The retinal pigment epithelium(RPE)is fundamental to sustaining retinal homeostasis.RPE abnormality leads to visual defects and blindness,including age-related macular degeneration(AMD).Although breakthroughs have bee...The retinal pigment epithelium(RPE)is fundamental to sustaining retinal homeostasis.RPE abnormality leads to visual defects and blindness,including age-related macular degeneration(AMD).Although breakthroughs have been made in the treatment of neovascular AMD,effective intervention for atrophic AMD is largely absent.The adequate knowledge of RPE pathology is hindered by a lack of the patients'RPE datasets,especially at the single-cell resolution.In the current study,we delved into a large-scale single-cell resource of AMD donors,in which RPE cells were occupied in a substantial proportion.Bulk RNA-seq datasets of atrophic AMD were integrated to extract molecular characteristics of RPE in the pathogenesis of atrophic AMD.Both in vivo and in vitro models revealed that carboxypeptidase X,M14 family member 2(CPXM2),was specifically expressed in the RPE cells of atrophic AMD,which might be induced by oxidative stress and involved in the epithelial-mesenchymal transition of RPE cells.Additionally,silencing of CPXM2 inhibited the mesenchymal phenotype of RPE cells in an oxidative stress cell model.Thus,our results demonstrated that CPXM2 played a crucial role in regulating atrophic AMD and might serve as a potential therapeutic target for atrophic AMD.展开更多
为了研究大型肉牛比利时蓝牛生长发育的遗传规律,筛选优异基因,试验基于Illumina Bovine SNP 50K芯片数据,采用PLINK软件对270头比利时蓝牛常染色体数据进行基因组长纯合片段(ROH)检测并基于选择信号分析,通过核苷酸多态性检测取前5%的...为了研究大型肉牛比利时蓝牛生长发育的遗传规律,筛选优异基因,试验基于Illumina Bovine SNP 50K芯片数据,采用PLINK软件对270头比利时蓝牛常染色体数据进行基因组长纯合片段(ROH)检测并基于选择信号分析,通过核苷酸多态性检测取前5%的单核苷酸多态性(single nucleotide polymorphism,SNP)位点,基于牛参考基因组(ARS-UCD1.2)对结果SNPs进行基因注释,对候选基因进行GO功能注释与KEGG信号通路富集分析,并计算染色体上ROH长度占基因组总长度的比例(FROH)。结果表明:在全部270个个体数据中共检测出1893个ROH片段,平均长度13.2311 Mb,平均FROH为0.0392;得到与生长发育相性状相关的基因有NEB、TET2、NEK11、NCKAP1、MYH15、EIF4A2、bta-miR-1248-1、DCAF8、PRORP、DOCK3、SYT15、MYEF2、ZDHHC13,与公牛生育能力相关的基因有CFAP61、DNAL1、BAG1。说明通过对比利时蓝牛生长发育性状相关分子标记的解析可以为比利时蓝牛遗传改良提供理论指导。展开更多
Background:Systemic lupus erythematosus(SLE)is a complex chronic autoimmune disease with no known cure.However,the regulatory mechanism of immunity-related genes is not fully understood in SLE.In order to explore new ...Background:Systemic lupus erythematosus(SLE)is a complex chronic autoimmune disease with no known cure.However,the regulatory mechanism of immunity-related genes is not fully understood in SLE.In order to explore new therapeutic targets,we used bioinformatical methods to analyze a series of data.Methods:After downloading and processing the data from Gene Expression Omnibus database,the differentially expressed genes of SLE were analyzed.CIBERSORT algorithm was used to analyze the immune infiltration of SLE.Based on single-cell RNA-sequencing data,the role of immune-related genes in SLE and its target organ(kidney)were analyzed.Key transcription factors affecting immune-related genes were identified.Cell-cell communication networks in SLE were analyzed.Results:In total,15 hub genes and 4 transcription factors were found in the bulk data.Monocytes and macrophages in GSE81622(SLE)showed more infiltration.There were four cell types were annotated in scRNA sequencing dataset(GSE135779),as follows T cells,monocyte,NK cells and B cells.Immunity-related genes were overexpressed in monocytes.Conclusion:The present study shows that immune-related genes affect SLE through monocytes and play an important role in target organ renal injury.展开更多
