Biophysics reports最新文献_第8页

Regulation of cellular senescence by innate immunity. 先天性免疫对细胞衰老的调节。

Biophysics reports Pub Date : 2023-12-31 DOI: 10.52601/bpr.2023.230032

Jinxiu Hou, Yi Zheng, Chengjiang Gao

引用次数: 0

Rapid quantification of 50 fatty acids in small amounts of biological samples for population molecular phenotyping. 快速量化少量生物样本中的 50 种脂肪酸，用于群体分子表型分析。

Biophysics reports Pub Date : 2023-12-31 DOI: 10.52601/bpr.2023.230042

Pinghui Liu, Qinsheng Chen, Lianglong Zhang, Chengcheng Ren, Biru Shi, Jingxian Zhang, Shuaiyao Wang, Ziliang Chen, Qi Wang, Hui Xie, Qingxia Huang, Huiru Tang

{"title":"Rapid quantification of 50 fatty acids in small amounts of biological samples for population molecular phenotyping.","authors":"Pinghui Liu, Qinsheng Chen, Lianglong Zhang, Chengcheng Ren, Biru Shi, Jingxian Zhang, Shuaiyao Wang, Ziliang Chen, Qi Wang, Hui Xie, Qingxia Huang, Huiru Tang","doi":"10.52601/bpr.2023.230042","DOIUrl":"10.52601/bpr.2023.230042","url":null,"abstract":"Efficient quantification of fatty-acid (FA) composition (fatty-acidome) in biological samples is crucial for understanding physiology and pathophysiology in large population cohorts. Here, we report a rapid GC-FID/MS method for simultaneous quantification of all FAs in numerous biological matrices. Within eight minutes, this method enabled simultaneous quantification of 50 FAs as fatty-acid methyl esters (FAMEs) in femtomole levels following the efficient transformation of FAs in all lipids including FFAs, cholesterol-esters, glycerides, phospholipids and sphingolipids. The method showed satisfactory inter-day and intra-day precision, stability and linearity (R2 > 0.994) within a concentration range of 2-3 orders of magnitude. FAs were then quantified in typical multiple biological matrices including human biofluids (urine, plasma) and cells, animal intestinal content and tissue samples. We also established a quantitative structure-retention relationship (QSRR) for analytes to accurately predict their retention time and aid their reliable identification. We further developed a novel no-additive retention index (NARI) with endogenous FAMEs reducing inter-batch variations to 15 seconds; such NARI performed better than the alkanes-based classical RI, making meta-analysis possible for data obtained from different batches and platforms. Collectively, this provides an inexpensive high-throughput analytical system for quantitative phenotyping of all FAs in 8-minutes multiple biological matrices in large cohort studies of pathophysiological effects.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"9 6","pages":"299-308"},"PeriodicalIF":0.0,"publicationDate":"2023-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10960574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208412","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

Nucleoside deaminases: the key players in base editing toolkit. 核苷脱氨酶：碱基编辑工具包中的关键角色。

Biophysics reports Pub Date : 2023-12-31 DOI: 10.52601/bpr.2023.230029

Jiangchao Xiang, Wenchao Xu, Jing Wu, Yaxin Luo, Bei Yang, Jia Chen

引用次数: 0

An artificial intelligence model for embryo selection in preimplantation DNA methylation screening in assisted reproductive technology. 辅助生殖技术植入前 DNA 甲基化筛查中胚胎选择的人工智能模型。

Biophysics reports Pub Date : 2023-12-31 DOI: 10.52601/bpr.2023.230035

Jianhong Zhan, Chuangqi Chen, Na Zhang, Shuhuai Zhong, Jiaming Wang, Jinzhou Hu, Jiang Liu

{"title":"An artificial intelligence model for embryo selection in preimplantation DNA methylation screening in assisted reproductive technology.","authors":"Jianhong Zhan, Chuangqi Chen, Na Zhang, Shuhuai Zhong, Jiaming Wang, Jinzhou Hu, Jiang Liu","doi":"10.52601/bpr.2023.230035","DOIUrl":"10.52601/bpr.2023.230035","url":null,"abstract":"Embryo quality is a critical determinant of clinical outcomes in assisted reproductive technology (ART). A recent clinical trial investigating preimplantation DNA methylation screening (PIMS) revealed that whole genome DNA methylation level is a novel biomarker for assessing ART embryo quality. Here, we reinforced and estimated the clinical efficacy of PIMS. We introduce PIMS-AI, an innovative artificial intelligence (AI) based model, to predict the probability of an embryo producing live birth and subsequently assist ART embryo selection. Our model demonstrated robust performance, achieving an area under the curve (AUC) of 0.90 in cross-validation and 0.80 in independent testing. In simulated embryo selection, PIMS-AI attained an accuracy of 81% in identifying viable embryos for patients. Notably, PIMS-AI offers significant advantages over conventional preimplantation genetic testing for aneuploidy (PGT-A), including enhanced embryo discriminability and the potential to benefit a broader patient population. In conclusion, our approach holds substantial promise for clinical application and has the potential to significantly improve the ART success rate.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"9 6","pages":"352-361"},"PeriodicalIF":0.0,"publicationDate":"2023-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10960573/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208409","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

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