An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure-猫眼课题宝

教授真核基因结构的本科生生物信息学课程

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2017

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M. M. Laakso;L. Paliulis;Paula A. Croonquist;Brianna Derr;E. Gracheva;Charles Hauser;C. Howell;Christopher J. Jones;J. Kagey;J. Kennell;S. Catherine Silver Key;H. Mistry;S. Robic;Jamie Siders Sanford;M. Santisteban;Chiyedza Small;Rebecca Spokony;Joyce Stamm;Melanie Van stry;Wilson Leung;S. C. Elgin

基因结构、转录、翻译和选择性剪接对许多学习生物学的本科生来说是具有挑战性的概念。这些主题通常涵盖在传统的讲座环境，但学生往往无法掌握和保留这些概念。为了解决这个问题，我们设计了一系列的六个模块，采用主动学习的方法，使用生物信息学工具，基因组浏览器，以帮助学生了解真核基因的结构和功能。学生学习如何使用由基因组学教育伙伴关系创建的UCSC基因组浏览器的镜像网站，同时完成模块，重点是基因结构，转录，剪接，翻译和选择性剪接。这些模块补充了短视频，说明了基因组浏览器的关键功能和处理转录本的基本概念。这些材料已被成功地用于在许多不同的环境中教授基因结构，从社区学院到四年制学院和大学，包括高级高中生到大学高年级学生。教师可以很容易地定制模块和/或选择一个子集为他们的课程。这些模块帮助我们的学生了解真核基因的结构和表达，同时获得使用基因组浏览器的技能，并为他们独立研究基因组注释项目做好准备。引文：Laakso，M.M.，Paliulis，L.V.，Croonquist，P.，Derr，B.，Gracheva，E.，豪瑟，C.，豪厄尔，C.，琼斯，C. J.，Kagey，J.D.，Kennell，J.，南卡罗来纳州，银钥匙，Mistry，H.，Robic，S.，Sanford，J.，M. Steban，斯莫尔，C.，斯波科尼河，Stamm，J.，货车斯特里，M.，梁伟，埃尔金，S.C.R. 2017.教授真核生物基因结构的本科生生物信息学课程。CourseSource. https://doi.org/10.24918/cs.2017.13 编辑：Mark Pauly，University of Nebraska-Omaha，Omaha NE接收时间：2016年12月1日;接受时间：2017年3月17日;发布时间：2017年6月26日版权所有：© 2017 Laakso，Paliulis，Croonquist，Derr，Gracheva，豪瑟，豪厄尔，琼斯，Kagey，肯内尔，银钥匙，米斯特里，罗比奇，桑福德，埃斯特万，斯莫尔，斯波科尼，斯塔姆，货车斯特里，梁，还有埃尔金。这是一篇开放获取的文章，根据知识共享署名-非商业性相同方式共享4.0国际许可证的条款分发，该许可证允许在任何媒体上不受限制的非商业性使用，分发和复制，前提是原作者和来源被记入。出版物的非商业使用不需要作者或出版商的许可。作者确认，他们拥有文本、图表、插图、摘要、摘要和辅助材料的版权，或已获得书面许可使用这些材料。利益冲突和资金声明：没有作者有一个财务，个人或专业利益冲突与这项工作有关。支持材料：S1。模块1：什么是基因？S2.模块2：基础知识模块3：基础知识模块4：剪接，S5。模块5：翻译，S6。模块6：选择性剪接，S7。浏览器视频，S8。基因和亚型视频，S9. RNA-Seq和TopHat视频，S10。短比赛视频，S11。拼接和相位视频，S12。跟踪视频，S13。模块1：什么是基因？答题卡，S14。模块2：抄写第一部分答题纸，S15。模块3：抄写第二部分答题纸，S16。模块4：拼接答题纸，S17。模块5：翻译答题纸，S18。模块6：可选拼接答题纸，S19。术语表和S20。性别决定小讲座。* 通信地址：1300 Eagle Road，St. Davids，PA，19087电子邮件：mlaakso@eastern.edu CourseSource|www.coursesource.org 2017|第04卷第1课

Gene structure, transcription, translation, and alternative splicing are challenging concepts for many undergraduates studying biology. These topics are typically covered in a traditional lecture environment, but students often fail to master and retain these concepts. To address this problem we have designed a series of six Modules that employ an active learning approach using a bioinformatics tool, the genome browser, to help students understand eukaryotic gene structure and functionality. Students learn how to use a mirror site of the UCSC Genome Browser created by the Genomics Education Partnership while completing the Modules, which focus on gene structure, transcription, splicing, translation, and alternative splicing. The Modules are supplemented with short videos that illustrate key functionalities of the genome browser and fundamental concepts in processing transcripts. These materials have been used successfully to teach gene structure in many different settings, from community colleges to 4-year colleges and universities, encompassing advanced high school students to college seniors. Instructors can easily customize the Modules and/or select a subset for their curriculum. The Modules have helped our students learn about eukaryotic gene structure and expression, simultaneously acquiring skills in the use of a genome browser, and have prepared them to pursue genome annotation projects as independent research. Citation: Laakso, M.M., Paliulis, L.V., Croonquist, P., Derr, B., Gracheva, E., Hauser, C., Howell, C., Jones, C.J., Kagey, J.D., Kennell, J., Silver Key, S.C., Mistry, H., Robic, S., Sanford, J., Santisteban, M., Small, C., Spokony, R., Stamm, J., Van Stry, M., Leung, W., Elgin, S.C.R. 2017. An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure. CourseSource. https://doi.org/10.24918/cs.2017.13 Editor: Mark Pauly, University of Nebraska-Omaha, Omaha NE Received: 12/01/2016; Accepted: 03/17/2017; Published: 06/26/2017 Copyright: © 2017 Laakso, Paliulis, Croonquist, Derr, Gracheva, Hauser, Howell, Jones, Kagey, Kennell, Silver Key, Mistry, Robic, Sanford, Santisteban, Small, Spokony, Stamm, Van Stry, Leung, and Elgin. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercialShareAlike 4.0 International License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited. No permission is required from the authors or the publishers for noncommercial use of the published materials. 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 have a financial, personal, or professional conflict of interest related to this work. Supporting Materials: S1. Module 1: What is a Gene?, S2. Module 2: Transcription Part I, S3. Module 3: Transcription Part II, S4. Module 4: Splicing, S5. Module 5: Translation, S6. Module 6: Alternative Splicing, S7. Browser video, S8. Genes and isoforms video, S9. RNA-Seq and TopHat video, S10. Short Match video, S11. Splicing and Phase video, S12. Tracks video, S13. Module 1: What is a Gene? Answer Sheet, S14. Module 2: Transcription Part I Answer Sheet, S15. Module 3: Transcription Part II Answer Sheet, S16. Module 4: Splicing Answer Sheet, S17. Module 5: Translation Answer Sheet, S18. Module 6: Alternative Splicing Answer Sheet, S19. Glossary of terms, and S20. Sex determination mini-lecture. *Correspondence to: 1300 Eagle Road, St. Davids, PA, 19087 Email: mlaakso@eastern.edu CourseSource | www.coursesource.org 2017 | Volume 04 1 Lesson

An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

教授真核基因结构的本科生生物信息学课程

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