[Objectives]To make full use of crop rhizosphere microbial resources.[Methods]Illumina NovaSeq sequencing platform was used to analyze the richness and diversity of microbial community structure in rhizosphere soil of...[Objectives]To make full use of crop rhizosphere microbial resources.[Methods]Illumina NovaSeq sequencing platform was used to analyze the richness and diversity of microbial community structure in rhizosphere soil of rice and maize crops in Baitu Town,Gaoyao District,Zhaoqing City.[Results]A total of 14936 OTUs of bacteria and 1905 OTUs of fungi were obtained from three samples of rice rhizosphere soil,and 13437 OTUs of bacteria and 1413 OTUs of fungi were obtained from three samples of maize rhizosphere soil.The diversity and richness of bacterial communities were higher than those of fungi.There are differences in soil bacterial and fungal communities among different crop samples.The analysis of species with bacteria difference at genus level among crop rhizosphere soil samples showed that 18 genera with significant differences were obtained from 6 samples;species analysis of fungi at the genus level showed that 3 genera with significant differences were obtained from 6 samples.[Conclusions]The research results of this paper have positive significance for the development and utilization of soil resources in Zhaoqing City and the full exploitation of rice and maize rhizosphere microbial resources.展开更多
Barley(Hordeum vulgare L.)is one of the earliest domesticated crop species and ranked as the fourth largest cereal production worldwide.Forward genetic studies in barley have greatly advanced plant genetics during the...Barley(Hordeum vulgare L.)is one of the earliest domesticated crop species and ranked as the fourth largest cereal production worldwide.Forward genetic studies in barley have greatly advanced plant genetics during the last century;however,most genes are identified by the conventional mapping method.Array genotyping and exome-capture sequencing have also been successfully used to target the causal mutation in barley populations,but these techniques are not widely adopted because of associated costs and partly due to the huge genome size of barley.This review summarizes three mapping cases of barley cuticle mutants in our laboratory with the help of RNA-sequencing.The causal mutations have been successfully identified for two of them and the target genes are located in the pericentromeric regions.Detailed information on the mapping-by-sequencing,mapping-and-sequencing,and RNA-sequencing assisted linkage mapping are presented and some limitations and challenges on the mapping assisted by RNA sequencing are also discussed.The alternative and elegant methods presented in this review may greatly accelerate forward genetics of barley mapping,especially for laboratories without large funding.展开更多
基金the National Natural Science Foundation of China(Grant Nos.81970821 and 82271100 to Q.L.).
文摘The retinal pigment epithelium(RPE)is fundamental to sustaining retinal homeostasis.RPE abnormality leads to visual defects and blindness,including age-related macular degeneration(AMD).Although breakthroughs have been made in the treatment of neovascular AMD,effective intervention for atrophic AMD is largely absent.The adequate knowledge of RPE pathology is hindered by a lack of the patients'RPE datasets,especially at the single-cell resolution.In the current study,we delved into a large-scale single-cell resource of AMD donors,in which RPE cells were occupied in a substantial proportion.Bulk RNA-seq datasets of atrophic AMD were integrated to extract molecular characteristics of RPE in the pathogenesis of atrophic AMD.Both in vivo and in vitro models revealed that carboxypeptidase X,M14 family member 2(CPXM2),was specifically expressed in the RPE cells of atrophic AMD,which might be induced by oxidative stress and involved in the epithelial-mesenchymal transition of RPE cells.Additionally,silencing of CPXM2 inhibited the mesenchymal phenotype of RPE cells in an oxidative stress cell model.Thus,our results demonstrated that CPXM2 played a crucial role in regulating atrophic AMD and might serve as a potential therapeutic target for atrophic AMD.
