Biophysical reports最新文献_第5页

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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

Cytosolic Ca²⁺ gradients and mitochondrial Ca²⁺ uptake in resting muscle fibers: A model analysis. 静息肌纤维中细胞质Ca2+梯度和线粒体Ca2+摄取:模型分析。

Biophysical reports Pub Date : 2023-09-13 DOI: 10.1016/j.bpr.2023.100117

Lorenzo Marcucci, Antonio Michelucci, Carlo Reggiani

{"title":"Cytosolic Ca2+ gradients and mitochondrial Ca2+ uptake in resting muscle fibers: A model analysis.","authors":"Lorenzo Marcucci, Antonio Michelucci, Carlo Reggiani","doi":"10.1016/j.bpr.2023.100117","DOIUrl":"https://doi.org/10.1016/j.bpr.2023.100117","url":null,"abstract":"Calcium ions (Ca2+) enter mitochondria via the mitochondrial Ca2+ uniporter, driven by electrical and concentration gradients. In this regard, transgenic mouse models, such as calsequestrin knockout (CSQ-KO) mice, with higher mitochondrial Ca2+ concentrations ([Ca2+]mito), should display higher cytosolic Ca2+ concentrations ([Ca2+]cyto). However, repeated measurements of [Ca2+]cyto in quiescent CSQ-KO fibers never showed a difference between WT and CSQ-KO. Starting from the consideration that fluorescent Ca2+ probes (Fura-2 and Indo-1) measure averaged global cytosolic concentrations, in this report we explored the role of local Ca2+ concentrations (i.e., Ca2+ microdomains) in regulating mitochondrial Ca2+ in resting cells, using a multicompartmental diffusional Ca2+ model. Progressively including the inward and outward fluxes of sarcoplasmic reticulum (SR), extracellular space, and mitochondria, we explored their contribution to the local Ca2+ distribution within the cell. The model predicts Ca2+ concentration gradients with hot spots or microdomains even at rest, minor but similar to those of evoked Ca2+ release. Due to their specific localization close to Ca2+ release units (CRU), mitochondria could take up Ca2+ directly from high-concentration microdomains, thus sensibly raising [Ca2+]mito, despite minor, possibly undetectable, modifications of the average [Ca2+]cyto.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"3 3","pages":"100117"},"PeriodicalIF":0.0,"publicationDate":"2023-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/2a/3c/main.PMC10412765.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10352078","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

Time-resolved burst variance analysis. 时间分辨突发方差分析。

Biophysical reports Pub Date : 2023-09-13 DOI: 10.1016/j.bpr.2023.100116

Ivan Terterov, Daniel Nettels, Dmitrii E Makarov, Hagen Hofmann

{"title":"Time-resolved burst variance analysis.","authors":"Ivan Terterov, Daniel Nettels, Dmitrii E Makarov, Hagen Hofmann","doi":"10.1016/j.bpr.2023.100116","DOIUrl":"https://doi.org/10.1016/j.bpr.2023.100116","url":null,"abstract":"Quantifying biomolecular dynamics has become a major task of single-molecule fluorescence spectroscopy methods. In single-molecule Förster resonance energy transfer (smFRET), kinetic information is extracted from the stream of photons emitted by attached donor and acceptor fluorophores. Here, we describe a time-resolved version of burst variance analysis that can quantify kinetic rates at microsecond to millisecond timescales in smFRET experiments of diffusing molecules. Bursts are partitioned into segments with a fixed number of photons. The FRET variance is computed from these segments and compared with the variance expected from shot noise. By systematically varying the segment size, dynamics at different timescales can be captured. We provide a theoretical framework to extract kinetic rates from the decay of the FRET variance with increasing segment size. Compared to other methods such as filtered fluorescence correlation spectroscopy, recurrence analysis of single particles, and two-dimensional lifetime correlation spectroscopy, fewer photons are needed to obtain reliable timescale estimates, which reduces the required measurement time.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"3 3","pages":"100116"},"PeriodicalIF":0.0,"publicationDate":"2023-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10406964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10344706","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

Real-time detection of virus antibody interaction by label-free common-path interferometry. 无标记共径干涉法实时检测病毒抗体相互作用。

