应用Illumina Mi Seq高通量测序技术测定核桃内生细菌的16S r DNA-V4变异区序列,使用Uparse等软件整理和统计样品序列数目和操作分类单元(OTUs)数量,分析内生细菌的丰度和α-多样性。获得了用于分析的有效序列63 183条,OTU数为103。稀...应用Illumina Mi Seq高通量测序技术测定核桃内生细菌的16S r DNA-V4变异区序列,使用Uparse等软件整理和统计样品序列数目和操作分类单元(OTUs)数量,分析内生细菌的丰度和α-多样性。获得了用于分析的有效序列63 183条,OTU数为103。稀释曲线表明测序深度充分,OTU数量接近于饱和。核桃样品的Chao1指数为105.143,Shannon多样性指数为1.823。核桃内生细菌主要分布于鞘氨醇单胞菌属(Sphingomonas,27.27%)、盐单胞菌属(Halomonas,27.27%)、土壤杆菌属(Agrobacterium,45.45%),这3个属是核桃内生细菌优势菌属。展开更多
Improving nutritional fruit quality and impacts important agro-traits such as biotic or abiotic stresses are extremely important for human civilization.Our previous study reported that manipulation of Sl MX1 gene enha...Improving nutritional fruit quality and impacts important agro-traits such as biotic or abiotic stresses are extremely important for human civilization.Our previous study reported that manipulation of Sl MX1 gene enhanced carotenoids accumulation and drought resistance in tomato.Here,RNA-Seq analysis proved to be a very useful tool to provide insights into the regulatory mechanisms of Sl MX1 involved in stress resistance and enhanced secondary metabolites.Physiological analysis showed that overexpression of Sl MX1 results in substantially increased broad-spectrum tolerance to a wide-range of abiotic and biotic(fungus,bacteria,virus and insects) stresses in tomato.This research appears to be of remarkable interest because enhanced terpenoids content has been achieved by increasing trichome density.In addition,we reported two types of trichome which seems to be aberrant types in tomato.This study unravels the mechanism of regulation of Sl MX1,which simultaneously modulates resistance and metabolic processes through regulating key structural and regulatory genes of the corresponding pathways.展开更多
The efficacy of triple therapy for Helicobacter pylori infection has dramatically declined over the last decade,largely related to increasing clarithromycin resistance rates.From a microbiological standpoint,bismuth q...The efficacy of triple therapy for Helicobacter pylori infection has dramatically declined over the last decade,largely related to increasing clarithromycin resistance rates.From a microbiological standpoint,bismuth quadruple therapy is the ideal replacement since it combines drugs for which resistance does not impair its efficacy.Nonetheless,several obstacles such as availability,complexity or tolerance prevent a general implementation of bismuth quadruple therapy,so nonbismuth quadruple regimens remain the best firstline treatment in clinical practice in many geographical areas.We review the rationale and efficacy of several optimization tools(increasing the length of duration,high-dose acid suppression,probiotics),which have been largely evaluated over the last 5 years to increase the effectiveness of standard triple therapy.Then,we update available evidence on the effectiveness of several non-bismuth quadruple therapies(sequential,concomitant,hybrid,miscellaneous therapy),which have gained interest lately.We also revise evidence on the efficacy of the aforementioned optimization tools for non-bismuth quadruples schemes and,finally we provide a novel regionalized therapeutic algorithm,based on novel formulas recently developed for predicting the outcome of non-bismuth quadruple regimens,upon local antibiotic resistance rates.展开更多
Obesity-related glomerulopathy(ORG)is an independent risk factor for chronic kid-ney disease and even progression to end-stage renal disease.Efforts have been undertaken to elucidate the mechanisms underlying the deve...Obesity-related glomerulopathy(ORG)is an independent risk factor for chronic kid-ney disease and even progression to end-stage renal disease.Efforts have been undertaken to elucidate the mechanisms underlying the development of ORG and substantial advances have been made in the treatment of ORG,but relatively little is known about cell-specific changes in gene expression.To define the transcriptomic landscape at single-cell resolution,we analyzed kidney samples from four patients with ORG and three obese control subjects without kidney disease using single-cell RNA sequencing.We