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Gluten extracted from wheat flour, demonstrating the extensible and plastic nature of this complex protein network. 从小麦粉中提取的面筋,展示了这种复杂蛋白质网络的可扩展性和可塑性。
Pub Date : 2022-01-01 DOI: 10.24918/cs.2022.13
E. Jones, E. Fogle
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引用次数: 0
Application of a bacterial experimental evolution system to visualize and teach evolution in action: A course-based undergraduate research experience. 应用细菌实验进化系统可视化并教授实际的进化:基于课程的本科生研究经验。
Pub Date : 2022-01-01 DOI: 10.24918/cs.2022.24
Collin Kessler, William Mazza, Kasey Christopher, Wook Kim

Concepts of evolution are typically taught through examples of extremely long timescales, which do not always resonate broadly. Here, we describe a course-based undergraduate research experience tailored for junior and senior undergraduate biology majors. Students visualize and learn in real-time how evolution can operate in bacteria in response to problems associated with a high-density lifestyle. Students directly evolve mutant strains, conduct whole genome sequencing to identify the causal mutations, carry out bioinformatics analysis to predict molecular consequences of the mutations, engineer their mutants to become antibiotic-resistant, and compete them head-to-head in a class-wide round-robin tournament to infer the properties of natural selection. The presented format is designed for a full semester, but the modular structure of the course allows instructors to make simple modifications for a shorter duration. A substantial portion of this course also focuses on scientific communication. Each student prepares a lab report structured as an original research article to gain experience in writing a publication quality manuscript. Individual components of their reports are prepared throughout the semester and are followed with instructor- and peer-based draft edits. Finally, students are tasked with working as a team to deliver an oral presentation, which drives them to come to a consensus on the interpretation of their group's data. Such a comprehensive research experience is difficult for a student to acquire without securing a research position in a faculty lab, but this course allows a large group of students to directly experience and actively contribute to open-ended and hypothesis-driven research.

进化论的概念通常是通过极长时间尺度的例子来教授的,这并不总是能引起广泛的共鸣。在这里,我们描述了一种基于课程的本科生研究经验,为大三和大四的生物学专业学生量身定制。学生实时可视化并学习进化如何在细菌中运作,以应对高密度生活方式带来的问题。学生们直接进化突变菌株,进行全基因组测序以确定突变的原因,进行生物信息学分析以预测突变的分子后果,设计他们的突变体使其具有抗生素耐药性,并在班级范围内的循环赛中与他们进行正面竞争,以推断自然选择的性质。所呈现的格式是为整个学期设计的,但课程的模块化结构允许教师在较短的时间内进行简单的修改。这门课程的很大一部分也侧重于科学传播。每个学生准备一份实验报告,作为一篇原创研究文章,以获得撰写出版质量手稿的经验。他们的报告的个别组成部分是在整个学期准备的,然后是导师和同行的草稿编辑。最后,学生们的任务是作为一个团队进行口头陈述,这促使他们对小组数据的解释达成共识。这样全面的研究经验对学生来说很难获得,如果没有在教师实验室获得研究职位,但这门课程允许一大群学生直接体验并积极参与开放式和假设驱动的研究。
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引用次数: 0
Bioinformatics is a BLAST: Engaging First-Year Biology Students on Campus Biodiversity Using DNA Barcoding 生物信息学是一个BLAST:利用DNA条形码吸引一年级生物学学生了解校园生物多样性
Pub Date : 2022-01-01 DOI: 10.24918/cs.2022.32
S. Unger, Mark A. Rollins
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.
