CourseSource最新文献

{"title":"Making Change Sustainable: Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) Meeting Review","authors":"Inimary T. Toby, Jason J. Williams, G. Lu, Chao Cai, K. Crandall, E. Dinsdale, Jennifer Drew, N. Edgington, Carlos C. Goller, Neal F. Grandgenett, B. Grant, Charles Hauser, Keith A. Johnson, Christopher J. Jones, N. Jue, J. Jungck, Jacob Kerby, Adam J. Kleinschmit, Kathryn G. Miller, William R. Morgan, Barbara Murdoch, G. Noutsios, Janelle Nunez-Castilla, M. Pauley, William R. Pearson, Sabrina D Robertson, S. Robic","doi":"10.24918/cs.2022.10","DOIUrl":"https://doi.org/10.24918/cs.2022.10","url":null,"abstract":"The purpose of the meeting described in this review was to decide how best to ensure the sustainability of the Network for Integrating Bioinformatics into Life Science Education (NIBLSE; pronounced “nibbles”). Biology research today generates large and complex datasets, and the analysis of these datasets is becoming increasingly critical to progress in the field. The long-term goal of NIBLSE is to address this need and achieve the full integration of bioinformatics into undergraduate life sciences education. Meeting participants supported several next steps for NIBLSE, including further development and dissemination of bioinformatics learning resources through our novel incubators and Faculty Mentoring Networks, vigorously pursuing assessment strategies for our learning resources, connecting learning resources with open educational resource (OER) textbooks, learning more about barriers to bioinformatics implementation for underrepresented groups, and developing future workshops and meetings. About half the participants at the meeting were newcomers to NIBLSE, a positive sign for the future. NIBLSE has many exciting opportunities available, and we welcome life science educators with any level of bioinformatics expertise as new members.","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69329298","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":"Responsible and Ethical Conduct of Research: Instruction on Plagiarism","authors":"Joseph Ross","doi":"10.24918/cs.2022.18","DOIUrl":"https://doi.org/10.24918/cs.2022.18","url":null,"abstract":"","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69329364","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":"Isolation and Functional Analysis of a Pancreatic Enzyme in an Introductory Student Lab","authors":"Peter J. Lyons","doi":"10.24918/cs.2022.39","DOIUrl":"https://doi.org/10.24918/cs.2022.39","url":null,"abstract":"Structure and function are correlated at all levels of biology. This topic is typically addressed early in an undergraduate class in general or molecular biology before students have gained much skill or knowledge in molecular biology. However, an understanding of the chemical bonds involved in forming and maintaining the structure of proteins is critical to understanding how enzymes function and how their activity can be regulated. Here, a laboratory activity is described that is suitable for undergraduate biology students. This activity examines the activity of carboxypeptidase A (CPA), an abundant pancreatic enzyme with a rich history in enzymology and structural biology. The abundance of CPA in pancreatic tissue allows for a series of common biochemical techniques to be easily performed under the constraints of an undergraduate teaching lab, including the separation of proteins by simple precipitation methods, the examination of resulting proteins by SDS-PAGE and Coomassie staining, and the analysis of enzyme function through the determination of constants such as Vmax and Km. These steps illustrate the importance of noncovalent bonds in protein structure and the use of common biochemical instruments in the lab, while providing students with an opportunity to hone analysis skills in their consideration of the resulting data. Finally, this lab may be modified in many ways to make it suitable for upper division classes, CURE approaches to the undergraduate lab, and even to the pre-college classroom.","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69329566","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":"Using Open-Source Bioinformatics and Visualization Tools to Explore the Structure and Function of SARS-CoV-2 Spike Protein","authors":"L. Listenberger, C. Joiner, C. Terrell","doi":"10.24918/cs.2022.5","DOIUrl":"https://doi.org/10.24918/cs.2022.5","url":null,"abstract":"The relationship between protein structure and function is a foundational concept in undergraduate biochemistry. We find this theme is best presented with assignments that encourage exploration and analysis. Here, we share a series of four assignments that use open-source, online molecular visualization and bioinformatics tools to examine the interaction between the SARSCoV-2 spike protein and the ACE2 receptor. The interaction between these two proteins initiates SARS-CoV-2 infection of human host cells and is the cause of COVID-19. In assignment I, students identify sequences with homology to the SARSCoV-2 spike protein and use them to build a primary sequence alignment. Students make connections to a linked primary research article as an example of how scientists use molecular and phylogenetic analysis to explore the origins of a novel virus. Assignments II through IV teach students to use an online molecular visualization tool for analysis of secondary, tertiary, and quaternary structure. Emphasis is placed on identification of noncovalent interactions that stabilize the SARS-CoV-2 spike protein and mediate its interaction with ACE2. We assigned this project to upper-level undergraduate biochemistry students at a public university and liberal arts college. Students in our courses completed the project as individual homework assignments. However, we can easily envision implementation of this project during multiple in-class sessions or in a biochemistry laboratory using in-person or remote learning. We share this project as a resource for instructors who aim to teach protein structure and function using inquiry-based molecular visualization activities. Citation: Listenberger LL, Joiner CM, Terrell CR. 2022. Using open-source bioinformatics and visualization tools to explore the structure and function of SARS-CoV-2 spike protein. CourseSource. https://doi.org/10.24918/cs.2022.5 Editor: Charles Hauser, St. Edward’s University Received: 1/5/2021; Accepted: 9/9/2021; Published: 3/18/2022 Copyright: © 2022 Listenberger, Joiner, and Terrell. 