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
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
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
Oviductus Ranae is the dried oviduct of female Rana tem-poraria chensinensis （David）, distributed mainly in North- eastern China. Oviductus Ranae is one of the best-known and highly valued oriental foods and medicin...Oviductus Ranae is the dried oviduct of female Rana tem-poraria chensinensis （David）, distributed mainly in North- eastern China. Oviductus Ranae is one of the best-known and highly valued oriental foods and medicines. Traditional Chinese medicine holds that Oviductus Ranae can nourish yin, moisten lung and replenish the kidney essence. Meanwhile, activities of Oviductus Ranae such as anti-aging, anti-lipemic, anti-oxidation and anti-fatigue have also been demonstrated by modern phar-macological studies. Previous studies have shown that Oviductus Ranae is mainly composed of proteins, which are up to 50% or more.展开更多
The mechanisms that regulate the specificity and maintenance of chicken muscle fiber types remain largely unknown. In mammals, CSRP3 has been shown to play a vital role in the maintenance of typical muscle structure a...The mechanisms that regulate the specificity and maintenance of chicken muscle fiber types remain largely unknown. In mammals, CSRP3 has been shown to play a vital role in the maintenance of typical muscle structure and function. This study investigated the role that CSRP3 plays in chicken skeletal muscle. First, the antibody against chicken CSRP3 protein was prepared, and the expression levels of the mRNA and protein of the CSRP3 gene in four chicken skeletal muscles with different myofiber compositions were compared. Then the effects of CSRP3 silencing on the expression profile of chicken myoblast transcriptomes were analyzed. The results showed that the expression levels of the mRNA and protein of the CSRP3 gene were both associated with the composition of fiber types in chicken skeletal muscles. A total of 650 genes with at least 1.5-fold differences(Q<0.05) were identified, of which 255 genes were upregulated and 395 genes were downregulated by CSRP3 silencing. Functional enrichment showed that several pathways, including adrenergic signaling in cardiomyocytes, adipocytokine signaling pathway and apelin signaling pathway, were significantly(P<0.05) enriched both in differentially expressed genes and all expressed genes. The co-expressed gene network suggested that CSRP3 silencing caused a compensatory upregulation(Q<0.05) of genes related to the assembly of myofibrils, muscle differentiation, and contraction. Meanwhile, two fast myosin heavy chain genes(MyH1B and MyH1E)were upregulated(Q<0.05) upon CSRP3 silencing. These results suggested that CSRP3 plays a crucial role in chicken myofiber composition, and affects the distribution of chicken myofiber types, probably by regulating the expression of MyH1B and MyH1E.展开更多
Few effective therapies have been developed for the treatment of lung squamous cell carcinoma （SQCC）, in part due to a lack of un- derstanding regarding the mechanisms underlying the initiation and development of th...Few effective therapies have been developed for the treatment of lung squamous cell carcinoma （SQCC）, in part due to a lack of un- derstanding regarding the mechanisms underlying the initiation and development of this disease. Whole transcriptome sequencing not only provides insight into the expression of all transcribed genes, but offers an efficient approach for identifying genetic variations, including gene fusions, mutations and alternative splicing. In this study, we performed whole transcriptome sequencing of 10 patients with stage IIIA lung SQCC, and discovered a large number of single nucleotide variants （SNVs： mean of 12.2 SNVs/Mb）, with C〉T/G〉A and A〉G/T〉C transitions being the most frequently observed. Additionally, a total of 132 gene fusions were identified based upon TopHat alignments, 70.5% （93/132） of which occurred as a result of intra-chromosomal rearrangements. Based on the number of supporting reads for each fusion, we further validated 20 of the 26 top gene fusions by RT-PCR and Sanger sequencing. Taken together, these data provide an in-depth view of transcriptional alterations in lung SQCC patients, and may be useful for identification of new therapeutic targets.展开更多
Small RNAs in Penicillium digitatum were identified and analyzed via transcriptome sequencing on the BGISEQ-500 platform. A total of 15 predicted miRNAs and 10718 novel siRNAs were found. Their length distribution, se...Small RNAs in Penicillium digitatum were identified and analyzed via transcriptome sequencing on the BGISEQ-500 platform. A total of 15 predicted miRNAs and 10718 novel siRNAs were found. Their length distribution, sequence, predicted construction, base bias, expression levels and potential targets were determined as well. Through pathway and KEGG enrichment analysis, the miRNA target genes were mostly involved in carbohydrate metabolism, transport and catabolism, translation and amino acid metabolism. The target genes involved in aflatoxin biosynthesis and proteasome had a higher rich factor value. The results will provide a theoretical foundation for understanding the developmental and pathogenic mechanisms of P. digitatum at the transcriptional level.展开更多
