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{"title":"A CURE for Salmonella: A Laboratory Course in Pathogen Microbiology and Genomics","authors":"Sophie K. Jurgensen, Joseph A. Harsh, J. B. Herrick","doi":"10.24918/cs.2021.24","DOIUrl":"https://doi.org/10.24918/cs.2021.24","url":null,"abstract":"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. Citation: Jurgensen SK, Harsh J, Herrick JB. 2021. A CURE for Salmonella: A Laboratory Course in Pathogen Microbiology and Genomics. CourseSource. https://doi.org/10.24918/cs.2021.24 Editor: William Morgan, College of Wooster Received: 5/19/2020; Accepted: 2/24/2021; Published: 9/15/2021 Copyright: © 2021 Jurgensen, Harsh, and Herrick. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited. Conflict of Interest and Funding Statement: None of the authors has a financial, personal, or professional conflict of interest related to this work. Supporting Materials: Supporting Files S1. CURE for Salmonella – Laboratory safety contract; S2. CURE for Salmonella – Pre-enrichment and enrichment media preparation; S3. CURE for Salmonella – Field sampling protocol; S4. CURE for Salmonella – Lab notebook grading rubric; S5. CURE for Salmonella – Pre-enrichment and enrichment inoculation protocol; S6. CURE for Salmonella – Plate media preparation; S7. CURE for Salmonella – Plating and purification protocol; S8. CU","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43584767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Fun Introductory Command Line Lesson: Next Generation Sequencing Quality Analysis with Emoji!","authors":"R. Jacques, William M. Maza, Sabrina D Robertson, Andrew Lonsdale, Caylin S. Murray, Jason J. Williams, R. Enke","doi":"10.24918/CS.2021.17","DOIUrl":"https://doi.org/10.24918/CS.2021.17","url":null,"abstract":"Radical innovations in DNA sequencing technology over the past decade have created an increased need for computational bioinformatics analyses in the 21st century STEM workforce. Recent evidence however demonstrates that there are significant barriers to teaching these skills at the undergraduate level including lack of faculty training, lack of student interest in bioinformatics, lack of vetted teaching materials, and overly full curricula. To this end, the James Madison University, Center for Genome & Metagenome Studies (JMU CGEMS) and other PUI collaborators are devoted to developing and disseminating engaging bioinformatics teaching materials specifically designed for streamlined integration into general undergraduate biology curriculum. Here, we have developed and integrated a fun introductory level lesson to command line next generation sequencing (NGS) analysis into a large enrollment core biology course. This one-off activity takes a crucial but mundane aspect of NGS quality control (QC) analysis and incorporates the use of Emoji data outputs using the software FASTQE to pique student interest. This amusing command line analysis is subsequently paired with a more rigorous research-grade software package called FASTP in which students complete sequence QC and filtering using a few simple commands. Collectively, this short lesson provides novice-level faculty and students an engaging entry point to learning basic genomics command line programming skills as a gateway to more complex and elaborated applications of computational bioinformatics analyses. Citation: St. Jacques RM, Maza WM, Robertson SD, Lonsdale A, Murray CS, Williams JJ, Enke RA. 2021. A fun introductory command line lesson: Next generation sequencing quality analysis with Emoji! CourseSource. https://doi.org/10.24918/cs.2021.17 Editor: Srebrenka Robic, Agnes Scott College Received: 8/22/2019; Accepted: 2/24/2021; Published: 4/13/2021 Copyright: © 2021 St. Jacques, Maza, Robertson, Lonsdale, Murray, Williams, and Enke. This is an open-access article distributed under the terms of the Creative Commons AttributionNonCommercial-ShareAlike 4.0 International License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited. Conflict of Interest and Funding Statement: None of the authors has a financial, personal, or professional conflict of interest related to this work. This work was supported by James Madison University 4-VA funding as well as National Science Foundation, Improving Undergraduate STEM Education Grant #1821657 awarded to R.A.E and the JMU College of Science and Mathematics. Supporting Materials: Supporting Files S1. FASTQE – Pre-class assignment; S2. FASTQE – Male5-oral1.fastq file; S3. FASTQE – Male5-oral2.fastq file; S4. FASTQE – Female2-oral1.fastq file; S5. FASTQE – Lecture slides; S6. FASTQE – Jupyter Notebook alternative implementation instructions; S7. FASTQE – Instructor","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46626585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adaptation and Facilitation of Small Group Activities in an Online