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 images used in supporting materials (Supporting File S3: Molecular Modeling – Summative Assessments and Data from Student Responses) are from journals that use the Creative Commons Attribution License. We cite the original source for each figure. The primary image includes student generated data and a cartoon from Pixabay, an online repository of copyright free art. 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. Molecular Modeling – BioMolViz Goals and Objectives; S2. Molecula","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69329786","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 Case Study for Teaching Toxicology: Using Whales as an Indicator for Environmental Health.","authors":"Bryanna Rupprecht,&nbsp;John Pierce Wise,&nbsp;Mindy Reynolds","doi":"10.24918/cs.2022.30","DOIUrl":"10.24918/cs.2022.30","url":null,"abstract":"<p><p>One of the challenges of teaching scientific courses is helping students understand research methods, biological models, and data analysis, which can be especially difficult in classes without a laboratory component. Within the field of toxicology, it is also important for students to understand how living organisms are affected by exposure to toxicants and how these toxicants can impact the ecosystem. Resources focusing on active learning pedagogy are scarce in the field of toxicology compared to other disciplines. In this activity, upper-level students in an introductory toxicology course learn to interpret data from primary literature, draw conclusions about how toxicants, specifically metals, can impact susceptible populations, and understand the One Environmental Health approach. Students work in small groups to answer questions concerning data from a paper and then share their responses with the entire class building their communication skills. The instructor serves as a moderator, allowing the students to work through concepts, intervening only when necessary. This approach enables a deeper level of understanding of content and allows the students to engage actively in the learning process. As such, students think critically through relevant problems and find connections to the real world. This lesson can be adapted for several levels of students and could be modified depending on the objectives of the course.</p>","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"9 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/22/05/nihms-1872638.PMC10501411.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10306677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pesticides in My Smoothie Bowl?","authors":"Shuangying Yu, S. Weir","doi":"10.24918/cs.2022.26","DOIUrl":"https://doi.org/10.24918/cs.2022.26","url":null,"abstract":"Teaching resources, especially active learning pedagogy, are scarce for toxicology compared to what is available for other disciplines. Ecological and human health risk assessment are important aspects of toxicology and are routinely used by government agencies to regulate the registration and usage of many chemicals. Most traditional toxicology classes do not cover how such risk assessments are carried out in real-world scenarios. We developed this case study to introduce concepts and processes of ecological and human health risk assessment in pesticide registration by the U.S. EPA. In Part 1, dialogues among three college friends introduce organic food, pesticides, and the concept of risk. Part 2 and Part 3 build on Part 1 and focus on ecological risk assessment and human health risk assessment, respectively. At the end of each section, students select appropriate exposure and toxicity endpoints to perform a mini-risk assessment and draw conclusions regarding risk. In Part 4, students examine real pesticide monitoring data in various foods and perform basic data organization and analysis. This case is appropriate for upper-level college students taking toxicology or other environmental science related courses. With modifications, the case study may also be suitable for introductory level environmental and biological science students.","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69329068","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":"The BioTAP Professional Development Model: Expanding Empirical Research on Graduate Student Teaching Professional Development","authors":"Kristen R. Miller, Judith S. Ridgway, G. Marbach‐Ad, E. Schussler, Grant E. Gardner","doi":"10.24918/cs.2021.44","DOIUrl":"https://doi.org/10.24918/cs.2021.44","url":null,"abstract":"The Biology Teaching Assistant Project (BioTAP) provides a year-long mentoring program for practitioners and researchers of Biology Graduate Teaching Assistant Teaching Professional Development (GTA TPD). The program participants, known as BioTAP Scholars, are guided through the process of implementing a research project on GTA TPD. The rationale for the program is that GTAs are critical to the instruction of STEM majors and therefore need TPD to build instructional skills known to support students’ academic performance. However, there is a paucity of empirical data documenting effective GTA TPD practices. Here we describe the BioTAP Scholars program that sought to increase this literature base. In this essay, we detail program activities, Scholar feedback about the program, and changes in Scholars’ confidence in conducting research over the length of the program. As a result of the program, BioTAP Scholars have contributed to and expanded the GTA TPD literature base. With this growing base of empirical data, STEM departments can make evidence-based decisions related to their GTA TPD programs. The BioTAP Scholars program provides a model that could be adapted to increase capacity for research in other aspects of STEM education.","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69329169","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 