RESUMEN
The COVID-19 pandemic has forced a shift in thinking regarding the safe delivery of wet laboratory courses. While we were fortunate to have the capacity to continue delivering wet laboratory experiments with physical distancing and other measures in place, modifications to the mechanisms of delivery within courses were necessary to minimize risk to students and teaching staff. One such modification was introduced in BCH370H, an introductory biochemistry laboratory course, where a OneNote Class Notebook (ONCN) was used as an electronic laboratory notebook (ELN) in place of the traditional hardbound paper laboratory notebook (PLN) used prior to the pandemic. The initial reasoning for switching to an ELN was around safety-allowing course staff and students to maintain physical distancing whenever possible and eliminating the need for teaching assistants to handle student notebooks; however, the benefits of the ONCN proved to be significantly more. OneNote acted not only as a place for students to record notes but the Class Notebook's unique features allowed easy integration of other important aspects of the course, including delivery of laboratory manuals, posting of student results, notetaking feedback, sharing of instructional materials with teaching assistants, and more. Student and teacher experiences with the ONCN as used within a fully in person biochemistry laboratory course, as well as learned best practices, are reviewed.
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Bioquímica , COVID-19 , Laboratorios , SARS-CoV-2 , Humanos , COVID-19/epidemiología , Bioquímica/educación , Estudiantes , Curriculum , PandemiasRESUMEN
Teaching chemistry and biology students about biologics design remains challenging despite its increasing importance in pharmaceutical development. Monoclonal antibodies, commonly called mAbs, are the most popular biologics. They have been developed into drugs to treat various diseases in the past decades. Multiple challenges exist for designing proper formulations to stabilize mAbs, such as preventing aggregation and mitigating viscosity. Molecular modeling and simulations can improve pharmaceutical products by examining the interactions between mAbs and other compounds, such as excipients. To introduce students to biopharmaceuticals, eight students at the Stevens Institute of Technology participated in a semester-long course to learn the challenges of pharmaceutical development and different computational skills to study biologics design. The students started with a limited background in this field. Throughout one semester, they were introduced to various literature and software tools for modeling antibodies and studying their interactions with excipients. This paper aims to develop a course structure to be replicated at other universities and institutions to teach biopharmaceutical development to students.
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Productos Biológicos , Estudiantes , Enseñanza , Humanos , Productos Biológicos/química , Modelos Moleculares , Anticuerpos Monoclonales/química , Diseño de FármacosRESUMEN
As biologists accumulate or encounter increasingly large and complex data sets, our field creates the need for students to develop skills in data exploration and visualization. Many biology courses lack the time for students to develop the skills needed to parse complex datasets and visualize them appropriately. We developed a new upper-level undergraduate biology course to focused on data exploration and communication without requiring previous coding experience. We emphasized data visualization principles and best practices and taught students how to manage and visualize data via Tableau and R. We also explored scientific ethics, how to refute misinformation, and inequities that can occur in data collection and usage.
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Biología , Estudiantes , Humanos , EnseñanzaRESUMEN
A computational biochemistry laboratory, fitted for bioinformatics students, is presented. The molecular dynamics package GROMACS is used to prepare and simulate a solvated protein. Students analyze the trajectory with different available tools (GROMACS and VMD) to probe the structural stability of the protein during the simulation. Students are also required to make use of Python libraries and write their own code to probe non-covalent interactions between the amino acid side chains. Based on these results, students characterize the system in a qualitatively approach but also assess the importance of each specific interaction through time. This work mobilizes biochemical concepts and programming skills, fostering critical thinking and group work and developing presenting skills.
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Biología Computacional/educación , Simulación de Dinámica Molecular , Receptor 3 Gatillante de la Citotoxidad Natural/química , Programas Informáticos , Estudiantes/psicología , Humanos , UniversidadesRESUMEN
This brief review explores the ever-increasing role that technological affordances may play in the 21C biochemistry and molecular biology curriculum. We consider the need to develop digital and creative fluencies in our students and the importance of creativity and visualization in learning science. The potential of virtual reality (VR) platforms to complement these goals are discussed with a number of examples. Finally, we look into the future where to see how VR might fit into a future curriculum.
