Biophysics reports最新文献_第6页

Surface engineering of lipid nanoparticles: targeted nucleic acid delivery and beyond. 脂质纳米颗粒的表面工程：定向核酸输送及其他。

Biophysics reports Pub Date : 2023-10-31 DOI: 10.52601/bpr.2023.230022

Yi Lin, Qiang Cheng, Tuo Wei

{"title":"Surface engineering of lipid nanoparticles: targeted nucleic acid delivery and beyond.","authors":"Yi Lin, Qiang Cheng, Tuo Wei","doi":"10.52601/bpr.2023.230022","DOIUrl":"10.52601/bpr.2023.230022","url":null,"abstract":"Harnessing surface engineering strategies to functionalize nucleic acid-lipid nanoparticles (LNPs) for improved performance has been a hot research topic since the approval of the first siRNA drug, patisiran, and two mRNA-based COVID-19 vaccines, BNT162b2 and mRNA-1273. Currently, efforts have been mainly made to construct targeted LNPs for organ- or cell-type-specific delivery of nucleic acid drugs by conjugation with various types of ligands. In this review, we describe the surface engineering strategies for nucleic acid-LNPs, considering ligand types, conjugation chemistries, and incorporation methods. We then outline the general purification and characterization techniques that are frequently used following the engineering step and emphasize the specific techniques for certain types of ligands. Next, we comprehensively summarize the currently accessible organs and cell types, as well as the other applications of the engineered LNPs. Finally, we provide considerations for formulating targeted LNPs and discuss the challenges of successfully translating the \"proof of concept\" from the laboratory into the clinic. We believe that addressing these challenges could accelerate the development of surface-engineered LNPs for targeted nucleic acid delivery and beyond.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"9 5","pages":"255-278"},"PeriodicalIF":0.0,"publicationDate":"2023-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10951480/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140186596","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

An efficient protocol for studying human pluripotent stem cell-derived myotube senescence. 研究人类多能干细胞衍生肌管衰老的高效方案。

Biophysics reports Pub Date : 2023-10-31 DOI: 10.52601/bpr.2023.230013

Qian Zhao, Ying Jing, Shuai Ma, Weiqi Zhang, Jing Qu, Si Wang, Guang-Hui Liu

引用次数: 0

CAR designs for solid tumors: overcoming hurdles and paving the way for effective immunotherapy. 用于实体瘤的 CAR 设计：克服障碍，为有效的免疫疗法铺平道路。

Biophysics reports Pub Date : 2023-10-31 DOI: 10.52601/bpr.2023.230020

Yuanbin Cui, Mintao Luo, Chuanyuan Gu, Yuxian He, Yao Yao, Peng Li

引用次数: 0

Decoding the mysteries of aging and its impact on human health. 破解衰老的奥秘及其对人类健康的影响。

Biophysics reports Pub Date : 2023-10-31 DOI: 10.52601/bpr.2023.230902

引用次数: 0

Chick chorioallantoic membrane model to investigate role of migrasome in angiogenensis. 用小鸡绒毛膜模型研究移行体在血管生成中的作用

Biophysics reports Pub Date : 2023-10-31 DOI: 10.52601/bpr.2023.230021

Cuifang Zhang, Helen He, Shuyao Yin, Mingyi Gao, Li Yu

{"title":"Chick chorioallantoic membrane model to investigate role of migrasome in angiogenensis.","authors":"Cuifang Zhang, Helen He, Shuyao Yin, Mingyi Gao, Li Yu","doi":"10.52601/bpr.2023.230021","DOIUrl":"10.52601/bpr.2023.230021","url":null,"abstract":"The development of the vascular system is essential for embryonic development, including processes such as angiogenesis. Angiogenesis plays a critical role in many normal physiological and pathological processes. It is driven by a set of angiogenic proteins, including angiogenic growth factors, chemokines, and extracellular matrix proteins. Among various animal model systems, the chorioallantoic membrane (CAM), a specialized and highly vascularized tissue of the avian embryo, has proven to be a valuable tool for analyzing the angiogenic potential of candidate cells or factors. In this protocol, we provide detailed procedures for establishing the CAM model to evaluate the function and mechanism of migrasomes in embryonic angiogenesis. This includes the CAM nylon mesh assay and CAM ex vivo sprouting assay to assess CAM angiogenesis, as well as the observation, purification, and delivery of migrasomes. Additionally, we describe the generation of T4-KO-mCherry-KI embryos using the CRISPR system within the CAM tissue to investigate the role of migrasomes in angiogenesis.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"9 5","pages":"241-254"},"PeriodicalIF":0.0,"publicationDate":"2023-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10951478/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140186594","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

