Biophysics reports最新文献_第5页

Assaying sarcoplasmic reticulum Ca²⁺-leak in mouse atrial myocytes. 测定小鼠心房肌细胞肌质网 Ca2+ 泄漏。

Biophysics reports Pub Date : 2024-10-31 DOI: 10.52601/bpr.2023.230044

Fan Xu, Jing-Jing Li, Eric Yang, Yi Zhang, Wenjun Xie

{"title":"Assaying sarcoplasmic reticulum Ca2+-leak in mouse atrial myocytes.","authors":"Fan Xu, Jing-Jing Li, Eric Yang, Yi Zhang, Wenjun Xie","doi":"10.52601/bpr.2023.230044","DOIUrl":"10.52601/bpr.2023.230044","url":null,"abstract":"More and more studies have suggested an essential role of sarcoplasmic reticulum (SR) Ca2+ leak of atrial myocytes in atrial diseases such as atrial fibrillation (AF). The increasing interest in atrial Ca2+ signaling makes it necessary to develop a more accurate approach for Ca2+ measurement in atrial myocytes due to obvious differences between atrial and ventricular Ca2+ handling. In the present study, we proposed a new approach for quantifying total SR Ca2+ leak in atrial myocytes with confocal line-scan Ca2+ images. With a very precious approximation of the histogram of normalized line-scan Ca2+ images by using a modified Gaussian distribution, we separated the signal pixel components from noisy pixels and extracted two new dimensionless parameters, F signals and R signals, to reflect the summation of signal pixels and their release components, respectively. In the presence of tetracaine blocking SR Ca2+ leak, the two parameters were very close to 0, and in atrial myocytes under normal conditions, the two parameters are well positive correlative with Ca2+ spark frequency and total signal mass, the two classic readouts for SR Ca2+ leak. Consistent with Ca2+ Spark readouts, the two parameters quantified a significant increase of SR Ca2+ leak in atrial myocytes from mice harboring a leaky type 2 ryanodine receptor mutation (RyR2-R2474S+/-) compared to the WT group. Collectively, this study proposed a simple and effective approach to quantify SR Ca2+ leak in atrial myocytes, which may benefit research on calcium signaling in atrial physiology and diseases.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 5","pages":"297-303"},"PeriodicalIF":0.0,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11554581/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633514","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

Modeling sarcoplasmic reticulum Ca²⁺ in rat cardiomyocytes. 建立大鼠心肌细胞肌浆网 Ca2+ 模型

Biophysics reports Pub Date : 2024-10-31 DOI: 10.52601/bpr.2024.240012

Yutong Su, Yongshen Liang, Menghao Xu, Beibei Gao, Siyuan Zhang, Eric Yang, Shuai Yin, Da Li, Zhangqin Huang, Wenjun Xie

{"title":"Modeling sarcoplasmic reticulum Ca2+ in rat cardiomyocytes.","authors":"Yutong Su, Yongshen Liang, Menghao Xu, Beibei Gao, Siyuan Zhang, Eric Yang, Shuai Yin, Da Li, Zhangqin Huang, Wenjun Xie","doi":"10.52601/bpr.2024.240012","DOIUrl":"10.52601/bpr.2024.240012","url":null,"abstract":"The sarcoplasmic reticulum (SR) primarily serves as the intracellular Ca2+ store in cardiac myocytes, mediating cellular function under cardiac physiology and diseases. However, the properties of cardiac SR Ca2+ have not yet been fully determined, particularly in rats and mice, which are the most commonly used experimental species in studies on cardiac physiology and diseases. Here, we developed a spatially detailed numerical model to deduce Ca2+ movements inside the junctional SR (jSR) cisternae of rat cardiomyocytes. Our model accurately reproduced the jSR Ca2+ kinetics of local and global SR Ca2+ releases reported in a recent experimental study. With this model, we revealed that jSR Ca2+ kinetics was mostly determined by the total release flux via type 2 ryanodine receptor (RyR2) channels but not by RyR2 positioning. Although Ca2+ diffusion in global SR was previously reported to be slow, our simulation demonstrated that Ca2+ diffused very quickly inside local jSR cisternae and the decrease in the diffusion coefficient resulted in a significant reduction of jSR Ca2+ depletion amplitude. Intracellular Ca2+ was typically experimentally detected with fluorescence dye. Our simulation revealed that when the dynamical characteristics of fluorescence dye exerted a minimal effect on actual Ca2+ mobility inside jSR, the reaction rate of the dye with Ca2+ could significantly affect apparent jSR Ca2+ kinetics. Therefore, loading a chemical fluorescence dye with fast kinetics, such as Fluo-5N, into SR is important for Ca2+ measurement inside SR. Overall, our model provides new insights into deciphering Ca2+ handling inside nanoscopic jSR cisternae in rat cardiomyocytes.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 5","pages":"328-335"},"PeriodicalIF":0.0,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11554579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633823","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