Classroom Intervention to Reduce Confirmation Bias","authors":"E. Hane, Evelyn Brister","doi":"10.24918/cs.2022.7","DOIUrl":"https://doi.org/10.24918/cs.2022.7","url":null,"abstract":"STEM students are often unable to recognize cognitive bias in their own disciplines, and simply describing cognitive bias to students has shown to be insufficient to improve critical thinking. However, habitual metacognitive techniques show promise for correcting cognitive biases, such as confirmation bias, a maladaptive cognitive strategy that specifically threatens the objectivity of scientists. As part of a course on metacognition in science, first-year STEM students were asked to give an oral presentation about a controversial socioscientific topic (e.g., GMO crops, de-extinction, or hydrofracking). The first year the course was offered, presentations exhibited confirmation bias at a high rate, despite instructions to examine multiple viewpoints about the scientific issue. In subsequent years, an intervention in the form of an interactive lecture/discussion/ activity about confirmation bias and two specifically-designed homework assignments asked the students to reflect on evidence, search processes and potential biases. This intervention was jointly developed by faculty members in biology and philosophy to focus on habitual metacognitive techniques. Compared to no intervention, the resultant presentations had a higher percentage of reliable sources and a lower percentage of citations that only supported their conclusion. These results indicate that after the intervention exercise, students were discriminating among sources more carefully (Mann-Whitney p=0.009) and were using more sources from the other side of the argument, including presenting more reasons that refute their own ideas (Mann-Whitney p=0.003). We find that providing classroom instruction supported by deliberate practice to counteract confirmation bias improves students’ evaluation of scientific evidence. Citation: Hane EN, Brister E. 2022. A classroom intervention to reduce confirmation bias. CourseSource. https://doi.org/10.24918/cs.2022.7 Editor: Katie Burnette, University of California Riverside Received: 6/16/2021; Accepted: 9/19/2021; Published: 3/3/2022 Copyright: © 2022 Hane and Brister. 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 authors affirm that they either own the copyright to or have received written permission to use the text, figures, tables, artwork, abstract, summaries, and supporting materials. 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. Confirmation Bias – Homework Assignment #1; S2. Confirmation Bias – Cognitive Bias Lecture Slides; S3. Confirmation Bias – Puzzle Activity Handout; S4. Confirmation Bias – Homework Assignment #2; S5. Confirmation Bias – Presentat","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69329811","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":"Does Organelle Shape Matter?: Exploring Patterns in Cell Shape and Structure with High-Throughput (HT) Imaging.","authors":"Carlos C Goller,&nbsp;Graham T Johnson,&nbsp;Kaitlyn Casimo","doi":"10.24918/cs.2022.3","DOIUrl":"https://doi.org/10.24918/cs.2022.3","url":null,"abstract":"<p><p>Organelle structure has been studied and visualized for decades; however, publicly available databases that use improved high-throughput microscopy of gene-edited cell lines have recently revolutionized the amount and quality of information now available for use in undergraduate classes. This lesson demonstrates how the use of high-throughput (HT) microscopy has generated data describing organelle structure and variability. Students access, analyze, and evaluate cell structure images using the Allen Institute for Cell Science's Allen Cell Explorer. Students synthesize the information to make recommendations and propose a future experiment. Using web-based tools and a realistic scenario that merges antimicrobial drug screens with eukaryotic cell perturbations and structure, this case study provides a guided tour of the powerful applications of high-throughput microscopy.</p>","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9385133/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40426418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Meiosis Remodeled: Inclusion of New Parts to Poppit Bead Models Enhances Understanding of Meiosis","authors":"J. LaFountain, G. K. Rickards","doi":"10.24918/cs.2022.2","DOIUrl":"https://doi.org/10.24918/cs.2022.2","url":null,"abstract":"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. Citation: LaFountain JR, Rickards GK. 2022. Meiosis remodeled: Inclusion of new parts to Poppit Bead models enhances understanding of meiosis. CourseSource. https://doi.org/10.24918/ cs.2022.2 Editor: Leocadia Paliulis, Bucknell University Received: 3/24/2021; Accepted: 10/7/2021; Published: 2/3/2022 Copyright: © 2022 LaFountain and Rickards. 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(s) and source are credited. The authors affirm that they own the copyright to all figures and drawings and written text, except for figures in supporting material entitled ‘Meiosis Survey’ where questions 25 – 30 contain drawings from a textbook, for which the authors have obtained permission and annotated on the drawings with this statement: ‘From CUMMINGS. Instructor’s edition for Cummings’ Human Heredity: Principles and Issues, Tenth Edition.' © 2014 Brooks/Cole, a part of Cengage, Inc. Reproduced by permission. www.cengage.com/permissions Conflict of Interest and Funding Statement: Neither of the authors has a financial, personal, or professional conflict of interest related to this work Supporting Materials: Supporting File S1. Meiosis remodeled – Meiosis survey PowerPoint slides *Correspondence to: James R. LaFountain Jr. 657 Cooke Hall, University at Buffalo North Campus, Buffalo, NY 14260. Email: jrl@buffalo.edu. Telephone: (716) 645-4965. Fax: (716) 645-2975 CourseSource | www.coursesource.org 2022 | Volume 09 1 Lesson","PeriodicalId":72713,"journal":{"name":"CourseSource","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69329400","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}