发布求助
文献互助 智能选刊 最新文献

Biophysics reports最新文献

筛选
英文 中文
Co-immunoprecipitation for identifying protein-protein interaction on lipid droplets. 共免疫沉淀法用于识别脂滴上蛋白质与蛋白质之间的相互作用。
Biophysics reports Pub Date : 2024-04-30 DOI: 10.52601/bpr.2024.240007
Xiaochuan Fu, Shuyan Zhang, Pingsheng Liu
{"title":"Co-immunoprecipitation for identifying protein-protein interaction on lipid droplets.","authors":"Xiaochuan Fu, Shuyan Zhang, Pingsheng Liu","doi":"10.52601/bpr.2024.240007","DOIUrl":"10.52601/bpr.2024.240007","url":null,"abstract":"<p><p>The lipid droplet (LD) is a conserved organelle that exists in almost all organisms, ranging from bacteria to mammals. Dysfunctions in LDs are linked to a range of human metabolic syndromes. The formation of protein complexes on LDs is crucial for maintaining their function. Investigating how proteins interact on LDs is essential for understanding the role of LDs. We have developed an effective method to uncover protein-protein interactions and protein complexes specifically on LDs. In this method, we conduct co-immunoprecipitation (co-IP) experiments using LD proteins extracted directly from isolated LDs, rather than utilizing proteins from cell lysates. To elaborate, we begin by purifying LDs with high-quality and extracting LD-associated proteins. Subsequently, the co-IP experiment is performed on these LD-associated proteins directly, which would enhance the co-IP experiment specificity of LD-associated proteins. This method enables researchers to directly unveil protein complexes on LDs and gain deeper insights into the functional roles of proteins associated with LDs.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 2","pages":"102-110"},"PeriodicalIF":0.0,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11103721/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141075374","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
Enrichment of ER tubule-derived microsomes by differential centrifugation and immunoprecipitation. 通过差速离心和免疫沉淀富集ER小管衍生微粒体。
Biophysics reports Pub Date : 2024-04-30 DOI: 10.52601/bpr.2023.230031
Yiduo Liu, Junjie Hu, Bing Yan
{"title":"Enrichment of ER tubule-derived microsomes by differential centrifugation and immunoprecipitation.","authors":"Yiduo Liu, Junjie Hu, Bing Yan","doi":"10.52601/bpr.2023.230031","DOIUrl":"10.52601/bpr.2023.230031","url":null,"abstract":"<p><p>The endoplasmic reticulum (ER) is an essential component of the endomembrane system in eukaryotes and plays a crucial role in protein and lipid synthesis, as well as the maintenance of calcium homeostasis. Morphologically, the ER is composed primarily of sheets and tubules. The tubular ER is composed of a network of tubular membrane structures, each with diameters ranging from 30 to 50 nanometers. In recent years, there has been in-depth research on the molecular mechanisms of membrane shaping and membrane fusion of the tubular ER. However, there is still limited understanding of the specific physiological functions of the tubular ER. Here, we report a protocol that combines differential centrifugation and immunoprecipitation to specifically enrich microsomes originating from the tubular ER in yeast. The ER tubule-derived microsomes can be further used for proteomic and lipidomic studies or other biochemical analyses.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 2","pages":"61-66"},"PeriodicalIF":0.0,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11103718/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141075890","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
Exploring lysosomal biology: current approaches and methods. 溶酶体生物学探索：当前的途径和方法。
Biophysics reports Pub Date : 2024-04-30 DOI: 10.52601/bpr.2023.230028
Qiuyuan Yin, Chonglin Yang
{"title":"Exploring lysosomal biology: current approaches and methods.","authors":"Qiuyuan Yin, Chonglin Yang","doi":"10.52601/bpr.2023.230028","DOIUrl":"10.52601/bpr.2023.230028","url":null,"abstract":"<p><p>Lysosomes are the degradation centers and signaling hubs in the cell. Lysosomes undergo adaptation to maintain cell homeostasis in response to a wide variety of cues. Dysfunction of lysosomes leads to aging and severe diseases including lysosomal storage diseases (LSDs), neurodegenerative disorders, and cancer. To understand the complexity of lysosome biology, many research approaches and tools have been developed to investigate lysosomal functions and regulatory mechanisms in diverse experimental systems. This review summarizes the current approaches and tools adopted for studying lysosomes, and aims to provide a methodological overview of lysosomal research and related fields.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 2","pages":"111-120"},"PeriodicalIF":0.0,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11103719/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141076476","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
Detection of ribophagy in yeast and mammals. 检测酵母和哺乳动物的核吞噬作用
Biophysics reports Pub Date : 2024-04-30 DOI: 10.52601/bpr.2024.240002
Miao Ye, Yuting Chen, Zhaojie Liu, Yigang Wang, Cong Yi
