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The Joy of Markov Models—Channel Gating and Transport Cycling Made Easy 马尔可夫模型的乐趣——通道选通和运输循环变得容易
Pub Date : 2021-03-30 DOI: 10.35459/TBP.2019.000125
G. Zifarelli, P. Zuccolini, S. Bertelli, M. Pusch
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.
离子通道和转运体的行为通常使用离散状态连续时间马尔可夫模型来建模。这些模型有助于解释实验数据,并可以通过测试特定的预测来指导实验设计。在这里,我们描述了一个计算工具,它允许我们创建选择复杂性的马尔可夫模型,并在宏观尺度上计算预测,以及在单分子尺度上。该程序计算稳态特性(电流,状态概率和周期频率),确定性宏观和随机时间过程,门控电流,驻留时间直方图,以及通道和转运体的功率谱。此外,视觉模拟模式允许我们跟踪单个通道或传输体随时间的随机行为。在对马尔可夫模型概念的基本介绍之后,讨论了现实生活中的例子,包括简单的K+通道模型,电压门控钠通道,3态配体门控通道和致电单输子。通过这种方式,本文具有模块化的体系结构,从基本主题到更高级的主题。这说明了markoveitor程序如何能够帮助学生在基本水平上探索马尔可夫模型,但也适合研究科学家测试和开发蛋白质功能机制的模型。
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引用次数: 3
A Flexible Laboratory Exercise Introducing Practical Aspects of Mean Squared Displacement 一个灵活的实验室练习,介绍均方位移的实用方面
Pub Date : 2021-03-22 DOI: 10.35459/TBP.2020.000157
Alexander B. C. Mantilla, N. Kuwada
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.
均方位移是表征热主导环境中粒子运动的标准生物物理工具,但很少在本科课程中正式介绍或讨论。在这里,我们提供了一个灵活和适应性强的实验或计算实验室活动,提供了均方位移和异常扩散的实用介绍,包括可选的实验协议和数据收集的计算模拟技术,并讨论了各种分析技术。该实验活动采用了面对面和完全在线两种方式,提供了重要研究技术的重要经验,有助于连接传统的本科课程和现代生物物理学研究。
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引用次数: 0
Quantitative Fundamentals of Molecular and Cellular Engineering by K. Dane Wittrup, Bruce Tidor, Benjamin J. Hackel, and Casim A. Sarkar 《分子和细胞工程的定量基础》,作者:K. Dane Wittrup, Bruce Tidor, Benjamin J. hackkel和Casim A. Sarkar
Pub Date : 2021-02-17 DOI: 10.35459/TBP.2020.00161
D. Hammer
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, as well as sophisticated tools for genetic manipulation (such as mutation, clustered regularly interspaced short palindromic repeats [CRISPR] editing, transfections, and knock downs), we are at the point that we can manipulate cells to do what we wish. The goals are simple: inhibit cell function when it has gone awry, but more so, manipulate and enhance cell function when desired. A current successful example is chimeric antigen receptor T-lymphocyte therapy, but many other examples will be forthcoming, and we need to prepare quantitative scientists for the challenges of predicting, designing, and quantifying cell behavior.
对于我们这些一直在教授分子和细胞工程的人来说,一个重要而有意义的新工具现在是可用的。Wittrup等人写了一本非常好的教科书,涵盖了这门学科的许多重要领域,并提供了大量的问题,这些问题应该对教师有很大的帮助。广义上讲,细胞工程是对细胞行为的量化和操作。一个人可以设计一个系统按照预期的方式工作的想法是工程学特有的,现在我们对细胞的各个部分及其工作方式有了更多的了解,以及用于基因操作的复杂工具(如突变、聚集规律间隔短回文重复序列[CRISPR]编辑、转染和敲除),我们就可以操纵细胞做我们想做的事情了。目标很简单:在细胞功能出错时抑制细胞功能,但更重要的是,在需要时操纵和增强细胞功能。目前一个成功的例子是嵌合抗原受体t淋巴细胞治疗,但许多其他的例子将会出现,我们需要为定量科学家准备预测、设计和定量细胞行为的挑战。
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引用次数: 0
Curiosity-Based Biophysics Projects in a High School Setting with Graduate Student Mentorship 以好奇心为基础的高中生物物理学项目与研究生导师
Pub Date : 2021-02-17 DOI: 10.35459/TBP.2019.000136
Cooper J. Galvin, Katherine N. Liu, A. Kennard, Sahil K. Tembulkar, Alexander Dunlap, Tao A. G. Large, Thao Pham, Derek J. Le, Aurora Alvarez-Buylla, Helen Nguyen, Ezequiel Ponce, Sophia Tran, Nikki Nguyen, Christina Ngo, Christina Tran, Gabriela Huynh, Patrick Allamandola, Z. Bryant
