In this paper,a standardized analysis method is established for identifying meat quality-related genes in Ordos finewool sheep using transcriptome sequencing data.A meticulously standardized approach is utilized to in...In this paper,a standardized analysis method is established for identifying meat quality-related genes in Ordos finewool sheep using transcriptome sequencing data.A meticulously standardized approach is utilized to investigate the genetic determinants of meat quality in Ordos fine-wool sheep through transcriptome sequencing analysis.Muscle samples from the longissimus dorsi of one-year-old sheep are collected under controlled conditions,and key texture properties—hardness,elasticity,and chewiness—are measured to categorize samples into high-and low-textural-value groups.Genes significantly associated with meat quality traits are identified through standardized RNA extraction,high-throughput sequencing,and differential gene expression analysis.Functional enrichment analysis reveals their involvement in biological processes such as extracellular matrix organization and metabolic pathways.The findings underscore the pivotal role of standardization in meat quality research,laying a solid scientific foundation for future research on meat quality improvement and molecular breeding.展开更多
In order to save manpower and time costs,and to achieve simultaneous detection of multiple animal-derived components in meat and meat products,this study used multiple nucleotide polymorphism(MNP)marker technology bas...In order to save manpower and time costs,and to achieve simultaneous detection of multiple animal-derived components in meat and meat products,this study used multiple nucleotide polymorphism(MNP)marker technology based on the principle of high-throughput sequencing,and established a multi-locus 10 animalderived components identification method of cattle,goat,sheep,donkey,horse,chicken,duck,goose,pigeon,quail in meat and meat products.The specific loci of each species could be detected and the species could be accurately identified,including 5 loci for cattle and duck,3 loci for sheep,9 loci for chicken and horse,10 loci for goose and pigeon,6 loci for quail and 1 locus for donkey and goat,and an adulteration model was established to simulate commercially available samples.The results showed that the method established in this study had high throughput,good repeatability and accuracy,and was able to identify 10 animalderived components simultaneously with 100%repeatability accuracy.The detection limit was 0.1%(m/m)in simulated samples of chicken,duck and horse.Using the method established in this study to test commercially available samples,4 samples from 14 commercially available samples were detected to be inconsistent with the labels,of which 2 did not contain the target ingredient and 2 were adulterated with small amounts of other ingredients.展开更多
Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocyt...Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocytes,microglia,and oligodendrocytes in the central nervous system,and satellite glial cells and Schwann cells in the peripheral nervous system.Despite the greater understanding of glial cell types and functional heterogeneity achieved through single-cell and single-nucleus RNA sequencing in animal models,few studies have investigated the transcriptomic profiles of glial cells in the human spinal cord.Here,we used high-throughput single-nucleus RNA sequencing and spatial transcriptomics to map the cellular and molecular heterogeneity of astrocytes,microglia,and oligodendrocytes in the human spinal cord.To explore the conservation and divergence across species,we compared these findings with those from mice.In the human spinal cord,astrocytes,microglia,and oligodendrocytes were each divided into six distinct transcriptomic subclusters.In the mouse spinal cord,astrocytes,microglia,and oligodendrocytes were divided into five,four,and five distinct transcriptomic subclusters,respectively.The comparative results revealed substantial heterogeneity in all glial cell types between humans and mice.Additionally,we detected sex differences in gene expression in human spinal cord glial cells.Specifically,in all astrocyte subtypes,the levels of NEAT1 and CHI3L1 were higher in males than in females,whereas the levels of CST3 were lower in males than in females.In all microglial subtypes,all differentially expressed genes were located on the sex chromosomes.In addition to sex-specific gene differences,the levels of MT-ND4,MT2A,MT-ATP6,MT-CO3,MT-ND2,MT-ND3,and MT-CO_(2) in all spinal cord oligodendrocyte subtypes were higher in females than in males.Collectively,the present dataset extensively characterizes glial cell heterogeneity and offers a valuable resource for exploring the cellular basis of spinal cordrelated illnesses,including chronic pain,amyotrophic lateral sclerosis,and multiple sclerosis.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
In recent years,intensive human activities have increased the intensity of desertification,driving continual desertification process of peripheral meadows.To investigate the effects of restoration on soil microbial co...In recent years,intensive human activities have increased the intensity of desertification,driving continual desertification process of peripheral meadows.To investigate the effects of restoration on soil microbial communities,we analyzed vegetation-soil relationships in the Hulun Buir Sandy Land,northern China.Through the use of high-throughput sequencing,we examined the structure and diversity in the bacterial and fungal communities within the 0-20 cm soil layer after 9-15 a of restoration.Different slope positions were analyzed and spatial heterogeneity was assessed.The results showed progressive improvements in soil properties and vegetation with the increase of restoration duration,and the following order was as follows:bottom slope>middle slope>crest slope.During the restoration in the Hulun Buir Sandy Land,the bacterial communities were dominated by Proteobacteria,Actinobacteria,and Acidobacteria,whereas the fungal communities were dominated by Ascomycota and Basidiomycota.Eutrophic bacterial abundance increased with the restoration duration,whereas oligotrophic bacterial and fungal abundance levels decreased.The soil bacterial abundance significantly increased with the increasing restoration duration,whereas the fungal diversity decreased after 11 a of restoration,except that at the crest slope.Redundancy analysis showed that pH,soil moisture content,total nitrogen,and vegetation-related factors affected the bacterial community structure(45.43%of the total variance explained).Canonical correspondence analysis indicated that pH,total phosphorus,and vegetation-related factors shaped the bacterial community structure(31.82%of the total variance explained).Structural equation modeling highlighted greater bacterial responses(R^(2)=0.49-0.79)to changes in environmental factors than those of fungi(R^(2)=0.20-0.48).The soil bacterial community was driven mainly by pH,soil moisture content,electrical conductivity,plant coverage,and litter dry weight.The abundance and diversity of the soil fungal community were mainly driven by plant coverage,litter dry weight,and herbaceous aboveground biomass,while there was no significant correlation between the soil fungal community structure and environmental factors.These findings highlighted divergent microbial succession patterns and environmental sensitivities during sandy grassland restoration.展开更多
OBJECTIVE: To corroborate the efficacy of Jintiange capsules(JTGs)( 金天格胶囊) in the treatment of osteoarthritis(OA) by exploring the potential mechanism of action of synovial mesenchymal stem cell exosomes(SMSC-Exo...OBJECTIVE: To corroborate the efficacy of Jintiange capsules(JTGs)( 金天格胶囊) in the treatment of osteoarthritis(OA) by exploring the potential mechanism of action of synovial mesenchymal stem cell exosomes(SMSC-Exos) and articular chondrocytes(ACs) through transcriptome sequencing(RNA-seq). METHODS: Type Ⅱ collagenase was used to induce OA in rats. The efficacy of JTGs was confirmed by macroscopic observation of articular cartilage, micro-CT observation, and safranin fast green staining. After SMSC-Exos and ACs were qualified, RNA-seq was used to screen differentially expressed mi RNAs and m RNAs. The target genes of differentially expressed mi RNAs in Synovial mesenchymal stem cells(SMSCs) were predicted based on the multi Mi R R package. The codifferentially expressed genes of SMSC-Exos and ACs were obtained by venny 2.1.0. The mi RNA-m RNA regulatory network was constructed by Cytoscape software. Based on the Omic Share platform, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis was performed on the m RNA regulated by key mi RNAs. Expression trend analysis was performed for co-differentially expressed genes. Correlation analysis was performed on micro-CT efficacy indicators, co-differentially expressed genes mRNA and miRNA. RESULTS: The efficacy of each administration group of JTGs was significant compared with the model group. SMSC-Exos and ACs were identified by their characteristics. The expression of rno-mi R-23a-3p, rnomi R-342-3p, rno-miR-146b-5p, rno-miR-501-3p, rnomiR-214-3p was down-regulated in OA pathological state, and the expression of rno-mi R-222-3p, rno-mi R-30e-3p, rno-mi R-676, and rno-miR-192-5p expression was upregulated, and the expression of all these mi RNAs was reversed after the intervention with JTGs containing serum. The co-differentially expressed genes were enriched in the interleukin 17 signaling pathway, tumor necrosis factor signaling pathway, transforming growth factor-β signaling pathway, etc. The expression trends of Ccl7, Akap12, Grem2, Egln3, Arhgdib, Ccl20, Mmp12, Pla2g2a, and Nr4a1 were significant. There was a correlation between micro-CT pharmacodynamic index, m RNA, and mi RNA. CONCLUSION: JTGs can improve the degeneration of joint cartilage and achieve the purpose of cartilage protection, which can be used for the treatment of OA. SMSCs-related mi RNA expression profiles were significantly altered after the intervention with JTGs containing serum. The 9 co-differentially expressed genes may be the key targets for the efficacy of JTGs in the treatment of OA rats, which can be used for subsequent validation.展开更多