To explore the mechanism of Agaricus blazei Murrill enrichment of the heavy metal cadmium,we employed Illumina high-throughput sequencing to analyze the transcriptomes of A.blazei mycelia treated with and without exog...To explore the mechanism of Agaricus blazei Murrill enrichment of the heavy metal cadmium,we employed Illumina high-throughput sequencing to analyze the transcriptomes of A.blazei mycelia treated with and without exogenous cadmium addition,and then the differentially expressed genes(DEGs)of the strains with high and low cadmium enrichment between the control and cadmium treatment were screened out.The results showed that the DEGs were mainly involved in steroid biosynthesis,antibiotic biosynthesis,protein processing in endoplasmic reticulum,glutathione metabolism and other pathways.Carbon metabolism and glutathione metabolism may play an important role in the response of A.blazei mycelium to cadmium stress.展开更多
Most phaeophytes （brown algae） and rhodophytes （red algae） dwell exclusively in marine habitats and play important roles in marine ecology and biodiversity. Many of these brown and red algae are also important res...Most phaeophytes （brown algae） and rhodophytes （red algae） dwell exclusively in marine habitats and play important roles in marine ecology and biodiversity. Many of these brown and red algae are also important resources for industries such as food, medicine and materials due to their unique metabolisms and me-tabolites. However, many fundamental questions surrounding their origins, early diversification, taxonomy, and special metabolisms remain unsolved because of poor molecular bases in brown and red algal study. As part of the 1 000 Plant Project, the marine macroalgal transcriptomes of 19 Phaeophyceae species and 21 Rhodophyta species from China＇s coast were sequenced, covering a total of 2 phyla, 3 classes, 11 orders, and 19 families. An average of 2 Gb per sample and a total 87.3 Gb of RNA-seq raw data were generated. Approxi-mately 15 000 to 25 000 unigenes for each brown algal sample and 5 000 to 10 000 unigenes for each red algal sample were annotated and analyzed. The annotation results showed obvious differences in gene expres-sion and genome characteristics between red algae and brown algae;these differences could even be seen between multicellular and unicellular red algae. The results elucidate some fundamental questions about the phylogenetic taxonomy within phaeophytes and rhodophytes, and also reveal many novel metabolic pathways. These pathways include algal CO2 fixation and particular carbohydrate metabolisms, and related gene/gene family characteristics and evolution in brown and red algae. These findings build on known algal genetic information and significantly improve our understanding of algal biology, biodiversity, evolution, and potential utilization of these marine algae.展开更多
Chiton(Ischnochiton hakodadensis) is one of marine mollusks well known for its eight separate shell plates. I. hakodadensis is important, which plays a vital role in the ecosystems it inhabits. So far, the genetic stu...Chiton(Ischnochiton hakodadensis) is one of marine mollusks well known for its eight separate shell plates. I. hakodadensis is important, which plays a vital role in the ecosystems it inhabits. So far, the genetic studies on the chiton are scarce due in part to insufficient genomic resources available for this species. In this study, we investigated the transcriptome of the chiton foot using Illumina sequencing technology. The reads were assembled and clustered into 256461 unigenes, of which 42247 were divided into diverse functional categories by Gene Ontology(GO) annotation terms, and 17256 mapped onto 365 pathways by KEGG pathway mapping. Meanwhile, a set of differentially expressed genes(DEGs) between distal and proximal muscles were identified as the foot adhesive locomotion associated, thus were useful for our future studies. Moreover, up to 679384 high-quality single nucleotide polymorphisms(SNPs) and 19814 simple sequence repeats(SSRs) were identified in this study, which are valuable for subsequent studies on genetic diversity and variation. The transcriptomic resource obtained in this study should aid to future genetic and genomic studies of chiton.展开更多
Species of Sargassum are distributed worldwide, and are of great ecological and economic importance in marine ecosystems and bioresources. In this study, transcriptome sequencings of six Sargassum species were perform...Species of Sargassum are distributed worldwide, and are of great ecological and economic importance in marine ecosystems and bioresources. In this study, transcriptome sequencings of six Sargassum species were performed for the first time using an Illumina platform. For each sample, a total of 2.1-2.5 Gb of nucle-otides are collected and assembled into 69 871-116 790 scaffolds, with an average length of 410-550 bp and N50 length of 756-1 462 bp. A total of 20 512-28 684 unigenes of each sample were annotated and compared well with known gene sequences from nr database. Clusters of Orthologous Groups （COG）, gene ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） analyses were also performed for further un-derstanding of gene functions and regulation pathways. Gene expression levels were calculated based on RPKM values and compared among these species, especially for those genes related to carbohydrate metab-olism. Cluster analyses indicated that the differences of global gene expression between S. fusiforme, which was nominated as Hizikia fusiformis before, and other five species were not significant. Further phylogenet-ic analysis of 108 orthologous genes confirmed that S. fusiforme had closer relationship with S. hemiphyllum rather than S. horneri. These transcriptome data provided valuable information for better understanding of genome and gene characteristics of Sargassum algae and benefiting comparative and phylogenetic studies of Phaeophyceae species in future studies.展开更多
