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
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
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
Life under tension: the relevance of force on biological polymers. 张力下的生命：力对生物聚合物的影响。
Biophysics reports Pub Date : 2024-02-29 DOI: 10.52601/bpr.2023.230019
Matthew T J Halma, Longfu Xu
{"title":"Life under tension: the relevance of force on biological polymers.","authors":"Matthew T J Halma, Longfu Xu","doi":"10.52601/bpr.2023.230019","DOIUrl":"10.52601/bpr.2023.230019","url":null,"abstract":"<p><p>Optical tweezers have elucidated numerous biological processes, particularly by enabling the precise manipulation and measurement of tension. One question concerns the biological relevance of these experiments and the generalizability of these experiments to wider biological systems. Here, we categorize the applicability of the information garnered from optical tweezers in two distinct categories: the direct relevance of tension in biological systems, and what experiments under tension can tell us about biological systems, while these systems do not reach the same tension as the experiment, still, these artificial experimental systems reveal insights into the operations of biological machines and life processes.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 1","pages":"48-56"},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11079598/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140912738","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
Catecholaminergic neurons orchestrate fasting-induced immune harmony. 儿茶酚胺能神经元协调空腹诱导的免疫和谐。
Biophysics reports Pub Date : 2024-02-29 DOI: 10.52601/bpr.2024.240901
Mengdi Guo, Weiyan Wang, Xiao Tu, Meiling Jiang, Cun-Jin Zhang
{"title":"Catecholaminergic neurons orchestrate fasting-induced immune harmony.","authors":"Mengdi Guo, Weiyan Wang, Xiao Tu, Meiling Jiang, Cun-Jin Zhang","doi":"10.52601/bpr.2024.240901","DOIUrl":"10.52601/bpr.2024.240901","url":null,"abstract":"","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 1","pages":"57-59"},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11079597/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140912517","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
APTAnet: an atom-level peptide-TCR interaction affinity prediction model. APTAnet：原子级多肽-TCR相互作用亲和力预测模型。
Biophysics reports Pub Date : 2024-02-29 DOI: 10.52601/bpr.2023.230037
Peng Xiong, Anyi Liang, Xunhui Cai, Tian Xia
{"title":"APTAnet: an atom-level peptide-TCR interaction affinity prediction model.","authors":"Peng Xiong, Anyi Liang, Xunhui Cai, Tian Xia","doi":"10.52601/bpr.2023.230037","DOIUrl":"10.52601/bpr.2023.230037","url":null,"abstract":"<p><p>The prediction of affinity between TCRs and peptides is crucial for the further development of TIL (Tumor-Infiltrating Lymphocytes) immunotherapy. Inspired by the broader research of drug-protein interaction (DPI), we propose an atom-level peptide-TCR interaction (PTI) affinity prediction model APTAnet using natural language processing methods. APTAnet model achieved an average ROC-AUC and PR-AUC of 0.893 and 0.877, respectively, in ten-fold cross-validation on 25,675 pairs of PTI data. Furthermore, experimental results on an independent test set from the McPAS database showed that APTAnet outperformed the current mainstream models. Finally, through the validation on 11 cases of real tumor patient data, we found that the APTAnet model can effectively identify tumor peptides and screen tumor-specific TCRs.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 1","pages":"1-14"},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11079603/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140912516","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
Screening for metastasis-related genes in mouse melanoma cells through sequential tail vein injection. 通过连续尾静脉注射筛选小鼠黑色素瘤细胞中的转移相关基因。
Biophysics reports Pub Date : 2024-02-29 DOI: 10.52601/bpr.2023.230043
Qinggang Hao, Rui Dong, Weiyu Bai, Dong Chang, Xinyi Yao, Yingru Zhang, Huangying Xu, Huiyan Li, Xiang Kui, Feng Wang, Yan Wang, Chengqin Wang, Yujie Lei, Yan Chen, Junling Shen, Lei Sang, Yan Bai, Jianwei Sun
{"title":"Screening for metastasis-related genes in mouse melanoma cells through sequential tail vein injection.","authors":"Qinggang Hao, Rui Dong, Weiyu Bai, Dong Chang, Xinyi Yao, Yingru Zhang, Huangying Xu, Huiyan Li, Xiang Kui, Feng Wang, Yan Wang, Chengqin Wang, Yujie Lei, Yan Chen, Junling Shen, Lei Sang, Yan Bai, Jianwei Sun","doi":"10.52601/bpr.2023.230043","DOIUrl":"10.52601/bpr.2023.230043","url":null,"abstract":"<p><p>Tumor metastasis, responsible for approximately 90% of cancer-associated mortality, remains poorly understood. Here in this study, we employed a melanoma lung metastasis model to screen for metastasis-related genes. By sequential tail vein injection of mouse melanoma B16F10 cells and the subsequently derived cells from lung metastasis into BALB/c mice, we successfully obtained highly metastatic B16F15 cells after five rounds of <i>in vivo</i> screening. RNA-sequencing analysis of B16F15 and B16F10 cells revealed a number of differentially expressed genes, some of these genes have previously been associated with tumor metastasis while others are novel discoveries. The identification of these metastasis-related genes not only improves our understanding of the metastasis mechanisms, but also provides potential diagnostic biomarkers and therapeutic targets for metastatic melanoma.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"10 1","pages":"15-21"},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11079599/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140912787","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
Establishment of a Fah-LSL mouse model to study BEC-to-hepatocyte conversion. 建立 Fah-LSL 小鼠模型，研究 BEC 向肝细胞的转化。
Biophysics reports Pub Date : 2023-12-31 DOI: 10.52601/bpr.2023.230034
Xingrui Wang, Wenjuan Pu, Huan Zhu, Mingjun Zhang, Bin Zhou
{"title":"Establishment of a Fah-LSL mouse model to study BEC-to-hepatocyte conversion.","authors":"Xingrui Wang, Wenjuan Pu, Huan Zhu, Mingjun Zhang, Bin Zhou","doi":"10.52601/bpr.2023.230034","DOIUrl":"10.52601/bpr.2023.230034","url":null,"abstract":"<p><p>The liver consists predominantly of hepatocytes and biliary epithelial cells (BECs), which serve distinct physiological functions. Although hepatocytes primarily replenish their own population during homeostasis and injury repair, recent findings have suggested that BECs can transdifferentiate into hepatocytes when hepatocyte-mediated liver regeneration is impaired. However, the cellular and molecular mechanisms governing this BEC-to-hepatocyte conversion remain poorly understood largely because of the inefficiency of existing methods for inducing lineage conversion. Therefore, this study introduces a novel mouse model engineered by the Zhou's lab, where hepatocyte senescence is induced by the deletion of the fumarylacetoacetate (<i>Fah</i>) gene. This model facilitates the efficient conversion of BECs to hepatocytes and allows for the simultaneous lineage tracing of BECs; consequently, a transitional liver progenitor cell population can be identified during lineage conversion. This study also outlines the technical procedures for utilizing this model to determine the underlying cellular and molecular mechanisms of BEC-to-hepatocyte conversion and provides new insights into liver regeneration and its underlying molecular mechanism.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"9 6","pages":"309-324"},"PeriodicalIF":0.0,"publicationDate":"2023-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10960572/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208410","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