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Exploring diet-microbiota interactions and therapeutic nutrition management in inflammatory bowel disease. 探讨炎症性肠病的饮食-微生物群相互作用和治疗性营养管理。
Biophysics reports Pub Date : 2025-06-30 DOI: 10.52601/bpr.2024.240050
Xinran Wang, Yiran Wang, Lulu Sun
{"title":"Exploring diet-microbiota interactions and therapeutic nutrition management in inflammatory bowel disease.","authors":"Xinran Wang, Yiran Wang, Lulu Sun","doi":"10.52601/bpr.2024.240050","DOIUrl":"10.52601/bpr.2024.240050","url":null,"abstract":"<p><p>Intestinal bowel disease (IBD) is a chronic, early-onset, recurrent gastrointestinal immune-related disease that has become globalized. Although the combination of genetic, environmental, and immunological factors leads to intestinal inflammation and barrier damage, the etiology of IBD is not clearly defined. In recent years, diet-microbiota interactions have been widely studied for their potential in pathogenesis and treatment for IBD. Meanwhile, the significant efficacy of exclusive enteral nutrition (EEN) has been observed in clinical practice with modulation in gut microbiota, but the specific mechanisms and optimization measures remain challenging. Therefore, we first describe the development of existing microbial research techniques and the perspectives that can be broadened. We then synthesize findings on how dietary components impact IBD progression and treatment through microbiota. Finally, based on correlating clinical and basic experiments, we summarize the current status and potential mechanisms of EEN for treating IBD, especially the contradictory points encountered in its application.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 3","pages":"180-197"},"PeriodicalIF":0.0,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12213664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562344","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
Assaying antigen-specific T cell trans-endothelial migration in vitro with the Transwell system: application in tumor immunology. 用Transwell系统测定抗原特异性T细胞体外跨内皮迁移：在肿瘤免疫学中的应用。
Biophysics reports Pub Date : 2025-06-30 DOI: 10.52601/bpr.2024.240032
Ruochan Zhang, Longchao Liu
{"title":"Assaying antigen-specific T cell trans-endothelial migration <i>in vitro</i> with the Transwell system: application in tumor immunology.","authors":"Ruochan Zhang, Longchao Liu","doi":"10.52601/bpr.2024.240032","DOIUrl":"10.52601/bpr.2024.240032","url":null,"abstract":"<p><p>T cells play a key role in tumor immune surveillance. Trafficking of T cells to the tumor microenvironment is critical for the success of cancer immunotherapies. The process of T cell trafficking involves a sequence of steps: initial rolling along the endothelium, firm adhesion, subsequent extravasation, and directed chemotactic movement toward the tumor site. It is emerging that tumor vasculature constitutes an important barrier to T cell infiltration. In this protocol, we summarize a method for assessing antigen-specific CD8<sup>+</sup>T cell trans-endothelial migration <i>in vitro</i> using the Transwell system. This technique is vital for studying the mechanisms of T cell extravasation and their interactions with the vascular endothelium, and provides a controllable experimental setup to investigate T cell trans-endothelial migration.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 3","pages":"156-163"},"PeriodicalIF":0.0,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12213703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562342","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
Correction to: Non-invasive micro-test technology and applications. 非侵入性微检测技术及应用。
Biophysics reports Pub Date : 2025-06-30 DOI: 10.52601/bpr.2025.250901
{"title":"Correction to: Non-invasive micro-test technology and applications.","authors":"","doi":"10.52601/bpr.2025.250901","DOIUrl":"https://doi.org/10.52601/bpr.2025.250901","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.52601/bpr.2024.240009.].</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 3","pages":"217"},"PeriodicalIF":0.0,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12213658/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562343","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
Electrophysiological analysis of cardiac KATP channel. 心脏KATP通道电生理分析。
Biophysics reports Pub Date : 2025-04-30 DOI: 10.52601/bpr.2024.240023