Background:Ursolic acid is a triterpenoid compound found in natural plants that exhibits antiproliferative effects in various cancer cells.Our study is the first to demonstrate the strong inhibitory effects of ursolic...Background:Ursolic acid is a triterpenoid compound found in natural plants that exhibits antiproliferative effects in various cancer cells.Our study is the first to demonstrate the strong inhibitory effects of ursolic acid on the proliferation of cutaneous T-cell lymphoma(CTCL)cells.We aimed to further investigate the underlying mechanism of the proliferation inhibition induced by ursolic acid in CTCL cells using transcriptome sequencing.Methods:Cell counting kit-8 assays were used to observe the effects of six traditional medicine monomers on the proliferation of CTCL cells.Transcriptome sequencing was used to identify differentially expressed genes after ursolic acid treatment.Bioinformatics analysis was performed to determine the potential mechanism.Real-time quantitative PCR and western blotting analyses were performed to confirm the sequencing results and verify the possible mechanisms of ursolic acid-mediated proliferation inhibition in CTCL cells.Results:Ursolic acid exhibited the strongest inhibitory effect on the proliferation of CTCL cells among the six traditional medicine monomers.Transcriptome sequencing analysis showed that 2,466 genes were significantly altered.Combined with Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis and protein-protein interaction network analysis,the interaction of various pathways and signaling molecules,such as tumor necrosis factor-α,NLR family pyrin domain containing 1,c-Jun N-terminal kinase,and melanoma differentiation-associated gene 5,accounted for the anti-tumor effects of ursolic acid in CTCL cells.Conclusion:Ursolic acid significantly inhibited the proliferation of CTCL cells,and our study laid a theoretical foundation for the future treatment of CTCL using ursolic acid.展开更多
Objective:To screen abnormally expressed lncRNAs in peripheral blood mononuclear cells from patients with COPD.Methods:The peripheral blood of 3 COPD patients and 3 normal controls were collected from our hospital,mon...Objective:To screen abnormally expressed lncRNAs in peripheral blood mononuclear cells from patients with COPD.Methods:The peripheral blood of 3 COPD patients and 3 normal controls were collected from our hospital,mononuclear cells were isolated,RNA was extracted and then transcriptome sequencing was performed.The expression difference between the two groups of samples was calculated based on p<0.05 and|log2FC|>1.Plot the difference lncRNA heat map and volcano map.The Lncpro database may predict mRNAs regulated by differential lncRNA,and perform the GO function and KEGG signaling clustering.Results:There were 67 lncRNAs between the COPD group and the control group that met the difference of p<0.05 and|log2FC|>1,of which 33 were up-regulated and 34 were down-regulated.Between the two groups.The target genes are mainly enriched in GO functions:regulatory functions of multicellular biological processes,regulatory functions of development processes,structured morphogenesis functions,system development functions,and development process functions.Target genes are mainly enriched in KEGG signaling pathways:multi-species apoptotic pathway,TGF-βsignaling pathway,complement and coagulation cascade pathway,colorectal cancer pathway and apoptosis pathway.Conclusion:Our results provide general information and possible regulatory functions and pathways of lncRNA expression changes in peripheral blood mononuclear cells of COPD,which may help clarify the underlying mechanism of COPD.展开更多
Objective To explore the characteristics of T cells and natural killer(NK)cells in cerebrospinal fluid of patients with multiple sclerosis(MS).Methods Cerebrospinal fluids from patients with relapsing-remitting multip...Objective To explore the characteristics of T cells and natural killer(NK)cells in cerebrospinal fluid of patients with multiple sclerosis(MS).Methods Cerebrospinal fluids from patients with relapsing-remitting multiple sclerosis(RRMS)and healthy controls attending the Second Hospital of Lanzhou University from January 2023to October 2024 were collected and analyzed by singlecell RNA sequencing(scRNA-seq)and flow cytometry,and T and NK cell characteristics were summarized and compared in the two groups.展开更多
