Biophysics reports最新文献

TurboID-based mapping of organelle membrane protein interactomes with digitonin-permeabilization. 基于turboid的细胞器膜蛋白相互作用组与洋地黄苷渗透的映射。

Biophysics reports Pub Date : 2025-08-31 DOI: 10.52601/bpr.2025.240051

Yang Sun, Lan Yang, Jingzi Zhang, Pu Tian, Shue Chen, Lei Fang, Zhi Hong

{"title":"TurboID-based mapping of organelle membrane protein interactomes with digitonin-permeabilization.","authors":"Yang Sun, Lan Yang, Jingzi Zhang, Pu Tian, Shue Chen, Lei Fang, Zhi Hong","doi":"10.52601/bpr.2025.240051","DOIUrl":"10.52601/bpr.2025.240051","url":null,"abstract":"Protein-protein interactions at organelle membranes bridge organelles in close proximity, facilitating regulated metabolite exchange and maintaining cellular homeostasis. Enzyme-catalyzed proximity labeling (PL) has been widely used to uncover the molecular composition of these interactions, but excessive labeling of irrelevant cytosolic proteins complicates data analysis. To address this, we developed a streamlined protocol that combines the TurboID system with digitonin-permeabilization to efficiently map protein interactions at organelle membranes in live mammalian cells. Digitonin selectively permeabilizes the plasma membrane, removing cytosolic proteins while preserving the integrity of inner membranes like the ER and mitochondria. This approach enhances spatial resolution in proteo-mic analysis, enabling a more precise map for protein interactome. Using this method, we successfully achieved proximal labeling of ER-localized proteins REEP1 and REEP6 to decipher their interaction networks, demonstrating its applicability for studying membrane-associated interactions with greater clarity and reduced contamination.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 4","pages":"219-231"},"PeriodicalIF":0.0,"publicationDate":"2025-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12418099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145042371","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

Advancements of algae-involved cancer treatment. 与藻类有关的癌症治疗进展。

Biophysics reports Pub Date : 2025-08-31 DOI: 10.52601/bpr.2024.240055

Tian Qiu, Xingrun Li, Hui Sun, Simeng Zhang, Yan An, Jianxiang Li, Xiaoyan Zhong

{"title":"Advancements of algae-involved cancer treatment.","authors":"Tian Qiu, Xingrun Li, Hui Sun, Simeng Zhang, Yan An, Jianxiang Li, Xiaoyan Zhong","doi":"10.52601/bpr.2024.240055","DOIUrl":"10.52601/bpr.2024.240055","url":null,"abstract":"Algae, especially microalgae, are versatile in terms of nutrition, feed, biofertilizers, biofuel, and so on. In the realm of oncotherapy, algal extracts have been extensively used as anti-cancer active ingredients; however, what has been ignored is the anti-cancer value induced by themselves. Thanks to their unparalleled advantages, for example, intrinsic tumor homing, immunogenicity, and in situ production of anti-cancer agents, algae pave a new way in anti-cancer research. Algae have been reported about selective cytotoxicity to cancer cells and could work for oxygen-dependent strategies such as photodynamic therapy, owing to their natural photosynthetic abilities. Interestingly, integrating with customized nanomaterials (NMs), algae have been demonstrated to have unprecedented potential in overcoming barriers to existing treatment methods. Thus, in this review, starting from the classification of algae, the diverse effects of algae are thoroughly introduced, followed by the current engineering strategies of algae; lastly, the emerging development of algae-based therapeutics is timely summarized with an emphasis on the intelligent creation of biohybrid systems by choosing algae and tailored NMs. This review presents a comprehensive exploration of engineered algae-involved innovative cancer therapy, with a discussion of the future challenges and outlook, which will help design creative therapy paradigms and facilitate their clinical applications.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 4","pages":"258-282"},"PeriodicalIF":0.0,"publicationDate":"2025-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12418101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145042800","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

Characterization of intrinsically disordered regions through scalar coupling-based solid-state NMR experiments. 通过基于标量耦合的固体核磁共振实验表征本质无序区。

