Field resistances of nine accessions of common wild rice （Oryza rufipogon Griff.） and one rice variety （IR24） were evaluated by using nine strains of bacterial blight pathogen （Xanthomonas oryzae pv. oryzae） fro...Field resistances of nine accessions of common wild rice （Oryza rufipogon Griff.） and one rice variety （IR24） were evaluated by using nine strains of bacterial blight pathogen （Xanthomonas oryzae pv. oryzae） from the Philippines. IR24 was highly susceptible to all the strains, and six common wild rice accessions resisted all the nine strains, with a resistance frequency of 67%. The accessions Yulin and Wanning were only susceptible to PXO280 and PXO71, respectively. The accession Gaozhou was susceptible to the three strains PXO79, PXO99 and PXO339, whereas resistant to the other six strains. It could be concluded that there is at least one resistance gene in each common wild rice accession. The functional markers of the genes xa5, xa13, Xa21 and Xa27 were used to detect the presence of these resistance genes in the nine tested wild rice accessions, and it was found that four wild rice accessions contained heterozygous xa13. Among the nine common wild rice accessions, five were homozygous for Xa27 and three homozygous for xa27, and the accession Laibin contained neither xa27 nor Xa27. In addition, there were no xa5 and Xa21 in all of these accessions.展开更多
Resistance to whitebacked planthopper(WBPH)in Chinese japonica riceChunjiang 06(CJ-06)was mediated by sucking inhibitory and ovicidal mecha-nism.The ovicidal reponse was a common self-defense mechanism againstWBPH in ...Resistance to whitebacked planthopper(WBPH)in Chinese japonica riceChunjiang 06(CJ-06)was mediated by sucking inhibitory and ovicidal mecha-nism.The ovicidal reponse was a common self-defense mechanism againstWBPH in japonica.The ovicidal gene and its chromosomal position had alreadybeen identified.The sucking inhibitory nature of CJ-06 caused a definenon-preference behavior of WBPH in fields.A single dominant gene governed展开更多
Tbx18,Wt1,and Tcf21 have been identified as epicardial markers during the early embryonic stage.However,the gene markers of mature epicardial cells remain unclear.Single-cell transcriptomic analysis was performed with...Tbx18,Wt1,and Tcf21 have been identified as epicardial markers during the early embryonic stage.However,the gene markers of mature epicardial cells remain unclear.Single-cell transcriptomic analysis was performed with the Seurat,Monocle,and CellphoneDB packages in R software with standard procedures.Spatial transcriptomics was performed on chilled Visium Tissue Optimization Slides(10x Genomics)and Visium Spatial Gene Expression Slides(10x Genomics).Spatial transcriptomics analysis was performed with Space Ranger software and R software.Immunofluorescence,whole-mount RNA in situ hybridization and X-gal staining were performed to validate the analysis results.Spatial transcriptomics analysis revealed distinct transcriptional profiles and functions between epicardial tissue and non-epicardial tissue.Several gene markers specific to postnatal epicardial tissue were identified,including Msln,C3,Efemp1,and Upk3b.Single-cell transcriptomic analysis revealed that cardiac cells from wildtype mouse hearts(from embryonic day 9.5 to postnatal day 9)could be categorized into six major cell types,which included epicardial cells.Throughout epicardial development,Wt1,Tbx18,and Upk3b were consistently expressed,whereas genes including Msln,C3,and Efemp1 exhibited increased expression during the mature stages of development.Pseudotime analysis further revealed two epicardial cell fates during maturation.Moreover,Upk3b,Msln,Efemp1,and C3 positive epicardial cells were enriched in extracellular matrix signaling.Our results suggested Upk3b,Efemp1,Msln,C3,and other genes were mature epicardium markers.Extracellular matrix signaling was found to play a critical role in the mature epicardium,thus suggesting potential therapeutic targets for heart regeneration in future clinical practice.展开更多
Lymphatic vessel networks have been identified in the meninges of mice,non-human primates,and humans[1].Meningeal lymphatic vessels(mLVs),composed of meningeal lymphatic endothelial cells(mLECs),are present in both ze...Lymphatic vessel networks have been identified in the meninges of mice,non-human primates,and humans[1].Meningeal lymphatic vessels(mLVs),composed of meningeal lymphatic endothelial cells(mLECs),are present in both zebrafish and mammals,although their anatomical distributions differ;they reside in the dura mater in mice,but are situated within the meninges in zebrafish[2].Moreover,the lymphatic marker genes expressed in these vessels differ between species[2].展开更多
AIM: To determine the gene expression profile data for the whole liver during development of dimethylni-trosamine (DMN)-induced hepatic fibrosis.METHODS: Marker genes were identified for different types of hepatic cel...AIM: To determine the gene expression profile data for the whole liver during development of dimethylni-trosamine (DMN)-induced hepatic fibrosis.METHODS: Marker genes were identified for different types of hepatic cells, including hepatic stellate cells (HSCs), Kupffer cells (including other inflammatory cells), and hepatocytes, using independent temporal DNA microarray data obtained from isolated hepatic cells. RESULTS: The cell-type analysis of gene expression gave several key results and led to formation of three hypotheses: (1) changes in the expression of HSC-specific marker genes during fibrosis were similar to gene expression data in in vitro cultured HSCs, suggesting a major role of the self-activating characteristics of HSCs in formation of fibrosis; (2) expression of mast cell-specific marker genes reached a peak during liver fibrosis, suggesting a possible role of mast cells in formation of fibrosis; and (3) abnormal expression of hepatocyte-specific marker genes was found across several metabolic pathways during fibrosis, including sulfur-containing amino acid metabolism, fatty acid metabolism, and drug metabolism, suggesting a mechanistic relationship between these abnormalities and symptoms of liver fibrosis. CONCLUSION: Analysis of marker genes for specific hepatic cell types can identify the key aspects of fibro-genesis. Sequential activation of inflammatory cells and the self-supporting properties of HSCs play an important role in development of fibrosis.展开更多
To correctly assess and properly manage the public health risks associated with exposure to contaminated water,it is necessary to identify the source of fecal pollution in a watershed.In this study,we evaluated the ef...To correctly assess and properly manage the public health risks associated with exposure to contaminated water,it is necessary to identify the source of fecal pollution in a watershed.In this study,we evaluated the efficacy of our two previously developed real time-quantitative PCR(qPCR)assays for the detection of swine-associated Bacteroidales genetic markers(gene 1-38,gene 3-53)in the Yangtze Delta watershed of southeastern China.The results indicated that the gene 1-38 and 3-53 markers exhibited high accuracy(92.5%,91.7%conditional probability,respectively)in detecting Bacteroidales spp.in water samples.According to binary logistic regression(BLR),these two swine-associated markers were well correlated(P<0.05)with fecal indicators(Escherichia coli and Enterococci spp.)and zoonotic pathogens(E.coli O157:H7,Salmonella spp.and Campylobacter spp.)in water samples.In contrast,concentrations of conventional fecal indicator bacteria(FIB)were not correlated with zoonotic pathogens,suggesting that they are noneffective at detecting fecal pollution events.Collectively,the results obtained in this study demonstrated that a swinetargeted qPCR assay based on two Bacteroidales genes markers(gene 1-38,gene 3-53)could be a useful tool in determining the swine-associated impacts of fecal contamination in a watershed.展开更多