为了向学生介绍分子多样性的概念,我们开发了一个简短的、引人入胜的在线课程,使用基本的生物信息学技术。学生们在了解当地校园物种多样性的同时,还被介绍了基本的生物信息学,方法是:1)根据给定的序列识别物种(执行基本的本地比对搜索工具[BLAST]分析);2)研究和记录每种物种的自然历史,并以简明的文字记录。为了评估学生对这一课的理解,我们使用李克特量表对学生进行了调查,并要求他们详细阐述对这一活动的书面反思。综合起来,学生的回答表明,94%的学生认为这节课帮助他们理解了DNA条形码以及如何使用它来识别物种。大多数学生(89.5%)表示他们很喜欢这节课,并给出了积极的反馈,包括“通过观察DNA序列,我真的对校园里不同的物种大开眼界”,“我喜欢搜索信息,从DNA序列中发现所有这些新信息”,最后,“数据库导航很有趣,识别物种感觉就像一个很酷的谜题。”我们的结果表明,这节课既吸引了学生,也让他们了解了如何使用DNA条形码作为识别当地物种生物多样性的工具。
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引用次数: 0
Analysis of Microbiomes Using Free Web-Based Tools in Online and In-Person Undergraduate Science Courses 在线和面对面本科科学课程中使用免费网络工具分析微生物组
Pub Date : 2022-01-01 DOI: 10.24918/cs.2022.35
A. Zelaya, N. Gerardo, L. Blumer, C. Beck
Our understanding of microbiomes, or the collection of microorganisms and their genes in a given environment, has been revolutionized by technological and computational advances. However, many undergraduate students do not get hands-on experiences with processing, analyzing, or interpreting these types of datasets. Recent global events have increased the need for effective educational activities that can be performed virtually and remotely. Here, we present a module that introduces STEM undergraduates to the bioinformatic and statistical analyses of bacterial communities using a combination of free, web-based data processing software. These lessons allow students to engage with the studies of microbiomes; gain valuable experiences processing large, high-throughput datasets; and practice their science communication skills. The lessons presented here walk students through two web-based platforms. The first ( DNA Subway ) is an easy-to-use wrapper of the popular QIIME (pronounced “chime”) pipeline, which performs quality control analysis of the raw sequence data and outputs a community matrix file with assigned bacterial taxonomies. The second, ranacapa , is an R Shiny App that allows students to compare microbial communities, perform statistical analyses and visualize community data. Students may communicate their findings with a written final report or oral presentation. While the lessons presented here use a sample dataset based on the gut-microbiome of the bean beetle ( Callosobruchus maculatus ), the materials are easily modified to use original next- generation amplicon sequence data from any host or environment. Additionally, options for alternative datasets are also provided facilitating flexibility within the curriculum.
我们对微生物组的理解,或在特定环境中微生物及其基因的集合,已经被技术和计算的进步彻底改变了。然而,许多本科生没有处理、分析或解释这些类型的数据集的实践经验。最近的全球事件增加了对可通过虚拟和远程方式进行的有效教育活动的需求。在这里,我们提出了一个模块,向STEM本科生介绍使用免费的基于网络的数据处理软件组合的细菌群落的生物信息学和统计分析。这些课程允许学生参与微生物组的研究;获得处理大型、高通量数据集的宝贵经验;并练习他们的科学交流技巧。这里展示的课程引导学生通过两个基于网络的平台。第一个(DNA Subway)是流行的QIIME(发音为“chime”)管道的一个易于使用的包装,QIIME对原始序列数据进行质量控制分析,并输出带有指定细菌分类的群落矩阵文件。第二个是ranacapa,这是一个R Shiny应用程序,允许学生比较微生物群落,进行统计分析并可视化社区数据。学生可以通过书面报告或口头报告来交流他们的发现。虽然本文所介绍的课程使用了基于豆甲虫肠道微生物组的样本数据集,但这些材料很容易修改,以使用来自任何宿主或环境的原始下一代扩增子序列数据。此外,还提供了替代数据集的选项,以促进课程中的灵活性。
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引用次数: 0
Garden Variety Mutations: Using Primary Data to Understand the Central Dogma in Large-Lecture Introductory Biology 园艺品种突变:用原始数据理解大型讲座生物学导论的中心法则
Pub Date : 2022-01-01 DOI: 10.24918/cs.2022.43
Jacob Woodbury, Jessie B. Arneson, Jacey Anderson, Larry B. Collins, A. Cavagnetto, William B. Davis, E. Offerdahl