{"title":"Detection of ribophagy in yeast and mammals.","authors":"Miao Ye, Yuting Chen, Zhaojie Liu, Yigang Wang, Cong Yi","doi":"10.52601/bpr.2024.240002","DOIUrl":"10.52601/bpr.2024.240002","url":null,"abstract":"<p><p>Ribophagy, the cellular process wherein ribosomes are selectively self-digested through autophagy, plays a pivotal role in maintaining ribosome turnover. Understanding the molecular regulatory mechanisms governing ribophagy is pivotal to uncover its significance. Consequently, the establishment of methods for detecting ribophagy becomes important. In this protocol, we have optimized, enriched, and advanced existing ribophagy detection techniques, including immunoblotting, fluorescence microscopy, and transmission electron microscopy (TEM), to precisely monitor and quantify ribophagic events. Particularly noteworthy is the introduction of TEM technology for yeast ribophagy detection. In summary, the delineated methods are applicable for detecting ribophagy in both yeast and mammals, laying a solid foundation for further exploring the physiological importance of ribophagy and its potential implications in diverse cellular environments.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 2","pages":"82-101"},"PeriodicalIF":0.0,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11103720/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141075696","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
Morphological determination of localization and function of Golgi proteins. 从形态学角度确定高尔基体蛋白的定位和功能。
Biophysics reports Pub Date : 2024-04-30 DOI: 10.52601/bpr.2024.240008
Yusheng Xing, Yannan Jian, Xiaodan Zhao, Yue Zhang, Zhenqian Zhang, Xing Zhang, Xiaoyan Zhang
{"title":"Morphological determination of localization and function of Golgi proteins.","authors":"Yusheng Xing, Yannan Jian, Xiaodan Zhao, Yue Zhang, Zhenqian Zhang, Xing Zhang, Xiaoyan Zhang","doi":"10.52601/bpr.2024.240008","DOIUrl":"10.52601/bpr.2024.240008","url":null,"abstract":"<p><p>In animal cells, the Golgi apparatus serves as the central hub of the endomembrane secretory pathway. It is responsible for the processing, modification, and sorting of proteins and lipids. The unique stacking and ribbon-like architecture of the Golgi apparatus forms the foundation for its precise functionality. Under cellular stress or pathological conditions, the structure of the Golgi and its important glycosylation modification function may change. It is crucial to employ suitable methodologies to study the structure and function of the Golgi apparatus, particularly when assessing the involvement of a target protein in Golgi regulation. This article provides a comprehensive overview of the diverse microscopy techniques used to determine the specific location of the target protein within the Golgi apparatus. Additionally, it outlines methods for assessing changes in the Golgi structure and its glycosylation modification function following the knockout of the target gene.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 2","pages":"121-132"},"PeriodicalIF":0.0,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11103716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141076650","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
Seeing is believing: observation of migrasomes. 眼见为实：观察迁移体。
Biophysics reports Pub Date : 2024-04-30 DOI: 10.52601/bpr.2023.230024
Yuwei Huang, Li Yu
{"title":"Seeing is believing: observation of migrasomes.","authors":"Yuwei Huang, Li Yu","doi":"10.52601/bpr.2023.230024","DOIUrl":"10.52601/bpr.2023.230024","url":null,"abstract":"<p><p>Migrasomes are a novel type of cell organelle that form on the retraction fibers at the rear of migrating cells. In recent years, numerous studies have unveiled the mechanisms of migrasome formation and have highlighted significant roles of migrasomes in both physiological and pathological processes. Building upon the strategies outlined in published works and our own research experiences, we have compiled a comprehensive set of protocols for observing migrasomes. These step-by-step instructions encompass various aspects such as cell culture, labeling, imaging, <i>in vitro</i> reconstitution, and statistical analysis. We believe that these protocols serve as a valuable resource for researchers exploring migrasome biology.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 2","pages":"67-81"},"PeriodicalIF":0.0,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11103717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141076908","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
EVEscape: Revealing potential escape sites based on the viral variation landscape. EVEscape：根据病毒变异景观揭示潜在逃逸点
Biophysics reports Pub Date : 2024-04-30 DOI: 10.52601/bpr.2024.240902
Yaling Li, Aiping Wu, Hang-Yu Zhou
{"title":"EVEscape: Revealing potential escape sites based on the viral variation landscape.","authors":"Yaling Li, Aiping Wu, Hang-Yu Zhou","doi":"10.52601/bpr.2024.240902","DOIUrl":"10.52601/bpr.2024.240902","url":null,"abstract":"","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 2","pages":"133-134"},"PeriodicalIF":0.0,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11103722/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141076475","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 optimized method of culturing neurons based on polyacrylamide gel. 基于聚丙烯酰胺凝胶的神经元培养优化方法。
Biophysics reports Pub Date : 2024-02-29 DOI: 10.52601/bpr.2023.230033
Yongjing Qiao, Jihong Gong, Ziqi Jin, Yiting Tu, Xiaofei Yang