Program in Biophysics, Stanford University, Stanford, CA 94305, USA Department of Bioengineering, Stanford University, Stanford, CA 94305, USA Department of Chemistry, Stanford University, Stanford, CA 94305, USA Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA Department of Mathematics, Stanford University, Stanford, CA 94305, USA Andrew P. Hill High School, San Jose, CA 95111, USA Program in Cancer Biology, Stanford University, Stanford, CA 94305, USA Department of Biology, Stanford University, Stanford, CA 94305, USA James Lick High School, San Jose, CA 95127, USA
美国斯坦福大学生物物理系,斯坦福,CA 94305,美国斯坦福大学生物工程系,斯坦福,CA 94305,美国斯坦福大学化学系,斯坦福,CA 94305,美国斯坦福大学医学院儿科,斯坦福,CA 94305,美国斯坦福大学数学系,斯坦福,CA 94305,美国安德鲁·p·希尔高中,加州圣何塞,CA 95111,美国斯坦福大学癌症生物学项目,斯坦福,CA 94305,美国斯坦福大学生物系,加州斯坦福94305;美国詹姆斯·利克高中,加州圣何塞95127
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引用次数: 1
A Practical Guide to Fluorescence Temporal and Spatial Correlation Spectroscopy 荧光时空相关光谱学实用指南
Pub Date : 2021-02-17 DOI: 10.35459/TBP.2019.000143
E. Pandzic, R. Whan
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.
本文的目的是介绍广泛使用的显微镜工具背后的基本原理:荧光波动相关光谱(FFCS)。我们介绍了单点采集(FCS)背后的基本原理及其对时空采样的扩展,该扩展是通过图像相关光谱(ICS)实现的。这篇文章是一本教育指南,介绍了FCS的理论概念和一些ICS技术,然后在MATLAB中进行交互式练习。在那里,学习者可以模拟数据时间序列和各种FFCS技术的应用,以及学习如何测量扩散系数、分子流和颗粒浓度。此外,每节后面都有一个简短的练习,通过模拟不同的场景来强化学习概念,寻求对结果的验证,并进行比较。此外,我们在整篇文章中邀请学习者查阅文献,了解FFCS技术的不同扩展,这些技术允许测量材料的不同物理化学性质。完成模块后,我们预计学习者将对FFCS领域有很好的了解,这将鼓励在未来的研究和教育实践中进一步探索和采用FFCS工具。
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引用次数: 0
Using Plant Cells of Nitellopsis obtusa for Biophysical Education 利用钝棘藜植物细胞进行生物体育教学
Pub Date : 2020-11-24 DOI: 10.35459/TBP.2019.000130
Vilmantas Pupkis, Rokas Buisas, Indre Lapeikaite, Vilma Kisnieriene
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.
提出在实验练习中使用巨型特征藻黑藻,使学生熟悉电生理学的基本概念,并提供一些简单的动手练习。所描述的概念实验包括动作电位(APs)的胞外登记和细胞质流特性的研究。学生需要记录ap的繁殖速度(在N. obtusa中发现为3.4±1.5 cm/s)和细胞质流动速度(66.7±9 μm/s)。提议的练习还涉及刺激后细胞质流的恢复动力学(恢复时间常数τ = 3.7±2.1 min)以及各种化学物质(例如KCl)对所有选定参数的影响的研究。实验结果表明,在生物物理学和细胞生物电现象的教学中,典型藻类是一种常规探索的模式系统。
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引用次数: 0
Project Symphony: A Biophysics Research Experience at a Primarily Undergraduate Institution 交响乐计划:初级本科院校的生物物理学研究经历
Pub Date : 2020-11-11 DOI: 10.35459/TBP.2019.000135
M. Muzzio, Sue Ellen Evangelista, Jacqueline Denver, Maria Lopez, Sunghee Lee
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 powerful learning tool, engaging students and stimulating their enthusiasm, thereby improving academic performance and persistence in science and preparing students for advanced degrees and careers in STEM fields (9–17). This report, the culmination of more than a decade’s work with undergraduate students, presents practices demonstrating that early exposure to the interdisciplinary field of biophysics can be effectively introduced at a primarily undergraduate institution (PUI) level through a well-structured research plan involving undergraduates with different STEM majors. The management of this group, called ‘‘Project Symphony’’ (18), overcame the challenges of sustaining research activities at a PUI via the incorporation of 2 essential elements of success: (a) establishment of a cooperative learning variant whereby students work together to maximize individual learning and each other’s learning; and (b) promotion of an integrated understanding via interdisciplinary biophysics projects.