BACKGROUND Esophageal squamous cell carcinoma(ESCC)is one of the most common malignancies worldwide,and its development comprises a multistep process from intraepithelial neoplasia(IN)to carcinoma(CA).However,the crit...BACKGROUND Esophageal squamous cell carcinoma(ESCC)is one of the most common malignancies worldwide,and its development comprises a multistep process from intraepithelial neoplasia(IN)to carcinoma(CA).However,the critical regulators and underlying molecular mechanisms remain largely unknown.AIM To explore the genes and infiltrating immune cells in the microenvironment that are associated with the multistage progression of ESCC to facilitate diagnosis and early intervention.METHODS A mouse model mimicking the multistage development of ESCC was established by providing warter containing 4-nitroquinoline 1-oxide(4NQO)to C57BL/6 mice.Moreover,we established a control group without 4NQO treatment of mice.Then,transcriptome sequencing was performed for esophageal tissues from patients with different pathological statuses,including low-grade IN(LGIN),high-grade IN(HGIN),and CA,and controlled normal tissue(NOR)samples.Differentially expressed genes(DEGs)were identified in the LGIN,HGIN,and CA groups,and the biological functions of the DEGs were analyzed via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses.The CIBERSORT algorithm was used to detect the pattern of immune cell infilt-ration.Immunohistochemistry(IHC)was also conducted to validate our results.Finally,the Luminex multiplex cytokine analysis was utilized to measure the serum cytokine levels in the mice.RESULTS Compared with those in the NOR group,a total of 681541,and 840 DEGs were obtained in the LGIN,HGIN,and CA groups,respectively.Using the intersection of the three sets of DEGs,we identified 86 genes as key genes involved in the development of ESCC.Enrichment analysis revealed that these genes were enriched mainly in the keratinization,epidermal cell differentiation,and interleukin(IL)-17 signaling pathways.CIBERSORT analysis revealed that,compared with those in the NOR group,M0 and M1 macrophages in the 4NQO group showed stronger infiltration,which was validated by IHC.Serum cytokine analysis revealed that,compared with those in the NOR group,IL-1βand IL-6 were upregulated,while IL-10 was downregulated in the LGIN,HGIN,and CA groups.Moreover,the expression of the representative key genes,such as S100a8 and Krt6b,was verified in external human samples,and the results of immunohistochemical staining were consistent with the findings in mice.CONCLUSION We identified a set of key genes represented by S100a8 and Krt6b and investigated their potential biological functions.In addition,we found that macrophage infiltration and abnormal alterations in the levels of inflam-mation-associated cytokines,such as IL-1β,IL-6,and IL-10,in the peripheral blood may be closely associated with the development of ESCC.展开更多
Nanopore direct RNA sequencing(DRS)provides the direct access to native RNA strands with full-length information,shedding light on rich qualitative and quantitative properties of gene expression profiles.Here with Nan...Nanopore direct RNA sequencing(DRS)provides the direct access to native RNA strands with full-length information,shedding light on rich qualitative and quantitative properties of gene expression profiles.Here with NanoTrans,we present an integrated computational framework that comprehensively covers all major DRS-based application scopes,including isoform clustering and quantification,poly(A)tail length estimation,RNA modification profiling,and fusion gene detection.In addition to its merit in providing such a streamlined one-stop solution,NanoTrans also shines in its workflow-orientated modular design,batch processing capability,all-in-one tabular and graphic report output,as well as automatic installation and configuration supports.Finally,by applying NanoTrans to real DRS datasets of yeast,Arabidopsis,as well as human embryonic kidney and cancer cell lines,we further demonstrate its utility,effectiveness,and efficacy across a wide range of DRS-based application settings.展开更多
High fish predation pressure can trigger"induced defense"in Daphnia species,resulting in phenotypic plasticity in morphology,behavior,or life-history traits.The molecular mechanisms of defense morphogenesis(...High fish predation pressure can trigger"induced defense"in Daphnia species,resulting in phenotypic plasticity in morphology,behavior,or life-history traits.The molecular mechanisms of defense morphogenesis(e.g.,the tail spine and helmet)in Daphnia remain unclear.In the pres-ent study,the tail spine,helmet,and body of Daphnia galeata under fish and non-fish kairomones conditions were collected for transcriptome analysis.A total of 24 candidate genes related to the morphological defense of D.galeata were identified,including 2 trypsin,one cuticle protein,1 C1qDC protein,and 2 ferritin genes.The function of the Dagcut gene(D.galeata cuticle protein gene)in relation to tail spine morphology was assessed using RNA interference(RNAi).Compared with the EGFP(Enhanced green fluorescent protein)treatment,after RNAi,the expression levels of the Dagcut gene(D.galeata cuticle protein gene)showed a significant decrease.Correspondingly,the tail spines of the offspring pro-duced by D.galeata after RNAi of the Dagcut gene appeared curved during the experiment.In whole-mount in situ hybridization,a clear signal site was detected on the tail spine of D.galeata before RNAi which disappeared after RNAi.Our results suggest that the Dagcut gene may play an important role in tail spine formation of D.galeata,and will provide a theoretical basis for studying the molecular mechanisms of the morpho-logical plasticityin cladocera inthefuture.展开更多
BACKGROUND Mesenchymal stem cells(MSCs)modulated by various exogenous signals have been applied extensively in regenerative medicine research.Notably,nanosecond pulsed electric fields(nsPEFs),characterized by short du...BACKGROUND Mesenchymal stem cells(MSCs)modulated by various exogenous signals have been applied extensively in regenerative medicine research.Notably,nanosecond pulsed electric fields(nsPEFs),characterized by short duration and high strength,significantly influence cell phenotypes and regulate MSCs differentiation via multiple pathways.Consequently,we used transcriptomics to study changes in messenger RNA(mRNA),long noncoding RNA(lncRNA),microRNA(miRNA),and circular RNA expression during nsPEFs application.AIM To explore gene expression profiles and potential transcriptional regulatory mechanisms in MSCs pretreated with nsPEFs.METHODS The impact of nsPEFs on the MSCs transcriptome was investigated through whole transcriptome sequencing.MSCs were pretreated with 5-pulse nsPEFs(100 ns at 10 kV/cm,1 Hz),followed by total RNA isolation.Each transcript was normalized by fragments per kilobase per million.Fold change and difference significance were applied to screen the differentially expressed genes(DEGs).Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to elucidate gene functions,complemented by quantitative polymerase chain reaction verification.RESULTS In total,263 DEGs were discovered,with 92 upregulated and 171 downregulated.DEGs were predominantly enriched in epithelial cell proliferation,osteoblast differentiation,mesenchymal cell differentiation,nuclear division,and wound healing.Regarding cellular components,DEGs are primarily involved in condensed chromosome,chromosomal region,actin cytoskeleton,and kinetochore.From aspect of molecular functions,DEGs are mainly involved in glycosaminoglycan binding,integrin binding,nuclear steroid receptor activity,cytoskeletal motor activity,and steroid binding.Quantitative real-time polymerase chain reaction confirmed targeted transcript regulation.CONCLUSION Our systematic investigation of the wide-ranging transcriptional pattern modulated by nsPEFs revealed the differential expression of 263 mRNAs,2 miRNAs,and 65 lncRNAs.Our study demonstrates that nsPEFs may affect stem cells through several signaling pathways,which are involved in vesicular transport,calcium ion transport,cytoskeleton,and cell differentiation.展开更多