The Chinese soft-shelled turtle(Pelodiscus sinensis)exhibits sexual dimorphism.Compared with females,males are considered to have higher economic value due to their accelerated growth,greater body mass,and longer skir...The Chinese soft-shelled turtle(Pelodiscus sinensis)exhibits sexual dimorphism.Compared with females,males are considered to have higher economic value due to their accelerated growth,greater body mass,and longer skirt width.Studies focused on these sex disparities have largely neglected potential sex differences in growth.Here,we performed RNA sequencing of muscle tissue components from 1-year-old specimens to reveal gene expression patterns in P.sinensis.In our male and female cohorts,our analysis revealed,respectively,388 and 526 upregulated differentially expressed genes(DEGs)and 1129 and 635 downregulated DEGs.Through weighted coexpression network analysis(WGCNA)and integration with phenotype data,we established two main gene modules:a light yellow module encompassing 191 genes(e.g.,ACACB,CTH,HADHA,and CTNNB)that demonstrated a positive correlation with population traits,and a black module comprising 298 genes(e.g.,CAV3,PIK3CD,SMAD3,and VEGFA)that demonstrated a negative correlation with population traits.We also performed a DEG evaluation and gene set enrichment analysis across individuals of different sizes and noted that pathways such as protein digestion and assimilation(ko04974),were substantially augmented in larger specimens.In these pathways,the collagen(COL)and solute carrier(SLC)gene families were noted to be crucial for sustaining body structure and facilitating nutrient and metabolite transportation.In conclusion,we elucidated the essential modules,pivotal genes,and pathways involved in gene expression differences among various P.sinensis size groupings.Our results provide novel insights for future studies on growth discrepancies in P.sinensis.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
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supported by the National Key Technology Research and Development Program of the Ministry of Science and Technology of China (No. 2011BAI03B00)the National Science and Technology Major Project of the Ministry of Science and Technology of China (No. 2011ZX09401-305)
文摘Oviductus Ranae is the dried oviduct of female Rana tem-poraria chensinensis （David）, distributed mainly in North- eastern China. Oviductus Ranae is one of the best-known and highly valued oriental foods and medicines. Traditional Chinese medicine holds that Oviductus Ranae can nourish yin, moisten lung and replenish the kidney essence. Meanwhile, activities of Oviductus Ranae such as anti-aging, anti-lipemic, anti-oxidation and anti-fatigue have also been demonstrated by modern phar-macological studies. Previous studies have shown that Oviductus Ranae is mainly composed of proteins, which are up to 50% or more.
基金supported by the earmarked fund for China Agriculture Research System (CARS-41)the earmarked fund for Jiangsu Agricultural Industry Technology System, China (JATS[2021]396)+6 种基金the Special Fund for Major Breeding Programs in Jiangsu Province (PZCZ201728)the Natural Science Foundation of Jiangsu Province (BK20161322, BK20211121, and BK20210955)the Projects of Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province (JQLAB-ZZ-201703)the Open Project Program of Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, China (JILAR-KF202020)the Yangzhou Science and Technology Support Program for Modem Agriculture (YZ2021029)the Jiangsu Provincal Agricultural Independent Innovation Fund Project (CX(21)2011-1)the Independent Scientific Foundation of Public Welfare Scientific Institutes of Jiangsu Province (BM2018026)。
文摘The mechanisms that regulate the specificity and maintenance of chicken muscle fiber types remain largely unknown. In mammals, CSRP3 has been shown to play a vital role in the maintenance of typical muscle structure and function. This study investigated the role that CSRP3 plays in chicken skeletal muscle. First, the antibody against chicken CSRP3 protein was prepared, and the expression levels of the mRNA and protein of the CSRP3 gene in four chicken skeletal muscles with different myofiber compositions were compared. Then the effects of CSRP3 silencing on the expression profile of chicken myoblast transcriptomes were analyzed. The results showed that the expression levels of the mRNA and protein of the CSRP3 gene were both associated with the composition of fiber types in chicken skeletal muscles. A total of 650 genes with at least 1.5-fold differences(Q<0.05) were identified, of which 255 genes were upregulated and 395 genes were downregulated by CSRP3 silencing. Functional enrichment showed that several pathways, including adrenergic signaling in cardiomyocytes, adipocytokine signaling pathway and apelin signaling pathway, were significantly(P<0.05) enriched both in differentially expressed genes and all expressed genes. The co-expressed gene network suggested that CSRP3 silencing caused a compensatory upregulation(Q<0.05) of genes related to the assembly of myofibrils, muscle differentiation, and contraction. Meanwhile, two fast myosin heavy chain genes(MyH1B and MyH1E)were upregulated(Q<0.05) upon CSRP3 silencing. These results suggested that CSRP3 plays a crucial role in chicken myofiber composition, and affects the distribution of chicken myofiber types, probably by regulating the expression of MyH1B and MyH1E.