AIM: To investigate the relationship of changes in expression of marker genes in functional categories or molecular networks comprising one functional category or multiple categories in progression of hepatic fibrosis...AIM: To investigate the relationship of changes in expression of marker genes in functional categories or molecular networks comprising one functional category or multiple categories in progression of hepatic fibrosis in hepatitis C (HCV) patients. METHODS: Marker genes were initially identified using DNA microarray data from a rat liver fibrosis model. The expression level of each fibrosis associated marker gene was analyzed using reverse transcription-polymerase chain reaction (RT-PCR) in clinical biopsy specimens from HCV-positive patients (n = 61). Analysis of changes in expression patterns and interactions of marker genes in functional categories was used to assess the biological mechanism of fibrosis. RESULTS: The profile data showed several biological changes associated with progression of hepatic fibrosis. Clustered genes in functional categories showed sequential changes in expression. Several sets of clustered genes, including those related to the extracellular matrix (ECM), inflammation, lipid metabolism, steroid metabolism, and some transcription factors important for hepatic biology showed expression changes in the immediate early phase (F1/F2) of fibrosis. Genes associated with aromatic amino acid (AA) metabolism, sulfur-containing AA metabolism and insulin/ Wnt signaling showed expression changes in the middle phase (F2/F3), and some genes related to glucose metabolism showed altered expression in the late phase of fibrosis (F3/F4). Therefore, molecular networks showing serial changes in gene expression are present in liver fibrosis progression in hepatitis C patients. CONCLUSION: Analysis of gene expression profiles from a perspective of functional categories or molecular networks provides an understanding of disease and suggests new diagnostic methods. Selected marker genes have potential utility for biological identification of advanced fibrosis.展开更多
Plant formation from in vitro-cultivated microspores involves a complex network of internal and environmental factors.Haploids/doubled haploids(DHs)derived from in vitro-cultured microspores are widely used in plant b...Plant formation from in vitro-cultivated microspores involves a complex network of internal and environmental factors.Haploids/doubled haploids(DHs)derived from in vitro-cultured microspores are widely used in plant breeding and genetic engineering.However,the mechanism underlying the developmental switch from regular pollen maturation towards microspore-derived plant regeneration remains poorly defined.Here,RNA-sequencing was employed to elucidate the transcriptional landscapes of four early stages of microspore embryogenesis(ME)in barley cultivars Golden Promise and Igri,which exhibit contrasting responsiveness to microspore-derived plant formation.Our experiments revealed fundamental regulatory networks,specific groups of genes,and transcription factor(TF)families potentially regulating the developmental switch.We identified a set of candidate genes crucial for genotype-dependent responsiveness/recalcitrance to ME.Our high-resolution temporal transcriptome atlas provides an important resource for future functional studies on the genetic control of microspore developmental transition.展开更多
AIM:To identify and assess the novel makers for detection of Shiga toxin producing Escherichia coli (STEC) O157:H7 with an integrated computational and experimental approach. METHODS:High-throughput NCBI blast (E-valu...AIM:To identify and assess the novel makers for detection of Shiga toxin producing Escherichia coli (STEC) O157:H7 with an integrated computational and experimental approach. METHODS:High-throughput NCBI blast (E-value cutoff e-5) was used to search homologous genes among all sequenced prokaryotic genomes of each gene encoded in each of the three strains of STEC O157:H7 with complete genomes,aiming to find unique genes in O157:H7 as its potential markers. To ensure that the identified markers from the three strains of STEC O157:H7 can serve as general markers for all the STEC O157:H7 strains,a genomic barcode approach was used to select the markers to minimize the possibility of choosing a marker gene as part of a transposable element. Effectiveness of the markers predicted was then validated by running polymerase chain reaction (PCR) on 18 strains of O157:H7 with 5 additional genomes used as negative controls. RESULTS:The blast search identified 20,16 and 20 genes,respectively,in the three sequenced strains of STEC O157:H7,which had no homologs in any of the other prokaryotic genomes. Three genes,wzy,Z0372 and Z0344,common to the three gene lists,were selected based on the genomic barcode approach. PCR showed an identification accuracy of 100% on the 18 tested strains and the 5 controls. CONCLUSION:The three identified novel markers,wzy,Z0372 and Z0344,are highly promising for the detection of STEC O157:H7,in complementary to the known markers.展开更多
[ Objective] This study was to construct an expression vector capable of excising selectable marker gene, further eliminating the effect of marker gene on the functional study of target gene. [ Method] By using Cre/Lo...[ Objective] This study was to construct an expression vector capable of excising selectable marker gene, further eliminating the effect of marker gene on the functional study of target gene. [ Method] By using Cre/LoxP site-specific recombination system, DsRed2-1 vector was modified by introducing LoxP se- quence and multiple cloning site sequence, then the TK gene was ligated into this vector for negative selection. [ Results] The fragments introduced were recom- bined at the molecular level under induced condition, and the specific red fluorescence was also observed in the recombinant vector transfected cells at the cellular level. [ Conclusion] It is feasible to use this Cre/loxP system to excise marker genes, showing a broad application prospect.展开更多