The calpain system is ubiquitous in cells, mainly comprising calpains and calpain inhibitors, and is a widespread calcium-dependent cysteine protease in organisms that is involved in many cellular processes such as mu...The calpain system is ubiquitous in cells, mainly comprising calpains and calpain inhibitors, and is a widespread calcium-dependent cysteine protease in organisms that is involved in many cellular processes such as muscle degradation in vivo and affects the tenderness of meat after animal slaughter. The study found 128 DEGs that probably regulated tenderness traits were selected from 16 significantly enriched GO terms by transcriptome sequencing analysis, and found that the developmental changes in the expression levels of the CAPN1 gene in the pectoral and leg muscles were significantly positively correlated ( P <0.05) with the cumulative growth values of live weight and comb weight. The developmental changes in the expression levels of the CAST gene in the pectoral and leg muscles were not significantly correlated with the cumulative growth values of live weight and comb weight. Our results helped demonstrate the potential molecular mechanisms of tenderness in chickens and provide valuable information for chicken breeding.展开更多
Single-cell transcriptome sequencing has been a rapidly developing and powerful biological tool in recent years,and it plays a vital role in describing tissue development,cell heterogeneity,stress response,etc.Cerebro...Single-cell transcriptome sequencing has been a rapidly developing and powerful biological tool in recent years,and it plays a vital role in describing tissue development,cell heterogeneity,stress response,etc.Cerebrovascular disease is one of the leading causes affecting human health in the world.Thus,it is important to understand the characteristics of cerebrovascular structure,function,and environmental response.Notably,single-cell transcriptome sequencing provides deeper insights into cerebrovascular research in health and disease states.This article will briefly introduce the basic structure and function of cerebrovascular endothelial cells(ECs),summarize the current research and new findings on cerebrovascular ECs at the single-cell transcriptome level,and discuss the challenges in this field.展开更多
Saccharina is one of the most important cold-water living marine brown algal genera. In this study we ana-lyzed the transcriptome of S. japonica, which belongs to the 1 000 Plants （OneKP） Project, by using a next-ge...Saccharina is one of the most important cold-water living marine brown algal genera. In this study we ana-lyzed the transcriptome of S. japonica, which belongs to the 1 000 Plants （OneKP） Project, by using a next-generation high-throughput DNA sequencing technique. About 5.16 GB of raw data were generated, and 65 536 scaffolds with an average length of 454 bp were assembled with SOAP de novo assembly method. In total, 19 040 unigenes were identified by BLAST;25 734 scaffolds were clustered into 37 Gene ontology functional groups;6 760 scaffolds were classified into 25 COG categories, as well as 2 665 scaffolds that were assigned to 306 KEGG pathways. Majority of the unigenes exhibited more similarities to algae including brown algae and diatom than other cyanobacteria, marine diatom, and plant. Saccharina japonica has the outstanding capability to accumulate halogen such as Br and I via halogenation processes from seawater. We acquired 42 different vanadium-dependent haloperoxidases （vHPO） in S. japonica transcriptome data, including 5 segments of vanadium-dependent iodoperoxidase （vIPO） and 37 segments of vanadium-de-pendent bromoperoxidase （vBPO）. Complicated analyses of identified fulllength S. japonica vBPO1 and S. japonica vBPO2 revealed the importance of vBPO among species of brown algae and the strong relationship between marine algal vBPOs and vIPOs. This study will enhance our understanding of the biological charac-teristics and economic values of S. japonica species.展开更多
OBJECTIVE:To explore the mechanism of Xianglian Huazhuo formula(香连化浊方,XLHZ)blocking the development of chronic atrophic gastritis(CAG)to gastric cancer(GC)through bioinformatics analysis and in vitro.METHODS:Path...OBJECTIVE:To explore the mechanism of Xianglian Huazhuo formula(香连化浊方,XLHZ)blocking the development of chronic atrophic gastritis(CAG)to gastric cancer(GC)through bioinformatics analysis and in vitro.METHODS:Pathological morphology of gastric mucosa of rats were observed.High-throughput sequencing was used to analyze the miRNA expression profile of gastric mucosa.The miRanda,miRDB and miRWalk databases were used to predict the differential target genes.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis were performed for differential target genes.Real-time quantitative reverse transcription polymerase chain reaction(qRTPCR)was used to verify the differentially expressed miRNAs and target genes.Western blot,EdU,wound healing and flow cytometry were used to observe the effect of XLHZ on epithelial-mesenchymal transition(EMT)markers,proliferation,migration,apoptosis and cell cycle of CAG cells in vitro.RESULTS:A total of five differentially expressed miRNAs and four differential target genes were screened in this study.GO analysis showed that the target genes were enriched in regulation of neuron development,regulation of transcription factor activity and regulation of RNA polymerase.KEGG pathways database differences in gene enrichment of target genes in the Wnt signaling pathway,Phospholipase D signaling pathway and mitogen-activated protein kinase signaling pathway.qRTPCR confirmed that miRNAs and its target genes were consistent with the screening results.In vitro,our study revealed that XLHZ could increase the expression of Ecadherin,decrease the expression of transforming growth factorβ1,vimentin andβ-catenin,inhibite the proliferation and migration of CAG cells,cause cell cycle arrest at G0/G1 and G2/M phase,induce the apoptosis of CAG cells,and prevent the progression of CAG to GC.CONCLUSION:This study provided a new idea for the mechanism of blocking the progression of CAG to GC by XLHZ,which may be related to the expression of miR-20a-3p,miR-320-3p,miR-34b-5p,miR-483-3p and miR-883-3p and their target genes transferrin receptor,nuclear receptor subfamily 4 member 2,delta like canonical Notch ligand 1 and a kinase anchor protein 12 in CAG.In the future,we will continue to investigate the linkage between the active ingredients of XLHZ and the relevant miRNAs and their target genes,so as to provide more sufficient experimental basis for clinically effective prevention of CAG to GC.展开更多
Objective Viral encephalitis is an infectious disease severely affecting human health.It is caused by a wide variety of viral pathogens,including herpes viruses,flaviviruses,enteroviruses,and other viruses.The laborat...Objective Viral encephalitis is an infectious disease severely affecting human health.It is caused by a wide variety of viral pathogens,including herpes viruses,flaviviruses,enteroviruses,and other viruses.The laboratory diagnosis of viral encephalitis is a worldwide challenge.Recently,high-throughput sequencing technology has provided new tools for diagnosing central nervous system infections.Thus,In this study,we established a multipathogen detection platform for viral encephalitis based on amplicon sequencing.Methods We designed nine pairs of specific polymerase chain reaction(PCR)primers for the 12 viruses by reviewing the relevant literature.The detection ability of the primers was verified by software simulation and the detection of known positive samples.Amplicon sequencing was used to validate the samples,and consistency was compared with Sanger sequencing.Results The results showed that the target sequences of various pathogens were obtained at a coverage depth level greater than 20×,and the sequence lengths were consistent with the sizes of the predicted amplicons.The sequences were verified using the National Center for Biotechnology Information BLAST,and all results were consistent with the results of Sanger sequencing.Conclusion Amplicon-based high-throughput sequencing technology is feasible as a supplementary method for the pathogenic detection of viral encephalitis.It is also a useful tool for the high-volume screening of clinical samples.展开更多
N^(6)-methyladenine(6mA)is a prevalent DNA modification and is involved in a wide range of human diseases.Previous studies have indicated that 6mA is enriched in mitochondrial DNA(mtDNA)of mammals.By employing an evol...N^(6)-methyladenine(6mA)is a prevalent DNA modification and is involved in a wide range of human diseases.Previous studies have indicated that 6mA is enriched in mitochondrial DNA(mtDNA)of mammals.By employing an evolved adenine deaminase,we developed a deaminase-mediated sequencing(DM-seq)method that could achieve genome-wide mapping of 6mA in mammalian mtDNA at single-base resolution.In this study,we used an engineered adenine deaminase,known as TadA8e protein,to map 6mA in mtDNA of hepatocellular carcinoma(HCC)by DM-seq.Through high-throughput sequencing,we identified sixteen 6mA sites in both HCC and adjacent normal tissue mtDNA.The results revealed an increased overall 6mA level in mtDNA associated with HCC.Furthermore,an elevation in 6mA level was observed alongside a decrease in the m RNA levels of the corresponding genes,indicating that increased6mA level hindered transcription processes related to these genes.These findings demonstrate that 6mA in mtDNA is correlated with HCC and provide evidence supporting the inhibitory effect of elevated 6mA level on subsequent transcriptional activity.This research illuminates the intricate relationship between 6mA modification and transcriptional regulation in the context of HCC,offering valuable insights into the role of 6mA modification in HCC pathogenesis.展开更多