report for the first time that immune cells,including T cells and B cells,are decreased in ORG patients.Further analysis indicated that SPP1 was significantly up-regulated in T cells and B cells.This gene is related to inflammation and cell proliferation.Analysis of differential gene expression in glomerular cells(endothelial cells,mesangial cells,and podocytes)showed that these cell types were mainly enriched in genes related to oxidative phosphorylation,cell adhesion,thermogenesis,and inflammatory pathways(PI3K-Akt signaling,MAPK signaling).Furthermore,we found that the podocytes of ORG patients were enriched in genes related to the fluid shear stress pathway.Moreover,an evaluation of cell-cell communications revealed that there were interactions between glomerular parietal epithelial cells and other cells in ORG patients,with major interactions between parietal epithelial cells and podocytes.Altogether,our identification of molecular events,cell types,and differentially expressed genes may facilitate the development of new preventive or therapeutic approaches for ORG.展开更多
Background Photosystem II(PSII)constitutes an intricate assembly of protein pigments,featuring extrinsic and intrinsic polypeptides within the photosynthetic membrane.The low-molecular-weight transmembrane protein Psb...Background Photosystem II(PSII)constitutes an intricate assembly of protein pigments,featuring extrinsic and intrinsic polypeptides within the photosynthetic membrane.The low-molecular-weight transmembrane protein PsbX has been identified in PSII,which is associated with the oxygen-evolving complex.The expression of PsbX gene protein is regulated by light.PsbX’s central role involves the regulation of PSII,facilitating the binding of quinone molecules to the Qb(PsbA)site,and it additionally plays a crucial role in optimizing the efficiency of photosynthesis.Despite these insights,a comprehensive understanding of the PsbX gene’s functions has remained elusive.Results In this study,we identified ten PsbX genes in Gossypium hirsutum L.The phylogenetic analysis results showed that 40 genes from nine species were classified into one clade.The resulting sequence logos exhibited substantial conservation across the N and C terminals at multiple sites among all Gossypium species.Furthermore,the ortholo-gous/paralogous,Ka/Ks ratio revealed that cotton PsbX genes subjected to positive as well as purifying selection pressure might lead to limited divergence,which resulted in the whole genome and segmental duplication.The expression patterns of GhPsbX genes exhibited variations across specific tissues,as indicated by the analysis.Moreover,the expression of GhPsbX genes could potentially be regulated in response to salt,intense light,and drought stresses.Therefore,GhPsbX genes may play a significant role in the modulation of photosynthesis under adverse abiotic conditions.Conclusion We examined the structure and function of PsbX gene family very first by using comparative genom-ics and systems biology approaches in cotton.It seems that PsbX gene family plays a vital role during the growth and development of cotton under stress conditions.Collectively,the results of this study provide basic information to unveil the molecular and physiological function of PsbX genes of cotton plants.展开更多
Grafting is commonly used to overcome soilborne diseases. However, its effects on the rhizodeposits as well as the linkages between the rhizosphere chemical niche and microbiome remained unknown. In this paper,signifi...Grafting is commonly used to overcome soilborne diseases. However, its effects on the rhizodeposits as well as the linkages between the rhizosphere chemical niche and microbiome remained unknown. In this paper,significant negative correlations between the bacterial alpha diversity and both the disease incidence(r = – 0.832,P = 0.005) and pathogen population(r = – 0.786, P = 0.012)were detected. Moreover, our results showed that the chemical diversity not only predicts bacterial alpha diversity but also can impact on overall microbial community structure(beta diversity) in the rhizosphere.Furthermore, some anti-fungal