Jianyi Huo, Hua-Qian Yang
{"title":"Electrophysiological analysis of cardiac K<sub>ATP</sub> channel.","authors":"Jianyi Huo, Hua-Qian Yang","doi":"10.52601/bpr.2024.240023","DOIUrl":"https://doi.org/10.52601/bpr.2024.240023","url":null,"abstract":"<p><p>ATP-sensitive potassium (K<sub>ATP</sub>) channels are integral components in excitable cells, particularly in cardiomyocytes, serving as critical regulators of cellular metabolism and electrical excitability. In instances of prolonged oxygen deprivation or heightened metabolic requirements, the opening of K<sub>ATP</sub> channels enables potassium efflux by virtue of a diminished ATP/ADP ratio. This process aids in maintaining membrane potential stability, thereby mitigating excessive excitability and cellular contraction, ultimately contributing significantly to cardiac protection. The accurate isolation of intact single cardiomyocytes and the electrophysiological evaluation of K<sub>ATP</sub> channels are pivotal processes in research on K<sub>ATP</sub> channels in cardiomyocytes <i>in vitro</i>. Here, we present a comprehensive protocol not only for the efficient isolation of viable cardiomyocytes from the adult mouse through the Langendorff perfusion method, but also for the recording of K<sub>ATP</sub> channel currents in single cardiomyocytes employing patch clamp technique.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 2","pages":"77-86"},"PeriodicalIF":0.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12035747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144038197","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
Proteomic analysis of B cells in peripheral lymphatic system reveals the dynamics during the systemic lupus erythematosus progression. 外周淋巴系统B细胞的蛋白质组学分析揭示了系统性红斑狼疮进展过程中的动力学。
Biophysics reports Pub Date : 2025-04-30 DOI: 10.52601/bpr.2024.240045
Liming Sun, Yuanyuan Yin, Yuqing Cao, Chunlei Chen, Yutong Guo, Zeming Cai, Jiarui Wu, Qingrun Li
{"title":"Proteomic analysis of B cells in peripheral lymphatic system reveals the dynamics during the systemic lupus erythematosus progression.","authors":"Liming Sun, Yuanyuan Yin, Yuqing Cao, Chunlei Chen, Yutong Guo, Zeming Cai, Jiarui Wu, Qingrun Li","doi":"10.52601/bpr.2024.240045","DOIUrl":"https://doi.org/10.52601/bpr.2024.240045","url":null,"abstract":"<p><p>In this study, we conducted a comprehensive proteomic analysis of B cells from the spleen, mesenteric lymph nodes (mLN), and peripheral blood mononuclear cells (PBMC) in a time-course model of systemic lupus erythematosus (SLE) using female MRL/lpr mice. By combining fluorescence-activated cell sorting (FACS) and 4D-Data-Independent Acquisition (4D-DIA) mass spectrometry, we quantified nearly 8000 proteins, identifying significant temporal and tissue-specific proteomic changes during SLE progression. PBMC-derived B cells exhibited early proteomic alterations by Week 9, while spleen-derived B cells showed similar changes by Week 12. We identified key regulatory proteins, including BAFF, BAFFR, and NFKB2, involved in B cell survival and activation, as well as novel markers such as CD11c and CD117, which have previously been associated with other immune cells. The study highlights the dynamic reprogramming of B cell proteomes across different tissues, with distinct contributions to SLE pathogenesis, providing valuable insights into the molecular mechanisms underlying B cell dysregulation in lupus. These findings offer potential therapeutic targets and biomarkers for SLE.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 2","pages":"129-142"},"PeriodicalIF":0.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12035744/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144051958","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 combined protocol for isolation, culture, and patch-clamp recording of dorsal root ganglion neurons. 背根神经节神经元的分离、培养和膜片钳记录的联合方案。
Biophysics reports Pub Date : 2025-04-30 DOI: 10.52601/bpr.2024.240036
Ruolin Wang, Yu Lu, Jianbo Zhao, Xueting Duan, Yang Chen, Zhuoyu Zhang, Rong Huang
