We report a summary of the results from an education research project that investigated student reasoning related to Michaelis-Menten enzyme kinetics and enzyme inhibition. We have previously discussed students' mathematical reasoning related to rate laws and reaction order, student conceptions of different types of enzyme inhibition (competitive, noncompetitive, and uncompetitive), and student understanding of representations used to describe enzyme kinetics (Michaelis-Menten graphs, Lineweaver-Burk plots, reaction schemes). In this paper, we bring together the different publications that resulted from this project to emphasize the implications for instruction gleaned from each study and discuss the additional insight provided by synthesizing the results across studies. For this work, the results from this project have been framed according to the refined consensus model of pedagogical content knowledge, a framework from science education that defines the knowledge and skills needed to transform content knowledge into teaching.ABSTRACT
Advances in fluorescent biosensors allow researchers to spatiotemporally monitor a diversity of biochemical reactions and secondary messengers. However, commercial microscopes for the specific application of Förster Resonance Energy Transfer (FRET) are prohibitively expensive to implement in the undergraduate classroom, owing primarily to the dynamic range required and need for ratiometric emission imaging. The purpose of this article is to provide a workflow to design a low-cost, FRET-enabled microscope and to equip the reader with sufficient knowledge to compare commercial light sources, optics, and cameras to modify the device for a specific application. We used this approach to construct a microscope that was assembled by undergraduate students with no prior microscopy experience that is suitable for most single-cell cyan and yellow fluorescent protein FRET applications. The utility of this design was demonstrated by measuring small metabolic oscillations by using a lactate FRET sensor expressed in primary mouse pancreatic islets, highlighting the biologically suitable signal-to-noise ratio and dynamic range of our compact microscope. The instructions in this article provide an effective teaching tool for undergraduate educators and students interested in implementing FRET in a cost-effective manner.ABSTRACT
Self-organization is ubiquitous in biology, with viruses providing an excellent illustration of bioassemblies being much more than the sum of their parts. Following nature's lead, molecular self-assembly has emerged as a new synthetic strategy in the past 3 decades or so. Self-assembly approaches promise to generate complex supramolecular architectures having molecular weights of 0.5 to 100 MDa and collective properties determined by the interplay between structural organization and composition. However, biophysical methods specific to mesoscopic self-assembly, and presentations of the challenges they aim to overcome, remain underrepresented in the educational laboratory curriculum. We present here a simple but effective model for laboratory instruction that introduces students to the world of intermolecular forces and virus assembly, and to a cutting-edge technology, atomic force microscopy nanoindentation, which is able to measure the mechanical properties of single virus shells in vitro. In addition, the model illustrates the important idea that, at nanoscale, phenomena often have an inherent interdisciplinary character.ABSTRACT
Characterizing the load–deformation relationships in both engineering materials and biologic tissues is a key component of undergraduate biomechanics and mechanobiology courses. These relationships are essential to determining the suitability of a given material for biomedical applications, such as identifying the root causes of implant failure and injury and quantifying the effects of mechanical cellular mechanotransduction. Typically, material characterization is done by using industry standard and research-grade material testing systems, which can cost tens to hundreds of thousands of dollars and require large amounts of dedicated laboratory space. This article presents a new design for a low-cost and portable alternative to these commercial systems, consisting of off-the-shelf and 3-dimensional printed components for teaching purposes. Student groups assemble their own devices and conduct material characterization experiments for both elastic and viscoelastic materials on their own time, outside of traditional laboratory settings. The “take-home” labs were pilot tested over a single semester, and preliminary results showed increased understanding of elastic and viscoelastic theory compared with lecture alone. These results suggest that the take-home tensile testing systems may be an effective means of providing a hands-on educational experience in courses in which traditional lab activities are not otherwise possible.ABSTRACT
The concepts and frameworks of soft matter physics and the laws of thermodynamics can be used to describe relevant developmental, physiologic, and pathologic events in which directed cell migration is involved, such as in cancer. Typically, this directionality has been associated with the presence of soluble long-range gradients of a chemoattractant, synergizing with many other guidance cues to direct the motion of cells. In particular, physical inputs have been shown to strongly influence cell locomotion. However, this type of cue has been less explored despite the importance in biology. In this paper, we describe recent in vitro works at the interface between physics and biology, showing how the motion of cells can be directed by using gradient-free environments with repeated local asymmetries. This rectification of cell migration, from random to directed, is a process reminiscent of the Feynman ratchet; therefore, this framework can be used to explain the mechanism behind directed cell motion.ABSTRACT