compounds including heptadecane and hexadecane were identified in the rhizosphere of grafted watermelon. We concluded that grafted watermelon can form a distinct rhizosphere chemical niche and thus recruit microbial communities with high diversity. Furthermore, the diverse bacteria and the antifungal compounds in the rhizosphere can potentially serve as biological and chemical barriers, respectively, to hinder pathogen invasion. These results not only lead us toward broadening the view of disease resistance mechanism of grafting, but also provide clues to control the microbial composition by manipulating the rhizosphere chemical niche.展开更多
Background:Heterogeneity of tumor cells and the tumor microenvironment(TME)is significantly associated with clinical outcomes and treatment responses in patients with urothelial carcinoma(UC).Comprehensive profiling o...Background:Heterogeneity of tumor cells and the tumor microenvironment(TME)is significantly associated with clinical outcomes and treatment responses in patients with urothelial carcinoma(UC).Comprehensive profiling of the cellular diversity and interactions between malignant cells and TME may clarify the mechanisms underlying UC progression and guide the development of novel therapies.This study aimed to extend our understanding of intra-tumoral heterogeneity and the immunosuppressive TME in UC and provide basic support for the development of novel UC therapies.Methods:Seven patients with UC were included who underwent curative surgery at our hospital between July 2020 and October 2020.We performed single-cell RNA sequencing(scRNA-seq)analysis in seven tumors with six matched adjacent normal tissues and integrated the results with two public scRNA-seq datasets.The functional properties and intercellular interactions between single cells were characterized,and the results were validated using multiplex immunofluorescence staining,flow cytometry,and bulk transcriptomic datasets.All statistical analyses were performed using the R package with two-sided tests.Wilcoxon-rank test,log-rank test,one-way analysis of variance test,and Pearson correlation analysis were used properly.Results:Unsupervised t-distributed stochastic neighbor embedding clustering analysis identified ten main cellular subclusters in urothelial tissues.Of them,seven urothelial subtypes were noted,and malignant urothelial cells were characterized with enhanced cellular proliferation and reduced immunogenicity.CD8^(+)T cell subclusters exhibited enhanced cellular cytotoxicity activities along with increased exhaustion signature in UC tissues,and the recruitment of CD4^(+)T regulatory cells was also increased in tumor tissues.Regarding myeloid cells,coordinated reprogramming of infiltrated neutrophils,M2-type polarized macrophages,and LAMP3^(+)dendritic cells contribute to immunosuppressive TME in UC tissues.Tumor tissues demonstrated enhanced angiog展开更多
Recently,single-cell RNA-seq technologies have been rapidly updated,leading to a revolution in biology.We previously developed Microwell-seq,a cost-effective and high-throughput single cell RNA sequencing(scRNA-seq)me...Recently,single-cell RNA-seq technologies have been rapidly updated,leading to a revolution in biology.We previously developed Microwell-seq,a cost-effective and high-throughput single cell RNA sequencing(scRNA-seq)method with a very simple device.Most cDNA libraries are sequenced using an expensive Illumina platform.Here,we present the first report showing combined Microwell-seq and BGI MGISEQ2000,a less expensive sequencing platform,to profile the whole transcriptome of 11,883 individual mouse adult adrenal gland cells and identify 18 transcriptionally distinct clusters.Moreover,we performed a single-cell comparative analysis of human and mouse adult adrenal glands to reveal the conserved genetic networks in these mammalian systems.These results provide new insights into the sophisticated adrenal gland hierarchy and provide a benchmark,low-cost strategy for highthroughput single-cell RNA study.展开更多