Meniscus injuries are widespread and the available treatments do not offer enough healing potential.Here,we provide critical support for using pigs as a biological model for meniscal degeneration and the development o...Meniscus injuries are widespread and the available treatments do not offer enough healing potential.Here,we provide critical support for using pigs as a biological model for meniscal degeneration and the development of cutting-edge therapies in orthopedics.We present a single-cell transcriptome atlas of the meniscus,consisting of cell clusters corresponding to four major cell types:chondrocytes,endothelial cells,smooth muscle cells,and immune cells.Five distinct chondrocyte subclusters(CH0–CH4)were annotated,of which only one was widespread in both the red and white zones,indicating a major difference in the cellular makeup of the zones.Subclusters distinct to the white zone appear responsible for cartilage-specific matrix deposition and protection against adverse microenvironmental factors,while those in the red zone exhibit characteristics of mesenchymal stem cells and are more likely to proliferate and migrate.Additionally,they induce remodeling actions in other chondrocyte subclusters and promote the proliferation and maturation of endothelial cells,inducing healing and vascularization processes.Considering that they have substantial remodeling capabilities,these subclusters should be of great interest for tissue engineering studies.We also show that the cellular makeup of the pig meniscus is comparable to that of humans,which supports the use of pigs as a model in orthopedic therapy development.展开更多
Gastric cancer(GC)remains one of the leading causes of cancer-related morbidity and mortality globally.Although significant progress has been made in treatment options,the survival rates for GC patients continue to be...Gastric cancer(GC)remains one of the leading causes of cancer-related morbidity and mortality globally.Although significant progress has been made in treatment options,the survival rates for GC patients continue to be low.This is primarily attributed to the intricate and insufficiently understood mechanisms of disease progression,as well as the considerable challenges associated with tumor hetero-geneity.The recent study by Tang et al provides a detailed single-cell RNA se-quencing analysis of GC across different stages,revealing dynamic changes in the tumor microenvironment and key immune responses.We aim to offer a compre-hensive interpretation of the study’s findings and propose several innovative directions for future academic research in gastric cancer.These include exploring advanced multi-omics approaches,leveraging spatial transcriptomics,integrating artificial intelligence for clinical applications,and developing novel immuno-therapy strategies.We further emphasize the importance of personalized medi-cine,early detection,and novel drug discovery techniques in improving GC treatment outcomes.展开更多
Head and neck cutaneous squamous cell carcinoma(HNCSCC)remains underexplored compared to oropharyngeal squamous cell carcinoma,particularly in relation to human papillomavirus(HPV)and molecular markers such as p16 and...Head and neck cutaneous squamous cell carcinoma(HNCSCC)remains underexplored compared to oropharyngeal squamous cell carcinoma,particularly in relation to human papillomavirus(HPV)and molecular markers such as p16 and p53.While p16 is a well-established surrogate for HPV in oropharyngeal cancer,our review highlights its unreliable role in HNCSCC,where positivity is instead associated with recurrence and metastasis.Similarly,p53 illustrates a dual role-wild-type as a genomic safeguard,mutated as an oncogenic driver-complicating prognostication.Methodological considerations,including the limitations of immunohistochemistry for HPV detection,underscore the need for multi-method and molecular validation in future studies.Ultraviolet radiation is posited as a key modifier of p16 function,decoupling expression from tumor suppression.To contextualize these findings,we draw parallels to glioblastoma(GBM),where subclonal evolution,p53 dysfunction,and intratumoral heterogeneity drive relapse despite aggressive multimodal therapies.GBM exemplifies how bulk-level biomarker generalizations often obscure dynamic cellular ecosystems,reinforcing the necessity of single-cell and spatial approaches.Multi-omics integration-encompassing genome,transcriptome,proteome,and tumor microenvironment mapping-coupled with single-cell RNA sequencing and spatial transcriptomics,offers a path forward for resolving subclonal dynamics in both HNCSCC and GBM.These technologies provide the resolution needed to track tumor-immunestromal co-evolution,identify therapy-resistant clones,and anticipate recurrence.We argue for a N-of-1,patient-and cell-centric paradigm that reframes biomarkers not as static surrogates but as dynamic readouts of cancer evolution across time and tissue contexts.Conceptually,we propose kinetic and microenvironmental frameworks(e.g.,“load-and-lock”barriers;dormancy and immunesynapse stabilization)as hypothesis-generating avenues to stall clonal handoffs and improve outcome prediction.Together,these perspectives argue for revised biomarker frameworks in HNCSCC and ethically inclusive,mechanism-anchored studies that bridge discovery with individualized care.By bridging insights from HNCSCC with the lessons of GBM,this review underscores the need for ethically inclusive,mechanistically informed frameworks that integrate subclonal evolution,biomarker re-interpretation,and precision-personalized hybrid models.Such an approach will be essential for advancing from one-size-fits-all strategies to individualized lifetime cancer care.展开更多
The internal microbial diversity and small molecular metabolites of Nuodeng ham in different processing years(the first,second and third year sample)were analyzed by high-throughput sequencing technology and gas chrom...The internal microbial diversity and small molecular metabolites of Nuodeng ham in different processing years(the first,second and third year sample)were analyzed by high-throughput sequencing technology and gas chromatography-time of flight mass spectrography(GC-TOF-MS)to study the effects of microorganisms and small molecular metabolites on the quality of ham in different processing years.The results showed that the dominant bacteria phyla of Nuodeng ham in different processing years were Proteobacteria and Firmicutes,the dominant fungi phyla were Ascomycota and Basidiomycota,while Staphylococcus and Aspergillus were the dominant bacteria and fungi of Nuodeng ham,respectively.Totally,252 kinds of small molecular metabolites were identified from Nuodeng ham in different processing years,and 12 different metabolites were screened through multivariate statistical analysis.Further metabolic pathway analysis showed that 23 metabolic pathways were related to ham fermentation,of which 8 metabolic pathways had significant effects on ham fermentation(Impact>0.01,P<0.05).The content of L-proline,phenyllactic acid,L-lysine,carnosine,taurine,D-proline,betaine and creatine were significantly positively correlated with the relative abundance of Staphylococcus and Serratia,but negatively correlated with the relative abundance of Halomonas,Aspergillus and Yamadazyma.展开更多
基金funded by the 2023 Inner Mongolia Public Institution High-Level Talent Introduction Scientific Research Support Project,and the Ordos Municipal Science and Technology Major Special Project(Grant No.2022EEDSKJZDZX021).
文摘In this paper,a standardized analysis method is established for identifying meat quality-related genes in Ordos finewool sheep using transcriptome sequencing data.A meticulously standardized approach is utilized to investigate the genetic determinants of meat quality in Ordos fine-wool sheep through transcriptome sequencing analysis.Muscle samples from the longissimus dorsi of one-year-old sheep are collected under controlled conditions,and key texture properties—hardness,elasticity,and chewiness—are measured to categorize samples into high-and low-textural-value groups.Genes significantly associated with meat quality traits are identified through standardized RNA extraction,high-throughput sequencing,and differential gene expression analysis.Functional enrichment analysis reveals their involvement in biological processes such as extracellular matrix organization and metabolic pathways.The findings underscore the pivotal role of standardization in meat quality research,laying a solid scientific foundation for future research on meat quality improvement and molecular breeding.