Introductory Biology Class","authors":"Patrick W. Cafferty","doi":"10.24918/CS.2021.9","DOIUrl":"https://doi.org/10.24918/CS.2021.9","url":null,"abstract":"In spring 2020, the sudden mid-semester closure of my campus in response to the global COVID-19 pandemic necessitated a rapid transition to emergency online learning. Consequently, I adapted the small group activities and facilitation methods of my face-to-face introductory biology class to a fully online format. During small group activities in the face-to-face classroom, students form teams of two or three and complete paper worksheets that are designed to promote dialogue among teammates, while learning assistants and I circulate around the classroom to provide assistance. Evidence suggests these small group activities are a highly effective form of active learning. Here, I describe how I adapted the content of these paper worksheets for use in my learning management system, how students performed collaborative group work together using videoconferencing software, and how learning assistants and I facilitated this group work in a completely online environment during the spring and summer 2020 semesters. I also discuss the limitations and benefits of online group work. Online group activities present many advantages over use of the same activities in the traditional face-to-face classroom including overcoming the many limitations of the physical classroom space","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69329243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Squirreling from Afar: Adapting Squirrel-Net Modules for Remote Teaching and Learning","authors":"Laurie J Dizney, J. Varner, Jennifer M. Duggan, H. Lanier, Patrice K Connors, Liesl P. Erb, E. Flaherty, Christopher J Yahnke, J. Hanson","doi":"10.24918/CS.2021.2","DOIUrl":"https://doi.org/10.24918/CS.2021.2","url":null,"abstract":"The shift from face-to-face instruction to remote teaching and learning has proven to be a challenging endeavor for many reasons, including lack of time, resources, and inspiration. Lab courses, the “hands-on” portion of many curricula, may be especially difficult to adapt to online learning given the common use of specialized equipment, materials, and techniques that require close supervision. Without the time and resources to creatively modify existing activities or create new ones, remote lab courses run the risk of becoming less effective, equitable, and/or engaging. Squirrel-Net has created four fieldbased activities for biology labs that are easy to implement, highly flexible for different course aims, and readily adaptable to a remote learning environment. In this essay, we briefly summarize the modules and propose several ways that each can be adjusted to accommodate online teaching and learning. By providing authentic learning opportunities through distance delivery we hope to promote widespread student engagement and creative solutions for instructors. Citation: Dizney L, Varner J, Duggan JM, Lanier HC, Connors PK, Erb LP, Flaherty EA, Yahnke CJ, Hanson JD. 2021. Squirreling from afar: Adapting Squirrel-Net modules for remote teaching and learning. CourseSource. https://doi.org/10.24918/cs.2021.2 Editor: Luanna Prevost, University of South Florida Received: 9/23/2020; Accepted: 12/21/2020; Published: 1/27/2021 Copyright: © 2021 Dizney, Varner, Duggan, Lanier, Connors, Erb, Flaherty, Yahnke, and Hanson. This is an open-access article distributed under the terms of the Creative Commons AttributionNonCommercial-ShareAlike 4.0 International License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited. The authors affirm that we own the copyright to all text, figures, tables, artwork, abstract, summaries, and supporting materials. Conflict of Interest and Funding Statement: This material is based upon work supported by the National Science Foundation under a collaborative grant (Nos. 2013483, 2013281, 2013308, and 2013320). PKC, JMD, and JV were supported by the 2019 CourseSource Writing Studio. Support for EAF was provided by the USDA National Institute of Food and Agriculture, Hatch Project 1019737. None of the authors has a financial, personal, or professional conflict of interest related to this work. *Correspondence to: 5000 N Willamette Blvd, Portland, OR 97203. Email: dizney@up.edu. CourseSource | www.coursesource.org 2021 | Volume 08 1 Essay","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69329127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the Lytic and Lysogenic Life Cycles of Bacteriophages","authors":"Jaimy Joy","doi":"10.24918/CS.2021.6","DOIUrl":"https://doi.org/10.24918/CS.2021.6","url":null,"abstract":"The goal of this lesson is to introduce students to the lytic and lysogenic cycles of T4 and lambda bacteriophages, respectively, using student-centered pedagogies. Bacteriophages are viruses that infect bacteria and are either virulent