Biophysics reports Pub Date : 2025-08-31 DOI: 10.52601/bpr.2025.240065

Tong Zeng, Juan Li, Chaowei Shi, Shengqi Xiang

{"title":"Characterization of intrinsically disordered regions through scalar coupling-based solid-state NMR experiments.","authors":"Tong Zeng, Juan Li, Chaowei Shi, Shengqi Xiang","doi":"10.52601/bpr.2025.240065","DOIUrl":"10.52601/bpr.2025.240065","url":null,"abstract":"Abnormal amyloid fibrils are characteristic features and common pathological mechanisms of various neurodegenerative diseases, often found in disease-related brain regions, leading to neuroinflammation and neuronal apoptosis. Many disease-associated amyloid fibrils consist of a rigid fibril core primarily composed of cross-β sheets, surrounded by a fuzzy coat formed by intrinsically disordered regions (IDR). Over the past two decades, substantial structural knowledge of the rigid fibril core has been accumulated through cryo-electron microscopy (cryo-EM) and solid-state nuclear magnetic resonance (ssNMR) based on cross-polarization. In contrast, the highly disordered conformations of the fuzzy coats have hindered their structural characterization. Here, we describe the application of two-dimensional (2D) heteronuclear single quantum coherence (HSQC) and three-dimensional (3D) HNCO, HNCA, and HN(CO)CA spectra, utilizing the scalar coupling-based 1H detection magic angle spinning (MAS) ssNMR techniques for backbone assignment of the IDR in amyloid fibrils, with the aim of further elucidating the conformational changes of the IDR during ligand binding processes.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 4","pages":"232-245"},"PeriodicalIF":0.0,"publicationDate":"2025-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12418100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145042715","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

Rapid generation of antigen-specific monoclonal antibodies from single mouse B cells. 从单个小鼠B细胞中快速产生抗原特异性单克隆抗体。

Biophysics reports Pub Date : 2025-08-31 DOI: 10.52601/bpr.2025.240067

Xuanxiu Ren, Yiwei Zhang, Gan Zhang, Shangyu Yang, Feiyang Yu, Rao Cheng, Zengqin Deng, Haiyan Zhao

{"title":"Rapid generation of antigen-specific monoclonal antibodies from single mouse B cells.","authors":"Xuanxiu Ren, Yiwei Zhang, Gan Zhang, Shangyu Yang, Feiyang Yu, Rao Cheng, Zengqin Deng, Haiyan Zhao","doi":"10.52601/bpr.2025.240067","DOIUrl":"10.52601/bpr.2025.240067","url":null,"abstract":"Identifying immunoglobulin (Ig) genes from antigen-specific B cells is crucial for understanding immune responses and generating monoclonal antibodies for diagnostic and therapeutic purposes. Despite single B cell PCR-based mouse antibody development is well established, several practical challenges remain. Here, we present an optimized protocol for the sequencing and cloning of variable regions of antibodies from single antigen-specific mouse B cells, along with high-throughput antibody expression and characterization. This method builds upon existing techniques, incorporating laboratory refinements and detailed troubleshooting insights. By integrating fluorescence-activated cell sorting (FACS) with reverse transcription polymerase chain reaction (RT-PCR) to amplify immunoglobulin heavy and light chain genes, along with a 12-well format for antibody expression, our refined approach enables efficient monoclonal antibody production and functional screening, thereby accelerating the antibody discovery workflow across a range of experimental applications.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 4","pages":"246-257"},"PeriodicalIF":0.0,"publicationDate":"2025-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12418097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145042134","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 single helicase-binding domain of DnaG couples with hexameric helicase DnaB in Bacillus stearothermophilus. 嗜热脂肪芽孢杆菌中单链解旋酶结合域与六聚链解旋酶DnaB偶联。

Biophysics reports Pub Date : 2025-08-31 DOI: 10.52601/bpr.2024.240059

Hao Luo, Wenlin Liu, Yingqin Zhou, Zhongchuan Liu, Yuyang Qin, Ganggang Wang

{"title":"A single helicase-binding domain of DnaG couples with hexameric helicase DnaB in Bacillus stearothermophilus.","authors":"Hao Luo, Wenlin Liu, Yingqin Zhou, Zhongchuan Liu, Yuyang Qin, Ganggang Wang","doi":"10.52601/bpr.2024.240059","DOIUrl":"10.52601/bpr.2024.240059","url":null,"abstract":"In bacterial DNA replication, helicase DnaB and primase DnaG form the primosome. Helicase DnaB unwinds double-stranded DNA (dsDNA) to provide templates for DNA polymerase, whereas primase DnaG supplies RNA primers to DNA polymerase for the synthesis of Okazaki fragments. How primase DnaG coordinates with helicase DnaB at the DNA replication fork remains unclear. In this study, the interactions between the helicase-binding domain of DnaG (DnaG (HBD)) and DnaB hexamer were studied. A stable ternary complex of DnaB6/dT16/DnaG(HBD) from Bacillus stearothermophilus was prepared and the homogeneity of the DnaB6/dT16/DnaG(HBD) complex was verified by dynamic light scattering. The stoichiometry of DnaG(HBD) to process DnaB6 was investigated by isothermal titration calorimetry. The results show that a single primase DnaG binds to DnaB6 in the presence of single-stranded DNA. Based on these results, a model is proposed to explain how the primase DnaG couples with the processing DnaB6 helicase during the Okazaki fragment synthesis cycle. These findings provide valuable insights into the coupling between dsDNA unwinding and RNA primer synthesis in DNA replication.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 4","pages":"283-290"},"PeriodicalIF":0.0,"publicationDate":"2025-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12418098/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145042767","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