Biophysical reports Pub Date : 2023-09-13 DOI: 10.1016/j.bpr.2023.100119

Samer Alhaddad, Houda Bey, Olivier Thouvenin, Pascale Boulanger, Claude Boccara, Martine Boccara, Ignacio Izeddin

{"title":"Real-time detection of virus antibody interaction by label-free common-path interferometry.","authors":"Samer Alhaddad, Houda Bey, Olivier Thouvenin, Pascale Boulanger, Claude Boccara, Martine Boccara, Ignacio Izeddin","doi":"10.1016/j.bpr.2023.100119","DOIUrl":"https://doi.org/10.1016/j.bpr.2023.100119","url":null,"abstract":"Viruses have a profound influence on all forms of life, motivating the development of rapid and minimally invasive methods for virus detection. In this study, we present a novel methodology that enables quantitative measurement of the interaction between individual biotic nanoparticles and antibodies in solution. Our approach employs a label-free, full-field common-path interferometric technique to detect and track biotic nanoparticles and their interactions with antibodies. It is based on the interferometric detection of light scattered by viruses in aqueous samples for the detection of individual viruses. We employ single-particle tracking analysis to characterize the size and properties of the detected nanoparticles, and to monitor the changes in their diffusive mobility resulting from interactions. To validate the sensitivity of our detection approach, we distinguish between particles having identical diffusion coefficients but different scattering signals, using DNA-loaded and DNA-devoid capsids of the Escherichia coli T5 virus phage. In addition, we have been able to monitor, in real time, the interaction between the bacteriophage T5 and purified antibodies targeting its major capsid protein pb8, as well as between the phage SPP1 and nonpurified anti-SPP1 antibodies present in rabbit serum. Interestingly, these virus-antibody interactions are observed within minutes. Finally, by estimating the number of viral particles interacting with antibodies at different concentrations, we successfully quantify the dissociation constant <math><mrow><msub><mi>K</mi><mi>d</mi></msub></mrow></math> of the virus-antibody reaction using single-particle tracking analysis.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"3 3","pages":"100119"},"PeriodicalIF":0.0,"publicationDate":"2023-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/5b/55/main.PMC10470184.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10142850","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

Evolution of drug resistance drives destabilization of flap region dynamics in HIV-1 protease. 耐药进化驱动HIV-1蛋白酶瓣区动力学的不稳定。

Biophysical reports Pub Date : 2023-09-13 DOI: 10.1016/j.bpr.2023.100121

Madhusudan Rajendran, Maureen C Ferran, Leora Mouli, Gregory A Babbitt, Miranda L Lynch

{"title":"Evolution of drug resistance drives destabilization of flap region dynamics in HIV-1 protease.","authors":"Madhusudan Rajendran, Maureen C Ferran, Leora Mouli, Gregory A Babbitt, Miranda L Lynch","doi":"10.1016/j.bpr.2023.100121","DOIUrl":"https://doi.org/10.1016/j.bpr.2023.100121","url":null,"abstract":"The HIV-1 protease is one of several common key targets of combination drug therapies for human immunodeficiency virus infection and acquired immunodeficiency syndrome. During the progression of the disease, some individual patients acquire drug resistance due to mutational hotspots on the viral proteins targeted by combination drug therapies. It has recently been discovered that drug-resistant mutations accumulate on the \"flap region\" of the HIV-1 protease, which is a critical dynamic region involved in nonspecific polypeptide binding during invasion and infection of the host cell. In this study, we utilize machine learning-assisted comparative molecular dynamics, conducted at single amino acid site resolution, to investigate the dynamic changes that occur during functional dimerization and drug binding of wild-type and common drug-resistant versions of the main protease. We also use a multiagent machine learning model to identify conserved dynamics of the HIV-1 main protease that are preserved across simian and feline protease orthologs. We find that a key conserved functional site in the flap region, a solvent-exposed isoleucine (Ile50) that controls flap dynamics is functionally targeted by drug resistance mutations, leading to amplified molecular dynamics affecting the functional ability of the flap region to hold the drugs. We conclude that better long-term patient outcomes may be achieved by designing drugs that target protease regions that are less dependent upon single sites with large functional binding effects.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"3 3","pages":"100121"},"PeriodicalIF":0.0,"publicationDate":"2023-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/6c/83/main.PMC10469570.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10149340","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: 1