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1. A research program-linked, course-based undergraduate research experience that allows undergraduates to participate in current research on mycobacterial gene regulation

   https://doi.org/10.3389/fmicb.2022.1025250  

   Roberts, Louis Anthony ; Shell, Scarlet S. ( January 2023 , Frontiers in Microbiology)

   Undergraduate instructional biology laboratories are typically taught within two paradigms. Some labs focus on protocols and techniques delivered in “cookbook” format with defined experimental outcomes. There is increasing momentum to alternatively employ student-driven, open-ended, and discovery-based strategies, oftenviacourse-based undergraduate research experiences (CUREs) using crowd-sourcing initiatives. A fraction of students also participate in funded research in faculty research labs, where they have opportunities to work on projects designed to expand the frontiers of human knowledge. These experiences are widely recognized as valuable but are not scalable, as most institutions have many more undergraduates than research lab positions. We sought to address this gap through our department’s curriculum by creating an opportunity for students to participate in the real-world research process within a laboratory course. We conceived, developed, and delivered an authentic, guided research experience to students in an upper-level molecular biology laboratory course. We refer to this model as a “research program-linked CURE.” The research questions come directly from a faculty member’s research lab and evolve along with that research program. Students study post-transcriptional regulation in mycobacteria. We use current molecular biology methodologies to test hypotheses like “UTRs affect RNA and protein expression levels,” “there is functional redundancy among RNA helicases,” and “carbon starvation alters mRNA 5′ end chemistries.” We conducted standard assessments and developed a customized “Skills and Concepts Inventory” survey to gauge how well the course met our student learning outcomes. We report the results of our assessments and describe challenges addressed during development and execution of the course, including organizing activities to fit within an instructional lab, balancing breadth with depth, and maintaining authenticity while giving students the experience of obtaining interpretable and novel results. Our data suggest student learning was enhanced through this truly authentic research approach. Further, students were able to perceive they were participants and contributors within an active research paradigm. Students reported increases in their self-identification as scientists, and a positive impact on their career trajectories. An additional benefit was reciprocation back to the funded research laboratory, by funneling course alumni, results, materials, and protocols.

    

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2. Teaching virtual protein‐centric CUREs and UREs using computational tools

   Bell, Anthony. ( September 2020 , Biochemistry and molecular biology education)

   Responding to the need to teach remotely due to COVID-19, we used readily available computational approaches (and developed associated tutorials (https://mdh-cures-community.squarespace.com/virtual-cures-and-ures)) to teach virtual Course-Based Undergraduate Research Experience (CURE) laboratories that fulfil generally accepted main components of CUREs or Undergraduate Research Experiences (UREs): Scientific Background, Hypothesis Development, Proposal, Experiments, Teamwork, Data Analysis, Conclusions, and Presentation1. We then developed and taught remotely, in three phases, protein-centric CURE activities that are adaptable to virtually any protein, emphasizing contributions of noncovalent interactions to structure, binding and catalysis (an ASBMB learning framework2 foundational concept). The courses had five learning goals (unchanged in the virtual format),focused on i) use of primary literature and bioinformatics, ii) the roles of non-covalent interactions, iii) keeping accurate laboratory notebooks, iv) hypothesis development and research proposal writing, and, v) presenting the project and drawing evidence based conclusions The first phase, Developing a Research Proposal, contains three modules, and develops hallmarks of a good student-developed hypothesis using available literature (PubMed3) and preliminary observations obtained using bioinformatics, Module 1: Using Primary Literature and Data Bases (Protein Data Base4, Blast5 and Clustal Omega6), Module 2: Molecular Visualization (PyMol7 and Chimera8), culminating in a research proposal (Module 3). Provided rubrics guide student expectations. In the second phase, Preparing the Proteins, students prepared necessary proteins and mutants using Module 4: Creating and Validating Models, which leads users through creating mutants with PyMol, homology modeling with Phyre29 or Missense10, energy minimization using RefineD11 or ModRefiner12, and structure validation using MolProbity13. In the third phase, Computational Experimental Approaches to Explore the Questions developed from the Hypothesis, students selected appropriate tools to perform their experiments, chosen from computational techniques suitable for a CURE laboratory class taught remotely. Questions, paired with computational approaches were selected from Modules 5: Exploring Titratable Groups in a Protein using H++14, 6: Exploring Small Molecule Ligand Binding (with SwissDock15), 7: Exploring Protein-Protein Interaction (with HawkDock16), 8: Detecting and Exploring Potential Binding Sites on a Protein (with POCASA17 and SwissDock), and 9: Structure-Activity Relationships of Ligand Binding & Drug Design (with SwissDock, Open Eye18 or the Molecular Operating Environment (MOE)19). All involve freely available computational approaches on publicly accessible web-based servers around the world (with the exception of MOE). Original literature/Journal club activities on approaches helped students suggest tie-ins to wet lab experiments they could conduct in the future to complement their computational approaches. This approach allowed us to continue using high impact CURE teaching, without changing our course learning goals. Quantitative data (including replicates) was collected and analyzed during regular class periods. Students developed evidence-based conclusions and related them to their research questions and hypotheses. Projects culminated in a presentation where faculty feedback was facilitated with the Virtual Presentation platform from QUBES20 These computational approaches are readily adaptable for topics accessible for first to senior year classes and individual research projects (UREs). We used them in both partial and full semester CUREs in various institutional settings. We believe this format can benefit faculty and students from a wide variety of teaching institutions under conditions where remote teaching is necessary. 

