Biophysical reports最新文献_第3页

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

The method for assessing the specificity of developing CAR therapies. 评估开发 CAR 疗法特异性的方法。

IF 2.4

Biophysical reports Pub Date : 2024-09-11 Epub Date: 2024-07-16 DOI: 10.1016/j.bpr.2024.100172

Ivan V Prikhodko, Georgy Th Guria

{"title":"The method for assessing the specificity of developing CAR therapies.","authors":"Ivan V Prikhodko, Georgy Th Guria","doi":"10.1016/j.bpr.2024.100172","DOIUrl":"10.1016/j.bpr.2024.100172","url":null,"abstract":"The effectiveness of antitumor chimeric antigen receptor (CAR) therapy mainly dealt with an elevated sensitivity of CAR cells to target cells. However, CAR therapies are associated with nonspecific side effects: on-target off-tumor toxicity. Sensitivity and specificity of CAR cells are the most important properties of the recognition process of target cells among other cells. Current developments are mainly concentrated on exploring molecular biology methods for designing CAR cells with the highest sensitivity, while the problem of the CAR cell specificity is rarely considered. For the assessment of CAR cell specificity, we suggest that, in addition to an elevated level of CAR-antigen affinity, the ability of CARs for clustering should be taken into account. We assume that the CAR cell cytotoxicity is determined by CAR clustering. The latter is treated within the framework of nucleation theory. The master equation for the probability of CAR cell cytotoxicity is derived. The size of a critical CAR cluster is found to be one of two most essential parameters. The conditions for necessary sensitivity and sufficient specificity are explored. Relevant parametric diagrams are derived. Possible applications of the method for assessing the specificity of developing CAR therapies are discussed.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100172"},"PeriodicalIF":2.4,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11344002/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141725187","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

Nonlinear classifiers for wet-neuromorphic computing using gene regulatory neural network. 使用基因调控神经网络的湿拟态计算非线性分类器

IF 2.4

Biophysical reports Pub Date : 2024-09-11 Epub Date: 2024-06-05 DOI: 10.1016/j.bpr.2024.100158

Adrian Ratwatte, Samitha Somathilaka, Sasitharan Balasubramaniam, Assaf A Gilad

{"title":"Nonlinear classifiers for wet-neuromorphic computing using gene regulatory neural network.","authors":"Adrian Ratwatte, Samitha Somathilaka, Sasitharan Balasubramaniam, Assaf A Gilad","doi":"10.1016/j.bpr.2024.100158","DOIUrl":"10.1016/j.bpr.2024.100158","url":null,"abstract":"The gene regulatory network (GRN) of biological cells governs a number of key functionalities that enable them to adapt and survive through different environmental conditions. Close observation of the GRN shows that the structure and operational principles resemble an artificial neural network (ANN), which can pave the way for the development of wet-neuromorphic computing systems. Genes are integrated into gene-perceptrons with transcription factors (TFs) as input, where the TF concentration relative to half-maximal RNA concentration and gene product copy number influences transcription and translation via weighted multiplication before undergoing a nonlinear activation function. This process yields protein concentration as the output, effectively turning the entire GRN into a gene regulatory neural network (GRNN). In this paper, we establish nonlinear classifiers for molecular machine learning using the inherent sigmoidal nonlinear behavior of gene expression. The eigenvalue-based stability analysis, tailored to system parameters, confirms maximum-stable concentration levels, minimizing concentration fluctuations and computational errors. Given the significance of the stabilization phase in GRNN computing and the dynamic nature of the GRN, alongside potential changes in system parameters, we utilize the Lyapunov stability theorem for temporal stability analysis. Based on this GRN-to-GRNN mapping and stability analysis, three classifiers are developed utilizing two generic multilayer sub-GRNNs and a sub-GRNN extracted from the Escherichia coli GRN. Our findings also reveal the adaptability of different sub-GRNNs to suit different application requirements.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100158"},"PeriodicalIF":2.4,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11231448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141289011","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

TSAT: Efficient evaluation software for NGS data of phage/mirror-image phage display selections. TSAT - 用于噬菌体/镜像噬菌体展示选择的 NGS 数据的高效评估软件。

IF 2.4

Biophysical reports Pub Date : 2024-09-11 Epub Date: 2024-06-21 DOI: 10.1016/j.bpr.2024.100166

Tim Altendorf, Jeannine Mohrlüder, Dieter Willbold

引用次数: 0

In silico thermal control of spiral wave dynamics in excitable cardiac tissue. 可兴奋心脏组织螺旋波动力学的硅学热控制。

IF 2.4

Biophysical reports Pub Date : 2024-09-11 Epub Date: 2024-07-02 DOI: 10.1016/j.bpr.2024.100170

Rupamanjari Majumder

引用次数: 0

Biophysical characterization of high-confidence, small human proteins. 高可信度小型人类蛋白质的生物物理特征。

IF 2.4

Biophysical reports Pub Date : 2024-09-11 Epub Date: 2024-06-22 DOI: 10.1016/j.bpr.2024.100167

A M Whited, Irwin Jungreis, Jeffre Allen, Christina L Cleveland, Jonathan M Mudge, Manolis Kellis, John L Rinn, Loren E Hough

{"title":"Biophysical characterization of high-confidence, small human proteins.","authors":"A M Whited, Irwin Jungreis, Jeffre Allen, Christina L Cleveland, Jonathan M Mudge, Manolis Kellis, John L Rinn, Loren E Hough","doi":"10.1016/j.bpr.2024.100167","DOIUrl":"10.1016/j.bpr.2024.100167","url":null,"abstract":"Significant efforts have been made to characterize the biophysical properties of proteins. Small proteins have received less attention because their annotation has historically been less reliable. However, recent improvements in sequencing, proteomics, and bioinformatics techniques have led to the high-confidence annotation of small open reading frames (smORFs) that encode for functional proteins, producing smORF-encoded proteins (SEPs). SEPs have been found to perform critical functions in several species, including humans. While significant efforts have been made to annotate SEPs, less attention has been given to the biophysical properties of these proteins. We characterized the distributions of predicted and curated biophysical properties, including sequence composition, structure, localization, function, and disease association of a conservative list of previously identified human SEPs. We found significant differences between SEPs and both larger proteins and control sets. In addition, we provide an example of how our characterization of biophysical properties can contribute to distinguishing protein-coding smORFs from noncoding ones in otherwise ambiguous cases.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100167"},"PeriodicalIF":2.4,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11305224/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141443861","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