生物物理学报:英文版最新文献_第3页

Measuring the size and growth of single cells. 测量单细胞的大小和生长情况。

生物物理学报:英文版 Pub Date : 2022-06-30 DOI: 10.52601/bpr.2022.210036

An Gong, Mingwei Min

引用次数: 0

Spatial transcriptomics: new dimension of understanding biological complexity. 空间转录组学:理解生物复杂性的新维度。

生物物理学报:英文版 Pub Date : 2022-06-30 DOI: 10.52601/bpr.2021.210037

Zhuxia Li, Guangdun Peng

{"title":"Spatial transcriptomics: new dimension of understanding biological complexity.","authors":"Zhuxia Li, Guangdun Peng","doi":"10.52601/bpr.2021.210037","DOIUrl":"https://doi.org/10.52601/bpr.2021.210037","url":null,"abstract":"Cells and tissues are exquisitely organized in a complex but ordered manner to form organs and bodies so that individuals can function properly. The spatial organization and tissue architecture represent a keynote property underneath all living organisms. Molecular architecture and cellular composition within intact tissues play a vital role in a variety of biological processes, such as forming the complicated tissue functionality, precise regulation of cell transition in all living activities, consolidation of central nervous system, cellular responses to immunological and pathological cues. To explore these biological events at a large scale and fine resolution, a genome-wide understanding of spatial cellular changes is essential. However, previous bulk RNA sequencing and single-cell RNA sequencing technologies could not obtain the important spatial information of tissues and cells, despite their ability to detect high content transcriptional changes. These limitations have prompted the development of numerous spatially resolved technologies which provide a new dimension to interrogate the regional gene expression, cellular microenvironment, anatomical heterogeneity and cell-cell interactions. Since the advent of spatial transcriptomics, related works that use these technologies have increased rapidly, and new methods with higher throughput and resolution have grown quickly, all of which hold great promise to accelerate new discoveries in understanding the biological complexity. In this review, we briefly discussed the historical evolution of spatially resolved transcriptome. We broadly surveyed the representative methods. Furthermore, we summarized the general computational analysis pipeline for the spatial gene expression data. Finally, we proposed perspectives for technological development of spatial multi-omics.","PeriodicalId":59621,"journal":{"name":"生物物理学报:英文版","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10189652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9597790","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: 2

Practical bioinformatics pipelines for single-cell RNA-seq data analysis. 用于单细胞RNA-seq数据分析的实用生物信息学管道。

生物物理学报:英文版 Pub Date : 2022-06-30 DOI: 10.52601/bpr.2022.210041

Jiangping He, Lihui Lin, Jiekai Chen

引用次数: 2

Single-cell multi-omics sequencing and its applications in studying the nervous system. 单细胞多组学测序及其在神经系统研究中的应用。

生物物理学报:英文版 Pub Date : 2022-06-30 DOI: 10.52601/bpr.2021.210031

Chaoyang Wang, Xiaoying Fan

引用次数: 0

Visualizing carboxyl-terminal domain of RNA polymerase II recruitment by FET fusion protein condensates with DNA curtains. 用FET融合蛋白凝聚体和DNA帷幕观察RNA聚合酶II募集的羧基末端结构域。

生物物理学报:英文版 Pub Date : 2022-04-30 DOI: 10.52601/bpr.2022.210027

Linyu Zuo, Jiawei Ding, Zhi Qi

{"title":"Visualizing carboxyl-terminal domain of RNA polymerase II recruitment by FET fusion protein condensates with DNA curtains.","authors":"Linyu Zuo, Jiawei Ding, Zhi Qi","doi":"10.52601/bpr.2022.210027","DOIUrl":"https://doi.org/10.52601/bpr.2022.210027","url":null,"abstract":"Many recent references show that living cells can form some membrane-less organelles by liquid-liquid phase separation (LLPS) of biomolecules, like proteins and nucleic acids. LLPS has been confirmed to link with many important biological functions in living cells, and one of the most important functions of biomolecular condensates is in the field of RNA transcription. Many studies confirm that mammalian RNA polymerase II (Pol II) molecules containing the CTD with different phosphorylation level are purposed to shuttle between initiation condensates and elongation condensates of RNA transcription. Traditional ensemble assays often experience difficulties in quantitively and directly recording the transient recruitment of Pol II CTD. Novel single-molecule approach - DNA curtains can be used to directly visualize biomolecular condensates formation and also recruitment of RNA polymerase II (Pol II) carboxyl-terminal domain (CTD) at the target sites in solution and in real time. This method can offer the potential for new insights into the mechanism of gene transcription. Here, we highlight the detailed protocol of DNA curtains method for studying LLPS.","PeriodicalId":59621,"journal":{"name":"生物物理学报:英文版","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10195810/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9600071","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

Driving force of biomolecular liquid-liquid phase separation probed by nuclear magnetic resonance spectroscopy. 核磁共振波谱法探测生物分子液-液相分离驱动力。

生物物理学报:英文版 Pub Date : 2022-04-30 DOI: 10.52601/bpr.2022.210034

Hanyu Zhang, Weiwei Fan, Gilbert Nshogoza, Yaqian Liu, Jia Gao, Jihui Wu, Yunyu Shi, Xiaoming Tu, Jiahai Zhang, Ke Ruan

引用次数: 0

Principles of fluorescence correlation spectroscopy applied to studies of biomolecular liquid-liquid phase separation. 荧光相关光谱原理在生物分子液-液相分离研究中的应用。

生物物理学报:英文版 Pub Date : 2022-04-30 DOI: 10.52601/bpr.2022.210047

Zhulou Wang, Huizhi Zhang, Lin Jian, Bo Ding, Keying Huang, Wolun Zhang, Qian Xiao, Shaohui Huang