The rapid growth of single-cell RNA-seq studies （scRNA-seq） demands efficient data storage, processing, and analysis. Big-data technology provides a framework that facilitates the comprehensive discovery of biologic...The rapid growth of single-cell RNA-seq studies （scRNA-seq） demands efficient data storage, processing, and analysis. Big-data technology provides a framework that facilitates the comprehensive discovery of biological signals from inter-institutional scRNA-seq datasets. The strategies to solve the stochastic and heterogeneous single-cell transcriptome signal are discussed in this article. After extensively reviewing the available big-data applications of next-generation sequencing （NGS）-based studies, we propose a workflow that accounts for the unique characteris- tics of scRNA-seq data and primary objectives of single-cell studies.展开更多
文摘应用Illumina Mi Seq高通量测序技术测定核桃内生细菌的16S r DNA-V4变异区序列,使用Uparse等软件整理和统计样品序列数目和操作分类单元(OTUs)数量,分析内生细菌的丰度和α-多样性。获得了用于分析的有效序列63 183条,OTU数为103。稀释曲线表明测序深度充分,OTU数量接近于饱和。核桃样品的Chao1指数为105.143,Shannon多样性指数为1.823。核桃内生细菌主要分布于鞘氨醇单胞菌属(Sphingomonas,27.27%)、盐单胞菌属(Halomonas,27.27%)、土壤杆菌属(Agrobacterium,45.45%),这3个属是核桃内生细菌优势菌属。
基金supported by the Major State Basic Research Development Program of China(2011CB100601)the National Natural Science Foundation of China(31070267)the Program for New Century Excellent Talents in University of Ministry of Education in China(NCET-09-0401)
文摘Improving nutritional fruit quality and impacts important agro-traits such as biotic or abiotic stresses are extremely important for human civilization.Our previous study reported that manipulation of Sl MX1 gene enhanced carotenoids accumulation and drought resistance in tomato.Here,RNA-Seq analysis proved to be a very useful tool to provide insights into the regulatory mechanisms of Sl MX1 involved in stress resistance and enhanced secondary metabolites.Physiological analysis showed that overexpression of Sl MX1 results in substantially increased broad-spectrum tolerance to a wide-range of abiotic and biotic(fungus,bacteria,virus and insects) stresses in tomato.This research appears to be of remarkable interest because enhanced terpenoids content has been achieved by increasing trichome density.In addition,we reported two types of trichome which seems to be aberrant types in tomato.This study unravels the mechanism of regulation of Sl MX1,which simultaneously modulates resistance and metabolic processes through regulating key structural and regulatory genes of the corresponding pathways.
文摘The efficacy of triple therapy for Helicobacter pylori infection has dramatically declined over the last decade,largely related to increasing clarithromycin resistance rates.From a microbiological standpoint,bismuth quadruple therapy is the ideal replacement since it combines drugs for which resistance does not impair its efficacy.Nonetheless,several obstacles such as availability,complexity or tolerance prevent a general implementation of bismuth quadruple therapy,so nonbismuth quadruple regimens remain the best firstline treatment in clinical practice in many geographical areas.We review the rationale and efficacy of several optimization tools(increasing the length of duration,high-dose acid suppression,probiotics),which have been largely evaluated over the last 5 years to increase the effectiveness of standard triple therapy.Then,we update available evidence on the effectiveness of several non-bismuth quadruple therapies(sequential,concomitant,hybrid,miscellaneous therapy),which have gained interest lately.We also revise evidence on the efficacy of the aforementioned optimization tools for non-bismuth quadruples schemes and,finally we provide a novel regionalized therapeutic algorithm,based on novel formulas recently developed for predicting the outcome of non-bismuth quadruple regimens,upon local antibiotic resistance rates.
基金supported by the Hunan Provincial Natural Science Foundation for Outstanding Youth(China)(No.2022JJ10093,2020JJ2020)the Scientific Research Fund of Hunan Provincial Health Commission(China)(No.B202303056777)+1 种基金the Major Research and Development Program of Hunan Province,China(No.2020SK2116)the Key Program of Hunan Provincial Health Commission(China)(No.202203052969).