{"title":"An optimized method of culturing neurons based on polyacrylamide gel.","authors":"Yongjing Qiao, Jihong Gong, Ziqi Jin, Yiting Tu, Xiaofei Yang","doi":"10.52601/bpr.2023.230033","DOIUrl":"10.52601/bpr.2023.230033","url":null,"abstract":"<p><p>Substrate stiffness is a microenvironment with a certain stiffness constructed by the extracellular matrix and adjacent cells, which plays an important role in the growth and development of cells and tissue formation. Studies have indicated that the stiffness of the brain is about 0.1-1 kPa. The physiological and pathological processes of the nervous system are mediated by the substrate stiffness that the neurons suffer. However, how substrate stiffness regulates these processes remains to be studied. Culturing neurons on substrates with different stiffness <i>in vitro</i> is one of the best methods to study the role of stiffness in regulating neuronal development and activity. In this study, by changing the preparation time and the activation time of polyacrylamide gel, we provide an improved method that achieves a low toxic substrate environment for better primary neuron adhesion and development. Hope that this method is convenient for those studying the role of substrate stiffness in neurons.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 1","pages":"41-47"},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11079600/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140912247","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
A practical guide for fast implementation of SNARE-mediated liposome fusion. 快速实现 SNARE 介导的脂质体融合的实用指南。
Biophysics reports Pub Date : 2024-02-29 DOI: 10.52601/bpr.2023.230017
Shen Wang, Cong Ma
{"title":"A practical guide for fast implementation of SNARE-mediated liposome fusion.","authors":"Shen Wang, Cong Ma","doi":"10.52601/bpr.2023.230017","DOIUrl":"10.52601/bpr.2023.230017","url":null,"abstract":"<p><p>Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNAER) family proteins are the engines of most intra-cellular and exocytotic membrane fusion pathways (Jahn and Scheller 2006). Over the past two decades, <i>in-vitro</i> liposome fusion has been proven to be a powerful tool to reconstruct physiological SNARE-mediated membrane fusion processes (Liu <i>et al.</i> 2017). The reconstitution of the membrane fusion process not only provides direct evidence of the capability of the cognate SNARE complex in driving membrane fusion but also allows researchers to study the functional mechanisms of regulatory proteins in related pathways (Wickner and Rizo 2017). Heretofore, a variety of delicate methods for <i>in-vitro</i> SNARE-mediated liposome fusion have been established (Bao <i>et al.</i> 2018; Diao <i>et al.</i> 2012; Duzgunes 2003; Gong <i>et al.</i> 2015; Heo <i>et al</i>. 2021; Kiessling <i>et al.</i> 2015; Kreye <i>et al.</i> 2008; Kyoung <i>et al.</i> 2013; Liu <i>et al.</i> 2017; Scott <i>et al.</i> 2003). Although technological advances have made reconstitution more physiologically relevant, increasingly elaborate experimental procedures, instruments, and data processing algorithms nevertheless hinder the non-experts from setting up basic SNARE-mediated liposome fusion assays. Here, we describe a low-cost, timesaving, and easy-to-handle protocol to set up a foundational <i>in-vitro</i> SNARE-mediated liposome fusion assay based on our previous publications (Liu <i>et al.</i> 2023; Wang and Ma 2022). The protocol can be readily adapted to assess various types of SNARE-mediated membrane fusion and the actions of fusion regulators by using appropriate alternative additives (<i>e</i>.<i>g</i>., proteins, macromolecules, chemicals, <i>etc</i>.). The total time required for one round of the assay is typically two days and could be extremely compressed into one day.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 1","pages":"31-40"},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11079601/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140912129","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
Generation and characterization of nanobodies targeting GPCR. 以 GPCR 为靶标的纳米抗体的生成和表征。
Biophysics reports Pub Date : 2024-02-29 DOI: 10.52601/bpr.2023.230026
Shenglan Zhang, Zhiran Fan, Jianfeng Liu
{"title":"Generation and characterization of nanobodies targeting GPCR.","authors":"Shenglan Zhang, Zhiran Fan, Jianfeng Liu","doi":"10.52601/bpr.2023.230026","DOIUrl":"10.52601/bpr.2023.230026","url":null,"abstract":"<p><p>G protein-coupled receptors (GPCRs) are a large family of cell membrane proteins that are important targets for drug discovery. Nanobodies, also known as VHH (variable domains of heavy chain-only antibodies, HcAbs) antibodies, are small antibody fragments derived from camelids that have gained significant attention as potential therapeutics for targeting GPCRs due to their advantages over conventional antibodies. However, there are challenges in developing nanobodies targeting GPCRs, among which epitope accessibility is the most significant because the cell membrane partially shields the GPCR surface. We developed a universal protocol for making nanobodies targeting GPCRs using the cell membrane extract of GPCR-overexpressing HEK293 cells as the llama/alpaca immunization antigen. We constructed an immune VHH library and identified nanobodies by phage display bio-panning. The monoclonal nanobodies were recombinantly expressed in <i>Escherichia coli (E. coli)</i> and purified to characterize their binding potency.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 1","pages":"22-30"},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11079602/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140912684","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
首页 上一页 下一页 尾页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们：info@booksci.cn Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：604180095
Book学术官方微信