文摘Background:Systemic lupus erythematosus(SLE)is a complex chronic autoimmune disease with no known cure.However,the regulatory mechanism of immunity-related genes is not fully understood in SLE.In order to explore new therapeutic targets,we used bioinformatical methods to analyze a series of data.Methods:After downloading and processing the data from Gene Expression Omnibus database,the differentially expressed genes of SLE were analyzed.CIBERSORT algorithm was used to analyze the immune infiltration of SLE.Based on single-cell RNA-sequencing data,the role of immune-related genes in SLE and its target organ(kidney)were analyzed.Key transcription factors affecting immune-related genes were identified.Cell-cell communication networks in SLE were analyzed.Results:In total,15 hub genes and 4 transcription factors were found in the bulk data.Monocytes and macrophages in GSE81622(SLE)showed more infiltration.There were four cell types were annotated in scRNA sequencing dataset(GSE135779),as follows T cells,monocyte,NK cells and B cells.Immunity-related genes were overexpressed in monocytes.Conclusion:The present study shows that immune-related genes affect SLE through monocytes and play an important role in target organ renal injury.
基金Supported by Guangdong Province Rural Science and Technology Commissioner Project(KTP20240693)Zhaoqing University Project(QN202329)+3 种基金Science and Technology Innovation Guidance Project of Zhaoqing(202304038001)Undergraduate Innovation and Entrepreneurship Training Program(202410580011&X202310580120)The Third Batch of Innovation Research Team of Zhaoqing University(05)Quality Engineering and Teaching Reform Project of Zhaoqing University(zlgc202229,zlgc202261).
文摘[Objectives]To make full use of crop rhizosphere microbial resources.[Methods]Illumina NovaSeq sequencing platform was used to analyze the richness and diversity of microbial community structure in rhizosphere soil of rice and maize crops in Baitu Town,Gaoyao District,Zhaoqing City.[Results]A total of 14936 OTUs of bacteria and 1905 OTUs of fungi were obtained from three samples of rice rhizosphere soil,and 13437 OTUs of bacteria and 1413 OTUs of fungi were obtained from three samples of maize rhizosphere soil.The diversity and richness of bacterial communities were higher than those of fungi.There are differences in soil bacterial and fungal communities among different crop samples.The analysis of species with bacteria difference at genus level among crop rhizosphere soil samples showed that 18 genera with significant differences were obtained from 6 samples;species analysis of fungi at the genus level showed that 3 genera with significant differences were obtained from 6 samples.[Conclusions]The research results of this paper have positive significance for the development and utilization of soil resources in Zhaoqing City and the full exploitation of rice and maize rhizosphere microbial resources.
基金grants from the National Natural Science Foundation of China(No.41621001,No.31870381,and No.31970352)by the Youth Innovation Promotion Association,CAS(2018463).
文摘Barley(Hordeum vulgare L.)is one of the earliest domesticated crop species and ranked as the fourth largest cereal production worldwide.Forward genetic studies in barley have greatly advanced plant genetics during the last century;however,most genes are identified by the conventional mapping method.Array genotyping and exome-capture sequencing have also been successfully used to target the causal mutation in barley populations,but these techniques are not widely adopted because of associated costs and partly due to the huge genome size of barley.This review summarizes three mapping cases of barley cuticle mutants in our laboratory with the help of RNA-sequencing.The causal mutations have been successfully identified for two of them and the target genes are located in the pericentromeric regions.Detailed information on the mapping-by-sequencing,mapping-and-sequencing,and RNA-sequencing assisted linkage mapping are presented and some limitations and challenges on the mapping assisted by RNA sequencing are also discussed.The alternative and elegant methods presented in this review may greatly accelerate forward genetics of barley mapping,especially for laboratories without large funding.