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Curriculum , Biología Molecular/educación , Realidad Virtual , HumanosRESUMEN
The recent COVID-19 pandemic has led to widespread lock-down strategies that force universities to perform all educational activities remotely. In this context, laboratory lessons pose a significant challenge. Here, I present an on-line tool that simulates the kinetics of chemical reactions. Enzymatic mechanisms can be easily modeled and followed through time. In addition, professors can customize the interface to hide the reaction mechanism. This setting will force students to design virtual experiments to uncover the mechanism and obtain the relevant enzymatic parameters. While some of the skills developed in a practical lesson cannot be simulated, this tool can be used to teach students important concepts about data acquisition and processing.
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Bioquímica/educación , COVID-19/epidemiología , Educación a Distancia , Pandemias , SARS-CoV-2 , Universidades , Realidad Virtual , Humanos , LaboratoriosRESUMEN
Structural biology education commonly employs molecular visualization software, such as PyMol, RasMol, and VMD, to allow students to appreciate structure-function relationships in biomolecules. In on-ground, classroom-based education, these programs are commonly used on University-owned devices with software preinstalled. Remote education typically involves the use of student-owned devices, which complicates the use of such software, owing to the fact that (a) student devices have differing configurations (e.g., Windows vs MacOS) and processing power, and (b) not all student devices are suitable for use with such software. Smartphones are near-ubiquitous devices, with smartphone ownership exceeding personal computer ownership, according to a recent survey. Here, we show the use of a smartphone-based augmented reality app, Augment, in a structural biology classroom exercise, which students installed independently without IT support. Post-lab attitudinal survey results indicate positive student experiences with this app. Based on our experiences, we suggest that smartphone-based molecular visualization software, such as that used in this exercise, is a powerful educational tool that is particularly well-suited for use in remote education.
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Realidad Aumentada , Educación a Distancia , Biología Molecular/educación , Teléfono Inteligente , Programas Informáticos , HumanosRESUMEN
Lab courses are a significant component of biochemistry and molecular biology (BMB) education. In teaching the labs, we combine established techniques with novel approaches. Lab formats have also moved from traditional cookbook style labs to guided inquiry to course-based undergraduate research experiences (CUREs), where faculty bring their own research interests into the course setting with a larger number of students in a much more restricted time frame. This presentation is designed to explore some of these ideas and challenge the reader to introduce research opportunities to all students, not just the smaller group of students in their research labs.
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Docentes , Laboratorios , Biología Molecular/educación , Enseñanza , Universidades , HumanosRESUMEN
Course-based Undergraduate Research Experiences (CUREs) can be a very effective means to introduce a large number of students to research. CUREs are often an extension of the instructor's research, which may make them difficult to replicate in other settings because of differences in expertise or facilities. The BASIL (Biochemistry Authentic Scientific Inquiry Lab) CURE has evolved over the past 4 years as faculty members with different backgrounds, facilities, and campus cultures have all contributed to a robust curriculum focusing on enzyme function prediction that is suitable for implementation in a wide variety of academic settings. © 2019 International Union of Biochemistry and Molecular Biology, 47(5):498-505, 2019.
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Bioquímica/educación , Proteínas/química , Investigación , Curriculum , Docentes , Humanos , Aprendizaje , Estudiantes , UniversidadesRESUMEN
Modeling is a practice of science that is underemphasized in biology classrooms in comparison to its central focus in the physical sciences. Visualizations of the submicroscopic world of molecules are becoming increasingly sophisticated with the evolution of new technologies. With this in mind, we introduced high school biology classrooms to a professional molecular modeling software program used by research biochemists to visualize proteins and other macromolecules. Analysis of surveys completed before and after the use of the program revealed significant student gains in their understandings of the nature of models. Student and teacher perceptions of the program showed an appreciation for the real/authentic nature of the program, and its affordances when utilizing the three-dimensional rendering of proteins. The teachers did report a general level of frustration regarding their lack of experience with the program and their inability to unlock its full potential due to not being able to access all of the program's features. However, we believe that the evidence at hand indicates that the value of introducing students to authentic molecular modeling tools in high school science classrooms outweighs the potential limitations. © 2018 by The International Union of Biochemistry and Molecular Biology, 46(3):230-236, 2018.