基金financially supported by National Key R&D Program(2021YFF0701905)。
文摘In order to save manpower and time costs,and to achieve simultaneous detection of multiple animal-derived components in meat and meat products,this study used multiple nucleotide polymorphism(MNP)marker technology based on the principle of high-throughput sequencing,and established a multi-locus 10 animalderived components identification method of cattle,goat,sheep,donkey,horse,chicken,duck,goose,pigeon,quail in meat and meat products.The specific loci of each species could be detected and the species could be accurately identified,including 5 loci for cattle and duck,3 loci for sheep,9 loci for chicken and horse,10 loci for goose and pigeon,6 loci for quail and 1 locus for donkey and goat,and an adulteration model was established to simulate commercially available samples.The results showed that the method established in this study had high throughput,good repeatability and accuracy,and was able to identify 10 animalderived components simultaneously with 100%repeatability accuracy.The detection limit was 0.1%(m/m)in simulated samples of chicken,duck and horse.Using the method established in this study to test commercially available samples,4 samples from 14 commercially available samples were detected to be inconsistent with the labels,of which 2 did not contain the target ingredient and 2 were adulterated with small amounts of other ingredients.
基金supported by the National Natural Science Foundation of China,No.82301403(to DZ)。
文摘Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocytes,microglia,and oligodendrocytes in the central nervous system,and satellite glial cells and Schwann cells in the peripheral nervous system.Despite the greater understanding of glial cell types and functional heterogeneity achieved through single-cell and single-nucleus RNA sequencing in animal models,few studies have investigated the transcriptomic profiles of glial cells in the human spinal cord.Here,we used high-throughput single-nucleus RNA sequencing and spatial transcriptomics to map the cellular and molecular heterogeneity of astrocytes,microglia,and oligodendrocytes in the human spinal cord.To explore the conservation and divergence across species,we compared these findings with those from mice.In the human spinal cord,astrocytes,microglia,and oligodendrocytes were each divided into six distinct transcriptomic subclusters.In the mouse spinal cord,astrocytes,microglia,and oligodendrocytes were divided into five,four,and five distinct transcriptomic subclusters,respectively.The comparative results revealed substantial heterogeneity in all glial cell types between humans and mice.Additionally,we detected sex differences in gene expression in human spinal cord glial cells.Specifically,in all astrocyte subtypes,the levels of NEAT1 and CHI3L1 were higher in males than in females,whereas the levels of CST3 were lower in males than in females.In all microglial subtypes,all differentially expressed genes were located on the sex chromosomes.In addition to sex-specific gene differences,the levels of MT-ND4,MT2A,MT-ATP6,MT-CO3,MT-ND2,MT-ND3,and MT-CO_(2) in all spinal cord oligodendrocyte subtypes were higher in females than in males.Collectively,the present dataset extensively characterizes glial cell heterogeneity and offers a valuable resource for exploring the cellular basis of spinal cordrelated illnesses,including chronic pain,amyotrophic lateral sclerosis,and multiple sclerosis.
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 Ecological Environment Survey and Assessment(2024-vertical-0107)the Fundamental Research Funds for the Central Public-interest Scientific Institution(2023YSKY-26)the Hulun Buir Grassland Ecological Restoration Comprehensive Survey Project(DD20230474).
文摘In recent years,intensive human activities have increased the intensity of desertification,driving continual desertification process of peripheral meadows.To investigate the effects of restoration on soil microbial communities,we analyzed vegetation-soil relationships in the Hulun Buir Sandy Land,northern China.Through the use of high-throughput sequencing,we examined the structure and diversity in the bacterial and fungal communities within the 0-20 cm soil layer after 9-15 a of restoration.Different slope positions were analyzed and spatial heterogeneity was assessed.The results showed progressive improvements in soil properties and vegetation with the increase of restoration duration,and the following order was as follows:bottom slope>middle slope>crest slope.During the restoration in the Hulun Buir Sandy Land,the bacterial communities were dominated by Proteobacteria,Actinobacteria,and Acidobacteria,whereas the fungal communities were dominated by Ascomycota and Basidiomycota.Eutrophic bacterial abundance increased with the restoration duration,whereas oligotrophic bacterial and fungal abundance levels decreased.The soil bacterial abundance significantly increased with the increasing restoration duration,whereas the fungal diversity decreased after 11 a of restoration,except that at the crest slope.Redundancy analysis showed that pH,soil moisture content,total nitrogen,and vegetation-related factors affected the bacterial community structure(45.43%of the total variance explained).Canonical correspondence analysis indicated that pH,total phosphorus,and vegetation-related factors shaped the bacterial community structure(31.82%of the total variance explained).Structural equation modeling highlighted greater bacterial responses(R^(2)=0.49-0.79)to changes in environmental factors than those of fungi(R^(2)=0.20-0.48).The soil bacterial community was driven mainly by pH,soil moisture content,electrical conductivity,plant coverage,and litter dry weight.The abundance and diversity of the soil fungal community were mainly driven by plant coverage,litter dry weight,and herbaceous aboveground biomass,while there was no significant correlation between the soil fungal community structure and environmental factors.These findings highlighted divergent microbial succession patterns and environmental sensitivities during sandy grassland restoration.
基金Shaanxi Province Key R&D Program (2022SF-238)Chinese Medicine Pharmaceutical Key Discipline of Shaanxi province (303061107)+1 种基金Discipline Innovation team Project of Shaanxi University of Chinese Medicine (2019-YL11)Shaanxi Province Key subject of pharmacy engineering of Shaanxi Provincial Traditional Chinese Medicine administration (2017001)。
文摘OBJECTIVE: To corroborate the efficacy of Jintiange capsules(JTGs)( 金天格胶囊) in the treatment of osteoarthritis(OA) by exploring the potential mechanism of action of synovial mesenchymal stem cell exosomes(SMSC-Exos) and articular chondrocytes(ACs) through transcriptome sequencing(RNA-seq). METHODS: Type Ⅱ collagenase was used to induce OA in rats. The efficacy of JTGs was confirmed by macroscopic observation of articular cartilage, micro-CT observation, and safranin fast green staining. After SMSC-Exos and ACs were qualified, RNA-seq was used to screen differentially expressed mi RNAs and m RNAs. The target genes of differentially expressed mi RNAs in Synovial mesenchymal stem cells(SMSCs) were predicted based on the multi Mi R R package. The codifferentially expressed genes of SMSC-Exos and ACs were obtained by venny 2.1.0. The mi RNA-m RNA regulatory network was constructed by Cytoscape software. Based on the Omic Share platform, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis was performed on the m RNA regulated by key mi RNAs. Expression trend analysis was performed for co-differentially expressed genes. Correlation analysis was performed on micro-CT efficacy indicators, co-differentially expressed genes mRNA and miRNA. RESULTS: The efficacy of each administration group of JTGs was significant compared with the model group. SMSC-Exos and ACs were identified by their characteristics. The expression of rno-mi R-23a-3p, rnomi R-342-3p, rno-miR-146b-5p, rno-miR-501-3p, rnomiR-214-3p was down-regulated in OA pathological state, and the expression of rno-mi R-222-3p, rno-mi R-30e-3p, rno-mi R-676, and rno-miR-192-5p expression was upregulated, and the expression of all these mi RNAs was reversed after the intervention with JTGs containing serum. The co-differentially expressed genes were enriched in the interleukin 17 signaling pathway, tumor necrosis factor signaling pathway, transforming growth factor-β signaling pathway, etc. The expression trends of Ccl7, Akap12, Grem2, Egln3, Arhgdib, Ccl20, Mmp12, Pla2g2a, and Nr4a1 were significant. There was a correlation between micro-CT pharmacodynamic index, m RNA, and mi RNA. CONCLUSION: JTGs can improve the degeneration of joint cartilage and achieve the purpose of cartilage protection, which can be used for the treatment of OA. SMSCs-related mi RNA expression profiles were significantly altered after the intervention with JTGs containing serum. The 9 co-differentially expressed genes may be the key targets for the efficacy of JTGs in the treatment of OA rats, which can be used for subsequent validation.
