Biophysical reports最新文献_第3页

Development of a digital amplifier system for cut-open oocyte electrophysiology. 开发用于切开卵母细胞电生理学的数字放大器系统。

IF 2.4

Biophysical reports Pub Date : 2024-12-11 Epub Date: 2024-10-15 DOI: 10.1016/j.bpr.2024.100185

Lucas J Koerner, Ian Delgadillo Bonequi, Ian S K Shogren, Abraham Stroschein, Jordan Haag, Linda M Boland

{"title":"Development of a digital amplifier system for cut-open oocyte electrophysiology.","authors":"Lucas J Koerner, Ian Delgadillo Bonequi, Ian S K Shogren, Abraham Stroschein, Jordan Haag, Linda M Boland","doi":"10.1016/j.bpr.2024.100185","DOIUrl":"10.1016/j.bpr.2024.100185","url":null,"abstract":"The cut-open oocyte Vaseline gap technique is a powerful electrophysiological method for the characterization of ion channels. However, traditional amplifiers for cut-open oocyte Vaseline gap are labor intensive and require significant user expertise. We introduce an innovative, open-source digital amplifier system with high-speed digitization and software-controlled electronics for computer-driven automation. This system compares well to existing commercial systems in terms of conventional specifications of step response (current peak at 25μs and decay of 36μs time constant), current noise (1.0 nA at 3-kHz bandwidth), and dynamic range (96.9 dB). Additionally, it unlocks new methods through close integration of the amplifier and software, including machine-learning techniques for tuning capacitive compensation waveforms, achieving a 100-fold suppression of mean-squared transient current, and impedance measurement methods to identify system components such as membrane capacitance and electrode resistances. For future extensions, the design has unique attributes such as real-time digital signal processing for feedback, multiple input and multiple output, and allows for user customization. By providing open-source access to the circuit board designs, control software, and field-programmable gate array code on GitHub, this approach aims to foster cross-disciplinary collaboration and facilitate instrument customization enabling previously inaccessible electrophysiology experiments.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100185"},"PeriodicalIF":2.4,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11549981/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An effective drift-diffusion model for pandemic propagation and uncertainty prediction. 用于流行病传播和不确定性预测的有效漂移-扩散模型。

IF 2.4

Biophysical reports Pub Date : 2024-12-11 Epub Date: 2024-09-11 DOI: 10.1016/j.bpr.2024.100182

Clara Bender, Abhimanyu Ghosh, Hamed Vakili, Preetam Ghosh, Avik W Ghosh

{"title":"An effective drift-diffusion model for pandemic propagation and uncertainty prediction.","authors":"Clara Bender, Abhimanyu Ghosh, Hamed Vakili, Preetam Ghosh, Avik W Ghosh","doi":"10.1016/j.bpr.2024.100182","DOIUrl":"10.1016/j.bpr.2024.100182","url":null,"abstract":"Predicting pandemic evolution involves complex modeling challenges, typically involving detailed discrete mathematics executed on large volumes of epidemiological data. Making them physics based provides added intuition as well as predictive value. Differential equations have the advantage of offering smooth, well-behaved solutions that try to capture overall predictive trends and averages. In this paper, the canonical susceptible-infected-recovered model is simplified, in the process generating quasi-analytical solutions and fitting functions that agree well with the numerics, as well as infection data across multiple countries. The equations provide an elegant way to visualize the evolution of the pandemic spread, by drawing equivalents with the similar dynamics of a particle, whose location over time represents the growing fraction of the population that is infected. This particle slides down a potential whose shape is set by model epidemiological parameters such as reproduction rate. Potential sources of errors and their growth over time are identified, and the uncertainties are mapped into a diffusive jitter that tends to push the particle away from its minimum. The combined physical understanding and analytical expressions offered by such an intuitive drift-diffusion model sets the foundation for their eventual extension to a multi-patch model while offering practical error bounds and could thus be useful in making policy decisions going forward.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100182"},"PeriodicalIF":2.4,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11775906/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142302323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Engineering stress as a motivation for filamentous virus morphology. 将工程应力作为丝状病毒形态的动力。

IF 2.4

Biophysical reports Pub Date : 2024-12-11 Epub Date: 2024-09-10 DOI: 10.1016/j.bpr.2024.100181

Andrew McMahon, Swetha Vijayakrishnan, Hafez El Sayyed, Danielle Groves, Michaela J Conley, Edward Hutchinson, Nicole C Robb