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Simulación de Dinámica Molecular , Aprendizaje Basado en Problemas , Estudiantes , Humanos , Práctica Profesional , Instituciones AcadémicasRESUMEN
A thorough understanding of the molecular biosciences requires the ability to visualize and manipulate molecules in order to interpret results or to generate hypotheses. While many instructors in biochemistry and molecular biology use visual representations, few indicate that they explicitly teach visual literacy. One reason is the need for a list of core content and competencies to guide a more deliberate instruction in visual literacy. We offer here the second stage in the development of one such resource for biomolecular three-dimensional visual literacy. We present this work with the goal of building a community for online resource development and use. In the first stage, overarching themes were identified and submitted to the biosciences community for comment: atomic geometry; alternate renderings; construction/annotation; het group recognition; molecular dynamics; molecular interactions; monomer recognition; symmetry/asymmetry recognition; structure-function relationships; structural model skepticism; and topology and connectivity. Herein, the overarching themes have been expanded to include a 12th theme (macromolecular assemblies), 27 learning goals, and more than 200 corresponding objectives, many of which cut across multiple overarching themes. The learning goals and objectives offered here provide educators with a framework on which to map the use of molecular visualization in their classrooms. In addition, the framework may also be used by biochemistry and molecular biology educators to identify gaps in coverage and drive the creation of new activities to improve visual literacy. This work represents the first attempt, to our knowledge, to catalog a comprehensive list of explicit learning goals and objectives in visual literacy. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):69-75, 2017.
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Bioquímica/educación , Gráficos por Computador , Procesamiento de Imagen Asistido por Computador/métodos , Aprendizaje , Biología Molecular/educación , Imagen Molecular/métodos , Proteínas/química , Objetivos , Humanos , Modelos Educacionales , Modelos Moleculares , EstudiantesRESUMEN
Analyzing protein structure has become an integral aspect of understanding systems of biochemical import. The laboratory experiment endeavors to introduce protein folding to ascertain structures of proteins for which the structure is unavailable, as well as to critically evaluate the quality of the prediction obtained. The model system used is the highly mutable influenza virus protein neuraminidase, which is the key target in the development of therapeutics. In light of recent pandemics, understanding how mutations confer drug resistance, which translates at the molecular level to understanding how different sequence variants differ, constitutes an area of great interest because of the ramifications in public health. This lab targets upper level undergraduate biochemistry students, and aims to introduce tools to be used to explore protein folding and protein visualization in the context of the neuraminidase case study. Students proceed to critically evaluate the folded models by comparison with crystallographic structures. When validity is established, they fold a neuraminidase sequence for which a structure is not available. Through structural alignment and visual inspection of the 150 loop, students gain molecular insight into two possible conformations of the protein, which are actively being studied. Folding the third chosen sequence mimics a true research environment in allowing students to generate a structure from a sequence for which a structure was not previously available, and to assess whether their particular variant has an open or closed loop. From this vantage, they are then challenged to speculate about the connection between loop conformation and drug susceptibility. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(4):361-376, 2016.
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Bioquímica/educación , Biología Computacional/educación , Evaluación Educacional , Variación Genética/genética , Neuraminidasa/química , Aprendizaje Basado en Problemas/métodos , Secuencia de Aminoácidos , Curriculum , Humanos , Modelos Moleculares , Neuraminidasa/genética , Conformación Proteica , Pliegue de Proteína , Relación Estructura-ActividadRESUMEN
In order to review the need assessment of enhancing the weightage of Applied Biochemistry in the undergraduate curriculum at Mahatma Gandhi Institute of Medical Sciences (MGIMS), Sevagram, a validated questionnaire was sent to 453 participants which include 387 undergraduate students, 11 interns, 23 postgraduate students, and 32 faculty members. A web-based data collection and analysis tool was designed for online questionnaire distribution, data collection, and analysis. Response rate was 100%. Most of the respondents agreed that the subject Biochemistry has relevance in clinical practice (81.24%) and applied based learning of Biochemistry by medical undergraduates would help in overall improvement in the health standards/patients care (83.44%). According to 65.12% respondents, most of the medical undergraduates read Biochemistry just for examination purpose only. Nearly half of the respondents agreed that minute details of biochemical reactions were not much useful in clinical practice (53.86%) and the vast majority of diagrammatic cycles memorized by the medical undergraduates had no relevance in clinical practice (51.21%), the decreased interest in learning the Applied Biochemistry was due to more amount of clinically irrelevant information taught to medical undergraduates (73.51%), there was a need to rethink for removing the diagrammatic biochemical cycles from curriculum for medical undergraduates (48.12%), the less learning of Applied Biochemistry or competencies would affect the clinical skills and knowledge of medical undergraduates (70.42%). The result of this study suggests that there is need for restructuring the Biochemistry curriculum with more clinical relevance. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:230-240, 2016.