Live-cell super-resolution imaging unconventional dynamics and assemblies of nuclear pore complexes. 活细胞超分辨率成像核孔复合体的非常规动态和组装。

Biophysics reports Pub Date : 2023-08-31 DOI: 10.52601/bpr.2023.230010

Xianxin Ye, Minzhu Guan, Yaorong Guo, Xiang Liu, Kunhao Wang, Tongsheng Chen, Shiqun Zhao, Liangyi Chen

{"title":"Live-cell super-resolution imaging unconventional dynamics and assemblies of nuclear pore complexes.","authors":"Xianxin Ye, Minzhu Guan, Yaorong Guo, Xiang Liu, Kunhao Wang, Tongsheng Chen, Shiqun Zhao, Liangyi Chen","doi":"10.52601/bpr.2023.230010","DOIUrl":"10.52601/bpr.2023.230010","url":null,"abstract":"Super-resolution microscopy has promoted the development of cell biology, but imaging proteins with low copy numbers in cellular structures remains challenging. The limited number of designated proteins within nuclear pore complexes (NPCs) impedes continuous observation in live cells, although they are often used as a standard for evaluating various SR methods. To address this issue, we tagged POM121 with Halo-SiR and imaged it using structured illumination microscopy with sparse deconvolution (Sparse-SIM). Remarkably, POM121-SiR exhibited more than six-fold fluorescence intensity and four-fold enhanced contrast compared to the same protein labeled with tandem-linked mCherry, while showing negligible photo-bleaching during SR imaging for 200 frames. Using this technique, we discovered various types of NPCs, including ring-like and cluster-like structures, and observed dynamic remodeling along with the sequential appearance of different Nup compositions. Overall, Halo-SiR with Sparse-SIM is a potent tool for extended SR imaging of dynamic structures of NPCs in live cells, and it may also help visualize proteins with limited numbers in general.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"9 4","pages":"206-214"},"PeriodicalIF":0.0,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10951474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140186590","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

Theoretical framework and experimental solution for the air-water interface adsorption problem in cryoEM. 低温电子显微镜中空气-水界面吸附问题的理论框架和实验解决方案。

Biophysics reports Pub Date : 2023-08-31 DOI: 10.52601/bpr.2023.230008

Joon S Kang, Xueting Zhou, Yun-Tao Liu, Kaituo Wang, Z Hong Zhou

{"title":"Theoretical framework and experimental solution for the air-water interface adsorption problem in cryoEM.","authors":"Joon S Kang, Xueting Zhou, Yun-Tao Liu, Kaituo Wang, Z Hong Zhou","doi":"10.52601/bpr.2023.230008","DOIUrl":"10.52601/bpr.2023.230008","url":null,"abstract":"As cryogenic electron microscopy (cryoEM) gains traction in the structural biology community as a method of choice for determining atomic structures of biological complexes, it has been increasingly recognized that many complexes that behave well under conventional negative-stain electron microscopy tend to have preferential orientation, aggregate or simply mysteriously \"disappear\" on cryoEM grids. However, the reasons for such misbehavior are not well understood, which limits systematic approaches to solving the problem. Here, we have developed a theoretical formulation that explains these observations. Our formulation predicts that all particles migrate to the air-water interface (AWI) to lower the total potential surface energy-rationalizing the use of surfactant, which is a direct solution to reduce the surface tension of the aqueous solution. By performing cryogenic electron tomography (cryoET) on the widely-tested sample, GroEL, we demonstrate that, in a standard buffer solution, nearly all particles migrate to the AWI. Gradually reducing the surface tension by introducing surfactants decreased the percentage of particles exposed to the surface. By conducting single-particle cryoEM, we confirm that suitable surfactants do not damage the biological complex, thus suggesting that they might provide a practical, simple, and general solution to the problem for high-resolution cryoEM. Applying this solution to a real-world AWI adsorption problem involving a more challenging membrane protein, namely, the ClC-1 channel, has resulted in its near-atomic structure determination using cryoEM.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"9 4","pages":"215-229"},"PeriodicalIF":0.0,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10951471/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140186591","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