Ca²⁺ sparks and beyond. Ca2+ 火花及其他

Biophysics reports Pub Date : 2024-10-31 DOI: 10.52601/bpr.2024.240909

Shi-Qiang Wang

引用次数: 0

Single-cell transcriptomics reveals neural stem cell trans-differentiation and cell subpopulations in whole heart decellularized extracellular matrix. 单细胞转录组学揭示了全心脱细胞细胞外基质中神经干细胞的跨分化和细胞亚群。

Biophysics reports Pub Date : 2024-08-31 DOI: 10.52601/bpr.2024.240011

Xiaoning Yang, Yuwei Zhao, Wei Liu, Zhongbao Gao, Chunlan Wang, Changyong Wang, Siwei Li, Xiao Zhang

{"title":"Single-cell transcriptomics reveals neural stem cell trans-differentiation and cell subpopulations in whole heart decellularized extracellular matrix.","authors":"Xiaoning Yang, Yuwei Zhao, Wei Liu, Zhongbao Gao, Chunlan Wang, Changyong Wang, Siwei Li, Xiao Zhang","doi":"10.52601/bpr.2024.240011","DOIUrl":"https://doi.org/10.52601/bpr.2024.240011","url":null,"abstract":"The whole heart decellularized extracellular matrix (ECM) has become a promising scaffold material for cardiac tissue engineering. Our previous research has shown that the whole heart acellular matrix possesses the memory function regulating neural stem cells (NSCs) trans-differentiating to cardiac lineage cells. However, the cell subpopulations and phenotypes in the trans-differentiation of NSCs have not been clearly identified. Here, we performed single-cell RNA sequencing and identified 2,765 cells in the recellularized heart with NSCs revealing the cellular diversity of cardiac and neural lineage, confirming NSCs were capable of trans-differentiating into the cardiac lineage while maintaining the original ability to differentiate into the neural lineage. Notably, the trans-differentiated heart-like cells have dual signatures of neuroectoderm and cardiac mesoderm. This study unveils an in-depth mechanism underlying the trans-differentiation of NSCs and provides a new opportunity and theoretical basis for cardiac regeneration.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 4","pages":"241-253"},"PeriodicalIF":0.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11399890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142303327","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

Met1-linked ubiquitination in cell signaling regulation. 细胞信号调节中与 Met1 链接的泛素化。

Biophysics reports Pub Date : 2024-08-31 DOI: 10.52601/bpr.2024.230030

Yanmin Guo, Yuqin Zhao, Yu-Sheng Cong

引用次数: 0

Studying large biomolecules as sedimented solutes with solid-state NMR. 利用固态核磁共振研究作为沉积溶质的大型生物分子。