OBJECTIVE: To explore the possibility of expression of exogenous gene in transduced bone marrow derived stromal cells (BMSCs). METHODS: The marker gene, pbLacZ, was transferred into cultured BMSCs and the expression o...OBJECTIVE: To explore the possibility of expression of exogenous gene in transduced bone marrow derived stromal cells (BMSCs). METHODS: The marker gene, pbLacZ, was transferred into cultured BMSCs and the expression of transduced gene by X-gal staining was examined. Then plasmid pcDNA3-rhBMP7 was delivered to cultured BMSCs. Through immunohistochemical staining and RT-PCR assay, the expression of rhBMP7 gene was detected. RESULTS: The exogenous gene could be expressed efficiently in transduced BMSCs. CONCLUSION: The present study provided a theoretical basis to gene therapy on the problems of bone and cartilage tissue.展开更多
Marker-aided selection has received more attention in recent years. This relies on the exploitation of dose linkage between molecular markers and target gene(s). We report here a randomly amplified polymorphic DNA (RA...Marker-aided selection has received more attention in recent years. This relies on the exploitation of dose linkage between molecular markers and target gene(s). We report here a randomly amplified polymorphic DNA (RAPD) marker tightly linked to the blast resistance gene Pi-ll(t) derived from Hongjiaozhan, which confers the resistance to race ZB1 of Pyricularia oryzae Cav.展开更多
BACKGROUND Hemorrhoids,a prevalent chronic condition globally,significantly impact patients'quality of life.While various surgical interventions,such as external stripping and internal ligation,procedure for prola...BACKGROUND Hemorrhoids,a prevalent chronic condition globally,significantly impact patients'quality of life.While various surgical interventions,such as external stripping and internal ligation,procedure for prolapse and hemorrhoids,and tissue selecting technique,are employed for treatment,they are often associated with postoperative complications,including unsatisfactory defecation,bleeding,and anal stenosis.In contrast,Xiaozhiling injection,a traditional Chinese medicine-based therapy,has emerged as a minimally invasive and effective alternative for internal hemorrhoids.This treatment offers distinct advantages,such as reduced dietary restrictions,broad applicability,and minimal induction of systemic inflammatory responses.Additionally,Xiaozhiling injection effectively eliminates hemorrhoid nuclei,prevents local tissue necrosis,preserves anal cushion integrity,and mitigates postoperative complications,including bleeding and prolapse.Despite its clinical efficacy,the molecular mechanisms underlying its therapeutic effects remain poorly understood,warranting further investigation.AIM To investigate the molecular mechanism underlying the therapeutic effect of Xiaozhiling injection in the treatment of internal hemorrhoids.METHODS An internal hemorrhoid model was established in rats,and the rats were randomly divided into a modeling group[control group(CK group)]and a treatment group.One week after injection,Stereo-seq and electron microscopy were used to study the changes in gene expression and subcellular structures in fibroblasts.RESULTS Single-cell sequencing revealed differences in the expression and transcript levels of the genes collagen 3 alpha 1,decorin,and actin alpha 2 in fibroblasts between the CK group and the treatment group.Spatial transcriptome analysis revealed that genes of the sphingosine kinase 1(Sphk1)/sphingosine-1-phosphate(S1P)pathway spatially overlapped with key genes of the transforming growth factor beta 1 pathway,namely,Sphk1,S1P receptor,and transforming growth factor beta 1,in the treatment group.The proportion of fibroblasts was lower in the treatment group than in the CK group,and Xiaozhiling treatment had a significant effect on the proportion of fibroblasts in hemorrhoidal tissue.Immunohistochemistry revealed a significant increase in the expression of a fibroblast marker.Electron microscopy showed that the endoplasmic reticulum of fibroblasts contained a large amount of glycogen,indicating cell activation.Fibroblast activation and the expression of key genes of the Sphk1-S1P pathway could be observed at the injection site,suggesting that after Xiaozhiling intervention,the Sphk1-S1P pathway could be activated to promote fibrosis.CONCLUSION Xiaozhiling injection exerts its therapeutic effects on internal hemorrhoids by promoting collagen synthesis and secretion in fibroblasts.After Xiaozhiling intervention,the Sphk1-S1P pathway can be activated to promote fibrosis.展开更多
Hybrid rice planting has been widely popularized and applied in the world. However, the high cost of seed production and the complicated procedures have become a bottleneck in the development of hybrid rice. The resea...Hybrid rice planting has been widely popularized and applied in the world. However, the high cost of seed production and the complicated procedures have become a bottleneck in the development of hybrid rice. The research progress on mixed sowing seed production techniques of hybrid rice was introduced from the aspects of rice resources creation, breeding, sowing seed technology research and cost benefit analysis. The production technology of the new mixed seeding combina- tion ＂Xinhunyou 6＂ was investigated, including the research and validation of benta- zon treatment period and dosage, mixing ratio of male and female parents, and the comparative test of different different sowing methods, which revealed that the mechanization technology of seed production of hybrid rice was mature and feasible and would be one of the most important development trend of technological devel- opment of hybrid rice production.展开更多
Corneal stem/progenitor cells are typical adult stem/progenitor cells.The human cornea covers the front of the eyeball,which protects the eye from the outside environment while allowing vision.The location and functio...Corneal stem/progenitor cells are typical adult stem/progenitor cells.The human cornea covers the front of the eyeball,which protects the eye from the outside environment while allowing vision.The location and function demand the cornea to maintain its transparency and to continuously renew its epithelial surface by replacing injured or aged cells through a rapid turnover process in which corneal stem/progenitor cells play an important role.Corneal stem/progenitor cells include mainly corneal epithelial stem cells,corneal endothelial cell progenitors and corneal stromal stem cells.Since the discovery of corneal epithelial stem cells(also known as limbal stem cells)in 1971,an increasing number of markers for corneal stem/progenitor cells have been proposed,but there is no consensus regarding the definitive markers for them.Therefore,the identification,isolation and cultivation of these cells remain challenging without a unified approach.In this review,we systematically introduce the profile of biological characterizations,such as anatomy,characteristics,isolation,cultivation and molecular markers,and clinical applications of the three categories of corneal stem/progenitor cells.展开更多
Breast cancer (BC), the most prevalent cancer type in women worldwide, exhibits significant heterogeneity across individual cases. The existing subtyping schemes for BC are all based on the expression of a few marker ...Breast cancer (BC), the most prevalent cancer type in women worldwide, exhibits significant heterogeneity across individual cases. The existing subtyping schemes for BC are all based on the expression of a few marker genes or proteins, which could not well capture samples sharing common or similar biology, which has substantially limited their applications.展开更多