{"title":"A combined protocol for isolation, culture, and patch-clamp recording of dorsal root ganglion neurons.","authors":"Ruolin Wang, Yu Lu, Jianbo Zhao, Xueting Duan, Yang Chen, Zhuoyu Zhang, Rong Huang","doi":"10.52601/bpr.2024.240036","DOIUrl":"https://doi.org/10.52601/bpr.2024.240036","url":null,"abstract":"<p><p>The dorsal root ganglion (DRG) neurons are crucial in transmitting sensory information from the peripheral nervous system to the central nervous system, including touch, pain, temperature, and proprioception. Understanding the functions and mechanisms of DRG neurons is essential for studying sensory processing and developing efficient treatments for sensory disorders. In addition, electrophysiological patch-clamp recording is a powerful and classical tool to study the functions and mechanisms of the nervous system. Building upon the strategies outlined in published works and our group's abundant research experience in DRG neurons' functions by patch-clamp, we have summarized and put forward a comprehensive step-by-step protocol combining juvenile rat DRG neuron isolation and culture, and patch-clamp recording. This protocol would be a powerful guidance document for neuroscience researchers to study sensory DRG neurons' physiological and pathological functions using electrophysiological tools.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 2","pages":"87-95"},"PeriodicalIF":0.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12035743/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144015045","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
Non-invasive micro-test technology and applications. 无创微检测技术及应用。
Biophysics reports Pub Date : 2025-04-30 DOI: 10.52601/bpr.2024.240009
Kai Sun, Yunqi Liu, Yanshu Pan, Dongwei Di, Jianfang Li, Feiyun Xu, Li Li, Yoshiharu Mimata, Yingying Chen, Lixia Xie, Siqi Wang, Wenqian Qi, Yan Tang, Huachun Sheng, Bing Wang, Ruixue Sun, Dingquan Tan, Daohong Fu, Ye Yin, Ao Xue, Yichao Shi, Wenjing Shao, Lei Gong, Zhijian Jiang, Wei Zhang, Qiangsheng Wu, Yaosheng Wang, Minglin Lang, Wenxiu Ye, Weifeng Xu, Shuhe Wei, Weiming Shi, Yue Jeff Xu
{"title":"Non-invasive micro-test technology and applications.","authors":"Kai Sun, Yunqi Liu, Yanshu Pan, Dongwei Di, Jianfang Li, Feiyun Xu, Li Li, Yoshiharu Mimata, Yingying Chen, Lixia Xie, Siqi Wang, Wenqian Qi, Yan Tang, Huachun Sheng, Bing Wang, Ruixue Sun, Dingquan Tan, Daohong Fu, Ye Yin, Ao Xue, Yichao Shi, Wenjing Shao, Lei Gong, Zhijian Jiang, Wei Zhang, Qiangsheng Wu, Yaosheng Wang, Minglin Lang, Wenxiu Ye, Weifeng Xu, Shuhe Wei, Weiming Shi, Yue Jeff Xu","doi":"10.52601/bpr.2024.240009","DOIUrl":"10.52601/bpr.2024.240009","url":null,"abstract":"<p><p>Non-invasive micro-test technology (NMT) reveals dynamic ionic/molecular concentration gradients by measuring fluxes of ions and small molecules in liquid media in 1D, 2D or 3D fashions with sensitivity up to pico- (10<sup>-12</sup>) or femto- (10<sup>-15</sup>) moles per cm<sup>2</sup> per second. NMT has been applied to study metabolism, signal transduction, genes and/or proteins physiological functions related to transmembrane ionic/molecular activities with live samples under normal conditions or stress. Data on ion and/or molecule homeostasis (IMH) by NMT in biomedical sciences, plant and crop sciences, environmental sciences, marine and space biology as well as traditional Chinese medicine are reviewed.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 2","pages":"96-111"},"PeriodicalIF":0.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12035745/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144010763","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
Application of metal stable isotopes labeling and elemental mass spectrometry for biomacromolecule profiling. 金属稳定同位素标记和元素质谱法在生物大分子分析中的应用。
Biophysics reports Pub Date : 2025-04-30 DOI: 10.52601/bpr.2024.240039
Ping Zhang, Ying Han, Yue Xu, Liang Gao
{"title":"Application of metal stable isotopes labeling and elemental mass spectrometry for biomacromolecule profiling.","authors":"Ping Zhang, Ying Han, Yue Xu, Liang Gao","doi":"10.52601/bpr.2024.240039","DOIUrl":"https://doi.org/10.52601/bpr.2024.240039","url":null,"abstract":"<p><p>Biomacromolecules including proteins and nucleic acids are widely recognized for their pivotal and irreplaceable role in maintaining the normal functions of biological systems. By combining metal stable isotope labeling with elemental mass spectrometry, researchers can quantify the amount and track the spatial distribution of specific biomacromolecules in complex biological systems. In this review, the probes classification and metal stable isotope labeling strategies are initially summarized. Secondly, the technical characteristics and working principle of the elemental mass spectrometry techniques including inductively coupled plasma mass spectrometry and secondary ion mass spectrometry are introduced to achieve highly sensitive detection of multiple biomacromolecules at molecular, cellular and tissue levels. Lastly, we underline the advantages and limitations of elemental mass spectrometry combined with metal stable isotope labeling strategies, and propose the perspectives for future developments.