Biophysics reports Pub Date : 2024-08-31 DOI: 10.52601/bpr.2024.240014

Fan Shi, Tong Zhang, Juan Li, Chaowei Shi, Shengqi Xiang

{"title":"Studying large biomolecules as sedimented solutes with solid-state NMR.","authors":"Fan Shi, Tong Zhang, Juan Li, Chaowei Shi, Shengqi Xiang","doi":"10.52601/bpr.2024.240014","DOIUrl":"https://doi.org/10.52601/bpr.2024.240014","url":null,"abstract":"Sedimentation solid-state NMR is a novel method for sample preparation in solid-state NMR (ssNMR) studies. It involves the sedimentation of soluble macromolecules such as large protein complexes. By utilizing ultra-high centrifugal forces, the molecules in solution are driven into a high-concentrated hydrogel, resulting in a sample suitable for solid-state NMR. This technique has the advantage of avoiding the need for chemical treatment, thus minimizing the loss of sample biological activity. Sediment ssNMR has been successfully applied to a variety of non-crystalline protein solids, significantly expanding the scope of solid-state NMR research. In theory, using this method, any biological macromolecule in solution can be transferred into a sedimented solute appropriate for solid-state NMR analysis. However, specialized equipment and careful handling are essential for effectively collecting and loading the sedimented solids to solid-state NMR rotors. To improve efficiency, we have designed a series of loading tools to achieve the loading process from the solution to the rotor in one step. In this paper, we illustrate the sample preparation process of sediment NMR using the H1.4-NCP167 complex, which consists of linker histone H1.4 and nucleosome core particle, as an example.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 4","pages":"201-212"},"PeriodicalIF":0.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11399891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142303329","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

The brain network hub degeneration in Alzheimer's disease. 阿尔茨海默病的大脑网络中枢退化。

Biophysics reports Pub Date : 2024-08-31 DOI: 10.52601/bpr.2024.230025

Suhui Jin, Jinhui Wang, Yong He

{"title":"The brain network hub degeneration in Alzheimer's disease.","authors":"Suhui Jin, Jinhui Wang, Yong He","doi":"10.52601/bpr.2024.230025","DOIUrl":"https://doi.org/10.52601/bpr.2024.230025","url":null,"abstract":"Alzheimer's disease (AD) has been conceptualized as a syndrome of brain network dysfunction. Recent imaging connectomics studies have provided unprecedented opportunities to map structural and functional brain networks in AD. By reviewing molecular, imaging, and computational modeling studies, we have shown that highly connected brain hubs are primarily distributed in the medial and lateral prefrontal, parietal, and temporal regions in healthy individuals and that the hubs are selectively and severely affected in AD as manifested by increased amyloid-beta deposition and regional atrophy, hypo-metabolism, and connectivity dysfunction. Furthermore, AD-related hub degeneration depends on the imaging modality with the most notable degeneration in the medial temporal hubs for morphological covariance networks, the prefrontal hubs for structural white matter networks, and in the medial parietal hubs for functional networks. Finally, the AD-related hub degeneration shows metabolic, molecular, and genetic correlates. Collectively, we conclude that the brain-network-hub-degeneration framework is promising to elucidate the biological mechanisms of network dysfunction in AD, which provides valuable information on potential diagnostic biomarkers and promising therapeutic targets for the disease.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 4","pages":"213-229"},"PeriodicalIF":0.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11399886/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142303330","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

Unlocking the secrets of TGR5: a new dawn in treating diabetic cardiomyopathy. 揭开 TGR5 的秘密：治疗糖尿病心肌病的新曙光。

Biophysics reports Pub Date : 2024-08-31 DOI: 10.52601/bpr.2024.240907

Jin Li, He Huang

引用次数: 0

Streamlined process for effective and strand-selective mitochondrial base editing using mitoBEs. 使用 mitoBEs 进行有效和链选择性线粒体碱基编辑的简化流程。

Biophysics reports Pub Date : 2024-08-31 DOI: 10.52601/bpr.2024.240010

Xiaoxue Zhang, Zongyi Yi, Wei Tang, Wensheng Wei

引用次数: 0

Decoder-seq: a technology for high sensitivity, high resolution, and low-cost spatial RNA sequencing. 解码器-测序：一种高灵敏度、高分辨率、低成本的空间 RNA 测序技术。

Biophysics reports Pub Date : 2024-06-30 DOI: 10.52601/bpr.2024.240903

Siquan Li, Jin Li, He Huang

引用次数: 0