Rare earth elements(REE)are applied as micro-fertilizer in large scale in China and there is growing concern about the environmental effects of REE accumulation in soils. Accumulation of REE was simulated in lab by ad...Rare earth elements(REE)are applied as micro-fertilizer in large scale in China and there is growing concern about the environmental effects of REE accumulation in soils. Accumulation of REE was simulated in lab by adding REE to three soils and the survival of Pseudomonas fluorescence X16 strain marked with luxAB gene in soils was detected. Curvilinear regression method was applied to analyze the survival pattern. The stimulation values, EC_(50) and NOEC values for X16 strain were calculated to compare the toxic intensity of REE in different soils. The stimulation(peak)values in red soil, yellow fluovo-aquic soil and yellow cinnamon soil, are 11.55～18.08,(0～2.13), 2.37～4.62 mg·kg^(-1) , respectively. EC_(50) values are 13.47～39.12, 6.59～56.18, 372～1034 (mg·kg^(-1)), respectively.NOEC values are 5.62 ～21.41, 0.00～4.53, 133.3～327.1 mg·kg^(-1), respectively. Tangents values of regression equation of the survival of X16 strain in red soil are the maximum ones indicating that REE accumulation in red soil has stronger inhibitory effects than in other two soils. The soil order, reflecting toxic intensity of REE is as follows: red soil>yellow fluovic-aquic soil>yellow cinnamon soil.展开更多
Maize（Zea mays L.） is a commercially important crop.Its yield can be reduced by mutations in biosynthetic and degradative pathways that cause death.In this paper,we describe the necrotic leaf（nec-t） mutant,which w...Maize（Zea mays L.） is a commercially important crop.Its yield can be reduced by mutations in biosynthetic and degradative pathways that cause death.In this paper,we describe the necrotic leaf（nec-t） mutant,which was obtained from an inbred line,81647.The nec-t mutant plants had yellow leaves with necrotic spots,reduced chlorophyll content,and the etiolated seedlings died under normal growth conditions.Transmission electron microscopy revealed scattered thylakoids,and reduced numbers of grana lamellae and chloroplasts per cell.Histochemical staining suggested that spot formation of nec-t leaves might be due to cell death.Genetic analysis showed that necrosis was caused by the mutation of a recessive locus.Using simple sequence repeat markers,the Nec-t gene was mapped between mmc0111 and bnlg2277 on the short arm of chromosome 2.A total of 1287 individuals with the mutant phenotype from a F_2 population were used for physical mapping.The Nec-t gene was located between markers T31 and H8 within a physical region of 131.7 kb.展开更多
Understanding consistencies and discrepancies in characterizing diversity and quantity of phytoplankton is essential for better modeling ecosystem change.In this study,eukaryotic phytoplankton in the Pearl River Estua...Understanding consistencies and discrepancies in characterizing diversity and quantity of phytoplankton is essential for better modeling ecosystem change.In this study,eukaryotic phytoplankton in the Pearl River Estuary,South China Sea were investigated using nuclear 18S rRNA and plastid 16S or 23S rRNA genes and pigment analysis.It was found that 18S abundance poorly explained the variations in total chlorophyll a(Chl-a).However,the ratios of log-transformed 18S abundance to Chl-a in the major phytoplankton groups were generally environment dependent,suggesting that the ratio has potential as an indicator of the physiological state of phytoplankton.The richness of 18S-based operational taxonomic units was positively correlated with the richness of 16S-based amplicon sequence variants of the whole phytoplankton community,but insignifcant or weak for individual phytoplankton groups.Overall,the 18S based,rather than the 16S based,community structure had a greater similarity to pigment-based estimations.Relative to the pigment data,the proportion of haptophytes in the 18S dataset,and diatoms and cryptophytes in the 16S dataset,were underestimated.This study highlights that 18S metabarcoding tends to refect biomass-based community organization of eukaryotic phytoplankton.Because there were lower copy numbers of plastid 16S than 18S per genome,metabarcoding of 16S probably approximates cell abundance-based community organization.Changes in biomass organization of the pigment-based community were sensitive to environmental changes.Taken together,multiple methodologies are recommended to be applied to more accurately profle the diversity and community composition of phytoplankton in natural ecosystems.展开更多
Pancreatic cancer(PC)is a commonly malignant tumor with a 5-year survival rate of only 10%.1 Cuproptosis is a newly discovered cell death mechanism closely associated with the development of tumors.This study mainly a...Pancreatic cancer(PC)is a commonly malignant tumor with a 5-year survival rate of only 10%.1 Cuproptosis is a newly discovered cell death mechanism closely associated with the development of tumors.This study mainly aimed to investigate cuproptosis-related genes(CRGs)and found the marker genes to construct a prognostic model for PC patients.Meanwhile,we explored their roles in immune infiltration and their relationship with drug sensitivity.After comparing the expression patterns of ten CRGs,we found these genes were differently expressed between the tumor and normal tissues.Then we further performed functional enrichment analysis,cluster analysis,and immunoeinfiltration correlation analysis.展开更多
基金supported by the Project of the National Ministry of Science and Technology,China (Grant No.2006AA10Z1C8)the Knowledge Innovative Program of the Chinese Academy of Sciences (Grant Nos.KSCX-YW-N-009-02 and KSCX1-YW-03)+1 种基金the National Basic Research Program of China (Grant No.2009CB126004)the Natural Science Foundation of Hainan Province,China (Grant No.309019)
文摘Field resistances of nine accessions of common wild rice （Oryza rufipogon Griff.） and one rice variety （IR24） were evaluated by using nine strains of bacterial blight pathogen （Xanthomonas oryzae pv. oryzae） from the Philippines. IR24 was highly susceptible to all the strains, and six common wild rice accessions resisted all the nine strains, with a resistance frequency of 67%. The accessions Yulin and Wanning were only susceptible to PXO280 and PXO71, respectively. The accession Gaozhou was susceptible to the three strains PXO79, PXO99 and PXO339, whereas resistant to the other six strains. It could be concluded that there is at least one resistance gene in each common wild rice accession. The functional markers of the genes xa5, xa13, Xa21 and Xa27 were used to detect the presence of these resistance genes in the nine tested wild rice accessions, and it was found that four wild rice accessions contained heterozygous xa13. Among the nine common wild rice accessions, five were homozygous for Xa27 and three homozygous for xa27, and the accession Laibin contained neither xa27 nor Xa27. In addition, there were no xa5 and Xa21 in all of these accessions.