文摘Obesity-related glomerulopathy(ORG)is an independent risk factor for chronic kid-ney disease and even progression to end-stage renal disease.Efforts have been undertaken to elucidate the mechanisms underlying the development of ORG and substantial advances have been made in the treatment of ORG,but relatively little is known about cell-specific changes in gene expression.To define the transcriptomic landscape at single-cell resolution,we analyzed kidney samples from four patients with ORG and three obese control subjects without kidney disease using single-cell RNA sequencing.We report for the first time that immune cells,including T cells and B cells,are decreased in ORG patients.Further analysis indicated that SPP1 was significantly up-regulated in T cells and B cells.This gene is related to inflammation and cell proliferation.Analysis of differential gene expression in glomerular cells(endothelial cells,mesangial cells,and podocytes)showed that these cell types were mainly enriched in genes related to oxidative phosphorylation,cell adhesion,thermogenesis,and inflammatory pathways(PI3K-Akt signaling,MAPK signaling).Furthermore,we found that the podocytes of ORG patients were enriched in genes related to the fluid shear stress pathway.Moreover,an evaluation of cell-cell communications revealed that there were interactions between glomerular parietal epithelial cells and other cells in ORG patients,with major interactions between parietal epithelial cells and podocytes.Altogether,our identification of molecular events,cell types,and differentially expressed genes may facilitate the development of new preventive or therapeutic approaches for ORG.
基金supported by National Natural Science Foundation of China(32060466)Chinese Academy of Agricultural Sciences。
文摘Background Photosystem II(PSII)constitutes an intricate assembly of protein pigments,featuring extrinsic and intrinsic polypeptides within the photosynthetic membrane.The low-molecular-weight transmembrane protein PsbX has been identified in PSII,which is associated with the oxygen-evolving complex.The expression of PsbX gene protein is regulated by light.PsbX’s central role involves the regulation of PSII,facilitating the binding of quinone molecules to the Qb(PsbA)site,and it additionally plays a crucial role in optimizing the efficiency of photosynthesis.Despite these insights,a comprehensive understanding of the PsbX gene’s functions has remained elusive.Results In this study,we identified ten PsbX genes in Gossypium hirsutum L.The phylogenetic analysis results showed that 40 genes from nine species were classified into one clade.The resulting sequence logos exhibited substantial conservation across the N and C terminals at multiple sites among all Gossypium species.Furthermore,the ortholo-gous/paralogous,Ka/Ks ratio revealed that cotton PsbX genes subjected to positive as well as purifying selection pressure might lead to limited divergence,which resulted in the whole genome and segmental duplication.The expression patterns of GhPsbX genes exhibited variations across specific tissues,as indicated by the analysis.Moreover,the expression of GhPsbX genes could potentially be regulated in response to salt,intense light,and drought stresses.Therefore,GhPsbX genes may play a significant role in the modulation of photosynthesis under adverse abiotic conditions.Conclusion We examined the structure and function of PsbX gene family very first by using comparative genom-ics and systems biology approaches in cotton.It seems that PsbX gene family plays a vital role during the growth and development of cotton under stress conditions.Collectively,the results of this study provide basic information to unveil the molecular and physiological function of PsbX genes of cotton plants.
基金supported by the National Basic Research Program of China (2015CB150503)National Natural Science Foundation of China (31301853)the Fundamental Research Funds for the Central Universities (KYZ201307)
文摘Grafting is commonly used to overcome soilborne diseases. However, its effects on the rhizodeposits as well as the linkages between the rhizosphere chemical niche and microbiome remained unknown. In this paper,significant negative correlations between the bacterial alpha diversity and both the disease incidence(r = – 0.832,P = 0.005) and pathogen population(r = – 0.786, P = 0.012)were detected. Moreover, our results showed that the chemical diversity not only predicts bacterial alpha diversity but also can impact on overall microbial community structure(beta diversity) in the rhizosphere.Furthermore, some anti-fungal compounds including heptadecane and hexadecane were identified in the rhizosphere of grafted watermelon. We concluded that grafted watermelon can form a distinct rhizosphere chemical niche and thus recruit microbial communities with high diversity. Furthermore, the diverse bacteria and the antifungal compounds in the rhizosphere can potentially serve as biological and chemical barriers, respectively, to hinder pathogen invasion. These results not only lead us toward broadening the view of disease resistance mechanism of grafting, but also provide clues to control the microbial composition by manipulating the rhizosphere chemical niche.