or temperate; virulent phages can only undergo the lytic cycle, which results in death of the host cell, while temperate phages can undergo either the lytic or lysogenic cycle, the latter of which results in the long-term association between host and virus. Bacteriophages significantly affect bacterial population in nature and are even attractive therapeutic interventions for some bacterial infections in humans. Therefore, this lesson was designed to educate students about the structure and function of bacteriophages and how viral infections can impact bacterial populations. The learning goals of this lesson are to understand how the lytic and lysogenic cycles of bacteriophages vary, affect bacterial growth, and are dictated by their unique genomes. To this end, the lesson incorporates a homework assignment for students before class, a series of in-class activities and critical thinking scenarios, and a homework assignment after class. This lesson was successfully employed in an upper-level undergraduate virology course for biology majors. Students were enthusiastic and expressed thoughtful and educated ideas during class discussion and through answers to open-ended questions. Taken together, this lesson provides an interactive and studentcentered approach to studying the form and function of bacteriophages, the most abundant organisms in the biosphere. Citation: Joy JP. 2021. Exploring the lytic and lysogenic life cycles of bacteriophages. CourseSource. https://doi.org/10.24918/cs.2021.6 Editor: Sue Merkel, Cornell University Received: 7/23/2020; Accepted: 11/19/2020; Published: 3/2/2021 Copyright: © 2021 Joy. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited. The author affirms that they either own the copyright to, utilize images under the Creative Commons Attribution 4.0 License, or have received written permission to use the text, figures, tables, artwork, abstract, summaries and supporting materials. Conflict of Interest and Funding Statement: The author does not have a financial, personal, or professional conflict of interest related to this work. Supporting Materials: Supporting File S1. Lytic and lysogenic – Bacteriophages in Medicine Pre-Class Homework Assignment; S2a. Lytic and lysogenic – Bacteriophage Replication Cycles In-Class Worksheet Section 1; S2b. Lytic and lysogenic – Bacteriophage Replication Cycles In-Class Worksheet Section 2; S2c. Lytic and lysogenic – Bacteriophage Replication Cycles In-Class Worksheet Section 3; S2d. Lytic and lysogenic – Bacterioph","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69329225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From Dirt to Streptomyces DNA","authors":"M. Brodkin","doi":"10.24918/cs.2021.32","DOIUrl":"https://doi.org/10.24918/cs.2021.32","url":null,"abstract":"The purpose of this semester-long Lesson is to give students an authentic, course-based undergraduate research experience during which they learn basic and advanced microbiological and molecular biology techniques. This project begins with the isolation of a suspected Streptomyces bacterium from a soil sample and concludes with its identification. Students collect data, regarding colony and cell morphology, biochemical characteristics, the production of secondary metabolites, and employs the PCR using custom-designed primers to the Streptomyces 16s rRNA gene. The project culminates with the identification of their soil isolate using the National Center for Biotechnology Information (NCBI) web site to perform nucleotide blasts. The blastn program provides the final piece of evidence used to confirm, or not, the identification of their isolate as a Streptomyces from 16s rRNA gene sequence data, hence the title “From Dirt to Streptomyces DNA. In addition, the Lesson focuses on the Streptomyces bacteria to address several ASM aligned goals and objectives. These include prokaryotic growth phases and ways in which interactions of microorganisms among themselves and with their environment is determined by their metabolic abilities. In addition, this Lesson illustrates how microbial metabolism is important to a relevant societal issue, the need for new antibiotic discovery particularly given the rise of antibiotic resistance strains of clinically relevant bacteria. It also illustrates the microbial diversity of soil and the developmental/physiological strategies employed in such a competitive environment. This Lesson hopes to impart both the thrill and challenges associated with scientific discovery. Citation: Brodkin MA. 2021. From dirt to Streptomyces DNA. CourseSource. https://doi.org/10.24918/cs.2021.32 Editor: Rachel Horak, American Society for Microbiology Received: 1/9/2020; Accepted: 4/30/2021; Published: 10/25/2021 Copyright: © 2021 Brodkin. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited. Bio-Protocol LLC has given written permission via email for protocol use in LAB 8 (S7). Qiagen has granted permission to use their protocol in LAB 8 (S7) with a written Image Transfer Agreement. Genewiz.com has given written permission via email to use screen shots from their web site in LAB 11(S10). NCBI NBLAST site is an open-source web site. Conflict of Interest and Funding Statement: The Widener University Provost Grant Program supported part of this work. The author does not have a financial, personal, or professional conflict of interest related to this work. Supporting Materials: Supporting Files S1. Dirt to DNA-Handout Introduction to the Actinobacteria (LAB 1); S2. Dirt to DNA-Handout Serial dilution and spread","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69329248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Engaging Undergraduates in Mechanisms of Tubular Reabsorption and Secretion in the Mammalian Kidney.","authors":"Kristen A. Roosa","doi":"10.24918/CS.2021.4","DOIUrl":"https://doi.org/10.24918/CS.2021.4","url":null,"abstract":"If students fail to see the connections among physiological systems, they can become overwhelmed with the amount of information they need to learn. Some students have particular difficulty with the renal system for this reason. This lesson was developed to emphasize two general models in physiology that can inform student understanding of tubular reabsorption and secretion. In this two-hour lesson, students learn the mechanisms of tubular reabsorption and secretion by drawing on their prior knowledge of transport across physiological membranes (general model 1). Students also apply their knowledge of the Starling forces of capillary exchange (representing general model 2) as they learn how tubular reabsorption is regulated. The lesson is a combination of mini-lectures, used to introduce learning outcomes and more specific information, and group active learning exercises that ask students to recall prior knowledge of the two general models in physiology, make predictions, and synthesize and organize their knowledge. This lesson has fit well in a structured, upper-division physiology course. Citation: Roosa KA. 2021. Engaging undergraduates in mechanisms of tubular reabsorption and secretion in the mammalian kidney. CourseSource. https://doi.org/10.24918/cs.2021.4 Editor: Justin Shaffer, Colorado School of Mines Received: 4/5/2020; Accepted: 10/21/2020; Published: 2/20/2021 Copyright: © 2021 Roosa. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited. All materials are CC BY NC Kristen A. Roosa unless noted otherwise. All materials not by K. Roosa are protected by the CC BY license and the author was attributed. Conflict of Interest and Funding Statement: The author has no financial, personal, or professional conflict of interest related to this work. Supporting Materials: Supporting Files S1. Reabsorption & Secretion – Lecture Presentation Slides; S2. Reabsorption & Secretion – Activity 1; S3. Reabsorption & Secretion – Activity 1 Key; S4. Reabsorption & Secretion – Activity 2; and S5. Reabsorption & Secretion – Activity 2 Key. *Correspondence to: Biology Department, State University of New York College at Oneonta. 108 Ravine Parkway Oneonta, NY 13820. Email: Kristen.Roosa@oneonta.edu. CourseSource | www.coursesource.org 2021 | Volume 08 1 Lesson","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69329377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Moths and Frogs and E. coli, Oh My!: Agent-based Modeling of Evolutionary Systems","authors":"A. Garretson, Lorelei D. Crerar","doi":"10.24918/cs.2021.35","DOIUrl":"https://doi.org/10.24918/cs.2021.35","url":null,"abstract":"In evolution classrooms, introducing and reinforcing the idea of genetic drift and random selection can be challenging, as can be reinforcing appropriate mental models of evolution. Agent-based models offer students the opportunity to conduct a model-based inquiry into the impacts of different features on the outcomes in evolutionary systems, helping to build, test, and expand their mental models of evolution. In this lesson—through independent investigation, model-based inquiry, and discussions with peers—students are introduced to the ways that agent-based models can be used to make predictions and test hypotheses about evolutionary systems. This lesson uses the NetLogo modeling environment, which comes preloaded with several useful teaching models and can be manipulated in an easy-to-use graphical interface. We use three models: a model of peppered moths focused on environmental pressures and natural selection, a red queen model focused on the competitive coevolution of snakes and frogs, and a genetic drift model of E. coli. Together, these models help reinforce evolutionary concepts in a hands-on, student-driven environment while improving their understanding of the utility of computing in evolution research. This lesson can be modified to suit courses of varying