基金Supported by National Natural Foundation of China,No.821742232019 Chinese and Western Medicine Clinical Collaborative Capacity Building Project for Major Difficult Diseases,No.2019-ZX-005。
文摘BACKGROUND Esophageal squamous cell carcinoma(ESCC)is one of the most common malignancies worldwide,and its development comprises a multistep process from intraepithelial neoplasia(IN)to carcinoma(CA).However,the critical regulators and underlying molecular mechanisms remain largely unknown.AIM To explore the genes and infiltrating immune cells in the microenvironment that are associated with the multistage progression of ESCC to facilitate diagnosis and early intervention.METHODS A mouse model mimicking the multistage development of ESCC was established by providing warter containing 4-nitroquinoline 1-oxide(4NQO)to C57BL/6 mice.Moreover,we established a control group without 4NQO treatment of mice.Then,transcriptome sequencing was performed for esophageal tissues from patients with different pathological statuses,including low-grade IN(LGIN),high-grade IN(HGIN),and CA,and controlled normal tissue(NOR)samples.Differentially expressed genes(DEGs)were identified in the LGIN,HGIN,and CA groups,and the biological functions of the DEGs were analyzed via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses.The CIBERSORT algorithm was used to detect the pattern of immune cell infilt-ration.Immunohistochemistry(IHC)was also conducted to validate our results.Finally,the Luminex multiplex cytokine analysis was utilized to measure the serum cytokine levels in the mice.RESULTS Compared with those in the NOR group,a total of 681541,and 840 DEGs were obtained in the LGIN,HGIN,and CA groups,respectively.Using the intersection of the three sets of DEGs,we identified 86 genes as key genes involved in the development of ESCC.Enrichment analysis revealed that these genes were enriched mainly in the keratinization,epidermal cell differentiation,and interleukin(IL)-17 signaling pathways.CIBERSORT analysis revealed that,compared with those in the NOR group,M0 and M1 macrophages in the 4NQO group showed stronger infiltration,which was validated by IHC.Serum cytokine analysis revealed that,compared with those in the NOR group,IL-1βand IL-6 were upregulated,while IL-10 was downregulated in the LGIN,HGIN,and CA groups.Moreover,the expression of the representative key genes,such as S100a8 and Krt6b,was verified in external human samples,and the results of immunohistochemical staining were consistent with the findings in mice.CONCLUSION We identified a set of key genes represented by S100a8 and Krt6b and investigated their potential biological functions.In addition,we found that macrophage infiltration and abnormal alterations in the levels of inflam-mation-associated cytokines,such as IL-1β,IL-6,and IL-10,in the peripheral blood may be closely associated with the development of ESCC.
基金facility support from the Single-Molecule Sequencing Platform at Sun Yat-sen University Cancer Center.This work is supported by the National Natural Science Foundation of China(32070592 to JXY,32000395 to JL,82272789 to LZ)Guangdong Basic and Applied Basic Research Foundation(2022A1515010717 and 2019A1515110762 to JXY and 2022A1515011873 to JL)+2 种基金Guangdong Pearl River Talents Program(2019QN01Y183 to JXY,2021QN02Y168 to JL)Guangzhou Municipal Science and Technology Bureau(202102020938 to JL)Young Talents Program of Sun Yat-sen University Cancer Center(YTP-SYSUCC-0042 to JXY and YTP-SYSUCC-0040 to JL)。
文摘Nanopore direct RNA sequencing(DRS)provides the direct access to native RNA strands with full-length information,shedding light on rich qualitative and quantitative properties of gene expression profiles.Here with NanoTrans,we present an integrated computational framework that comprehensively covers all major DRS-based application scopes,including isoform clustering and quantification,poly(A)tail length estimation,RNA modification profiling,and fusion gene detection.In addition to its merit in providing such a streamlined one-stop solution,NanoTrans also shines in its workflow-orientated modular design,batch processing capability,all-in-one tabular and graphic report output,as well as automatic installation and configuration supports.Finally,by applying NanoTrans to real DRS datasets of yeast,Arabidopsis,as well as human embryonic kidney and cancer cell lines,we further demonstrate its utility,effectiveness,and efficacy across a wide range of DRS-based application settings.
基金supported by National Natural Science Foundation of China(No.31870451,31370470 and 32001155)the State Key Laboratory of Lake Science and Environment Foundation(2022SKL011).
文摘High fish predation pressure can trigger"induced defense"in Daphnia species,resulting in phenotypic plasticity in morphology,behavior,or life-history traits.The molecular mechanisms of defense morphogenesis(e.g.,the tail spine and helmet)in Daphnia remain unclear.In the pres-ent study,the tail spine,helmet,and body of Daphnia galeata under fish and non-fish kairomones conditions were collected for transcriptome analysis.A total of 24 candidate genes related to the morphological defense of D.galeata were identified,including 2 trypsin,one cuticle protein,1 C1qDC protein,and 2 ferritin genes.The function of the Dagcut gene(D.galeata cuticle protein gene)in relation to tail spine morphology was assessed using RNA interference(RNAi).Compared with the EGFP(Enhanced green fluorescent protein)treatment,after RNAi,the expression levels of the Dagcut gene(D.galeata cuticle protein gene)showed a significant decrease.Correspondingly,the tail spines of the offspring pro-duced by D.galeata after RNAi of the Dagcut gene appeared curved during the experiment.In whole-mount in situ hybridization,a clear signal site was detected on the tail spine of D.galeata before RNAi which disappeared after RNAi.Our results suggest that the Dagcut gene may play an important role in tail spine formation of D.galeata,and will provide a theoretical basis for studying the molecular mechanisms of the morpho-logical plasticityin cladocera inthefuture.
基金Supported by the National Natural Science Foundation,China,No.82272568,81902247,and 32201013Natural Science Foundation of Shandong Province,China,No.ZR2021QH275+1 种基金Natural Science Foundation of Jinan City,China,No.202225070Guangdong Basic and Applied Basic Research Foundation,China,No.2022A1515220056.
文摘BACKGROUND Mesenchymal stem cells(MSCs)modulated by various exogenous signals have been applied extensively in regenerative medicine research.Notably,nanosecond pulsed electric fields(nsPEFs),characterized by short duration and high strength,significantly influence cell phenotypes and regulate MSCs differentiation via multiple pathways.Consequently,we used transcriptomics to study changes in messenger RNA(mRNA),long noncoding RNA(lncRNA),microRNA(miRNA),and circular RNA expression during nsPEFs application.AIM To explore gene expression profiles and potential transcriptional regulatory mechanisms in MSCs pretreated with nsPEFs.METHODS The impact of nsPEFs on the MSCs transcriptome was investigated through whole transcriptome sequencing.MSCs were pretreated with 5-pulse nsPEFs(100 ns at 10 kV/cm,1 Hz),followed by total RNA isolation.Each transcript was normalized by fragments per kilobase per million.Fold change and difference significance were applied to screen the differentially expressed genes(DEGs).Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to elucidate gene functions,complemented by quantitative polymerase chain reaction verification.RESULTS In total,263 DEGs were discovered,with 92 upregulated and 171 downregulated.DEGs were predominantly enriched in epithelial cell proliferation,osteoblast differentiation,mesenchymal cell differentiation,nuclear division,and wound healing.Regarding cellular components,DEGs are primarily involved in condensed chromosome,chromosomal region,actin cytoskeleton,and kinetochore.From aspect of molecular functions,DEGs are mainly involved in glycosaminoglycan binding,integrin binding,nuclear steroid receptor activity,cytoskeletal motor activity,and steroid binding.Quantitative real-time polymerase chain reaction confirmed targeted transcript regulation.CONCLUSION Our systematic investigation of the wide-ranging transcriptional pattern modulated by nsPEFs revealed the differential expression of 263 mRNAs,2 miRNAs,and 65 lncRNAs.Our study demonstrates that nsPEFs may affect stem cells through several signaling pathways,which are involved in vesicular transport,calcium ion transport,cytoskeleton,and cell differentiation.