文摘Resistance to whitebacked planthopper(WBPH)in Chinese japonica riceChunjiang 06(CJ-06)was mediated by sucking inhibitory and ovicidal mecha-nism.The ovicidal reponse was a common self-defense mechanism againstWBPH in japonica.The ovicidal gene and its chromosomal position had alreadybeen identified.The sucking inhibitory nature of CJ-06 caused a definenon-preference behavior of WBPH in fields.A single dominant gene governed
基金supported by grants from the National Natural Science Foundation of China(Grant No.:82270281)Chongqing Medical University Program for Youth Innovation in Future Medicine(Grant No.:W0133)+2 种基金Senior Medical Talents Program of Chongqing for Young and Middle-aged,China(Program No.:JianlinDu[2022])Postdoctoral Research Funding of the Second Affiliated Hospital of Chongqing Medical University,China(Grant No.:rsc-postdoctor114)and Kuanren Talents Program of the Second Affiliated Hospital of Chongqing Medical University,China(Program No.:kryc-gg-2102).
文摘Tbx18,Wt1,and Tcf21 have been identified as epicardial markers during the early embryonic stage.However,the gene markers of mature epicardial cells remain unclear.Single-cell transcriptomic analysis was performed with the Seurat,Monocle,and CellphoneDB packages in R software with standard procedures.Spatial transcriptomics was performed on chilled Visium Tissue Optimization Slides(10x Genomics)and Visium Spatial Gene Expression Slides(10x Genomics).Spatial transcriptomics analysis was performed with Space Ranger software and R software.Immunofluorescence,whole-mount RNA in situ hybridization and X-gal staining were performed to validate the analysis results.Spatial transcriptomics analysis revealed distinct transcriptional profiles and functions between epicardial tissue and non-epicardial tissue.Several gene markers specific to postnatal epicardial tissue were identified,including Msln,C3,Efemp1,and Upk3b.Single-cell transcriptomic analysis revealed that cardiac cells from wildtype mouse hearts(from embryonic day 9.5 to postnatal day 9)could be categorized into six major cell types,which included epicardial cells.Throughout epicardial development,Wt1,Tbx18,and Upk3b were consistently expressed,whereas genes including Msln,C3,and Efemp1 exhibited increased expression during the mature stages of development.Pseudotime analysis further revealed two epicardial cell fates during maturation.Moreover,Upk3b,Msln,Efemp1,and C3 positive epicardial cells were enriched in extracellular matrix signaling.Our results suggested Upk3b,Efemp1,Msln,C3,and other genes were mature epicardium markers.Extracellular matrix signaling was found to play a critical role in the mature epicardium,thus suggesting potential therapeutic targets for heart regeneration in future clinical practice.
基金supported by the National Natural Science Foundation of China(32220103006 and 82271524).
文摘Lymphatic vessel networks have been identified in the meninges of mice,non-human primates,and humans[1].Meningeal lymphatic vessels(mLVs),composed of meningeal lymphatic endothelial cells(mLECs),are present in both zebrafish and mammals,although their anatomical distributions differ;they reside in the dura mater in mice,but are situated within the meninges in zebrafish[2].Moreover,the lymphatic marker genes expressed in these vessels differ between species[2].
文摘AIM: To determine the gene expression profile data for the whole liver during development of dimethylni-trosamine (DMN)-induced hepatic fibrosis.METHODS: Marker genes were identified for different types of hepatic cells, including hepatic stellate cells (HSCs), Kupffer cells (including other inflammatory cells), and hepatocytes, using independent temporal DNA microarray data obtained from isolated hepatic cells. RESULTS: The cell-type analysis of gene expression gave several key results and led to formation of three hypotheses: (1) changes in the expression of HSC-specific marker genes during fibrosis were similar to gene expression data in in vitro cultured HSCs, suggesting a major role of the self-activating characteristics of HSCs in formation of fibrosis; (2) expression of mast cell-specific marker genes reached a peak during liver fibrosis, suggesting a possible role of mast cells in formation of fibrosis; and (3) abnormal expression of hepatocyte-specific marker genes was found across several metabolic pathways during fibrosis, including sulfur-containing amino acid metabolism, fatty acid metabolism, and drug metabolism, suggesting a mechanistic relationship between these abnormalities and symptoms of liver fibrosis. CONCLUSION: Analysis of marker genes for specific hepatic cell types can identify the key aspects of fibro-genesis. Sequential activation of inflammatory cells and the self-supporting properties of HSCs play an important role in development of fibrosis.