跨学科科学、技术、工程和数学(STEM)教育得到了越来越多的关注,为学生更好地理解应对复杂挑战做好了准备(1-3)。特别是在本科阶段,为学生提供跨学科整合知识的机会具有公认的价值(4-7)。除了核心技术知识外,传授行为技能也是有益的,这些技能使学生能够通过有效的沟通、时间管理和团队合作与他人良好相处(8)。本科生研究经验被认为是一种强大的学习工具,可以吸引学生并激发他们的热情,从而提高学习成绩和对科学的坚持,并为学生获得STEM领域的高级学位和职业生涯做好准备(9-17)。这份报告是十多年来与本科生合作的成果,它提出了一些实践,证明通过一个结构良好的研究计划,让不同STEM专业的本科生参与进来,可以在主要的本科生机构(PUI)层面有效地早期接触生物物理跨学科领域。这个名为“交响乐项目”(18)的小组的管理层通过结合两个成功的基本要素,克服了在PUI维持研究活动的挑战:(a)建立合作学习变体,让学生共同努力,最大限度地提高个人学习和彼此学习;(b)通过跨学科生物物理项目促进综合理解。
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引用次数: 0
Machine Learning in a Molecular Modeling Course for Chemistry, Biochemistry, and Biophysics Students. 面向化学、生物化学和生物物理学学生的分子建模课程中的机器学习。
Pub Date : 2020-08-01 Epub Date: 2020-08-13 DOI: 10.35459/tbp.2019.000140
Jacob M Remington, Jonathon B Ferrell, Marlo Zorman, Adam Petrucci, Severin T Schneebeli, Jianing Li

Recent advances in computer hardware and software, particularly the availability of machine learning libraries, allow the introduction of data-based topics such as machine learning into the Biophysical curriculum for undergraduate and/or graduate levels. However, there are many practical challenges of teaching machine learning to advanced-level students in the 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, pedagogical tools, and assessments of student learning, to develop the new methodology to incorporate the basis of machine learning 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 machine learning 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 machine learning algorithms. This work establishes a framework for future teaching approaches that unite machine learning and any existing course in the biophysical curriculum, while also pinpointing the critical challenges that educators and students will likely face.

计算机硬件和软件的最新进展,特别是机器学习库的可用性,允许将基于数据的主题(如机器学习)引入本科和/或研究生水平的生物物理课程。然而,向生物物理学专业的高级学生教授机器学习存在许多实际挑战,这些学生通常没有丰富的计算背景。为了克服这些挑战,我们提出了一项教育研究,包括课程主题的设计,教学工具和学生学习的评估,以开发新的方法,将机器学习的基础纳入现有的生物物理选修课程,并让学生参与解决跨学科领域问题的练习。总的来说,我们观察到学生们有足够的好奇心来学习和应用机器学习算法来预测分子性质。值得注意的是,来自学生的反馈表明,必须注意确保学生为理解使用机器学习算法所需的数据驱动概念和基本编码方面做好准备。这项工作为未来的教学方法建立了一个框架,将机器学习与生物物理课程中的任何现有课程结合起来,同时也指出了教育工作者和学生可能面临的关键挑战。
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引用次数: 2
Reflections on undergraduate research mentoring. 关于大学生科研指导的几点思考。
Pub Date : 2020-08-01 DOI: 10.35459/tbp.2019.000112
Nicholas B Whitticar, Craig S Nunemaker

Recruiting talented high school and college students to consider a career in the biomedical or biophysical sciences is important, yet often difficult. Encouraging students in regions like Appalachia adds additional challenges due to socioeconomic hurdles and misperceptions. This brief report contains the reflections of a research mentor engaging with students as a high school physics teacher, a principal investigator at research-intensive university, and as a principal investigator at a predominantly undergraduate-focused research university, as well as the viewpoint of a former undergraduate student in the mentor's lab. Different hurdles stand in the way of success at each level. A key issue at the high school level is engaging students in 'real science', the discovery of new knowledge and ideas. With undergraduate students at a larger research institution, a key issue is for the student to have opportunities to engage in meaningful scientific research. At a smaller and more rural research institution, especially in Appalachia, many students have socioeconomic concerns and misconceptions of what scientific careers entail. Regardless of background and environment, there are certain students who thrive on the scientific curiosity to discover new things. All they need is that opportunity to engage in meaningful scientific discovery to become interested in a scientific career.