基金Supported by Science and Technology Support Planning Project of Sichuan Province(2021YFYZ0031SASA2024CZYX002)National Modern Agricultural Technology System Construction of China(CARS-41-G07)。
文摘The calpain system is ubiquitous in cells, mainly comprising calpains and calpain inhibitors, and is a widespread calcium-dependent cysteine protease in organisms that is involved in many cellular processes such as muscle degradation in vivo and affects the tenderness of meat after animal slaughter. The study found 128 DEGs that probably regulated tenderness traits were selected from 16 significantly enriched GO terms by transcriptome sequencing analysis, and found that the developmental changes in the expression levels of the CAPN1 gene in the pectoral and leg muscles were significantly positively correlated ( P <0.05) with the cumulative growth values of live weight and comb weight. The developmental changes in the expression levels of the CAST gene in the pectoral and leg muscles were not significantly correlated with the cumulative growth values of live weight and comb weight. Our results helped demonstrate the potential molecular mechanisms of tenderness in chickens and provide valuable information for chicken breeding.
文摘Single-cell transcriptome sequencing has been a rapidly developing and powerful biological tool in recent years,and it plays a vital role in describing tissue development,cell heterogeneity,stress response,etc.Cerebrovascular disease is one of the leading causes affecting human health in the world.Thus,it is important to understand the characteristics of cerebrovascular structure,function,and environmental response.Notably,single-cell transcriptome sequencing provides deeper insights into cerebrovascular research in health and disease states.This article will briefly introduce the basic structure and function of cerebrovascular endothelial cells(ECs),summarize the current research and new findings on cerebrovascular ECs at the single-cell transcriptome level,and discuss the challenges in this field.
基金The National Natural Science Foundation of China under contract Nos 41206116,31140070 and 31271397Technology Project of Ocean and Fisheries of Guangdong Province under contract No.A201201E03+1 种基金the Fundamental Research Funds for the Central Universities under contract No.201262003the algal transcriptome sequencing was supported by OneKP Project(www.onekp.com)
文摘Saccharina is one of the most important cold-water living marine brown algal genera. In this study we ana-lyzed the transcriptome of S. japonica, which belongs to the 1 000 Plants （OneKP） Project, by using a next-generation high-throughput DNA sequencing technique. About 5.16 GB of raw data were generated, and 65 536 scaffolds with an average length of 454 bp were assembled with SOAP de novo assembly method. In total, 19 040 unigenes were identified by BLAST;25 734 scaffolds were clustered into 37 Gene ontology functional groups;6 760 scaffolds were classified into 25 COG categories, as well as 2 665 scaffolds that were assigned to 306 KEGG pathways. Majority of the unigenes exhibited more similarities to algae including brown algae and diatom than other cyanobacteria, marine diatom, and plant. Saccharina japonica has the outstanding capability to accumulate halogen such as Br and I via halogenation processes from seawater. We acquired 42 different vanadium-dependent haloperoxidases （vHPO） in S. japonica transcriptome data, including 5 segments of vanadium-dependent iodoperoxidase （vIPO） and 37 segments of vanadium-de-pendent bromoperoxidase （vBPO）. Complicated analyses of identified fulllength S. japonica vBPO1 and S. japonica vBPO2 revealed the importance of vBPO among species of brown algae and the strong relationship between marine algal vBPOs and vIPOs. This study will enhance our understanding of the biological charac-teristics and economic values of S. japonica species.
基金Construction Project of National Clinical Research Base of Traditional Chinese Medicine(Science Letter[2018]No.131,State Office of Traditional Chinese Medicine)Natural Science Foundation of Hebei Province:Study on the Mechanism of Action of Traditional Chinese Medicine on Disease and Syndrome(No.H2023423001)+6 种基金Key Research Project of the Ministry of Science and Technology(No.2018YFC1704100)Key Research Project of the Ministry of Science and Technology:Li Diangui Famous Old Chinese Medicine of Traditional Chinese Medicine Academic View Characteristic,Diagnosis and Treatment Methods and Experience of Prevention and Control of Major Diseases(No.2018YFC1704102)Provincial Science and Technology Program of Hebei Province:Prevention and Treatment of Gastric Cancer by Blocking the"Inflammation-Cancer Transformation"Based on the Theory of Turbidimetric Toxicity(No.21377724D)Provincial Science and Technology Program of Hebei Province:to Study the Clinical Efficacy and Mechanism of Huazhuo Jiedu Formula in the Treatment of Chronic Atrophic Gastritis based on Epidermal Growth Factor Receptor/Mitogen Activated Protein Kinase/Extracellular Signal-Regulated Kinase Signaling Pathway(No.21377740D)Scientific Research Project of Hebei Administration of Traditional Chinese Medicine:Clinical Study of Huazhuo Jiedu Formula Blocking the Pathological Evolution of Chronic Atrophic Gastritis(No.2022026)Scientific Research Project of Hebei Administration of Traditional Chinese Medicine:Study on the Medication Rules of Spleen and Stomach Diseases of Famous Yanzhao Medical Doctors Based on Data Mining(No.2022032)Scientific Research Project of Hebei Administration of Traditional Chinese Medicine:to Explore the Mechanism of Xianglian Huazhuo Formula in the Treatment of Chronic Atrophic Gastritis based on Transcriptomics(No.2023022)。
文摘OBJECTIVE:To explore the mechanism of Xianglian Huazhuo formula(香连化浊方,XLHZ)blocking the development of chronic atrophic gastritis(CAG)to gastric cancer(GC)through bioinformatics analysis and in vitro.METHODS:Pathological morphology of gastric mucosa of rats were observed.High-throughput sequencing was used to analyze the miRNA expression profile of gastric mucosa.The miRanda,miRDB and miRWalk databases were used to predict the differential target genes.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis were performed for differential target genes.Real-time quantitative reverse transcription polymerase chain reaction(qRTPCR)was used to verify the differentially expressed miRNAs and target genes.Western blot,EdU,wound healing and flow cytometry were used to observe the effect of XLHZ on epithelial-mesenchymal transition(EMT)markers,proliferation,migration,apoptosis and cell cycle of CAG cells in vitro.RESULTS:A total of five differentially expressed miRNAs and four differential target genes were screened in this study.GO analysis showed that the target genes were enriched in regulation of neuron development,regulation of transcription factor activity and regulation of RNA polymerase.KEGG pathways database differences in gene enrichment of target genes in the Wnt signaling pathway,Phospholipase D signaling pathway and mitogen-activated protein kinase signaling pathway.qRTPCR confirmed that miRNAs and its target genes were consistent with the screening results.In vitro,our study revealed that XLHZ could increase the expression of Ecadherin,decrease the expression of transforming growth factorβ1,vimentin andβ-catenin,inhibite the proliferation and migration of CAG cells,cause cell cycle arrest at G0/G1 and G2/M phase,induce the apoptosis of CAG cells,and prevent the progression of CAG to GC.CONCLUSION:This study provided a new idea for the mechanism of blocking the progression of CAG to GC by XLHZ,which may be related to the expression of miR-20a-3p,miR-320-3p,miR-34b-5p,miR-483-3p and miR-883-3p and their target genes transferrin receptor,nuclear receptor subfamily 4 member 2,delta like canonical Notch ligand 1 and a kinase anchor protein 12 in CAG.In the future,we will continue to investigate the linkage between the active ingredients of XLHZ and the relevant miRNAs and their target genes,so as to provide more sufficient experimental basis for clinically effective prevention of CAG to GC.
基金supported by the National Key Research and Development Program(grant number:2022YFC2305304).