基金supported by the National Key Research and Development Program of China(No.2016YFD0501105)the Science and Technology Department of Zhejiang Province(No.2015C02044)the National Natural Science Foundation of China(No.31301492)
文摘To correctly assess and properly manage the public health risks associated with exposure to contaminated water,it is necessary to identify the source of fecal pollution in a watershed.In this study,we evaluated the efficacy of our two previously developed real time-quantitative PCR(qPCR)assays for the detection of swine-associated Bacteroidales genetic markers(gene 1-38,gene 3-53)in the Yangtze Delta watershed of southeastern China.The results indicated that the gene 1-38 and 3-53 markers exhibited high accuracy(92.5%,91.7%conditional probability,respectively)in detecting Bacteroidales spp.in water samples.According to binary logistic regression(BLR),these two swine-associated markers were well correlated(P<0.05)with fecal indicators(Escherichia coli and Enterococci spp.)and zoonotic pathogens(E.coli O157:H7,Salmonella spp.and Campylobacter spp.)in water samples.In contrast,concentrations of conventional fecal indicator bacteria(FIB)were not correlated with zoonotic pathogens,suggesting that they are noneffective at detecting fecal pollution events.Collectively,the results obtained in this study demonstrated that a swinetargeted qPCR assay based on two Bacteroidales genes markers(gene 1-38,gene 3-53)could be a useful tool in determining the swine-associated impacts of fecal contamination in a watershed.
文摘AIM: To investigate the relationship of changes in expression of marker genes in functional categories or molecular networks comprising one functional category or multiple categories in progression of hepatic fibrosis in hepatitis C (HCV) patients. METHODS: Marker genes were initially identified using DNA microarray data from a rat liver fibrosis model. The expression level of each fibrosis associated marker gene was analyzed using reverse transcription-polymerase chain reaction (RT-PCR) in clinical biopsy specimens from HCV-positive patients (n = 61). Analysis of changes in expression patterns and interactions of marker genes in functional categories was used to assess the biological mechanism of fibrosis. RESULTS: The profile data showed several biological changes associated with progression of hepatic fibrosis. Clustered genes in functional categories showed sequential changes in expression. Several sets of clustered genes, including those related to the extracellular matrix (ECM), inflammation, lipid metabolism, steroid metabolism, and some transcription factors important for hepatic biology showed expression changes in the immediate early phase (F1/F2) of fibrosis. Genes associated with aromatic amino acid (AA) metabolism, sulfur-containing AA metabolism and insulin/ Wnt signaling showed expression changes in the middle phase (F2/F3), and some genes related to glucose metabolism showed altered expression in the late phase of fibrosis (F3/F4). Therefore, molecular networks showing serial changes in gene expression are present in liver fibrosis progression in hepatitis C patients. CONCLUSION: Analysis of gene expression profiles from a perspective of functional categories or molecular networks provides an understanding of disease and suggests new diagnostic methods. Selected marker genes have potential utility for biological identification of advanced fibrosis.
基金funded by National Science Center in Poland Grant (2015/18/M/NZ3/00348) to Iwona·Zursupported by Czech Science Foundation Grant (21-02929S) to Ales Pecinka+2 种基金European Regional Development Fund project TANGENC (CZ.02.01.01/00/ 22_008/0004581)funded by Ad Agri F (CZ.02.01.01/00/22_008/0004635)supplied by the project “e-Infrastruktura CZ” (e-INFRA CZ LM2018140) supported by the Ministry of Education, Youth and Sports of the Czech Republic
文摘Plant formation from in vitro-cultivated microspores involves a complex network of internal and environmental factors.Haploids/doubled haploids(DHs)derived from in vitro-cultured microspores are widely used in plant breeding and genetic engineering.However,the mechanism underlying the developmental switch from regular pollen maturation towards microspore-derived plant regeneration remains poorly defined.Here,RNA-sequencing was employed to elucidate the transcriptional landscapes of four early stages of microspore embryogenesis(ME)in barley cultivars Golden Promise and Igri,which exhibit contrasting responsiveness to microspore-derived plant formation.Our experiments revealed fundamental regulatory networks,specific groups of genes,and transcription factor(TF)families potentially regulating the developmental switch.We identified a set of candidate genes crucial for genotype-dependent responsiveness/recalcitrance to ME.Our high-resolution temporal transcriptome atlas provides an important resource for future functional studies on the genetic control of microspore developmental transition.
基金Supported by National Natural Science Foundation of China, No. 30872415National Science Foundation, No. DBI-0354771, ITR-IIS-0407204, DBI-0542119, CCF0621700+1 种基金National Institutes of Health, No. 1R01GM075331 and 1R01GM081682BioEnergy Science Center, US Department of Energy BioEnergy Research Center supported by the Office of Biological and Environmental Research in DOE Office of Science
文摘AIM:To identify and assess the novel makers for detection of Shiga toxin producing Escherichia coli (STEC) O157:H7 with an integrated computational and experimental approach. METHODS:High-throughput NCBI blast (E-value cutoff e-5) was used to search homologous genes among all sequenced prokaryotic genomes of each gene encoded in each of the three strains of STEC O157:H7 with complete genomes,aiming to find unique genes in O157:H7 as its potential markers. To ensure that the identified markers from the three strains of STEC O157:H7 can serve as general markers for all the STEC O157:H7 strains,a genomic barcode approach was used to select the markers to minimize the possibility of choosing a marker gene as part of a transposable element. Effectiveness of the markers predicted was then validated by running polymerase chain reaction (PCR) on 18 strains of O157:H7 with 5 additional genomes used as negative controls. RESULTS:The blast search identified 20,16 and 20 genes,respectively,in the three sequenced strains of STEC O157:H7,which had no homologs in any of the other prokaryotic genomes. Three genes,wzy,Z0372 and Z0344,common to the three gene lists,were selected based on the genomic barcode approach. PCR showed an identification accuracy of 100% on the 18 tested strains and the 5 controls. CONCLUSION:The three identified novel markers,wzy,Z0372 and Z0344,are highly promising for the detection of STEC O157:H7,in complementary to the known markers.