基金supported by the grants from the National Natural Science Foundation of China (No. 81272618) to YiLong WuGuangdong Provincial Key Laboratory of Lung Cancer Translational Medicine (No. 2012A061400006)Special Fund for Research in the Public Interest from National Health and Family Planning Commission of PRC (No. 201402031)
文摘Few effective therapies have been developed for the treatment of lung squamous cell carcinoma （SQCC）, in part due to a lack of un- derstanding regarding the mechanisms underlying the initiation and development of this disease. Whole transcriptome sequencing not only provides insight into the expression of all transcribed genes, but offers an efficient approach for identifying genetic variations, including gene fusions, mutations and alternative splicing. In this study, we performed whole transcriptome sequencing of 10 patients with stage IIIA lung SQCC, and discovered a large number of single nucleotide variants （SNVs： mean of 12.2 SNVs/Mb）, with C〉T/G〉A and A〉G/T〉C transitions being the most frequently observed. Additionally, a total of 132 gene fusions were identified based upon TopHat alignments, 70.5% （93/132） of which occurred as a result of intra-chromosomal rearrangements. Based on the number of supporting reads for each fusion, we further validated 20 of the 26 top gene fusions by RT-PCR and Sanger sequencing. Taken together, these data provide an in-depth view of transcriptional alterations in lung SQCC patients, and may be useful for identification of new therapeutic targets.
文摘Small RNAs in Penicillium digitatum were identified and analyzed via transcriptome sequencing on the BGISEQ-500 platform. A total of 15 predicted miRNAs and 10718 novel siRNAs were found. Their length distribution, sequence, predicted construction, base bias, expression levels and potential targets were determined as well. Through pathway and KEGG enrichment analysis, the miRNA target genes were mostly involved in carbohydrate metabolism, transport and catabolism, translation and amino acid metabolism. The target genes involved in aflatoxin biosynthesis and proteasome had a higher rich factor value. The results will provide a theoretical foundation for understanding the developmental and pathogenic mechanisms of P. digitatum at the transcriptional level.
文摘To explore the mechanism of Agaricus blazei Murrill enrichment of the heavy metal cadmium,we employed Illumina high-throughput sequencing to analyze the transcriptomes of A.blazei mycelia treated with and without exogenous cadmium addition,and then the differentially expressed genes(DEGs)of the strains with high and low cadmium enrichment between the control and cadmium treatment were screened out.The results showed that the DEGs were mainly involved in steroid biosynthesis,antibiotic biosynthesis,protein processing in endoplasmic reticulum,glutathione metabolism and other pathways.Carbon metabolism and glutathione metabolism may play an important role in the response of A.blazei mycelium to cadmium stress.