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3. Interactive and Adaptable Cloud-based Virtual Equipment and Laboratories for 21st Century Science and Engineering Education

   https://doi.org/10.29007/7wf8  

   Cherner, Yakov ; Cima, Michael ; Barone, Paul ; Van Dyke, Bruce ; Lotring, Arnold ( February 2020 , EPiC Series in Education Science)

   This paper presents and discusses the use of simulation-based customizable online learning activities, virtual laboratories, and comprehensive e-Learning environments for teaching subjects such as materials science, chemistry, and biomanufacturing. The virtual equipment and lab assignments have been used for: (i) authentic online experimentation, (ii) homework and control assignments with traditional and blended courses, (iii) preparing students for hands-on work in real labs, (iv) lecture demonstrations, and (v) performance-based assessment of students’ ability to apply gained theoretical knowledge for operating actual equipment and solving practical problems. Using the associated learning and content management system (LCMS) and authoring tools, instructors kept track of student performance and designed new virtual experiments and more personalized learning assignments for students. Virtual X-Ray Laboratory and Web-based Environment for Single-Use Upstream Bioprocessing have been used to illustrate the implementation of the concept of Interactive and Adjustable Cloud-based e-Learning Tools. The virtual labs and e-learning environments have been used at two-year and four-year colleges and universities in the USA, UK, Tanzania and some other countries. The virtual X-Ray lab has also been integrated with the MITx course delivered via the MOOC (massive open online course) edX platform for Massachusetts Institute of Technology undergraduate students.

    

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4. Low-Barrier Strategies to Increase Student-Centered Learning Low-Barrier Strategies to Increase Student-Centered Learning

   Friend, Nicole Erin Woodcock ( July 2021 , ASEE annual conference exposition proceedings)