文摘Objective Viral encephalitis is an infectious disease severely affecting human health.It is caused by a wide variety of viral pathogens,including herpes viruses,flaviviruses,enteroviruses,and other viruses.The laboratory diagnosis of viral encephalitis is a worldwide challenge.Recently,high-throughput sequencing technology has provided new tools for diagnosing central nervous system infections.Thus,In this study,we established a multipathogen detection platform for viral encephalitis based on amplicon sequencing.Methods We designed nine pairs of specific polymerase chain reaction(PCR)primers for the 12 viruses by reviewing the relevant literature.The detection ability of the primers was verified by software simulation and the detection of known positive samples.Amplicon sequencing was used to validate the samples,and consistency was compared with Sanger sequencing.Results The results showed that the target sequences of various pathogens were obtained at a coverage depth level greater than 20×,and the sequence lengths were consistent with the sizes of the predicted amplicons.The sequences were verified using the National Center for Biotechnology Information BLAST,and all results were consistent with the results of Sanger sequencing.Conclusion Amplicon-based high-throughput sequencing technology is feasible as a supplementary method for the pathogenic detection of viral encephalitis.It is also a useful tool for the high-volume screening of clinical samples.
基金supported by the National Natural Science Foundation of China(No.22277093)the Key Research and Development Project of Hubei Province(No.2023BCB094)。
文摘N^(6)-methyladenine(6mA)is a prevalent DNA modification and is involved in a wide range of human diseases.Previous studies have indicated that 6mA is enriched in mitochondrial DNA(mtDNA)of mammals.By employing an evolved adenine deaminase,we developed a deaminase-mediated sequencing(DM-seq)method that could achieve genome-wide mapping of 6mA in mammalian mtDNA at single-base resolution.In this study,we used an engineered adenine deaminase,known as TadA8e protein,to map 6mA in mtDNA of hepatocellular carcinoma(HCC)by DM-seq.Through high-throughput sequencing,we identified sixteen 6mA sites in both HCC and adjacent normal tissue mtDNA.The results revealed an increased overall 6mA level in mtDNA associated with HCC.Furthermore,an elevation in 6mA level was observed alongside a decrease in the m RNA levels of the corresponding genes,indicating that increased6mA level hindered transcription processes related to these genes.These findings demonstrate that 6mA in mtDNA is correlated with HCC and provide evidence supporting the inhibitory effect of elevated 6mA level on subsequent transcriptional activity.This research illuminates the intricate relationship between 6mA modification and transcriptional regulation in the context of HCC,offering valuable insights into the role of 6mA modification in HCC pathogenesis.
基金supported by the National Centre for Research and Development TECHMATSTRATEG-Ⅲ/0027/2019,POWR.03.02.00-00-I006/17the IDUB UAM。
文摘Meniscus injuries are widespread and the available treatments do not offer enough healing potential.Here,we provide critical support for using pigs as a biological model for meniscal degeneration and the development of cutting-edge therapies in orthopedics.We present a single-cell transcriptome atlas of the meniscus,consisting of cell clusters corresponding to four major cell types:chondrocytes,endothelial cells,smooth muscle cells,and immune cells.Five distinct chondrocyte subclusters(CH0–CH4)were annotated,of which only one was widespread in both the red and white zones,indicating a major difference in the cellular makeup of the zones.Subclusters distinct to the white zone appear responsible for cartilage-specific matrix deposition and protection against adverse microenvironmental factors,while those in the red zone exhibit characteristics of mesenchymal stem cells and are more likely to proliferate and migrate.Additionally,they induce remodeling actions in other chondrocyte subclusters and promote the proliferation and maturation of endothelial cells,inducing healing and vascularization processes.Considering that they have substantial remodeling capabilities,these subclusters should be of great interest for tissue engineering studies.We also show that the cellular makeup of the pig meniscus is comparable to that of humans,which supports the use of pigs as a model in orthopedic therapy development.
基金Supported by Scientific Research Project of Putian University,No.2022059Special Project for Outstanding Young Talents of Putian University,No.2024072Natural Science Foundation of Fujian Province,No.2023J01160.
文摘Gastric cancer(GC)remains one of the leading causes of cancer-related morbidity and mortality globally.Although significant progress has been made in treatment options,the survival rates for GC patients continue to be low.This is primarily attributed to the intricate and insufficiently understood mechanisms of disease progression,as well as the considerable challenges associated with tumor hetero-geneity.The recent study by Tang et al provides a detailed single-cell RNA se-quencing analysis of GC across different stages,revealing dynamic changes in the tumor microenvironment and key immune responses.We aim to offer a compre-hensive interpretation of the study’s findings and propose several innovative directions for future academic research in gastric cancer.These include exploring advanced multi-omics approaches,leveraging spatial transcriptomics,integrating artificial intelligence for clinical applications,and developing novel immuno-therapy strategies.We further emphasize the importance of personalized medi-cine,early detection,and novel drug discovery techniques in improving GC treatment outcomes.
文摘Head and neck cutaneous squamous cell carcinoma(HNCSCC)remains underexplored compared to oropharyngeal squamous cell carcinoma,particularly in relation to human papillomavirus(HPV)and molecular markers such as p16 and p53.While p16 is a well-established surrogate for HPV in oropharyngeal cancer,our review highlights its unreliable role in HNCSCC,where positivity is instead associated with recurrence and metastasis.Similarly,p53 illustrates a dual role-wild-type as a genomic safeguard,mutated as an oncogenic driver-complicating prognostication.Methodological considerations,including the limitations of immunohistochemistry for HPV detection,underscore the need for multi-method and molecular validation in future studies.Ultraviolet radiation is posited as a key modifier of p16 function,decoupling expression from tumor suppression.To contextualize these findings,we draw parallels to glioblastoma(GBM),where subclonal evolution,p53 dysfunction,and intratumoral heterogeneity drive relapse despite aggressive multimodal therapies.GBM exemplifies how bulk-level biomarker generalizations often obscure dynamic cellular ecosystems,reinforcing the necessity of single-cell and spatial approaches.Multi-omics integration-encompassing genome,transcriptome,proteome,and tumor microenvironment mapping-coupled with single-cell RNA sequencing and spatial transcriptomics,offers a path forward for resolving subclonal dynamics in both HNCSCC and GBM.These technologies provide the resolution needed to track tumor-immunestromal co-evolution,identify therapy-resistant clones,and anticipate recurrence.We argue for a N-of-1,patient-and cell-centric paradigm that reframes biomarkers not as static surrogates but as dynamic readouts of cancer evolution across time and tissue contexts.Conceptually,we propose kinetic and microenvironmental frameworks(e.g.,“load-and-lock”barriers;dormancy and immunesynapse stabilization)as hypothesis-generating avenues to stall clonal handoffs and improve outcome prediction.Together,these perspectives argue for revised biomarker frameworks in HNCSCC and ethically inclusive,mechanism-anchored studies that bridge discovery with individualized care.By bridging insights from HNCSCC with the lessons of GBM,this review underscores the need for ethically inclusive,mechanistically informed frameworks that integrate subclonal evolution,biomarker re-interpretation,and precision-personalized hybrid models.Such an approach will be essential for advancing from one-size-fits-all strategies to individualized lifetime cancer care.
基金supported by Major Science and Technology Projects of Yunnan Science and Technology Plan(2019ZG003)Yunnan Young and Middle-aged Academic and Technical Leader Reserve Talent Project(202105AC160068)。
文摘The internal microbial diversity and small molecular metabolites of Nuodeng ham in different processing years(the first,second and third year sample)were analyzed by high-throughput sequencing technology and gas chromatography-time of flight mass spectrography(GC-TOF-MS)to study the effects of microorganisms and small molecular metabolites on the quality of ham in different processing years.The results showed that the dominant bacteria phyla of Nuodeng ham in different processing years were Proteobacteria and Firmicutes,the dominant fungi phyla were Ascomycota and Basidiomycota,while Staphylococcus and Aspergillus were the dominant bacteria and fungi of Nuodeng ham,respectively.Totally,252 kinds of small molecular metabolites were identified from Nuodeng ham in different processing years,and 12 different metabolites were screened through multivariate statistical analysis.Further metabolic pathway analysis showed that 23 metabolic pathways were related to ham fermentation,of which 8 metabolic pathways had significant effects on ham fermentation(Impact>0.01,P<0.05).The content of L-proline,phenyllactic acid,L-lysine,carnosine,taurine,D-proline,betaine and creatine were significantly positively correlated with the relative abundance of Staphylococcus and Serratia,but negatively correlated with the relative abundance of Halomonas,Aspergillus and Yamadazyma.