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 2","pages":"112-128"},"PeriodicalIF":0.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12035746/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033964","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
Host cytoskeleton and membrane network remodeling in the regulation of viral replication. 病毒复制调控过程中的宿主细胞骨架和膜网络重塑。
Biophysics reports Pub Date : 2025-02-28 DOI: 10.52601/bpr.2024.240040
Xuedi Gao, Xinming Chen, Letian Yu, Shuangshuang Zhao, Yaming Jiu
{"title":"Host cytoskeleton and membrane network remodeling in the regulation of viral replication.","authors":"Xuedi Gao, Xinming Chen, Letian Yu, Shuangshuang Zhao, Yaming Jiu","doi":"10.52601/bpr.2024.240040","DOIUrl":"10.52601/bpr.2024.240040","url":null,"abstract":"<p><p>Viral epidemics pose major threats to global health and economies. A hallmark of viral infection is the reshaping of host cell membranes and cytoskeletons to form organelle-like structures, known as viral factories, which support viral genome replication. Viral infection in many cases induces the cytoskeletal network to form cage-like structures around viral factories, including actin rings, microtubule cages, and intermediate filament cages. Viruses hijack various organelles to create these replication factories, such as viroplasms, spherules, double-membrane vesicles, tubes, and nuclear viral factories. This review specifically examines the roles of cytoskeletal elements and the endomembrane system in material transport, structural support, and biochemical regulation during viral factory formation. Furthermore, we discuss the broader implications of these interactions for viral replication and highlight potential future research directions.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 1","pages":"34-45"},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11891074/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607564","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
Single-molecule techniques in studying the molecular mechanisms of DNA synapsis in non-homologous end-joining repair. 非同源末端连接修复中DNA突触分子机制的单分子研究。
Biophysics reports Pub Date : 2025-02-28 DOI: 10.52601/bpr.2024.240043
Yuhao Jiang, Chao Zhao, Chenyang Zhang, Weilin Li, Di Liu, Bailin Zhao
{"title":"Single-molecule techniques in studying the molecular mechanisms of DNA synapsis in non-homologous end-joining repair.","authors":"Yuhao Jiang, Chao Zhao, Chenyang Zhang, Weilin Li, Di Liu, Bailin Zhao","doi":"10.52601/bpr.2024.240043","DOIUrl":"10.52601/bpr.2024.240043","url":null,"abstract":"<p><p>DNA double-strand breaks (DSBs) are the most severe form of DNA damage, primarily repaired by the non-homologous end joining (NHEJ) pathway. A critical step in this process is DNA synapsis, where the two broken ends are brought together to facilitate timely repair. Deficiencies in NHEJ synapsis can lead to improper DNA end configurations, potentially resulting in chromosomal translocations. NHEJ synapsis is a highly dynamic, multi-protein mediated assembly process. Recent advances in single-molecule techniques have led to significant progress in understanding the molecular mechanisms driving NHEJ synapsis. In this review, we summarize single-molecule methods developed for studying NHEJ synapsis, with a particular focus on the single-molecule fluorescence resonance energy transfer (smFRET) technique. We discuss the various molecular mechanisms of NHEJ synapsis uncovered through these studies and explore the coupling between synapsis and other steps in NHEJ. Additionally, we highlight the strategies, limitations, and future directions for single-molecule studies of NHEJ synapsis.</p>","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"11 1","pages":"46-55"},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11891076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607568","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
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