Intracellular calcium imaging for agonist screening. 细胞内钙显像用于激动剂筛选。

Biophysics reports Pub Date : 2025-06-30 DOI: 10.52601/bpr.2024.240026

Haojie Wang, Bo Yang, Liangzhu Mo, Hua-Qian Yang

引用次数: 0

Neuronal synaptic architecture revealed by cryo-correlative light and electron microscopy. 低温相关光镜和电镜显示的神经元突触结构。

Biophysics reports Pub Date : 2025-06-30 DOI: 10.52601/bpr.2024.240035

Pei Wang, Buyun Tian, Xiaojun Xu, Huiqin Luan, Yan Zhang, Wenhao Sun, Liqiao Hu, Yuanyuan Li, Yuchen Yao, Weixing Li, Shuli Zhang, Xia Li, Wei Feng, Wei Ji, Yanhong Xue

引用次数: 0

Modulating mitochondrial dynamics in CMT2A: a multifaceted platform for drug discovery and evaluation. 调节线粒体动力学在CMT2A：药物发现和评估的多方面平台。

Biophysics reports Pub Date : 2025-06-30 DOI: 10.52601/bpr.2024.240037

Yang Liu, Chen Yan, Borui Cao, Dejun Kong, Jiaqi Li, Wenlei Li, Yingjie Guo, Zhongyang Yuan, Yumiao Gao, Yubo Zhang, Ran Sui, Guo Chen, Xiaojiang Hao, Quan Chen

{"title":"Modulating mitochondrial dynamics in CMT2A: a multifaceted platform for drug discovery and evaluation.","authors":"Yang Liu, Chen Yan, Borui Cao, Dejun Kong, Jiaqi Li, Wenlei Li, Yingjie Guo, Zhongyang Yuan, Yumiao Gao, Yubo Zhang, Ran Sui, Guo Chen, Xiaojiang Hao, Quan Chen","doi":"10.52601/bpr.2024.240037","DOIUrl":"10.52601/bpr.2024.240037","url":null,"abstract":"Mitochondrial dynamics, encompassing fusion and fission processes, plays a crucial role in regulating mitochondrial distribution, motility, and material exchange within cells, particularly in the nervous system. Mitofusin-2 (MFN2), a GTPase localized to the outer mitochondrial membrane, mediates mitochondrial fusion through dimerization and conformational changes. Mutations in MFN2 are causal for Charcot-Marie-Tooth disease type 2A (CMT2A), an inherited peripheral neuropathy for which no curative treatment currently exists. Herein, we have developed a comprehensive mitochondrial drug-screening and evaluation platform to facilitate the identification of potential therapeutic candidates. This work builds upon our previous research with S89, a small molecule agonist derived from spiramine alkaloids that promotes mitochondrial fusion by interacting with endogenous MFN1 and effectively mitigates axonal degeneration in CMT2A patient-derived motor neurons. This platform integrates three sequential stages of assessment: (1) initial screening in Mfn knockout mouse embryonic fibroblasts (MEFs) to identify compounds capable of reversibly rescuing mitochondrial fragmentation; (2) evaluation in primary neuronal cultures derived from CMT2A mouse dorsal root ganglia and cortex to assess the compounds' efficacy in restoring mitochondrial morphology, axonal transport, and neurite outgrowth; and (3) final assessment in CMT2A patient-derived induced pluripotent stem cell (iPSC)-differentiated motor neurons to determine the candidates' therapeutic potential in human peripheral nervous system cells. This multi-tiered approach facilitates rapid compound screening with increasing physiological relevance, enhancing the efficiency and translational potential of identifying therapeutic candidates for CMT2A.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 3","pages":"143-155"},"PeriodicalIF":0.0,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12213711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562346","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 integrative approach for imaging and quantitative analysis of gut microbiota growth in vivo using fluorescent D-amino acid labeling and fluorescence in situ hybridization. 利用荧光d -氨基酸标记和荧光原位杂交技术对体内肠道微生物群生长进行成像和定量分析的综合方法。