{"title":"Engineering stress as a motivation for filamentous virus morphology.","authors":"Andrew McMahon, Swetha Vijayakrishnan, Hafez El Sayyed, Danielle Groves, Michaela J Conley, Edward Hutchinson, Nicole C Robb","doi":"10.1016/j.bpr.2024.100181","DOIUrl":"10.1016/j.bpr.2024.100181","url":null,"abstract":"Many viruses are pleomorphic in shape and size, with pleomorphism often thought to correlate with infectivity, pathogenicity, or virus survival. For example, influenza and respiratory syncytial virus particles range in size from small spherical virions to filaments reaching many micrometers in length. We have used a pressure vessel model to investigate how the length and width of spherical and filamentous virions can vary for a given critical stress and fluorescence super-resolution microscopy along with image analysis tools to fit imaged influenza viruses to the model. We have shown that influenza virion dimensions fit within the theoretical limits of the model, suggesting that filament formation may be a way to increase an individual virus's volume without particle rupture. We have also used cryoelectron microscopy to investigate influenza and respiratory syncytial virus dimensions at the extrema of the model and used the pressure vessel model to explain the lack of alternative virus particle geometries. Our approach offers insight into the possible purpose of filamentous virus morphology and is applicable to a wide range of other biological entities, including bacteria and fungi.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100181"},"PeriodicalIF":2.4,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11447354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142302324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Thank you to our reviewers. 感谢我们的审稿人。

IF 2.4

Biophysical reports Pub Date : 2024-12-07 DOI: 10.1016/j.bpr.2024.100188

引用次数: 0

Magnetic field platform for experiments on well-mixed and spatially structured microbial populations. 用于对微生物种群进行充分混合和空间结构实验的磁场平台。

IF 2.4

Biophysical reports Pub Date : 2024-09-11 Epub Date: 2024-06-17 DOI: 10.1016/j.bpr.2024.100165

Akila Bandara, Enoki Li, Daniel A Charlebois

引用次数: 0

Advanced analysis of single-molecule spectroscopic data. 单分子光谱数据高级分析。

IF 2.4

Biophysical reports Pub Date : 2024-09-11 Epub Date: 2024-08-02 DOI: 10.1016/j.bpr.2024.100173

Joshua L Botha, Bertus van Heerden, Tjaart P J Krüger

{"title":"Advanced analysis of single-molecule spectroscopic data.","authors":"Joshua L Botha, Bertus van Heerden, Tjaart P J Krüger","doi":"10.1016/j.bpr.2024.100173","DOIUrl":"10.1016/j.bpr.2024.100173","url":null,"abstract":"We present Full SMS, a multipurpose graphical user interface (GUI)-based software package for analyzing single-molecule spectroscopy (SMS) data. SMS typically delivers multiparameter data-such as fluorescence brightness, lifetime, and spectra-of molecular- or nanometer-scale particles such as single dye molecules, quantum dots, or fluorescently labeled biological macromolecules. Full SMS allows an unbiased statistical analysis of fluorescence brightness through level resolution and clustering, analysis of fluorescence lifetimes through decay fitting, as well as the calculation of second-order correlation functions and the display of fluorescence spectra and raster-scan images. Additional features include extensive data filtering options, a custom HDF5-based file format, and flexible data export options. The software is open source and written in Python but GUI based so it may be used without any programming knowledge. A multiprocess architecture was employed for computational efficiency. The software is also designed to be easily extendable to include additional import data types and analysis capabilities.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100173"},"PeriodicalIF":2.4,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11374972/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141891106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Lipid loss and compositional change during preparation of simple two-component liposomes. 制备简单双组分脂质体过程中的脂质损失和成分变化。

IF 2.4

Biophysical reports Pub Date : 2024-09-11 Epub Date: 2024-08-21 DOI: 10.1016/j.bpr.2024.100174

Eunice Kim, Olivia Graceffa, Rachel Broweleit, Ali Ladha, Andrew Boies, Sanyukta Prakash Mudakannavar, Robert J Rawle

{"title":"Lipid loss and compositional change during preparation of simple two-component liposomes.","authors":"Eunice Kim, Olivia Graceffa, Rachel Broweleit, Ali Ladha, Andrew Boies, Sanyukta Prakash Mudakannavar, Robert J Rawle","doi":"10.1016/j.bpr.2024.100174","DOIUrl":"10.1016/j.bpr.2024.100174","url":null,"abstract":"Liposomes are used as model membranes in many scientific fields. Various methods exist to prepare liposomes, but common procedures include thin-film hydration followed by extrusion, freeze-thaw, and/or sonication. These procedures can produce liposomes at specific concentrations and lipid compositions, and researchers often assume that the concentration and composition of their liposomes are similar or identical to what would be expected if no lipid loss occurred. However, lipid loss and concomitant biasing of lipid composition can in principle occur at any preparation step due to nonideal mixing, lipid-surface interactions, etc. Here, we report a straightforward HPLC-ELSD method to quantify the lipid concentration and composition of liposomes and apply that method to study the preparation of simple cholesterol/POPC liposomes. We examine common liposome preparation steps, including vortexing during resuspension, lipid film hydration, extrusion, freeze-thaw, and sonication. We found that the resuspension step can play an outsized role in determining the lipid loss (up to ∼50% under seemingly rigorous procedures). The extrusion step yielded smaller lipid losses (∼10-20%). Freeze-thaw and sonication could both be employed to improve lipid yields. Hydration times up to 60 min and increasing cholesterol concentrations up to 50 mol % had little influence on lipid recovery. Fortunately, even conditions with large lipid loss did not substantially influence the target membrane composition, as long as the lipid mixture was below the cholesterol solubility limit. From our results, we identify best practices for producing maximum levels of lipid recovery and minimal changes to lipid composition during liposome preparation for cholesterol/POPC liposomes.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100174"},"PeriodicalIF":2.4,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406089/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142037898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Numerical model for electrogenic transport by the ATP-dependent potassium pump KdpFABC. 依赖 ATP 的钾泵 KdpFABC 的电氮运输数值模型。