基金The National Natural Science Foundation of China under contract Nos 31140070,31271397 and 41206116the algal transcrip-tome sequencing was supported by 1KP Project(www.onekp.com)
文摘Most phaeophytes （brown algae） and rhodophytes （red algae） dwell exclusively in marine habitats and play important roles in marine ecology and biodiversity. Many of these brown and red algae are also important resources for industries such as food, medicine and materials due to their unique metabolisms and me-tabolites. However, many fundamental questions surrounding their origins, early diversification, taxonomy, and special metabolisms remain unsolved because of poor molecular bases in brown and red algal study. As part of the 1 000 Plant Project, the marine macroalgal transcriptomes of 19 Phaeophyceae species and 21 Rhodophyta species from China＇s coast were sequenced, covering a total of 2 phyla, 3 classes, 11 orders, and 19 families. An average of 2 Gb per sample and a total 87.3 Gb of RNA-seq raw data were generated. Approxi-mately 15 000 to 25 000 unigenes for each brown algal sample and 5 000 to 10 000 unigenes for each red algal sample were annotated and analyzed. The annotation results showed obvious differences in gene expres-sion and genome characteristics between red algae and brown algae;these differences could even be seen between multicellular and unicellular red algae. The results elucidate some fundamental questions about the phylogenetic taxonomy within phaeophytes and rhodophytes, and also reveal many novel metabolic pathways. These pathways include algal CO2 fixation and particular carbohydrate metabolisms, and related gene/gene family characteristics and evolution in brown and red algae. These findings build on known algal genetic information and significantly improve our understanding of algal biology, biodiversity, evolution, and potential utilization of these marine algae.
基金grant support from the National Natural Science Foundation of China (Nos. 31130054, 31472258)the AoShan Talents Program of Qingdao National Laboratory for Marine Science and Technology (No. 2015ASTP-ES02)the Fundamental Research Funds for the Central Universities (No. 201564009)
文摘Chiton(Ischnochiton hakodadensis) is one of marine mollusks well known for its eight separate shell plates. I. hakodadensis is important, which plays a vital role in the ecosystems it inhabits. So far, the genetic studies on the chiton are scarce due in part to insufficient genomic resources available for this species. In this study, we investigated the transcriptome of the chiton foot using Illumina sequencing technology. The reads were assembled and clustered into 256461 unigenes, of which 42247 were divided into diverse functional categories by Gene Ontology(GO) annotation terms, and 17256 mapped onto 365 pathways by KEGG pathway mapping. Meanwhile, a set of differentially expressed genes(DEGs) between distal and proximal muscles were identified as the foot adhesive locomotion associated, thus were useful for our future studies. Moreover, up to 679384 high-quality single nucleotide polymorphisms(SNPs) and 19814 simple sequence repeats(SSRs) were identified in this study, which are valuable for subsequent studies on genetic diversity and variation. The transcriptomic resource obtained in this study should aid to future genetic and genomic studies of chiton.
基金The National Natural Science Foundation of China under contract Nos 31140070,31271397 and 41206116the algal transcrip-tome sequencing was supported by 1KP Project(www.onekp.com)
文摘Species of Sargassum are distributed worldwide, and are of great ecological and economic importance in marine ecosystems and bioresources. In this study, transcriptome sequencings of six Sargassum species were performed for the first time using an Illumina platform. For each sample, a total of 2.1-2.5 Gb of nucle-otides are collected and assembled into 69 871-116 790 scaffolds, with an average length of 410-550 bp and N50 length of 756-1 462 bp. A total of 20 512-28 684 unigenes of each sample were annotated and compared well with known gene sequences from nr database. Clusters of Orthologous Groups （COG）, gene ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） analyses were also performed for further un-derstanding of gene functions and regulation pathways. Gene expression levels were calculated based on RPKM values and compared among these species, especially for those genes related to carbohydrate metab-olism. Cluster analyses indicated that the differences of global gene expression between S. fusiforme, which was nominated as Hizikia fusiformis before, and other five species were not significant. Further phylogenet-ic analysis of 108 orthologous genes confirmed that S. fusiforme had closer relationship with S. hemiphyllum rather than S. horneri. These transcriptome data provided valuable information for better understanding of genome and gene characteristics of Sargassum algae and benefiting comparative and phylogenetic studies of Phaeophyceae species in future studies.
基金This work was supported by the National Natural Science Foundation of China(No.82003808).