基金supported by grants from the National Nature Science Foundation(No.81970658)Natural Science Foundation of Shanghai(No.20ZR1434100)
文摘Background:Heterogeneity of tumor cells and the tumor microenvironment(TME)is significantly associated with clinical outcomes and treatment responses in patients with urothelial carcinoma(UC).Comprehensive profiling of the cellular diversity and interactions between malignant cells and TME may clarify the mechanisms underlying UC progression and guide the development of novel therapies.This study aimed to extend our understanding of intra-tumoral heterogeneity and the immunosuppressive TME in UC and provide basic support for the development of novel UC therapies.Methods:Seven patients with UC were included who underwent curative surgery at our hospital between July 2020 and October 2020.We performed single-cell RNA sequencing(scRNA-seq)analysis in seven tumors with six matched adjacent normal tissues and integrated the results with two public scRNA-seq datasets.The functional properties and intercellular interactions between single cells were characterized,and the results were validated using multiplex immunofluorescence staining,flow cytometry,and bulk transcriptomic datasets.All statistical analyses were performed using the R package with two-sided tests.Wilcoxon-rank test,log-rank test,one-way analysis of variance test,and Pearson correlation analysis were used properly.Results:Unsupervised t-distributed stochastic neighbor embedding clustering analysis identified ten main cellular subclusters in urothelial tissues.Of them,seven urothelial subtypes were noted,and malignant urothelial cells were characterized with enhanced cellular proliferation and reduced immunogenicity.CD8^(+)T cell subclusters exhibited enhanced cellular cytotoxicity activities along with increased exhaustion signature in UC tissues,and the recruitment of CD4^(+)T regulatory cells was also increased in tumor tissues.Regarding myeloid cells,coordinated reprogramming of infiltrated neutrophils,M2-type polarized macrophages,and LAMP3^(+)dendritic cells contribute to immunosuppressive TME in UC tissues.Tumor tissues demonstrated enhanced angiog
基金This work was supported by grants from the National Natural Science Foundation of China(81770188,31722027,and 31701290)the National Key Program on Stem Cell and Translational Research(2017YFA0103401).
文摘Recently,single-cell RNA-seq technologies have been rapidly updated,leading to a revolution in biology.We previously developed Microwell-seq,a cost-effective and high-throughput single cell RNA sequencing(scRNA-seq)method with a very simple device.Most cDNA libraries are sequenced using an expensive Illumina platform.Here,we present the first report showing combined Microwell-seq and BGI MGISEQ2000,a less expensive sequencing platform,to profile the whole transcriptome of 11,883 individual mouse adult adrenal gland cells and identify 18 transcriptionally distinct clusters.Moreover,we performed a single-cell comparative analysis of human and mouse adult adrenal glands to reveal the conserved genetic networks in these mammalian systems.These results provide new insights into the sophisticated adrenal gland hierarchy and provide a benchmark,low-cost strategy for highthroughput single-cell RNA study.
基金supported by Baylor Research Institute start-up funding,USA to WL
文摘The rapid growth of single-cell RNA-seq studies （scRNA-seq） demands efficient data storage, processing, and analysis. Big-data technology provides a framework that facilitates the comprehensive discovery of biological signals from inter-institutional scRNA-seq datasets. The strategies to solve the stochastic and heterogeneous single-cell transcriptome signal are discussed in this article. After extensively reviewing the available big-data applications of next-generation sequencing （NGS）-based studies, we propose a workflow that accounts for the unique characteris- tics of scRNA-seq data and primary objectives of single-cell studies.