IF 2.4

Biophysical reports Pub Date : 2024-09-11 Epub Date: 2024-06-29 DOI: 10.1016/j.bpr.2024.100169

Adel Hussein, Xihui Zhang, David L Stokes

{"title":"Numerical model for electrogenic transport by the ATP-dependent potassium pump KdpFABC.","authors":"Adel Hussein, Xihui Zhang, David L Stokes","doi":"10.1016/j.bpr.2024.100169","DOIUrl":"10.1016/j.bpr.2024.100169","url":null,"abstract":"In vitro assays of ion transport are an essential tool for understanding molecular mechanisms associated with ATP-dependent pumps. Because ion transport is generally electrogenic, principles of electrophysiology are applicable, but conventional tools like patch-clamp are ineffective due to relatively low turnover rates of the pumps. Instead, assays have been developed to measure either voltage or current generated by transport activity of a population of molecules either in cell-derived membrane fragments or after reconstituting purified protein into proteoliposomes. In order to understand the nuances of these assays and to characterize effects of various operational parameters, we have developed a numerical model to simulate data produced by two relevant assays: fluorescence from voltage-sensitive dyes and current recorded by capacitive coupling on solid supported membranes. Parameters of the model, which has been implemented in Python, are described along with underlying principles of the computational algorithm. Experimental data from KdpFABC, a K+ pump associated with P-type ATPases, are presented, and model parameters have been adjusted to mimic these data. In addition, effects of key parameters such as nonselective leak conductance and turnover rate are demonstrated. Finally, simulated data are used to illustrate the effects of capacitive coupling on measured current and to compare alternative methods for quantification of raw data.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100169"},"PeriodicalIF":2.4,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11304011/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141478089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An efficient EPR spin-labeling method enables insights into conformational changes in DNA. 通过高效的 EPR 自旋标记法，可以深入了解 DNA 的构象变化。

IF 2.4

Biophysical reports Pub Date : 2024-09-11 Epub Date: 2024-06-28 DOI: 10.1016/j.bpr.2024.100168

Melanie Hirsch, Lukas Hofmann, Idan Yakobov, Shirin Kahremany, Hila Sameach, Yulia Shenberger, Lada Gevorkyan-Airapetov, Sharon Ruthstein

引用次数: 0

Tunable intracellular transport on converging microtubule morphologies. 汇聚微管形态上的可调细胞内运输。

IF 2.4

Biophysical reports Pub Date : 2024-09-11 Epub Date: 2024-07-10 DOI: 10.1016/j.bpr.2024.100171

Niranjan Sarpangala, Brooke Randell, Ajay Gopinathan, Oleg Kogan

{"title":"Tunable intracellular transport on converging microtubule morphologies.","authors":"Niranjan Sarpangala, Brooke Randell, Ajay Gopinathan, Oleg Kogan","doi":"10.1016/j.bpr.2024.100171","DOIUrl":"10.1016/j.bpr.2024.100171","url":null,"abstract":"A common type of cytoskeletal morphology involves multiple microtubules converging with their minus ends at the microtubule organizing center (MTOC). The cargo-motor complex will experience ballistic transport when bound to microtubules or diffusive transport when unbound. This machinery allows for sequestering and subsequent dispersal of dynein-transported cargo. The general principles governing dynamics, efficiency, and tunability of such transport in the MTOC vicinity are not fully understood. To address this, we develop a one-dimensional model that includes advective transport toward an attractor (such as the MTOC) and diffusive transport that allows particles to reach absorbing boundaries (such as cellular membranes). We calculated the mean first passage time (MFPT) for cargo to reach the boundaries as a measure of the effectiveness of sequestering (large MFPT) and diffusive dispersal (low MFPT). We show that the MFPT experiences a dramatic growth, transitioning from a low to high MFPT regime (dispersal to sequestering) over a window of cargo on-/off-rates that is close to in vivo values. Furthermore, increasing either the on-rate (attachment) or off-rate (detachment) can result in optimal dispersal when the attractor is placed asymmetrically. Finally, we also describe a regime of rare events where the MFPT scales exponentially with motor velocity and the escape location becomes exponentially sensitive to the attractor positioning. Our results suggest that structures such as the MTOC allow for the sensitive control of the spatial and temporal features of transport and corresponding function under physiological conditions.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100171"},"PeriodicalIF":2.4,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11345624/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141602294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0