文摘Background:Ursolic acid is a triterpenoid compound found in natural plants that exhibits antiproliferative effects in various cancer cells.Our study is the first to demonstrate the strong inhibitory effects of ursolic acid on the proliferation of cutaneous T-cell lymphoma(CTCL)cells.We aimed to further investigate the underlying mechanism of the proliferation inhibition induced by ursolic acid in CTCL cells using transcriptome sequencing.Methods:Cell counting kit-8 assays were used to observe the effects of six traditional medicine monomers on the proliferation of CTCL cells.Transcriptome sequencing was used to identify differentially expressed genes after ursolic acid treatment.Bioinformatics analysis was performed to determine the potential mechanism.Real-time quantitative PCR and western blotting analyses were performed to confirm the sequencing results and verify the possible mechanisms of ursolic acid-mediated proliferation inhibition in CTCL cells.Results:Ursolic acid exhibited the strongest inhibitory effect on the proliferation of CTCL cells among the six traditional medicine monomers.Transcriptome sequencing analysis showed that 2,466 genes were significantly altered.Combined with Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis and protein-protein interaction network analysis,the interaction of various pathways and signaling molecules,such as tumor necrosis factor-α,NLR family pyrin domain containing 1,c-Jun N-terminal kinase,and melanoma differentiation-associated gene 5,accounted for the anti-tumor effects of ursolic acid in CTCL cells.Conclusion:Ursolic acid significantly inhibited the proliferation of CTCL cells,and our study laid a theoretical foundation for the future treatment of CTCL using ursolic acid.
文摘Objective:To screen abnormally expressed lncRNAs in peripheral blood mononuclear cells from patients with COPD.Methods:The peripheral blood of 3 COPD patients and 3 normal controls were collected from our hospital,mononuclear cells were isolated,RNA was extracted and then transcriptome sequencing was performed.The expression difference between the two groups of samples was calculated based on p<0.05 and|log2FC|>1.Plot the difference lncRNA heat map and volcano map.The Lncpro database may predict mRNAs regulated by differential lncRNA,and perform the GO function and KEGG signaling clustering.Results:There were 67 lncRNAs between the COPD group and the control group that met the difference of p<0.05 and|log2FC|>1,of which 33 were up-regulated and 34 were down-regulated.Between the two groups.The target genes are mainly enriched in GO functions:regulatory functions of multicellular biological processes,regulatory functions of development processes,structured morphogenesis functions,system development functions,and development process functions.Target genes are mainly enriched in KEGG signaling pathways:multi-species apoptotic pathway,TGF-βsignaling pathway,complement and coagulation cascade pathway,colorectal cancer pathway and apoptosis pathway.Conclusion:Our results provide general information and possible regulatory functions and pathways of lncRNA expression changes in peripheral blood mononuclear cells of COPD,which may help clarify the underlying mechanism of COPD.
文摘Objective To explore the characteristics of T cells and natural killer(NK)cells in cerebrospinal fluid of patients with multiple sclerosis(MS).Methods Cerebrospinal fluids from patients with relapsing-remitting multiple sclerosis(RRMS)and healthy controls attending the Second Hospital of Lanzhou University from January 2023to October 2024 were collected and analyzed by singlecell RNA sequencing(scRNA-seq)and flow cytometry,and T and NK cell characteristics were summarized and compared in the two groups.
基金supported by the National Natural Science Foundation of China(32302992)the Central Public-Interest Scientific Institution Basal Research Fund+1 种基金CAFS(No.2023TD36 and YFI202406)the National Freshwater Aquatic Germplasm Resource Center(FGRC18537).
文摘The Chinese soft-shelled turtle(Pelodiscus sinensis)exhibits sexual dimorphism.Compared with females,males are considered to have higher economic value due to their accelerated growth,greater body mass,and longer skirt width.Studies focused on these sex disparities have largely neglected potential sex differences in growth.Here,we performed RNA sequencing of muscle tissue components from 1-year-old specimens to reveal gene expression patterns in P.sinensis.In our male and female cohorts,our analysis revealed,respectively,388 and 526 upregulated differentially expressed genes(DEGs)and 1129 and 635 downregulated DEGs.Through weighted coexpression network analysis(WGCNA)and integration with phenotype data,we established two main gene modules:a light yellow module encompassing 191 genes(e.g.,ACACB,CTH,HADHA,and CTNNB)that demonstrated a positive correlation with population traits,and a black module comprising 298 genes(e.g.,CAV3,PIK3CD,SMAD3,and VEGFA)that demonstrated a negative correlation with population traits.We also performed a DEG evaluation and gene set enrichment analysis across individuals of different sizes and noted that pathways such as protein digestion and assimilation(ko04974),were substantially augmented in larger specimens.In these pathways,the collagen(COL)and solute carrier(SLC)gene families were noted to be crucial for sustaining body structure and facilitating nutrient and metabolite transportation.In conclusion,we elucidated the essential modules,pivotal genes,and pathways involved in gene expression differences among various P.sinensis size groupings.Our results provide novel insights for future studies on growth discrepancies in P.sinensis.
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.