The ability to interpret and create an argument from data is a crucial skill for budding scientists, yet one that is seldom practiced in introductory courses. During this argumentation module, students in a large lecture class will work in groups to understand how a single mutation can lead to an obvious phenotypic change among tomatoes. Before the module begins, students are provided with background information on mutations and techniques to give them a starting point to explain what they will see in the data. In class, students will use data from the primary literature to understand the relationship between single amino acid mutations and phenotypic variation within the context of a “big question” about garden tomatoes that ripen without turning red. Over two days, small groups will negotiate data, create and evaluate hypotheses
从数据中解释和创建论点的能力对崭露头角的科学家来说是一项至关重要的技能,但在入门课程中很少练习。在这个论证模块中,学生将在一个大型课堂上分组学习,了解单个突变如何导致番茄明显的表型变化。在该模块开始之前,学生将获得有关突变和技术的背景信息,以便为他们解释他们将在数据中看到的内容提供一个起点。在课堂上,学生将使用原始文献中的数据来理解单个氨基酸突变与表型变异之间的关系,这是一个“大问题”的背景下,关于花园西红柿成熟而不变红。在两天的时间里,小组将讨论数据,创建和评估假设
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引用次数: 0
Video Making Tips for Laboratory Instructors 实验室教官视频制作技巧
Pub Date : 2022-01-01 DOI: 10.24918/cs.2022.45
J. E. Patrick, John Z. Zhu
Demonstration videos are an excellent way to introduce students to new laboratory techniques, but many available videos are of low quality, too long, lack human diversity, and the main narrator is someone other than the instructor of the course. Videos may feature terminology and equipment different from what the students will use and the availability of the video is also not controlled by the lab instructor. Lab instructors can enhance the lab experience of students by making their own demonstrations videos. The current cell phone camera technology allows instructors to make custom videos. We watched many successful how-to style YouTube videos and distilled several techniques. We then applied these techniques to make more engaging videos for our students. Many of our videos have found success on YouTube. In this paper, we break down our video making techniques for demonstrating laboratory equipment and protocols. We hope the readers will find inspiration to make their own demonstration videos to aide their students.
演示视频是向学生介绍新的实验技术的一种极好的方式,但许多可用的视频质量低,太长,缺乏人类多样性,主要讲述者不是课程的讲师。视频中的术语和设备可能与学生将要使用的不同,视频的可用性也不受实验室教师的控制。实验室教师可以通过制作自己的演示视频来增强学生的实验室体验。目前的手机摄像技术允许教师制作定制视频。我们观看了许多成功的YouTube视频,从中提炼出一些技巧。然后我们应用这些技术为我们的学生制作更吸引人的视频。我们的很多视频都在YouTube上获得了成功。在本文中,我们打破了我们的视频制作技术,以展示实验室设备和协议。我们希望读者能从中找到灵感,制作自己的示范视频来帮助他们的学生。
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引用次数: 0
Transitioning Two-Stage Exams to an Online Class 将两阶段考试转变为在线课程
Pub Date : 2022-01-01 DOI: 10.24918/cs.2022.29
Jill A. Parsell, Allissa M. Blystone, Adrienne E. Williams
Students often find biology courses to be very difficult and isolating, particularly if they identify as part of a group that has been historically excluded from STEM. Some of this anxiety and isolation comes from high-stakes exams. We decided to use the collaborative structure of two-stage exams to try to overcome the isolation of assessment. In two-stage exams, students take an individual exam, and then immediately get into groups and take the exam again, discussing the questions and the rationale behind the answers. Their exam scores are a combination of the two attempts. Our move to emergency online learning because of the COVID-19 pandemic forced us to try our two-stage exams online. In this Teaching Tools and Strategies essay, we discuss our process of offering two-stage exams online at two different institutions: a two-year Community College and four-year Research University. We share feedback from the students and discuss our iterative improvements to two-stage exam use.
