Biophysical reports最新文献_第3页

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

Establishing Riboglow-FLIM to visualize noncoding RNAs inside live zebrafish embryos. 建立Riboglow FLIM以可视化活斑马鱼胚胎内的非编码RNA。

Biophysical reports Pub Date : 2023-09-26 eCollection Date: 2023-12-13 DOI: 10.1016/j.bpr.2023.100132

Nadia Sarfraz, Harrison J Lee, Morgan K Rice, Emilia Moscoso, Luke K Shafik, Eric Glasgow, Suman Ranjit, Ben J Lambeck, Esther Braselmann

{"title":"Establishing Riboglow-FLIM to visualize noncoding RNAs inside live zebrafish embryos.","authors":"Nadia Sarfraz, Harrison J Lee, Morgan K Rice, Emilia Moscoso, Luke K Shafik, Eric Glasgow, Suman Ranjit, Ben J Lambeck, Esther Braselmann","doi":"10.1016/j.bpr.2023.100132","DOIUrl":"10.1016/j.bpr.2023.100132","url":null,"abstract":"The central role of RNAs in health and disease calls for robust tools to visualize RNAs in living systems through fluorescence microscopy. Live zebrafish embryos are a popular system to investigate multicellular complexity as disease models. However, RNA visualization approaches in whole organisms are notably underdeveloped. Here, we establish our RNA tagging and imaging platform Riboglow-FLIM for complex cellular imaging applications by systematically evaluating FLIM capabilities. We use adherent mammalian cells as models for RNA visualization. Additional complexity of analyzing RNAs in whole mammalian animals is achieved by injecting these cells into a zebrafish embryo system for cell-by-cell analysis in this model of multicellularity. We first evaluate all variable elements of Riboglow-FLIM quantitatively before assessing optimal use in whole animals. In this way, we demonstrate that a model noncoding RNA can be detected robustly and quantitatively inside live zebrafish embryos using a far-red Cy5-based variant of the Riboglow platform. We can clearly resolve cell-to-cell heterogeneity of different RNA populations by this methodology, promising applicability in diverse fields.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"3 4","pages":"100132"},"PeriodicalIF":0.0,"publicationDate":"2023-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/93/31/main.PMC10568559.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241618","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

Model-based trajectory classification of anchored molecular motor-biopolymer interactions. 锚定分子马达-生物聚合物相互作用的基于模型的轨迹分类。

Biophysical reports Pub Date : 2023-09-14 eCollection Date: 2023-12-13 DOI: 10.1016/j.bpr.2023.100130

John B Linehan, Gerald Alan Edwards, Vincent Boudreau, Amy Shaub Maddox, Paul S Maddox

{"title":"Model-based trajectory classification of anchored molecular motor-biopolymer interactions.","authors":"John B Linehan, Gerald Alan Edwards, Vincent Boudreau, Amy Shaub Maddox, Paul S Maddox","doi":"10.1016/j.bpr.2023.100130","DOIUrl":"10.1016/j.bpr.2023.100130","url":null,"abstract":"During zygotic mitosis in many species, forces generated at the cell cortex are required for the separation and migration of paternally provided centrosomes, pronuclear migration, segregation of genetic material, and cell division. Furthermore, in some species, force-generating interactions between spindle microtubules and the cortex position the mitotic spindle asymmetrically within the zygote, an essential step in asymmetric cell division. Understanding the mechanical and molecular mechanisms of microtubule-dependent force generation and therefore asymmetric cell division requires identification of individual cortical force-generating units in vivo. There is no current method for identifying individual force-generating units with high spatiotemporal resolution. Here, we present a method to determine both the location and the relative number of microtubule-dependent cortical force-generating units using single-molecule imaging of fluorescently labeled dynein. Dynein behavior is modeled to classify trajectories of cortically bound dynein according to whether they are interacting with a microtubule. The categorization strategy recapitulates well-known force asymmetries in C. elegans zygote mitosis. To evaluate the robustness of categorization, we used RNAi to deplete the tubulin subunit TBA-2. As predicted, this treatment reduced the number of trajectories categorized as engaged with a microtubule. Our technique will be a valuable tool to define the molecular mechanisms of dynein cortical force generation and its regulation as well as other instances wherein anchored motors interact with biopolymers (e.g., actin, tubulin, DNA).","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"3 4","pages":"100130"},"PeriodicalIF":0.0,"publicationDate":"2023-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ca/1e/main.PMC10558742.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41159112","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