招募有才华的高中生和大学生考虑从事生物医学或生物物理科学的职业是很重要的,但往往是困难的。由于社会经济障碍和误解,鼓励阿巴拉契亚等地区的学生增加了额外的挑战。这份简短的报告包含了一位研究导师作为一名高中物理教师、一所研究型大学的首席研究员、一所主要以本科生为重点的研究型大学的首席研究员与学生接触的反思,以及导师实验室中一名前本科生的观点。在每个阶段,成功的道路上都有不同的障碍。高中阶段的一个关键问题是让学生参与“真正的科学”,即发现新知识和新思想。对于一个较大的研究机构的本科生来说,一个关键问题是学生有机会从事有意义的科学研究。在一个更小、更偏远的研究机构,特别是在阿巴拉契亚地区,许多学生都有社会经济方面的担忧,并且对科学事业的要求有误解。不管背景和环境如何,有一些学生在科学好奇心的驱使下茁壮成长,发现新事物。他们所需要的只是有机会从事有意义的科学发现,从而对科学事业产生兴趣。
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引用次数: 2
Stochastic Modelling of Reaction–Diffusion Processes by Radek Erban and S. Jonathan Chapman Radek Erban和S.Jonathan Chapman对反应-扩散过程的随机建模
Pub Date : 2020-06-01 DOI: 10.35459/tbp.2020.000155
P. Nelson
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 now allows routine study of single cells and even single molecules, so corresponding analytical tools that go beyond ensemble averaging are needed, just to extract the lessons that are latent in our datasets. Most of us also took classes in which chemical reactions were studied in imagined ‘‘well-stirred’’ conditions, and diffusion was studied separately in contexts where chemical reactions were not important. However, a vesicle of neurotransmitter must travel across a synapse while being degraded; a morphogen must bind and activate receptors while establishing a spatial gradient; and so on. This book’s title expresses the authors’ aim to establish a framework capable of handling biophysically relevant situations like these. Student interest in this topic is strong. My own students are at least implicitly aware that results from even the simplest stochastic simulation seem more ‘‘lifelike’’ than deterministic results, and they are always excited to see the gradual emergence of deterministic behavior as copy numbers get large. I realized some time ago that stochastic simulation belongs in any biophysics curriculum, starting from the very first introductory course and reappearing as appropriate at later stages. However, it was not so easy to find appropriate course materials. Erban and Chapman now give us a concise, elegant, and practical survey of numerical methods that are useful for such analyses, although at a level somewhat higher than first-year courses. An advanced undergraduate who is comfortable with ordinary differential equations and conditional probability and the associated mathemat-
随机模拟已成为科学工具包中不可或缺的工具。作为学生,我们都被告知,由于热运动,分子之间不断推挤,化学反应依赖于分子之间的偶然相遇。然而,我们中的大多数人都上了化学和物理课,在这些课上,注意力很快转移到了大量的分子上,在观察总体浓度时,这些分子固有的随机性被抹去了;然后,我们建立并求解了确定性速率方程。然而,细胞中的一些关键因子只出现在少数拷贝中(对于某些基因来说,可能只有一个拷贝)。此外,实验技术现在允许对单细胞甚至单分子进行常规研究,因此需要超越系综平均的相应分析工具,只是为了提取我们数据集中潜在的教训。我们大多数人还参加了在想象的“无井”条件下研究化学反应的课程,在化学反应不重要的情况下分别研究扩散。然而,神经递质的小泡在降解时必须穿过突触;形态发生素必须结合并激活受体,同时建立空间梯度;这本书的标题表达了作者的目标,即建立一个能够处理此类生物物理相关情况的框架。学生对这个话题很感兴趣。我自己的学生至少含蓄地意识到,即使是最简单的随机模拟的结果似乎也比确定性结果更“逼真”,而且随着拷贝数的增加,他们总是很兴奋地看到确定性行为的逐渐出现。不久前,我意识到随机模拟属于任何生物物理课程,从第一门入门课程开始,并在后期适当地重新出现。然而,要找到合适的课程材料并不容易。Erban和Chapman现在为我们提供了一个简洁、优雅、实用的数值方法调查,这些方法对此类分析很有用,尽管其水平略高于一年级课程。一名精通常微分方程、条件概率和相关数学的高级本科生-
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引用次数: 0
期刊
Biophysicist (Rockville, Md.)
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