基金Supported by Doctoral Funds of Xinjiang Production and Construction Corps(2011BB014)Guidance Program of Xinjiang Academy of Agricultural Reclamation Sciences(YYD201110)
文摘[ Objective] This study was to construct an expression vector capable of excising selectable marker gene, further eliminating the effect of marker gene on the functional study of target gene. [ Method] By using Cre/LoxP site-specific recombination system, DsRed2-1 vector was modified by introducing LoxP se- quence and multiple cloning site sequence, then the TK gene was ligated into this vector for negative selection. [ Results] The fragments introduced were recom- bined at the molecular level under induced condition, and the specific red fluorescence was also observed in the recombinant vector transfected cells at the cellular level. [ Conclusion] It is feasible to use this Cre/loxP system to excise marker genes, showing a broad application prospect.
文摘OBJECTIVE: To explore the possibility of expression of exogenous gene in transduced bone marrow derived stromal cells (BMSCs). METHODS: The marker gene, pbLacZ, was transferred into cultured BMSCs and the expression of transduced gene by X-gal staining was examined. Then plasmid pcDNA3-rhBMP7 was delivered to cultured BMSCs. Through immunohistochemical staining and RT-PCR assay, the expression of rhBMP7 gene was detected. RESULTS: The exogenous gene could be expressed efficiently in transduced BMSCs. CONCLUSION: The present study provided a theoretical basis to gene therapy on the problems of bone and cartilage tissue.
文摘Marker-aided selection has received more attention in recent years. This relies on the exploitation of dose linkage between molecular markers and target gene(s). We report here a randomly amplified polymorphic DNA (RAPD) marker tightly linked to the blast resistance gene Pi-ll(t) derived from Hongjiaozhan, which confers the resistance to race ZB1 of Pyricularia oryzae Cav.
基金Supported by the National Natural Science Foundation of China,No.81774118the Foreign Cooperation Project of Science and Technology Department of Fujian Province,No.2023I0021the Medical Innovation Project of Fujian Province,No.2024CXB013.
文摘BACKGROUND Hemorrhoids,a prevalent chronic condition globally,significantly impact patients'quality of life.While various surgical interventions,such as external stripping and internal ligation,procedure for prolapse and hemorrhoids,and tissue selecting technique,are employed for treatment,they are often associated with postoperative complications,including unsatisfactory defecation,bleeding,and anal stenosis.In contrast,Xiaozhiling injection,a traditional Chinese medicine-based therapy,has emerged as a minimally invasive and effective alternative for internal hemorrhoids.This treatment offers distinct advantages,such as reduced dietary restrictions,broad applicability,and minimal induction of systemic inflammatory responses.Additionally,Xiaozhiling injection effectively eliminates hemorrhoid nuclei,prevents local tissue necrosis,preserves anal cushion integrity,and mitigates postoperative complications,including bleeding and prolapse.Despite its clinical efficacy,the molecular mechanisms underlying its therapeutic effects remain poorly understood,warranting further investigation.AIM To investigate the molecular mechanism underlying the therapeutic effect of Xiaozhiling injection in the treatment of internal hemorrhoids.METHODS An internal hemorrhoid model was established in rats,and the rats were randomly divided into a modeling group[control group(CK group)]and a treatment group.One week after injection,Stereo-seq and electron microscopy were used to study the changes in gene expression and subcellular structures in fibroblasts.RESULTS Single-cell sequencing revealed differences in the expression and transcript levels of the genes collagen 3 alpha 1,decorin,and actin alpha 2 in fibroblasts between the CK group and the treatment group.Spatial transcriptome analysis revealed that genes of the sphingosine kinase 1(Sphk1)/sphingosine-1-phosphate(S1P)pathway spatially overlapped with key genes of the transforming growth factor beta 1 pathway,namely,Sphk1,S1P receptor,and transforming growth factor beta 1,in the treatment group.The proportion of fibroblasts was lower in the treatment group than in the CK group,and Xiaozhiling treatment had a significant effect on the proportion of fibroblasts in hemorrhoidal tissue.Immunohistochemistry revealed a significant increase in the expression of a fibroblast marker.Electron microscopy showed that the endoplasmic reticulum of fibroblasts contained a large amount of glycogen,indicating cell activation.Fibroblast activation and the expression of key genes of the Sphk1-S1P pathway could be observed at the injection site,suggesting that after Xiaozhiling intervention,the Sphk1-S1P pathway could be activated to promote fibrosis.CONCLUSION Xiaozhiling injection exerts its therapeutic effects on internal hemorrhoids by promoting collagen synthesis and secretion in fibroblasts.After Xiaozhiling intervention,the Sphk1-S1P pathway can be activated to promote fibrosis.
基金Supported by the National High-tech R&D Program(863 Program)(2014AA10A603)the Key Science and Technology Program during the"13thFive Year Plan"of Anhui Province(1604a0702008)+1 种基金the Special Fund for Agro-scientific Research in the Public Interest(201503130)the Project for the Team of Science and Technology Innovation of Anhui Academy of Agricultural Sciences(15C0108)~~
文摘Hybrid rice planting has been widely popularized and applied in the world. However, the high cost of seed production and the complicated procedures have become a bottleneck in the development of hybrid rice. The research progress on mixed sowing seed production techniques of hybrid rice was introduced from the aspects of rice resources creation, breeding, sowing seed technology research and cost benefit analysis. The production technology of the new mixed seeding combina- tion ＂Xinhunyou 6＂ was investigated, including the research and validation of benta- zon treatment period and dosage, mixing ratio of male and female parents, and the comparative test of different different sowing methods, which revealed that the mechanization technology of seed production of hybrid rice was mature and feasible and would be one of the most important development trend of technological devel- opment of hybrid rice production.
