Biophysical reports最新文献

{"title":"Correlating single-molecule rupture mechanics with cell population adhesion by yeast display","authors":"Mariana Sá Santos, Haipei Liu, V. Schittny, R. Vanella, M. A. Nash","doi":"10.1016/j.bpr.2021.100035","DOIUrl":"https://doi.org/10.1016/j.bpr.2021.100035","url":null,"abstract":"","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87143788","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}

{"title":"PySOFI: an open source Python package for SOFI","authors":"Yuting Miao, S. Weiss, Xiyu Yi","doi":"10.1101/2021.10.16.464651","DOIUrl":"https://doi.org/10.1101/2021.10.16.464651","url":null,"abstract":"Super-resolution optical fluctuation imaging (SOFI) is a highly democratizable technique that provides optical super-resolution (SR) without requirement of sophisticated imaging instruments. An open source package for SOFI algorithm is needed to support not only the utilization of SOFI, but also the community adoption and participation for further development of SOFI. In this work, we developed PySOFI, an open source python package for SOFI analysis that offers the flexibility to inspect, test, modify, improve and extend the algorithm. We provide a complete documentation for the package and a collection of Jupyter Notebooks to demonstrate the usage of the package. We discuss the architecture of PySOFI, illustrate how to use each functional module, and demonstrate how to extend the PySOFI package with additional modules. We expect PySOFI to facilitate efficient adoption, testing, modification, dissemination and prototyping of new SOFI-relevant algorithms.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"43 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80345839","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}

{"title":"Surface tension and viscosity of protein condensates quantified by micropipette aspiration.","authors":"Huan Wang, Fleurie M Kelley, Dragomir Milovanovic, Benjamin S Schuster, Zheng Shi","doi":"10.1016/j.bpr.2021.100011","DOIUrl":"10.1016/j.bpr.2021.100011","url":null,"abstract":"<p><p>The material properties of biomolecular condensates have been suggested to play important biological and pathological roles. Despite the rapid increase in the number of biomolecules identified that undergo liquid-liquid phase separation, quantitative studies and direct measurements of the material properties of the resulting condensates have been severely lagging behind. Here, we develop a micropipette-based technique that uniquely, to our knowledge, allows quantifications of both the surface tension and viscosity of biomolecular condensates, independent of labeling and surface-wetting effects. We demonstrate the accuracy and versatility of this technique by measuring condensates of LAF-1 RGG domains and a polymer-based aqueous two-phase system. We further confirm our measurements using established condensate fusion and fluorescence recovery after photobleaching assays. We anticipate the micropipette-based technique will be widely applicable to biomolecular condensates and will resolve several limitations regarding current approaches.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/64/90/main.PMC9563586.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9628862","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}

{"title":"Multimodal single-molecule microscopy with continuously controlled spectral resolution.","authors":"Jonathan Jeffet, Ariel Ionescu, Yael Michaeli, Dmitry Torchinsky, Eran Perlson, Timothy D Craggs, Yuval Ebenstein","doi":"10.1016/j.bpr.2021.100013","DOIUrl":"10.1016/j.bpr.2021.100013","url":null,"abstract":"<p><p>Color is a fundamental contrast mechanism in fluorescence microscopy, providing the basis for numerous imaging and spectroscopy techniques. Building on spectral imaging schemes that encode color into a fixed spatial intensity distribution, here, we introduce continuously controlled spectral-resolution (CoCoS) microscopy, which allows the spectral resolution of the system to be adjusted in real-time. By optimizing the spectral resolution for each experiment, we achieve maximal sensitivity and throughput, allowing for single-frame acquisition of multiple color channels with single-molecule sensitivity and 140-fold larger fields of view compared with previous super-resolution spectral imaging techniques. Here, we demonstrate the utility of CoCoS in three experimental formats, single-molecule spectroscopy, single-molecule Förster resonance energy transfer, and multicolor single-particle tracking in live neurons, using a range of samples and 12 distinct fluorescent markers. A simple add-on allows CoCoS to be integrated into existing fluorescence microscopes, rendering spectral imaging accessible to the wider scientific community.</p>","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"1 1","pages":"100013"},"PeriodicalIF":2.4,"publicationDate":"2021-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/5b/1c/main.PMC9680784.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10648101","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}

{"title":"Cooled SPAD array detector for low light-dose fluorescence laser scanning microscopy","authors":"E. Slenders, Eleonora Perego, M. Buttafava, G. Tortarolo, E. Conca, Sabrina Zappone, Agnieszka Pierzyńska-Mach, F. Villa, E. M. Petrini, A. Barberis, A. Tosi, G. Vicidomini","doi":"10.1101/2021.08.03.454878","DOIUrl":"https://doi.org/10.1101/2021.08.03.454878","url":null,"abstract":"The single-photon timing and sensitivity performance and the imaging ability of asynchronous-readout single-photon avalanche diode (SPAD) array detectors have opened up enormous perspectives in fluorescence (lifetime) laser scanning microscopy (FLSM), such as super-resolution image scanning microscopy and high-information content fluorescence fluctuation spectroscopy (FFS). However, the strengths of these FLSM techniques depend on the many different characteristics of the detector, such as dark-noise, photon-detection efficiency, after-pulsing probability, and optical-cross talk, whose overall optimization is typically a trade-off between these characteristics. To mitigate this trade-off, we present a novel SPAD array detector with an active cooling system, which substantially reduces the dark-noise without significantly deteriorating any other detector characteristics. In particular, we show that lowering the temperature of the sensor to −15°C significantly improves the signal-to-noise ratio due to a 10-fold decrease in the dark-count rate compared to room temperature. As a result, for imaging, the laser power can be decreased by more than a factor of three, which is particularly beneficial for live-cell super-resolution imaging, as demonstrated in fixed and living cells expressing GFP-tagged proteins. For FFS, together with the benefit of the reduced laser power, we show that cooling the detector is necessary to remove artifacts in the correlation function, such as spurious negative correlations observed in the hot elements of the detector, i.e., elements whose dark-noise is substantially higher than the median value. Overall, this detector represents a further step towards the integration of SPAD array detectors in any FLSM system. SIGNIFICANCE Single-photon avalanche diode (SPAD) array detectors are revolutionizing fluorescence laser-scanning microscopy (FLSM). Thanks to their single-photon timing and sensitivity ability and their imaging faculty, a SPAD array detector transforms any FLSM into a super-resolution microscope, and opens a whole range of possibilities for the study of sample dynamics by means of fluorescence fluctuation spectroscopy (FFS). However, dark-noise can be a severe problem for both imaging and FFS. For imaging, the signal overcomes noise only for a relatively high illumination intensity, which can be detrimental for live-cell experiments. For FFS, the noise leads to artifacts in the correlation curves, potentially leading to wrong conclusions about the sample. We show that lowering the temperature of the detector to −15°C solves both problems","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82117145","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}

{"title":"Apolar chemical environments compact unfolded RNAs and can promote folding","authors":"Shamal M Gunawardhana, Erik D. Holmstrom","doi":"10.1016/j.bpr.2021.100004","DOIUrl":"https://doi.org/10.1016/j.bpr.2021.100004","url":null,"abstract":"","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"75 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87380558","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}

{"title":"A mean shift algorithm for drift correction in localization microscopy","authors":"Frank J Fazekas, Thomas R. Shaw, Sumin Kim, Ryan A. Bogucki, S. Veatch","doi":"10.1016/j.bpr.2021.100008","DOIUrl":"https://doi.org/10.1016/j.bpr.2021.100008","url":null,"abstract":"","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88733797","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}