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Bioquímica/educación , Competencia Clínica , Curriculum/normas , Educación de Pregrado en Medicina , Modelos Educacionales , Evaluación de Necesidades , Humanos , Aprendizaje , Estudiantes de MedicinaRESUMEN
A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and simulations. In particular, modern computational tools are employed to elucidate the relationship between structure, dynamics, and function in proteins. Computer-based laboratory protocols that we introduced in three modules allow students to visualize the secondary, super-secondary, and tertiary structures of proteins, analyze non-covalent interactions in protein-ligand complexes, develop three-dimensional structural models (homology model) for new protein sequences and evaluate their structural qualities, and study proteins' intrinsic dynamics to understand their functions. In the fourth module, students are assigned to an authentic research problem, where they apply their laboratory skills (acquired in modules 1-3) to answer conceptual biophysical questions. Through this process, students gain in-depth understanding of protein dynamics-the missing link between structure and function. Additionally, the requirement of term papers sharpens students' writing and communication skills. Finally, these projects result in new findings that are communicated in peer-reviewed journals.
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Bioquímica/educación , Proteínas/química , Proteínas/fisiología , Universidades , Laboratorios , Modelos Moleculares , Biología Molecular/educación , Conformación Proteica , Relación Estructura-ActividadRESUMEN
Computational molecular docking is a fast and effective in silico method for the analysis of binding between a protein receptor model and a ligand. The visualization and manipulation of protein to ligand binding in three-dimensional space represents a powerful tool in the biochemistry curriculum to enhance student learning. The DockoMatic tutorial described herein provides a framework by which instructors can guide students through a drug screening exercise. Using receptor models derived from readily available protein crystal structures, docking programs have the ability to predict ligand binding properties, such as preferential binding orientations and binding affinities. The use of computational studies can significantly enhance complimentary wet chemical experimentation by providing insight into the important molecular interactions within the system of interest, as well as guide the design of new candidate ligands based on observed binding motifs and energetics. In this laboratory tutorial, the graphical user interface, DockoMatic, facilitates docking job submissions to the docking engine, AutoDock 4.2. The purpose of this exercise is to successfully dock a 17-amino acid peptide, α-conotoxin TxIA, to the acetylcholine binding protein from Aplysia californica-AChBP to determine the most stable binding configuration. Each student will then propose two specific amino acid substitutions of α-conotoxin TxIA to enhance peptide binding affinity, create the mutant in DockoMatic, and perform docking calculations to compare their results with the class. Students will also compare intermolecular forces, binding energy, and geometric orientation of their prepared analog to their initial α-conotoxin TxIA docking results.
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Bioquímica/educación , Biología Computacional , Péptidos/metabolismo , Receptores de Superficie Celular/metabolismo , Estudiantes , Sitios de Unión , Simulación del Acoplamiento MolecularRESUMEN
As non-scientific conceptions interfere with learning processes, teachers need both, to know about them and to address them in their classrooms. For our study, based on 182 eleventh graders, we analyzed the level of conceptual understanding by implementing the "draw and write" technique during a computer-supported gene technology module. To give participants the hierarchical organizational level which they have to draw, was a specific feature of our study. We introduced two objective category systems for analyzing drawings and inscriptions. Our results indicated a long- as well as a short-term increase in the level of conceptual understanding and in the number of drawn elements and their grades concerning the DNA structure. Consequently, we regard the "draw and write" technique as a tool for a teacher to get to know students' alternative conceptions. Furthermore, our study points the modification potential of hands-on and computer-supported learning modules.