文摘Corneal stem/progenitor cells are typical adult stem/progenitor cells.The human cornea covers the front of the eyeball,which protects the eye from the outside environment while allowing vision.The location and function demand the cornea to maintain its transparency and to continuously renew its epithelial surface by replacing injured or aged cells through a rapid turnover process in which corneal stem/progenitor cells play an important role.Corneal stem/progenitor cells include mainly corneal epithelial stem cells,corneal endothelial cell progenitors and corneal stromal stem cells.Since the discovery of corneal epithelial stem cells(also known as limbal stem cells)in 1971,an increasing number of markers for corneal stem/progenitor cells have been proposed,but there is no consensus regarding the definitive markers for them.Therefore,the identification,isolation and cultivation of these cells remain challenging without a unified approach.In this review,we systematically introduce the profile of biological characterizations,such as anatomy,characteristics,isolation,cultivation and molecular markers,and clinical applications of the three categories of corneal stem/progenitor cells.
基金supported by grants from the National Natural Science Foundation of China(No.T2350010,W2431059)the Key University Laboratory of Metabolism and Health of Guangdong,Southern University of Science and Technology(China)(No.2022KSYS007)supported by the Center for Scientific and Engineering Computing at Southern University of Science and Technology(SUSTech).
文摘Breast cancer (BC), the most prevalent cancer type in women worldwide, exhibits significant heterogeneity across individual cases. The existing subtyping schemes for BC are all based on the expression of a few marker genes or proteins, which could not well capture samples sharing common or similar biology, which has substantially limited their applications.
文摘Rare earth elements(REE)are applied as micro-fertilizer in large scale in China and there is growing concern about the environmental effects of REE accumulation in soils. Accumulation of REE was simulated in lab by adding REE to three soils and the survival of Pseudomonas fluorescence X16 strain marked with luxAB gene in soils was detected. Curvilinear regression method was applied to analyze the survival pattern. The stimulation values, EC_(50) and NOEC values for X16 strain were calculated to compare the toxic intensity of REE in different soils. The stimulation(peak)values in red soil, yellow fluovo-aquic soil and yellow cinnamon soil, are 11.55～18.08,(0～2.13), 2.37～4.62 mg·kg^(-1) , respectively. EC_(50) values are 13.47～39.12, 6.59～56.18, 372～1034 (mg·kg^(-1)), respectively.NOEC values are 5.62 ～21.41, 0.00～4.53, 133.3～327.1 mg·kg^(-1), respectively. Tangents values of regression equation of the survival of X16 strain in red soil are the maximum ones indicating that REE accumulation in red soil has stronger inhibitory effects than in other two soils. The soil order, reflecting toxic intensity of REE is as follows: red soil>yellow fluovic-aquic soil>yellow cinnamon soil.
基金financially supported by the grants from the Agriculture Thoroughbred Industrialization of Shandong Province(No.2011-7)the Ministry of Agriculture of China(Nos.2008ZX08003-003 and 2009ZX08003-023B)the National High-tech‘863' Program of China(No. 2012AA101104)
文摘Maize（Zea mays L.） is a commercially important crop.Its yield can be reduced by mutations in biosynthetic and degradative pathways that cause death.In this paper,we describe the necrotic leaf（nec-t） mutant,which was obtained from an inbred line,81647.The nec-t mutant plants had yellow leaves with necrotic spots,reduced chlorophyll content,and the etiolated seedlings died under normal growth conditions.Transmission electron microscopy revealed scattered thylakoids,and reduced numbers of grana lamellae and chloroplasts per cell.Histochemical staining suggested that spot formation of nec-t leaves might be due to cell death.Genetic analysis showed that necrosis was caused by the mutation of a recessive locus.Using simple sequence repeat markers,the Nec-t gene was mapped between mmc0111 and bnlg2277 on the short arm of chromosome 2.A total of 1287 individuals with the mutant phenotype from a F_2 population were used for physical mapping.The Nec-t gene was located between markers T31 and H8 within a physical region of 131.7 kb.
基金This work was supported by the National Natural Science Foundation of China(nos.41976128 and 31970486)the Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)(no.311021004).
文摘Understanding consistencies and discrepancies in characterizing diversity and quantity of phytoplankton is essential for better modeling ecosystem change.In this study,eukaryotic phytoplankton in the Pearl River Estuary,South China Sea were investigated using nuclear 18S rRNA and plastid 16S or 23S rRNA genes and pigment analysis.It was found that 18S abundance poorly explained the variations in total chlorophyll a(Chl-a).However,the ratios of log-transformed 18S abundance to Chl-a in the major phytoplankton groups were generally environment dependent,suggesting that the ratio has potential as an indicator of the physiological state of phytoplankton.The richness of 18S-based operational taxonomic units was positively correlated with the richness of 16S-based amplicon sequence variants of the whole phytoplankton community,but insignifcant or weak for individual phytoplankton groups.Overall,the 18S based,rather than the 16S based,community structure had a greater similarity to pigment-based estimations.Relative to the pigment data,the proportion of haptophytes in the 18S dataset,and diatoms and cryptophytes in the 16S dataset,were underestimated.This study highlights that 18S metabarcoding tends to refect biomass-based community organization of eukaryotic phytoplankton.Because there were lower copy numbers of plastid 16S than 18S per genome,metabarcoding of 16S probably approximates cell abundance-based community organization.Changes in biomass organization of the pigment-based community were sensitive to environmental changes.Taken together,multiple methodologies are recommended to be applied to more accurately profle the diversity and community composition of phytoplankton in natural ecosystems.
基金the Ethics Committee of the Second Affiliated Hospital of Nanchang University(approval numbers:(2023)CDYFYYLK(05e023)).
文摘Pancreatic cancer(PC)is a commonly malignant tumor with a 5-year survival rate of only 10%.1 Cuproptosis is a newly discovered cell death mechanism closely associated with the development of tumors.This study mainly aimed to investigate cuproptosis-related genes(CRGs)and found the marker genes to construct a prognostic model for PC patients.Meanwhile,we explored their roles in immune infiltration and their relationship with drug sensitivity.After comparing the expression patterns of ten CRGs,we found these genes were differently expressed between the tumor and normal tissues.Then we further performed functional enrichment analysis,cluster analysis,and immunoeinfiltration correlation analysis.