Biophysics reports Pub Date : 2025-06-30 DOI: 10.52601/bpr.2024.240044

Yingjun Zhou, Liyuan Lin, Wei Wang

{"title":"An integrative approach for imaging and quantitative analysis of gut microbiota growth in vivo using fluorescent D-amino acid labeling and fluorescence in situ hybridization.","authors":"Yingjun Zhou, Liyuan Lin, Wei Wang","doi":"10.52601/bpr.2024.240044","DOIUrl":"10.52601/bpr.2024.240044","url":null,"abstract":"The profound influence of gut microbiota on human health has been well-recognized; however, substantial gaps remain in our understanding of the highly diverse and dynamic processes of microbial growth and activities in the gut. Conventional methods, which primarily rely on DNA sequencing, provide limited insights into these aspects. This paper presents a protocol that integrates fluorescent D-amino acid (FDAA) metabolic labeling with fluorescence in situ hybridization (FISH) for imaging and quantitatively analyzing the in vivo growth of gut microbiota. By administering two FDAAs sequentially through mouse gavage, we label the peptidoglycan of gut bacteria in their native environment, allowing the labeling signals on bacterial cell walls to serve as markers of cellular proliferation and division. We have also demonstrated that the intensity of FDAA labeling directly correlates with the metabolic activity of gut bacteria. Additionally, FISH is employed to distinguish specific bacterial taxa of interest via fluorescence microscopy or flow cytometry. This integrative method greatly enhances our capacity to visualize and measure the in vivo growth and metabolic states of various gut bacteria, thereby illuminating the previously obscured \"dark matter\" in the gut ecosystem.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 3","pages":"172-179"},"PeriodicalIF":0.0,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12213662/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562341","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

Synovial sarcoma extracellular vesicles induce fatty liver. 滑膜肉瘤细胞外囊泡诱发脂肪肝。

Biophysics reports Pub Date : 2025-06-30 DOI: 10.52601/bpr.2024.240041

Tao Ren, Zhiheng Zhou, Huirong Hong, Bohong Cen, Jun Xiao, Guofen Chen, Yang Zhang, Jianlong Li

{"title":"Synovial sarcoma extracellular vesicles induce fatty liver.","authors":"Tao Ren, Zhiheng Zhou, Huirong Hong, Bohong Cen, Jun Xiao, Guofen Chen, Yang Zhang, Jianlong Li","doi":"10.52601/bpr.2024.240041","DOIUrl":"10.52601/bpr.2024.240041","url":null,"abstract":"Synovial sarcoma leads to pathological changes in multiple organs. To investigate the mechanism by which synovial sarcoma induces fatty liver through extracellular vesicles (EVs), the synovial sarcoma SW-982 cells were orthotopically implanted, or SW-982 derived EVs were extracted and used to \"educate\" nude mice. Liver tissues were then subjected to H&E and Oil-Red O (ORO) staining, and qPCR analysis. EVs were characterized using TEM and Nanosight. The bio-distribution of EVs in vivo was verified using the fluorescent dye Burgundy staining, followed by Odyssey imaging. Immunofluorescence (IF) and flow cytometry were used to confirm cellular uptake of EVs. Rab27a knockdown (KD) efficiency was validated by Western blot, and lipid droplet deposition in the liver from mice bearing with SW-982-Rab27a-KD cells was observed by staining with ORO. After three weeks of orthotopic implantation of SW-982 cells in nude mice, qPCR and H&E showed no tumor metastasis in liver tissues, while ORO staining revealed lipid deposition in the liver, and EVs diameters were confirmed by Nanosight and TEM to be approximately 141 nm in size. In vivo, EVs were taken up by liver Kupffer cells (KCs). After \"educating\" nude mice with EVs, lipid deposition in the liver was observed. In rescue experiments, Rab27a knockdown reduced EV secretion from the tumor, and KC inactivation led to decreased lipid deposition in the liver. It is shown that synovial sarcoma EVs mediate fatty liver through Kupffer cells.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 3","pages":"209-216"},"PeriodicalIF":0.0,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12213661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562265","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