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ADN/química , Biología Molecular/educación , Enseñanza/métodos , Adolescente , Comprensión , Computadores , Femenino , Humanos , Aprendizaje , Masculino , Encuestas y CuestionariosRESUMEN
The activity of mushroom tyrosinase can be measured by monitoring the conversion of phenolic compounds into quinone derivatives using spectrophotometry. This article describes a series of experiments which characterize the functional properties of tyrosinase, the analysis of the resulting data using R to determine the kinetic parameters, and the exploration of the structural properties of tyrosinase-inhibitor complexes. Tyrosinase assay development and subsequent activity measurements, in the presence of varying pH, substrate concentration and inhibitors, offers the opportunity to learn the enzyme characterization skills relevant to a research laboratory setting. Combining the activity studies with an exploration of the nature of the tyrosinase-inhibitor interactions enables a structural understanding of the experimental observations.
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Agaricus/química , Bioquímica/educación , Monofenol Monooxigenasa/química , Aprendizaje Basado en Problemas/métodos , Agaricus/enzimología , Pruebas de Enzimas/métodos , Humanos , Laboratorios , Modelos Biológicos , Investigación/educación , Espectrofotometría/métodos , UniversidadesRESUMEN
Teaching the subject of the electron transport chain is one of the most challenging aspects of the chemistry curriculum at the high school level. This article presents an educational program called "Electron Transport Chain" which consists of 14 visual animations including a biochemistry quiz. The program was created in the Adobe Flash CS3 Professional animation program and is designed for high school chemistry students. Our goal is to develop educational materials that facilitate the comprehension of this complex subject through dynamic animations which show the course of the electron transport chain and simultaneously explain its nature. We record the process of the electron transport chain, including connections with oxidative phosphorylation, in such a way as to minimize the occurrence of discrepancies in interpretation. The educational program was evaluated in high schools through the administration of a questionnaire, which contained 12 opened-ended items and which required participants to evaluate the graphics of the animations, chemical content, student preferences, and its suitability for high school biochemistry teaching.
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Recursos Audiovisuales , Bioquímica/educación , Instrucción por Computador/métodos , Enseñanza/métodos , Comprensión , Curriculum , Transporte de Electrón , Humanos , Aprendizaje , EstudiantesRESUMEN
The sequencing of whole genomes and the analysis of genetic information continues to fundamentally change biological and medical research. Unfortunately, the people best suited to interpret this data (biologically trained researchers) are commonly discouraged by their own perceived computational limitations. To address this, we developed a course to help alleviate this constraint. Remarkably, in addition to equipping our undergraduates with an informatic toolset, we found our course design helped prepare our students for collaborative research careers in unexpected ways. Instead of simply offering a traditional lecture- or laboratory-based course, we chose a guided inquiry method, where an instructor-selected research question is examined by students in a collaborative analysis with students contributing to experimental design, data collection, and manuscript reporting. While students learn the skills needed to conduct bioinformatic research throughout all sections of the course, importantly, students also gain experience in working as a team and develop important communication skills through working with their partner and the class as a whole, and by contributing to an original research article. Remarkably, in its first three semesters, this novel computational genetics course has generated 45 undergraduate authorships across three peer-reviewed articles. More importantly, the students that took this course acquired a positive research experience, newfound informatics technical proficiency, unprecedented familiarity with manuscript preparation, and an earned sense of achievement. Although this course deals with analyses of genetic systems, we suggest the basic concept of integrating actual research projects into a 16-week undergraduate course could be applied to numerous other research-active academic fields.
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Biología Computacional/educación , Biología Computacional/métodos , Educación Profesional/métodos , Genoma , Análisis de Secuencia de ADN , Humanos , Manuscritos como AsuntoRESUMEN
The Forensic Science Education Programs Accreditation Commission (FEPAC) requires accredited programs offer a "coherent curriculum" to ensure each student gains a "thorough grounding of the natural sciences." Part of this curriculum includes completion of a minimum of 15 semester-hours forensic science coursework, nine of which can involve a class in forensic DNA biology. Departments that have obtained or are pursuing FEPAC accreditation can meet this requirement by offering a stand-alone forensic DNA biology course; however, materials necessary to instruct students are often homegrown and not standardized; in addition, until recently, the community lacked commercially available books, lab manuals, and teaching materials, and many of the best pedagogical resources were scattered across various peer-reviewed journals. The curriculum discussed below is an attempt to synthesize this disparate information, and although certainly not the only acceptable methodology, the below discussion represents "a way" for synthesizing and aggregating this information into a cohesive, comprehensive whole.