Transient barriers are fundamental to cell supramolecular organization and assembly. Discontinuities between spaces can be generated by a physical barrier but also by thermodynamic barriers achieved by phase separation of molecules. However, because of the transient nature and the lack of a visible barrier, the existence of phase separation is difficult to demonstrate experimentally. We describe an approach based on the 2-dimensional pair correlation function (2D-pCF) analysis of the spatial connectivity in a cell. The educational aim of the article is to present both a model suitable for explaining diffusion barrier measurements to a broad range of courses and examples of biological situations. If there are no barriers to diffusion, particles could diffuse equally in all directions. In this situation the pair correlation function introduced in this article is independent of the direction and is uniform in all directions. However, in the presence of obstacles, the shape of the 2D-pCF is distorted to reflect how the obstacle position and orientation change the flow of molecules. In the example shown in this article, measurements of diffusion of enhanced green fluorescent protein moving in live cells show the lack of connectivity at the nucleolus surface for shorter distances. We also observe a gradual increase in the connectivity for longer distances or times, presumably because of molecular trajectories around the nucleolus.ABSTRACT
Transmitted light imaging is an important tool in biophysics for applications that include sample analysis, recording samples whose viability is compromised by high levels of illumination (e.g., live cell tracking), and finding regions of interest in a sample. Koehler transillumination is a powerful illumination method used in commercial microscopes; yet commercial Koehler condensers are expensive, are difficult to integrate into tabletop systems, and make learning the concepts of Koehler illumination difficult because of their closed-box nature. Here, we show a protocol to build a simple 4f Koehler illumination system that offers advantages with respect to commercial condensers in terms of simplicity, cost, and compatibility with tabletop systems, such as open-source light sheet fluorescence microscopes. We include step-by-step instructions that can be followed by advanced undergraduate or graduate students without experience in optics on how to align and assemble the illuminator, along with a list of the necessary parts for assembly. We also include supplemental material that describes 4 supporting educational activities students can conduct with the apparatus and helps in the understanding of key concepts relevant to Koehler illumination and optics. The performance of the system is comparable to that of commercial condensers and significantly better, in terms of illumination homogeneity and depth of field (optical sections are possible), than that of LED flashlights, such as those found in low-cost diagnostic devices and tabletop systems.ABSTRACT
Machine Learning in a Molecular Modeling Course for Chemistry, Biochemistry, and Biophysics Students
Recent advances in computer hardware and software, particularly the availability of machine learning (ML) libraries, allow the introduction of data-based topics such as ML into the biophysical curriculum for undergraduate and graduate levels. However, there are many practical challenges of teaching ML to advanced level students in biophysics majors, who often do not have a rich computational background. Aiming to overcome such challenges, we present an educational study, including the design of course topics, pedagogic tools, and assessments of student learning, to develop the new methodology to incorporate the basis of ML in an existing biophysical elective course and engage students in exercises to solve problems in an interdisciplinary field. In general, we observed that students had ample curiosity to learn and apply ML algorithms to predict molecular properties. Notably, feedback from the students suggests that care must be taken to ensure student preparations for understanding the data-driven concepts and fundamental coding aspects required for using ML algorithms. This work establishes a framework for future teaching approaches that unite ML and any existing course in the biophysical curriculum, while also pinpointing the critical challenges that educators and students will likely face.ABSTRACT
As a former high school physics teacher, attracting students to consider careers in the science, technology, engineering, and mathematics (STEM) fields has been a long-term interest. Consequently, undergraduate students have often played prominent roles in my laboratory's research activities. Approximately 50 students have been involved in research in my lab either through summer research programs (including first-year medical students), for academic credit, as volunteer interns, or because of other academic requirements. Among those student researchers, 29 were coauthor on 1 or more peer-reviewed publications, with 12 students as first or co-first author. Many of these students went on to pursue
Scientists in developing countries face several challenges, including limited funding and a smaller and less connected scientific community. One opportunity of growth is to host scientific meetings in these countries to highlight the importance of scientific research in society. As early career investigators, we organized a biophysics symposium in Costa Rica, a developing country, with the goal of increasing the awareness of and interest in biophysics and biomedical research. In this report, we discuss our experience organizing this event to serve as a practical guide with actionable points to organize meetings of this kind in developing countries.Science and networking
On 16 March 2020, an abrupt change entered my daily life, as it did for many others in the United Kingdom. All of a sudden, instead of working in a laboratory fabricating microfluidic devices, operating single-molecule detection setups, and preparing for my weekly undergraduate teaching, I found myself scrambling to bag up everything I might need from my office so that I could be productive from home for an indefinite period of time. It seemed a bit surreal, only having been back in the country for 2 weeks after attending the Biophysical Society meeting in San Diego, California, and taking
Stochastic simulation has become an indispensable tool in the scientific toolkit. We were all told as students that molecules jostle one another incessantly because of thermal motion and that chemical reactions rely on the resulting chance encounters between molecules. However, most of us took chemistry and physics classes in which attention quickly shifted to vast collections of molecules, for which the inherent randomness washed out when viewing overall concentrations; we then formulated and solved deterministic rate equations. However, some key actors in cells appear in only a small number of copies (perhaps just one, for some genes). Moreover, experimental technique