<div style="text-align:justify;"> Circulating extracellular RNAs (exRNAs) are very important potential biomarkers of disease. But few have been reported the extracellular RNA profiles in serum. In this...<div style="text-align:justify;"> Circulating extracellular RNAs (exRNAs) are very important potential biomarkers of disease. But few have been reported the extracellular RNA profiles in serum. In this study, we tried to use RNA-seq technology to analyze the extracellular RNA by using low volume peripheral blood serum and compared the sequencing results between different volumes of serum (500 μl, 1.5 ml, 2.5 ml, 3.5 ml). According to the results, we found that most of the exRNA in the serum is lncRNA, protein_coding and MT-rRNA. And when the volume of serum is between 0.5 - 3.5 ml, the numbers and reads of exRNA, including the reads of circRNA, have not changed significantly. It indicates that the sequencing result of exRNA in serum has no significance with the initial serum volume. </div>展开更多
White-rot fungi are the only organisms that can completely degrade all components of lignocellulosic biomass, including the recalcitrant lignin polymer. Lignin degradation is important for the industrial application o...White-rot fungi are the only organisms that can completely degrade all components of lignocellulosic biomass, including the recalcitrant lignin polymer. Lignin degradation is important for the industrial application of lignocellulosic biomass as a raw material for producing value-added chemicals and </span><span style="font-family:Verdana;">materials. Therefore, elucidating the lignin degradation mechanism in white-rot</span><span style="font-family:Verdana;"> fungi will help researchers develop efficient and eco-friendly methods enabling the production of value-added chemicals from lignocellulosic biomass. A transcriptome analysis is an effective way to compare gene expression patterns between different samples under diverse conditions and can provide insights into biological processes. The democratization of next-generation sequencing technology, especially RNA-sequencing, has made transcriptome sequencing and analysis a common research approach for many laboratories. </span><span style="font-family:Verdana;">In this review, we focus on the transcriptome profiles of two well-characterized</span><span style="font-family:Verdana;"> white-rot fungi (</span><i><span style="font-family:Verdana;">Phanerochaete</span></i><span style="font-family:Verdana;"> <i>chrysosporium</i></span><span style="font-family:Verdana;"> and </span><i><span style="font-family:Verdana;">Dichomitus</span></i><span style="font-family:Verdana;"> <i>squalens</i></span><span style="font-family:Verdana;">) in response to various lignocellulosic materials. The application of RNA-seq technology combining with other techniques remains the best approach for investigating fungal secretomes and elucidating the mechanisms of fungal responses to lignocellulose.展开更多
Knee arthrofibrosis,characterized by excessive matrix protein production and deposition,substantially impairs basic daily functions,causing considerable distress and financial burden.However,the underlying pathomechan...Knee arthrofibrosis,characterized by excessive matrix protein production and deposition,substantially impairs basic daily functions,causing considerable distress and financial burden.However,the underlying pathomechanisms remain unclear.Here,we characterized the heterogeneous cell populations and cellular pathways by combination of flow cytometry and single-cell RNA-seq analysis of synovial tissues from six patients with or without knee arthrofibrosis.Increased macrophages and fibroblasts were observed with decreased numbers of fibroblast-like synoviocytes,endothelial cells,vascular smooth muscle cells,and T cells in the arthrofibrosis group compared with negative controls.展开更多
Alzheimer’s disease(AD)is the most common form of dementia.In addition to the lack of effective treatments,there are limitations in diagnostic capabilities.The complexity of AD itself,together with a variety of other...Alzheimer’s disease(AD)is the most common form of dementia.In addition to the lack of effective treatments,there are limitations in diagnostic capabilities.The complexity of AD itself,together with a variety of other diseases often observed in a patient’s history in addition to their AD diagnosis,make deciphering the molecular mechanisms that underlie AD,even more important.Large datasets of single-cell RNA sequencing,single-nucleus RNA-sequencing(snRNA-seq),and spatial transcriptomics(ST)have become essential in guiding and supporting new investigations into the cellular and regional susceptibility of AD.However,with unique technology,software,and larger databases emerging;a lack of integration of these data can contribute to ineffective use of valuable knowledge.Importantly,there was no specialized database that concentrates on ST in AD that offers comprehensive differential analyses under various conditions,such as sex-specific,region-specific,and comparisons between AD and control groups until the new Single-cell and Spatial RNA-seq databasE for Alzheimer’s Disease(ssREAD)database(Wang et al.,2024)was introduced to meet the scientific community’s growing demand for comprehensive,integrated,and accessible data analysis.展开更多
【目的】旨在解析杜洛克猪剩余采食量的社会遗传效应(The social genetic effects of residual feed intake,SGE-RFI)的分子调控机制,揭示其通过能量代谢途径影响群体行为的生物学基础,为提高猪只饲料利用效率提供理论依据。【方法】通...【目的】旨在解析杜洛克猪剩余采食量的社会遗传效应(The social genetic effects of residual feed intake,SGE-RFI)的分子调控机制,揭示其通过能量代谢途径影响群体行为的生物学基础,为提高猪只饲料利用效率提供理论依据。【方法】通过RNA测序技术对杜洛克猪肝脏组织进行全转录组分析,系统筛选与SGE-RFI性状相关的关键差异表达基因,并采用功能富集方法解析其参与的生物学通路。【结果】鉴定出360个显著差异表达基因,功能分析表明这些基因主要富集于线粒体氧化磷酸化和ATP代谢等能量代谢相关通路,提示其可能通过调控机体能量稳态间接影响社会行为。载脂蛋白基因簇APOA1、APOC3和APOA4的协同表达改变,揭示了社会遗传效应调控过程中神经内分泌系统与脂代谢的交互作用。【结论】本研究构建了杜洛克猪SGE-RFI的多维度调控网络,不仅为解析群体行为遗传机制提供了新视角,更为精准选育低剩余采食量种猪和优化群体饲养管理方案奠定了分子基础。展开更多