{"title":"Principles of fluorescence correlation spectroscopy applied to studies of biomolecular liquid-liquid phase separation.","authors":"Zhulou Wang, Huizhi Zhang, Lin Jian, Bo Ding, Keying Huang, Wolun Zhang, Qian Xiao, Shaohui Huang","doi":"10.52601/bpr.2022.210047","DOIUrl":"https://doi.org/10.52601/bpr.2022.210047","url":null,"abstract":"Fluorescence correlation spectroscopy (FCS) investigates the temporal relationship of fluctuating fluorescence signals reflecting underlying molecular processes occurring in a solution sample or a single live cell. This review article introduces the principles of two basic and most used FCS techniques: fluorescence auto-correlation spectroscopy (FACS) and fluorescence cross-correlation spectroscopy (FCCS). Combined, FACS and FCCS techniques can quantitatively analyze multiple properties of molecule or nanoparticle samples, including molar concentration, diffusion coefficient and hydrodynamic radius, homo- or hetero-interaction, fluorescence brightness, etc. Not surprisingly, FCS techniques have long been used to investigate molecular mechanisms of biomolecular phase separation, first in the lipid bilayer and more recently in cell cytosol and nucleoplasm. The latter applications are especially exciting since a whole new class of membraneless cellular organelles have been discovered, which are proposed to be results of biomolecule liquid-liquid phase separation (LLPS). LLPS research can benefit significantly from the multifunctionality and single-molecule sensitivity of a variety of FCS techniques, particularly for live-cell studies. This review illustrates how FACS and FCCS techniques can be used to investigate multiple aspects of the molecular mechanisms of LLPS, and summarizes FCS applications to LLPS research in vivo and in vitro.","PeriodicalId":59621,"journal":{"name":"生物物理学报:英文版","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10195812/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9603156","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: 2

Theoretical modelling of liquid-liquid phase separation: from particle-based to field-based simulation. 液-液相分离的理论建模:从基于颗粒的模拟到基于场的模拟。

生物物理学报:英文版 Pub Date : 2022-04-30 DOI: 10.52601/bpr.2022.210029

Lin-Ge Li, Zhonghuai Hou

{"title":"Theoretical modelling of liquid-liquid phase separation: from particle-based to field-based simulation.","authors":"Lin-Ge Li, Zhonghuai Hou","doi":"10.52601/bpr.2022.210029","DOIUrl":"https://doi.org/10.52601/bpr.2022.210029","url":null,"abstract":"Liquid-liquid phase separation (LLPS) has proved to be ubiquitous in living cells, forming membraneless organelles (MLOs) and dynamic condensations essential in physiological processes. However, some underlying mechanisms remain challenging to unravel experimentally, making theoretical modeling an indispensable aspect. Here we present a protocol for understanding LLPS from fundamental physics to detailed modeling procedures. The protocol involves a comprehensive physical picture on selecting suitable theoretical approaches, as well as how and what to interpret and resolve from the results. On the particle-based level, we elaborate on coarse-grained simulation procedures from building up models, identifying crucial interactions to running simulations to obtain phase diagrams and other concerned properties. We also outline field-based theories which give the system's density profile to determine phase diagrams and provide dynamic properties by studying the time evolution of density field, enabling us to characterize LLPS systems with larger time and length scales and to further include other nonequilibrium factors such as chemical reactions.","PeriodicalId":59621,"journal":{"name":"生物物理学报:英文版","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10195811/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9603154","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

Measuring the elasticity of liquid-liquid phase separation droplets with biomembrane force probe. 用生物膜力探针测量液液相分离液滴的弹性。

生物物理学报:英文版 Pub Date : 2022-04-30 DOI: 10.52601/bpr.2022.210038

Min Sun, Hui Chen, Qinghua Ji, Jianhui Xiao, Yanzhe Hou, Jizhong Lou

{"title":"Measuring the elasticity of liquid-liquid phase separation droplets with biomembrane force probe.","authors":"Min Sun, Hui Chen, Qinghua Ji, Jianhui Xiao, Yanzhe Hou, Jizhong Lou","doi":"10.52601/bpr.2022.210038","DOIUrl":"https://doi.org/10.52601/bpr.2022.210038","url":null,"abstract":"Numerous biomacromolecules undergo liquid-liquid phase separation (LLPS) inside living cells and LLPS plays important roles in their functions. The droplets formed by LLPS molecules are complex fluids and their behavior follows fluid mechanics, thus studies on rheological and material properties are required to gain full insight into the biophysical mechanism of these droplets. Biophysical force spectroscopy techniques are particularly useful in this aspect. Indeed, atomic force microscopy and optical tweezers have been used to quantify the elasticity and the viscoelasticity of LLPS droplets. The Biomembrane Force Probe (BFP) is a single-molecule technique designed to investigate liquid-like objects and is more suitable to quantify the material properties of LLPS droplets, but its usage on LLPS droplets is not yet described. Here we present an experimental protocol to measure the Young's modulus of LLPS droplets using BFP, we believe that the application of BFP on phase separation studies can be expanded and will be very helpful in deciphering the underlying principles of LLPS.","PeriodicalId":59621,"journal":{"name":"生物物理学报:英文版","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10195813/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9603155","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

Cellular and animal models to investigate pathogenesis of amyloid aggregation in neurodegenerative diseases. 研究神经退行性疾病中淀粉样蛋白聚集的细胞和动物模型。

生物物理学报:英文版 Pub Date : 2022-02-28 DOI: 10.52601/bpr.2022.210033

Houfang Long, Shuyi Zeng, Dan Li

引用次数: 1