学生们经常发现生物课程非常困难和孤立,特别是如果他们认为自己是历史上被排除在STEM之外的群体的一部分。这种焦虑和孤立有些来自高风险的考试。我们决定采用两阶段考试的协作结构来克服评估的孤立性。在两阶段的考试中,学生们参加单独的考试,然后立即分成小组,再次参加考试,讨论问题和答案背后的基本原理。他们的考试成绩是这两种尝试的结合。由于COVID-19大流行,我们转向紧急在线学习,迫使我们尝试在线进行两阶段考试。在这篇教学工具和策略文章中,我们讨论了我们在两所不同的机构提供两阶段在线考试的过程:两年制社区学院和四年制研究型大学。我们分享来自学生的反馈,并讨论我们对两阶段考试使用的迭代改进。
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引用次数: 1
Animal Behaviour Case Study Lessons in Communication, Migration, and Parental Care Using the Jigsaw Approach 动物行为案例研究课程在沟通,迁移和亲代照顾使用拼图方法
Pub Date : 2022-01-01 DOI: 10.24918/cs.2022.25
L. Phillips, Kevin K Duclos, Mindi M. Summers
Animal behaviour courses integrate concepts across biological disciplines and are particularly well suited for collaborative, student-focused teaching strategies. Case Studies can positively impact students by placing their learning in context while providing an opportunity to do quick research and have rich discussions with both their peers and instructional team. Case Studies can also enrich the learning environment and help to produce a safe, collaborative space for asking questions and developing critical thinking skills. Here we describe three Case Study lesson plans using the Jigsaw approach that allows students to explore animal communication, migration, and parental care. Each Case Study includes 16 primary literature summaries on four different animal groups. In the Jigsaw approach, students are first sorted into four “expert groups” where they receive primary literature summaries exploring proximate and ultimate approaches to a specific animal’s behaviour (e.g., neurobiology, physiology, genetics, and evolution). One student from each “expert group” (e.g., ants, birds, etc.) then joins and shares their group’s knowledge in a “jigsaw group.” By the end of each lesson, students will have read one primary literature article summary, prepared and delivered an oral brief, and summarized and then presented their expert group’s findings to the new Jigsaw group members. Through this collaborative peer-to-peer learning activity, students gain skills in interpreting, analyzing and synthesizing scientific literature. They also have the opportunity to practice communicating scientific findings effectively and concisely, sharing how animal behaviour is studied, and explaining how behaviour is influenced by both proximate and ultimate factors
动物行为课程整合了生物学科的概念,特别适合以学生为中心的合作教学策略。案例研究可以通过将学生的学习置于情境中,同时提供快速研究和与同龄人和教学团队进行丰富讨论的机会,对学生产生积极影响。案例研究还可以丰富学习环境,帮助创造一个安全、协作的空间,供学生提问和培养批判性思维技能。在这里,我们描述了三个案例研究课程计划,使用拼图方法,让学生探索动物交流,迁徙和亲代照顾。每个案例研究包括16个主要文献摘要,涉及四个不同的动物群体。在拼图方法中,学生们首先被分为四个“专家组”,在那里他们接受主要的文献摘要,探索特定动物行为的近似和最终方法(例如,神经生物学,生理学,遗传学和进化)。每个“专家小组”(例如蚂蚁、鸟类等)中有一名学生加入“拼图小组”,分享他们小组的知识。在每节课结束时,学生们将阅读一篇主要的文献文章摘要,准备并发表口头简报,总结并向拼图小组的新成员展示他们专家组的发现。通过这种协作式的点对点学习活动,学生可以获得解释、分析和综合科学文献的技能。他们也有机会练习有效而简洁地交流科学发现,分享动物行为是如何被研究的,并解释行为是如何受到近因和终极因素的影响的
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引用次数: 0
A Modeling Exercise in Sexual Selection using a Student-Created Bird Species 用学生创造的鸟类进行性选择的建模练习
Pub Date : 2022-01-01 DOI: 10.24918/cs.2022.20
Ashley B. Heim, Anna E. Freundlich, E. Holt
Evolution-centered lessons at the undergraduate level can often be jargon-heavy, propagate misconceptions if taught ineffectively, and be uninteresting to students who may not see the relevancy of such concepts. This activity provides a fun and hands-on way for introductory biology students to learn about sexual selection and fitness and encourages students to consider what traits the “flashier” sex may use to attract the “less flashy” sex and how sexual selection and fitness are related. In this activity, after reading a short scenario, half of the students in the class are assigned as “flashy birds” and required to create a model of a flashy bird (of a fictitious species) that they believe will attract the less flashy sex of this same species using materials (e.g., modeling dough and other craft materials). The other half of the students are assigned as “less flashy birds” and required to compile a list of traits and behaviors that they would prefer to see in their flashier counterparts. Once modeling is complete, students in “flashy bird” groups are asked to share the birds they created at the front of the class and justify why they gave their individuals particular characteristics and behaviors. Students in the less flashy bird groups then “vote” on which flashy bird they prefer given its unique traits, based on the lists they compiled of desired characteristics. This is a highly student-centered activity which can be easily adapted to meet the needs of your students, your learning goals and objectives, and your curriculum. 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. Modeling Exercise in Sexual Selection - Lesson Timeline; S2. Modeling Exercise in Sexual Selection - Powerpoint Slides; S3. Modeling Exercise in Sexual Selection - Handout & Answer Key; S4. Modeling Exercise in Sexual Selection - Sample Exam Questions; and S5. Modeling Exercise in Sexual Selection - Sample Bird Model/Trait List Rubric.