文摘<div style="text-align:justify;"> Circulating extracellular RNAs (exRNAs) are very important potential biomarkers of disease. But few have been reported the extracellular RNA profiles in serum. In this study, we tried to use RNA-seq technology to analyze the extracellular RNA by using low volume peripheral blood serum and compared the sequencing results between different volumes of serum (500 μl, 1.5 ml, 2.5 ml, 3.5 ml). According to the results, we found that most of the exRNA in the serum is lncRNA, protein_coding and MT-rRNA. And when the volume of serum is between 0.5 - 3.5 ml, the numbers and reads of exRNA, including the reads of circRNA, have not changed significantly. It indicates that the sequencing result of exRNA in serum has no significance with the initial serum volume. </div>
文摘White-rot fungi are the only organisms that can completely degrade all components of lignocellulosic biomass, including the recalcitrant lignin polymer. Lignin degradation is important for the industrial application of lignocellulosic biomass as a raw material for producing value-added chemicals and </span><span style="font-family:Verdana;">materials. Therefore, elucidating the lignin degradation mechanism in white-rot</span><span style="font-family:Verdana;"> fungi will help researchers develop efficient and eco-friendly methods enabling the production of value-added chemicals from lignocellulosic biomass. A transcriptome analysis is an effective way to compare gene expression patterns between different samples under diverse conditions and can provide insights into biological processes. The democratization of next-generation sequencing technology, especially RNA-sequencing, has made transcriptome sequencing and analysis a common research approach for many laboratories. </span><span style="font-family:Verdana;">In this review, we focus on the transcriptome profiles of two well-characterized</span><span style="font-family:Verdana;"> white-rot fungi (</span><i><span style="font-family:Verdana;">Phanerochaete</span></i><span style="font-family:Verdana;"> <i>chrysosporium</i></span><span style="font-family:Verdana;"> and </span><i><span style="font-family:Verdana;">Dichomitus</span></i><span style="font-family:Verdana;"> <i>squalens</i></span><span style="font-family:Verdana;">) in response to various lignocellulosic materials. The application of RNA-seq technology combining with other techniques remains the best approach for investigating fungal secretomes and elucidating the mechanisms of fungal responses to lignocellulose.
基金The Shanghai Science and Technology Committee(22dz1204700)the MOST Key R&D Program of China(2022YFC2304703,2020YFA0907200)+2 种基金Innovative research team of high-level local universities in Shanghai,the National Natural Science Foundation of China(32270202,82272579,82272570,62372286)the Shanghai Talent Development Fund(No.2021057)the Shanghai Jiao Tong University Science and Technology Innovation Special Fund(No.2021JCPT02).
文摘Knee arthrofibrosis,characterized by excessive matrix protein production and deposition,substantially impairs basic daily functions,causing considerable distress and financial burden.However,the underlying pathomechanisms remain unclear.Here,we characterized the heterogeneous cell populations and cellular pathways by combination of flow cytometry and single-cell RNA-seq analysis of synovial tissues from six patients with or without knee arthrofibrosis.Increased macrophages and fibroblasts were observed with decreased numbers of fibroblast-like synoviocytes,endothelial cells,vascular smooth muscle cells,and T cells in the arthrofibrosis group compared with negative controls.
文摘Alzheimer’s disease(AD)is the most common form of dementia.In addition to the lack of effective treatments,there are limitations in diagnostic capabilities.The complexity of AD itself,together with a variety of other diseases often observed in a patient’s history in addition to their AD diagnosis,make deciphering the molecular mechanisms that underlie AD,even more important.Large datasets of single-cell RNA sequencing,single-nucleus RNA-sequencing(snRNA-seq),and spatial transcriptomics(ST)have become essential in guiding and supporting new investigations into the cellular and regional susceptibility of AD.However,with unique technology,software,and larger databases emerging;a lack of integration of these data can contribute to ineffective use of valuable knowledge.Importantly,there was no specialized database that concentrates on ST in AD that offers comprehensive differential analyses under various conditions,such as sex-specific,region-specific,and comparisons between AD and control groups until the new Single-cell and Spatial RNA-seq databasE for Alzheimer’s Disease(ssREAD)database(Wang et al.,2024)was introduced to meet the scientific community’s growing demand for comprehensive,integrated,and accessible data analysis.
文摘【目的】旨在解析杜洛克猪剩余采食量的社会遗传效应(The social genetic effects of residual feed intake,SGE-RFI)的分子调控机制,揭示其通过能量代谢途径影响群体行为的生物学基础,为提高猪只饲料利用效率提供理论依据。【方法】通过RNA测序技术对杜洛克猪肝脏组织进行全转录组分析,系统筛选与SGE-RFI性状相关的关键差异表达基因,并采用功能富集方法解析其参与的生物学通路。【结果】鉴定出360个显著差异表达基因,功能分析表明这些基因主要富集于线粒体氧化磷酸化和ATP代谢等能量代谢相关通路,提示其可能通过调控机体能量稳态间接影响社会行为。载脂蛋白基因簇APOA1、APOC3和APOA4的协同表达改变,揭示了社会遗传效应调控过程中神经内分泌系统与脂代谢的交互作用。【结论】本研究构建了杜洛克猪SGE-RFI的多维度调控网络,不仅为解析群体行为遗传机制提供了新视角,更为精准选育低剩余采食量种猪和优化群体饲养管理方案奠定了分子基础。
