Visualizing the Invisible: A Guide to Designing, Printing, and Incorporating Dynamic 3D Molecular Models to Teach Structure–Function Relationships

Understanding the intricate relationship between macromolecular structure and function represents a central goal of undergraduate biology education (1–3). In teaching complex three-dimensional (3D) concepts, instructors typically depend on static two-dimensional (2D) textbook images or computer-based visualization software, which can lead to unintended misconceptions (4–6). While chemical and molecular kits exist, these models cannot handle the size and detail of macromolecules. Consequently, students may graduate in the life sciences without understanding how structure underlies function or acquiring skills to translate between 2D and 3D molecular models (5, 7). Building on recent technological advances, 3D printing (3DP) potentiates an era in which students learn through direct interaction with dynamic 3D structural models. With 3DP, instructors have the opportunity to use tailor-made models of virtually any size molecule. For example, protein models can be designed to relate enzyme active site structures to kinetic activity. Furthermore, instructors can use diverse printing materials and accessories to demonstrate molecular properties, dynamics, and interactions (Fig. 1). In this article and supplemental guide, we present an example of how to incorporate a 3D model-based lesson on DNA supercoiling in an undergraduate biochemistry classroom and best practices for designing and printing 3D models

Video guide to design flexible DNA.mp4

Model file name: Video guide to design flexible DNA.mp4 Authors: Michelle E Howell, Karin van Dijk, Christine S Booth, Tomas Helikar, Brian A Couch, Rebecca L Roston This 30-minute video includes step-by-step instructions to design and 3-D print a long flexible DNA model that mimics the structure and function of DNA. The instructions are applicable for designing the model using open-source 3-D computer graphics software Blender 2.79 which is available for download at https://www.blender.org/download/. .mp4 file download (70 MB) below

Experimental Validation of a Fundamental Model for PCR Efficiency

Recently a theoretical analysis of PCR efficiency has been published by Booth et al., (2010). The PCR yield is the product of three efficiencies: (i) the annealing efficiency is the fraction of templates that form binary complexes with primers during annealing, (ii)the polymerase binding efficiency is the fraction of binary complexes that bind to polymerase to form ternary complexes and (iii)the elongation efficiency is the fraction of ternary complexes that extend fully. Yield is controlled by the smallest of the three efficiencies and control could shift from one type of efficiency to another over the course of a PCR experiment. Experiments have been designed that are specifically controlled by each one of the efficiencies and the results are consistent with the mathematical model. The experimental data has also been used to quantify six key parameters of the theoretical model. An important application of the fully characterized model is to calculate initial template concentration from real-time PCR data. Given the PCR protocol, the midpoint cycle number (where the template concentration is half that of the final concentration) can be theoretically determined and graphed for a variety of initial DNA concentrations. Real-time results can be used to calculate the midpoint cycle number and consequently the initial DNA concentration, using this graph. The application becomes particularly simple if a conservative PCR protocol is followed where only the annealing efficiency is controlling

Efficiency of the Polymerase Chain Reaction

The polymerase chain reaction (PCR) has found wide application in biochemistry and molecular biology such as gene expression studies, mutation detection, forensic analysis and pathogen detection. Increasingly quantitative real time PCR is used to assess copy numbers from overall yield. In this study the yield is analyzed as a function of several processes: (1) thermal damage of the template and polymerase occurs during the denaturing step, (2) competition exists between primers and templates to either anneal or form dsDNA, (3) polymerase binding to annealed products (primer/ssDNA) to form ternary complexes and (4) extension of ternary complexes. Explicit expressions are provided for the efficiency of each process, therefore reaction conditions can be directly linked to the overall yield. Examples are provided where different processes play the yield-limiting role. The analysis will give researchers a unique understanding of the factors that control the reaction and will aid in the interpretation of experimental results

Visualizing the Invisible: A Guide to Designing, Printing, and Incorporating Dynamic 3D Molecular Models to Teach Structure–Function Relationships

Understanding the intricate relationship between macromolecular structure and function represents a central goal of undergraduate biology education (1–3). In teaching complex three-dimensional (3D) concepts, instructors typically depend on static two-dimensional (2D) textbook images or computer-based visualization software, which can lead to unintended misconceptions (4–6). While chemical and molecular kits exist, these models cannot handle the size and detail of macromolecules. Consequently, students may graduate in the life sciences without understanding how structure underlies function or acquiring skills to translate between 2D and 3D molecular models (5, 7)

Student Understanding of DNA Structure–Function Relationships Improves from Using 3D Learning Modules with Dynamic 3D Printed Models

Understanding the relationship between molecular structure and function represents an important goal of undergraduate life sciences. Although evidence suggests that handling physical models supports gains in student understanding of structure–function relationships, such models have not been widely implemented in biochemistry classrooms. Three-dimensional (3D) printing represents an emerging cost-effective means of producing molecular models to help students investigate structure–function concepts. We developed three interactive learning modules with dynamic 3D printed models to help biochemistry students visualize biomolecular structures and address particular misconceptions. These modules targeted specific learning objectives related to DNA and RNA structure, transcription factor-DNA interactions, and DNA supercoiling dynamics. We also designed accompanying assessments to gauge student learning. Students responded favorably to the modules and showed normalized learning gains of 49% with respect to their ability to understand and relate molecular structures to biochemical functions. By incorporating accurate 3D printed structures, these modules represent a novel advance in instructional design for biomolecular visualization. We provide instructors with the materials necessary to incorporate each module in the classroom, including instructions for acquiring and distributing the models, activities, and assessments. 9 supplemental files attached (below

Relationship between homocysteine and cardiorespiratory fitness is sex-dependent

Abstract Elevated plasma homocysteine is recognized as an independent risk factor for cardiovascular disease. Recently, there have been conflicting reports of the relationship between physical activity and homocysteine. A more objective measure of physical activity is cardiorespiratory fitness; however, its relationship with homocysteine has yet to be investigated. The aim of this study was to determine the relationship between cardiorespiratory fitness and plasma homocysteine. Cross-sectional associations between cardiorespiratory fitness (VO 2 max) and plasma homocysteine were examined in 49 men and 11 women. A submaximal bicycle test was used to determine VO 2 max and plasma homocysteine was measured using high performance liquid chromatography with fluorescence detection. Dietary analysis determined B vitamin intake. There was a significant inverse relationship between plasma homocysteine concentration and VO 2 max in women (r ϭ Ϫ0.81, P ϭ 0.003) but not in men (r ϭ Ϫ0.09, P ϭ 0.95). There were no significant relationships between plasma homocysteine and age, BMI, body fat, total cholesterol, and LDL cholesterol. In summary, elevated cardiorespiratory fitness is associated with decreased plasma homocysteine concentrations in women

Bridging Medical Simulation with Computer Science and Engineering: A Growing Field of Study

Objectives: The aim of this study was to determine if having on-site technological expertise will allow for the facile navigation of high fidelity manikins within nursing programs as well as to assess if the level of understanding and interest among engineering students would increase as a result of attending a class related to the technology used in healthcare simulation. Methods: Two assessments were applied to engineering students attending a class of technology used in healthcare simulation. A pre-test was designed to measure the understanding and interest of students in the engineering/computer science courses before attending a simulation class. A post-test assessment was used to measure their improvement in understanding and interest to learn more about simulation technologies. Participants: Engineering students attending 6 different engineering programs (Computer Science, Computer Engineering, Mechanical Engineering, Biomedical Engineering, Electrical Engineering and Technology Management) and having different educational levels (undergraduate and graduate)