在本科阶段,以进化论为中心的课程通常会有大量的术语,如果教授得不好,就会传播误解,而且对于那些可能看不到这些概念的相关性的学生来说,也会变得无趣。这个活动为生物学入门的学生提供了一种有趣的实践方式来学习性选择和适应性,并鼓励学生思考“华丽”的性别可能会用什么特征来吸引“不那么华丽”的性别,以及性选择和适应性是如何相关的。在这个活动中,在阅读了一个简短的场景后,班上一半的学生被分配为“浮华的鸟”,并被要求使用材料(例如建模面团和其他工艺材料)制作一个他们认为会吸引同一物种中不那么浮华的性别的浮华鸟的模型。另一半的学生被分到“不太浮华的小鸟”组,他们被要求列出一份清单,列出他们希望在浮华的同伴身上看到的特征和行为。一旦建模完成,学生在“华丽的鸟”组被要求分享他们在班级前面创造的鸟,并证明为什么他们给他们的个人特定的特征和行为。然后,不那么光鲜亮丽的鸟组的学生根据他们所期望的特征列表,“投票”出他们更喜欢哪只光鲜亮丽的鸟,因为它有独特的特征。这是一个高度以学生为中心的活动,可以很容易地适应你的学生的需要,你的学习目标和目的,以及你的课程。知识共享署名-非商业-相同方式共享4.0国际许可协议条款,允许在任何媒体上不受限制的非商业使用、分发和复制,前提是要注明原作者和来源。利益冲突和资金声明:作者没有与本研究相关的财务、个人或专业利益冲突。支持材料:支持文件性选择的建模练习-课程时间S2。性选择的建模练习-投影片;S3。性选择的建模练习-讲义和答案;S4。性选择的建模练习-样题和S5。性选择中的建模练习-鸟类模型/特征列表样本。
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引用次数: 0
Escape Zoom!: Reviewing Introductory Evolution Content Using an Escape Room Format 逃避放大!:使用密室逃生模式回顾入门级进化内容
Pub Date : 2022-01-01 DOI: 10.24918/cs.2022.21
Ashley B. Heim, Michelle K. Smith
Reviewing and integrating key concepts and learning goals at the end of a biology course can be overwhelming to students and instructors alike. Often end-of-term review sessions in preparation for final exams are heavily based on memorization, and content coverage may be favored over students’ deeper understanding of fewer key ideas. We developed a final exam review for a virtual introductory evolution course using an “escape room” format, which consisted of unique activities— including puzzles, role-playing, and literature searches—aligned with course learning goals. Similar to a traditional escape room, students needed to collaboratively solve or complete each activity before moving on to the subsequent task. Our escape room activity was conducted virtually via Zoom and included both whole-class and smaller breakout room interactions. We recommend instructors utilize escape rooms as an engaging and effective way to review key concepts in their courses.
在生物学课程结束时回顾和整合关键概念和学习目标对学生和教师来说都是压倒性的。为期末考试做准备的期末复习课通常很大程度上是建立在死记硬背的基础上的,而内容覆盖可能比学生对较少的关键思想的深入理解更受欢迎。我们为一门虚拟的进化论入门课程设计了一套期末考试复习系统,采用了“密室逃生”的形式,它由独特的活动组成——包括谜题、角色扮演和文献搜索——与课程学习目标保持一致。与传统的密室逃生类似,学生们需要在进入下一个任务之前,共同解决或完成每个活动。我们的密室逃生活动是通过Zoom虚拟进行的,包括整个班级和较小的分组讨论室互动。我们建议教师利用密室逃生作为一种有效的方法来复习课程中的关键概念。
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引用次数: 0
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