   Evidence has shown that facilitating student-centered learning (SCL) in STEM classrooms enhances student learning and satisfaction [1]–[3]. However, despite increased support from educational and government bodies to incorporate SCL practices [1], minimal changes have been made in undergraduate STEM curriculum [4]. Faculty often teach as they were taught, relying heavily on traditional lecture-based teaching to disseminate knowledge [4]. Though some faculty express the desire to improve their teaching strategies, they feel limited by a lack of time, training, and incentives [4], [5]. To maximize student learning while minimizing instructor effort to change content, courses can be designed to incorporate simpler, less time-consuming SCL strategies that still have a positive impact on student experience. In this paper, we present one example of utilizing a variety of simple SCL strategies throughout the design and implementation of a 4-week long module. This module focused on introductory tissue engineering concepts and was designed to help students learn foundational knowledge within the field as well as develop critical technical skills. Further, the module sought to develop important professional skills such as problem-solving, teamwork, and communication. During module design and implementation, evidence-based SCL teaching strategies were applied to ensure students developed important knowledge and skills within the short timeframe. Lectures featured discussion-based active learning exercises to encourage student engagement and peer collaboration [6]–[8]. The module was designed using a situated perspective, acknowledging that knowing is inseparable from doing [9], and therefore each week, the material taught in the two lecture sessions was directly applied to that week’s lab to reinforce students’ conceptual knowledge through hands-on activities and experimental outcomes. Additionally, the majority of assignments served as formative assessments to motivate student performance while providing instructors with feedback to identify misconceptions and make real-time module improvements [10]–[12]. Students anonymously responded to pre- and post-module surveys, which focused on topics such as student motivation for enrolling in the module, module expectations, and prior experience. Students were also surveyed for student satisfaction, learning gains, and graduate student teaching team (GSTT) performance. Data suggests a high level of student satisfaction, as most students’ expectations were met, and often exceeded. Students reported developing a deeper understanding of the field of tissue engineering and learning many of the targeted basic lab skills. In addition to hands-on skills, students gained confidence to participate in research and an appreciation for interacting with and learning from peers. Finally, responses with respect to GSTT performance indicated a perceived emphasis on a learner-centered and knowledge/community-centered approaches over assessment-centeredness [13]. Overall, student feedback indicated that SCL teaching strategies can enhance student learning outcomes and experience, even over the short timeframe of this module. Student recommendations for module improvement focused primarily on modifying the lecture content and laboratory component of the module, and not on changing the teaching strategies employed. The success of this module exemplifies how instructors can implement similar strategies to increase student engagement and encourage in-depth discussions without drastically increasing instructor effort to re-format course content. Introduction. 

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5. Systematic Analysis of Graphics-Based Hardware and Software for Virtual Reality Instructional Framework

   Chandramouli, Magesh ( June 2019 , ASEE annual conference exposition proceedings)

   This paper explains the design of a prototype desktop and augmented Virtual Reality (VR) framework as a medium to deliver instructional materials to the students in an introductory computer animation course. This framework was developed as part of a Teaching Innovation Grant to propose a cost-effective and innovative instructional frameworks to engage and stimulate students. Desktop-based virtual reality presents a 3-dimensional (3D) world using the display of a standard desktop computer available in most of the PC labs on campus. This is a required course at this university that has students not only from the primary department, but from other colleges/departments as well. Desktop VR has been chosen as a medium for this study due to the ease-of-access and affordability; this framework can be visualized and accessed with the available computers in PC labs available in university campuses. The proposed research is intended to serve as a low-cost framework that can be accessed by all students. The concepts of ‘computer graphics, modeling & animation’, instead of being presented using conventional methods such as notes or power point presentations, are presented in an interactive manner on a desktop display. This framework allows the users to interact with the objects on the display not only via the standard mouse and keyboard, but also using multiple forms of HCI such as Touchscreen, Touchpad, and 3D Mouse. Hence, the modules were developed from scratch for access via regular desktop PCs. Such a framework helps effective pedagogical strategies such as active learning (AL) and project-based learning (PBL), which are especially relevant to a highly lab-oriented course such as this course titled ‘Introduction to Animation’. Finally, the framework has also been tested on a range of VR media to check its accessibility. On the whole, this proposed framework can be used to not only teach basic modeling and animation concepts such as spatial coordinates, coordinate systems, transformation, and parametric curves, but it is also used to teach basic graphics programming concepts. Hence, instead of a touchscreen, the modules have to be developed from scratch for access via regular desktop PCs. Such a framework helps effective pedagogical strategies such as active learning (AL) and project-based learning (PBL), which are especially relevant to a highly lab-oriented course such as this animation course. 

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