Using giant characeaen algae Nitellopsis obtusa in laboratory exercises is proposed to familiarize students with basic concepts of electrophysiology and provide some simple hands-on practice. The described concept experiments present extracellular registration of action potentials (APs) and investigation of cytoplasmic streaming properties. Students are expected to register the propagation velocity of APs (found to be 3.4 ± 1.5 cm/s in N. obtusa), as well as the velocity of cytoplasmic streaming (66.7 ± 9 μm/s). Proposed exercises also concern recovery dynamics of cytoplasmic streaming after a stimulation (recovery time constant τ = 3.7 ± 2.1 min) as well as investigation of an effect of various chemicals (e.g., KCl) on all selected parameters. The experiments endorse characeaen algae as a model system to be routinely explored in education of biophysics and bioelectrical phenomena of the cell.ABSTRACT
In this article, I describe a new curriculum for introductory physics for the life sciences, a 2-semester sequence usually required of all biology majors. Because biology-related applications on the macroscale are complex and require mathematics beyond introductory calculus, the focus is entirely on applications from molecular and cellular biology. Topics that are more relevant for engineering have been removed, and topics relevant to biology have been added. The curriculum is designed around 2 main themes: diffusion and electric dipoles. Diffusion illustrates the concepts of conservation of momentum and energy and provides the framework for introducing entropy from the perspective of statistical mechanics. Electric dipoles illustrate the basic concepts of electromagnetic theory and provide the framework for understanding light waves and light interactions with biomolecules. These themes are supported by small computational activities to help students understand the physics without advanced mathematics. This curriculum has been piloted over the past 4 years at Michigan State University and should be applicable to many colleges and universities.ABSTRACT
The aim of this article is to introduce the basic principles behind the widely used microscopy tool: fluorescence fluctuation correlation spectroscopy (FFCS). We present the fundamentals behind single spot acquisition (FCS) and its extension to spatiotemporal sampling, which is implemented through image correlation spectroscopy (ICS). The article is an educational guide that introduces theoretic concepts of FCS and some of the ICS techniques, followed by interactive exercises in MATLAB. There, the learner can simulate data time series and the application of various FFCS techniques, as well as learn how to measure diffusion coefficients, molecular flow, and concentration of particles. Additionally, each section is followed by a short exercise to reinforce learning concepts by simulating different scenarios, seek verification of outcomes, and make comparisons. Furthermore, we invite the learner throughout the article to consult the literature for different extensions of FFCS techniques that allow measurements of different physicochemical properties of materials. Upon completion of the modules, we anticipate the learner will gain a good understanding in the field of FFCS that will encourage further exploration and adoption of the FFCS tools in future research and educational practices.ABSTRACT
The behavior of ion channels and transporters is often modeled using discrete state continuous-time Markov models. Such models are helpful for the interpretation of experimental data and can guide the design of experiments by testing specific predictions. Here, we describe a computational tool that allows us to create Markov models of chosen complexity and to calculate the predictions on a macroscopic scale, as well on a single-molecule scale. The program calculates steady-state properties (current, state probabilities, and cycle frequencies), deterministic macroscopic and stochastic time courses, gating currents, dwell-time histograms, and power spectra of channels and transporters. In addition, a visual simulation mode allows us to follow the time-dependent stochastic behavior of a single channel or transporter. After a basic introduction into the concept of Markov models, real-life examples are discussed, including a model of a simple K+ channel, a voltage-gated sodium channel, a 3-state ligand-gated channel, and an electrogenic uniporter. In this manner, the article has a modular architecture, progressing from basic to more advanced topics. This illustrates how the MarkovEditor program can serve students to explore Markov models at a basic level but is also suited for research scientists to test and develop models on the mechanisms of protein function.ABSTRACT
Mean squared displacement is a standard biophysical tool for characterizing the motion of particles in a thermally dominated environment, yet it is rarely formally introduced or discussed in undergraduate curriculum. Here, we provide a flexible and adaptable experimental or computational lab activity that provides a practical introduction to mean squared displacement and anomalous diffusion that includes optional experimental protocols and computational simulation techniques for data collection and discusses a variety of analysis techniques. This lab activity has been implemented both face-to-face and completely online and provides crucial experience in important research techniques, helping to bridge traditional undergraduate curriculum and modern biophysics research.ABSTRACT
Increased attention has been conferred upon interdisciplinary science, technology, engineering, and math (STEM) education to prepare students for deeper understanding to address complex challenges (1–3). Particularly at the undergraduate level, there is recognized value in providing opportunities for students to integrate knowledge across disciplinary boundaries (4–7). In addition to core technical knowledge, it is beneficial to confer behavioral skills that allow students to perform well with others through effective communication, time management, and teamwork (8). Undergraduate research experiences have been considered to be a powerfulInterdisciplinary research experience in biophysics
We describe a project-based learning (PBL) program that combines student-driven projects with year-long mentorship to inspire high school students to pursue science, technology, engineering, and math (STEM). Previous studies indicate that PBL improves learning outcomes, teamwork, and long-term interest (1–4). Separate work suggests that long-term mentorship (LTM) programs can promote a pipeline into higher education and STEM for students from underrepresented backgrounds (5, 6). We sought to combine PBL and LTM through a single program called Future Advancers of Science and Technology (FAST). FAST was started at Andrew P. Hill HighIntroduction
For those of us who have been teaching molecular and cellular engineering, an important and significant new tool is now available. Wittrup et al. have written a very nice textbook that spans many of the important areas of this discipline and provides a substantial number of problems that should prove a significant aid to instructors. Cellular engineering, broadly defined, is the quantification and manipulation of cell behavior. The idea that one can design a system to behave as intended is endemic to engineering, and now that we have more knowledge about the parts of a cell and how they work,
Computational Cell Physiology: With Examples in Python introduces key cellular mechanisms that cover a wide range of cell physiology topics, particularly associated with excitable cells such as nerve, muscle, and endocrine cells. The book is written by Dr. Stephen M. Baylor, Professor Emeritus of Physiology at the University of Pennsylvania, whose expertise lies in excitation-contraction coupling in vertebrate skeletal muscle and the role of the calcium ion as an intracellular chemical messenger. What makes this book stand out from the rest is that it uses a relatively easy-to-learn programming language, Python, to describe and computationally simulate the mechanisms in