Xenopus cell-free extracts and their applications in cell biology study. 无细胞爪蟾提取物及其在细胞生物学研究中的应用。

Biophysics reports Pub Date : 2023-08-31 DOI: 10.52601/bpr.2023.230016

Junjun Liu, Chuanmao Zhang

{"title":"Xenopus cell-free extracts and their applications in cell biology study.","authors":"Junjun Liu, Chuanmao Zhang","doi":"10.52601/bpr.2023.230016","DOIUrl":"10.52601/bpr.2023.230016","url":null,"abstract":"Xenopus has proven to be a remarkably versatile model organism in the realm of biological research for numerous years, owing to its straightforward maintenance in laboratory settings and its abundant provision of ample-sized oocytes, eggs, and embryos. The cell cycle of these oocytes, eggs, and early embryos exhibits synchrony, and extracts derived from these cells serve various research purposes. Many fundamental concepts in biochemistry, cell biology, and development have been elucidated through the use of cell-free extracts derived from Xenopus cells. Over the past few decades, a wide array of cell-free extracts has been prepared from oocytes, eggs, and early embryos of different Xenopus species at varying cell cycle stages. Each of these extracts possesses distinct characteristics. This review provides a concise overview of the Xenopus species employed in laboratory research, the diverse types of cell-free extracts available, and their respective properties. Furthermore, this review delves into the extensive investigation of spindle assembly in Xenopus egg extracts, underscoring the versatility and potency of these cell-free systems in the realm of cell biology.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"9 4","pages":"195-205"},"PeriodicalIF":0.0,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10951473/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140186588","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

Deep learning-enabled fast DNA-PAINT imaging in cells. 基于深度学习的细胞快速 DNA-PAINT 成像。

Biophysics reports Pub Date : 2023-08-31 DOI: 10.52601/bpr.2023.230014

Min Zhu, Luhao Zhang, Luhong Jin, Yunyue Chen, Haixu Yang, Baohua Ji, Yingke Xu

引用次数: 0

Tumor type classification and candidate cancer-specific biomarkers discovery via semi-supervised learning. 通过半监督学习发现肿瘤类型分类和候选癌症特异性生物标志物。

Biophysics reports Pub Date : 2023-04-30 DOI: 10.52601/bpr.2023.230005

Peng Chen, Zhenlei Li, Zhaolin Hong, Haoran Zheng, Rong Zeng

{"title":"Tumor type classification and candidate cancer-specific biomarkers discovery via semi-supervised learning.","authors":"Peng Chen, Zhenlei Li, Zhaolin Hong, Haoran Zheng, Rong Zeng","doi":"10.52601/bpr.2023.230005","DOIUrl":"10.52601/bpr.2023.230005","url":null,"abstract":"Identifying cancer-related differentially expressed genes provides significant information for diagnosing tumors, predicting prognoses, and effective treatments. Recently, deep learning methods have been used to perform gene differential expression analysis using microarray-based high-throughput gene profiling and have achieved good results. In this study, we proposed a new robust multiple-datasets-based semi-supervised learning model, MSSL, to perform tumor type classification and candidate cancer-specific biomarkers discovery across multiple tumor types and multiple datasets, which addressed the following long-lasting obstacles: (1) the data volume of the existing single dataset is not enough to fully exert the advantages of deep learning; (2) a large number of datasets from different research institutions cannot be effectively used due to inconsistent internal variances and low quality; (3) relatively uncommon cancers have limited effects on deep learning methods. In our article, we applied MSSL to The Cancer Genome Atlas (TCGA) and the Gene Expression Comprehensive Database (GEO) pan-cancer normalized-level3 RNA-seq data and got 97.6% final classification accuracy, which had a significant performance leap compared with previous approaches. Finally, we got the ranking of the importance of the corresponding genes for each cancer type based on classification results and validated that the top genes selected in this way were biologically meaningful for corresponding tumors and some of them had been used as biomarkers, which showed the efficacy of our method.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"9 2","pages":"57-66"},"PeriodicalIF":0.0,"publicationDate":"2023-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10518520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41168715","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