student levels and has been successfully adapted to online or lecture-based learning environments. Citation: Garretson A, Crerar LD. 2021. Moths and Frogs and E. coli, Oh My!: Agent-based Modeling of Evolutionary Systems. CourseSource. https://doi.org/10.24918/cs.2021.35 Editor: William Morgan, College of Wooster Received: 7/20/2020; Accepted: 4/19/2021; Published: 11/3/2021 Copyright: © 2021 Garretson and Crerar. This lesson manuscript is released to the “public domain” under Attribution-NonCommercial 4.0 International (CC BY-NC 4.0). Under this license, authors retain ownership of the copyright to their article, but allow anyone to download, reuse, reprint, modify, distribute, and/or copy the article, as long as the original authors and source are cited and the intended use is not for commercial purposes. It is considered professional etiquette to provide attribution of the original work if this data package is shared in whole or by individual components. The authors shall not be liable for any damages resulting from misinterpretation or misuse of the lesson manuscript or its components. The authors affirm that we own the copyright to the text, figures, tables, artwork, abstract, summaries, and supporting materials. Conflict of Interest and Funding Statement: This work was supported in part by the George Mason University STEM Accelerator Program and the National Science Foundation Graduate Research Fellowship Program under Grant No. 1842191. Neither of the authors has a financial, personal, or professional conflict of interest related to this work. Supporting Materials: Supporting Files S1. Agent-based modeling – Presentation slides; S2. Agent-based modeling – Pre-test; S3. Agent-b","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69329316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Understanding Host-Pathogen Interactions With the Use of Galleria mellonella","authors":"Brendaliz Santiago-Narvaez","doi":"10.24918/CS.2021.1","DOIUrl":"https://doi.org/10.24918/CS.2021.1","url":null,"abstract":"The Galleria mellonella; the larvae of the Greater Wax Moth, is a safe and effective means to study host-pathogen interactions in the undergraduate setting. The use of animal models in the teaching classroom provides an opportunity to discuss proper animal use and the benefits of alternative model systems in research. In this lesson, we developed a laboratory experience for students to learn about the use of G. mellonella as a model to study bacterial virulence. Students evaluate the virulence of a suite of microbes by injecting larvae and analyzing their survival over time. Students gain the opportunity to reinforce basic microbiology techniques such as aseptic technique and bacterial enumeration, while learning about new methods involving animal use in research. Students learn how to report their data using survival plots. More importantly, this lesson gives students a hands-on experience working with an in vivo system and complements discussions of innate immunity and bacterial virulence by providing a visual and quantitative approach to the study of virulence. Citation: Santiago-Narvaez B. 2021. Understanding host-pathogen interactions with the use of Galleria mellonella. CourseSource. https://doi.org/10.24918/cs.2021.1 Editor: Rachel Horak, American Society for Microbiology Received: 10/4/2020; Accepted: 9/29/2020; Published: 1/26/2021 Copyright: © 2021 Santiago-Narvaez. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited. Conflict of Interest and Funding Statement: The author has no financial, personal, or professional conflict of interest related to this work. Supporting Materials: Supporting Files S1. Host/Pathogen – Reagent List and Materials; S2. Host/Pathogen – G. mellonella Articles; S3. Host/Pathogen – G. mellonella Lab Presentation; S4. Host/Pathogen – G. mellonella Laboratory Exercise Handout; S5. Host/Pathogen – Excel Spreadsheet for Survival Curves; S6. Host/Pathogen – Figure Assignment Instructions; S7. Host/Pathogen – Figure Rubric; S8. Host/Pathogen – Survival Curve Analysis; and S9. Host/Pathogen – Class Data Google Doc Template. *Correspondence to: 1000 Holt Avenue Box 2743 Winter Park, FL 32789. Email: bsantiagonarvaez@rollins.edu. CourseSource | www.coursesource.org 2020 | Volume 07 1 Lesson","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69328677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How Do Kidneys Make Urine From Blood? Qualitative and Quantitative Approaches to Filtration, Secretion, Reabsorption, and Excretion","authors":"Gregory J. Crowther","doi":"10.24918/cs.2021.42","DOIUrl":"https://doi.org/10.24918/cs.2021.42","url":null,"abstract":"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 HCO 3- 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.","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69329119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}