Biophysical reports最新文献_第4页

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

Estimation of the mass density of biological matter from refractive index measurements. 通过折射率测量估算生物物质的质量密度。

IF 2.4

Biophysical reports Pub Date : 2024-06-12 Epub Date: 2024-04-24 DOI: 10.1016/j.bpr.2024.100156

Conrad Möckel, Timon Beck, Sara Kaliman, Shada Abuhattum, Kyoohyun Kim, Julia Kolb, Daniel Wehner, Vasily Zaburdaev, Jochen Guck

{"title":"Estimation of the mass density of biological matter from refractive index measurements.","authors":"Conrad Möckel, Timon Beck, Sara Kaliman, Shada Abuhattum, Kyoohyun Kim, Julia Kolb, Daniel Wehner, Vasily Zaburdaev, Jochen Guck","doi":"10.1016/j.bpr.2024.100156","DOIUrl":"10.1016/j.bpr.2024.100156","url":null,"abstract":"The quantification of physical properties of biological matter gives rise to novel ways of understanding functional mechanisms. One of the basic biophysical properties is the mass density (MD). It affects the dynamics in sub-cellular compartments and plays a major role in defining the opto-acoustical properties of cells and tissues. As such, the MD can be connected to the refractive index (RI) via the well known Lorentz-Lorenz relation, which takes into account the polarizability of matter. However, computing the MD based on RI measurements poses a challenge, as it requires detailed knowledge of the biochemical composition of the sample. Here we propose a methodology on how to account for assumptions about the biochemical composition of the sample and respective RI measurements. To this aim, we employ the Biot mixing rule of RIs alongside the assumption of volume additivity to find an approximate relation of MD and RI. We use Monte-Carlo simulations and Gaussian propagation of uncertainty to obtain approximate analytical solutions for the respective uncertainties of MD and RI. We validate this approach by applying it to a set of well-characterized complex mixtures given by bovine milk and intralipid emulsion and employ it to estimate the MD of living zebrafish (Danio rerio) larvae trunk tissue. Our results illustrate the importance of implementing this methodology not only for MD estimations but for many other related biophysical problems, such as mechanical measurements using Brillouin microscopy and transient optical coherence elastography.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"4 2","pages":"100156"},"PeriodicalIF":2.4,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11090064/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140892265","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. 感谢我们的评论员。

Biophysical reports Pub Date : 2023-12-03 eCollection Date: 2023-12-13 DOI: 10.1016/j.bpr.2023.100136

引用次数: 0

Phasor Identifier: A Cloud-based Analysis of Phasor-FLIM Data on Python Notebooks 相量标识符:基于云的Python笔记本相量胶片数据分析

Biophysical reports Pub Date : 2023-11-01 DOI: 10.1016/j.bpr.2023.100135

Mario Bernardi, Francesco Cardarelli

引用次数: 0

Trustworthy in silico Cell Labeling via Ensemble-based Image Translation 可信赖的基于集成的图像翻译的硅细胞标记

Biophysical reports Pub Date : 2023-10-01 DOI: 10.1016/j.bpr.2023.100133

Sara Imboden, Xuanqing Liu, Marie C. Payne, Cho-Jui Hsieh, Neil Y.C. Lin

引用次数: 0

Thioflavin T indicates membrane potential in mammalian cells and can affect it in a blue light dependent manner. 硫黄素T指示哺乳动物细胞的膜电位，并以蓝光依赖的方式影响它。

Biophysical reports Pub Date : 2023-10-01 DOI: 10.1016/j.bpr.2023.100134

Emily Skates, Hadrien Delattre, Zoe Schofield, Munehiro Asally, Orkun S. Soyer

{"title":"Thioflavin T indicates membrane potential in mammalian cells and can affect it in a blue light dependent manner.","authors":"Emily Skates, Hadrien Delattre, Zoe Schofield, Munehiro Asally, Orkun S. Soyer","doi":"10.1016/j.bpr.2023.100134","DOIUrl":"https://doi.org/10.1016/j.bpr.2023.100134","url":null,"abstract":"The fluorescent benzothiazole dye Thioflavin T (ThT) is widely used as a marker for protein aggregates, most commonly in the context of neurodegenerative disease research and diagnosis. Recently, this same dye was shown to indicate membrane potential in bacteria due to its cationic nature. This finding prompted a question whether ThT fluorescence is linked to the membrane potential in mammalian cells, which would be important for appropriate utilisation of ThT in research and diagnosis. Here, we show that ThT localises into the mitochondria of HeLa cells in a membrane-potential dependent manner. Specifically, ThT colocalised in cells with the mitochondrial membrane-potential indicator Tetramethylrhodamine methyl ester (TMRM) and gave similar temporal responses as TMRM to treatment with a protonophore, carbonyl cyanide-4-(trifluoromethoxy) phenylhydrazone (FCCP). Additionally, we found that presence of ThT together with exposure to blue light (λ = 405 nm), but neither factor alone, caused depolarisation of mitochondrial membrane potential. This additive effect of the concentration and blue light was recapitulated by a mathematical model implementing the potential-dependent distribution of ThT and its effect on mitochondrial membrane potential through photosensitization. These results show that ThT can act as a mitochondrial membrane potential indicator in mammalian cells, when used at low concentrations and with low blue-light exposure. However, it causes dissipation of the mitochondrial membrane potential depending additively on its concentrations and blue light exposure. This conclusion motivates a re-evaluation of ThT’s use at micromolar range in live-cell analyses, and indicates that this dye can enable future studies on the potential connections between membrane potential dynamics and protein aggregation.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"40 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136128399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2