Leaf color mutants are ideal materials for studying many plant physiological and metabolic processes such as photosynthesis,photomorphogenesis,hormone physiology and disease resistance.In this study,the genetically st...Leaf color mutants are ideal materials for studying many plant physiological and metabolic processes such as photosynthesis,photomorphogenesis,hormone physiology and disease resistance.In this study,the genetically stable yellow-green leaf mutant ygl16 was identified from mutated“Xinong 1B”.Compared with the wild type,the pigment concentration and photosynthetic capacity of the ygl16 decreased significantly.The ultrastructural observation showed that the distribution of thylakoid lamellae was irregular in ygl16 chloroplasts,and the grana and matrix lamellae were blurred and loose in varied degrees,and the chloroplast structure was disordered,while the osmiophilic corpuscles increased.The results of the genetic analysis and mapping showed that the phenotype of ygl16 was controlled by a pair of recessive nuclear gene.The gene located in the 56Kb interval between RM25654 and R3 on the long arm of chromosome 10.The sequencing results showed that the 121st base of the first intron of the candidate gene OsPORB/FGL changed from A to T in the interval.qRT-PCR results showed that the expression of chlorophyll synthase-related genes in the mutant decreased.展开更多
DNA microarray technology is an extremely effective technique for studying gene expression patterns in cells, and the main challenge currently faced by this technology is how to analyze the large amount of gene expres...DNA microarray technology is an extremely effective technique for studying gene expression patterns in cells, and the main challenge currently faced by this technology is how to analyze the large amount of gene expression data generated. To address this, this paper employs a mixed-effects model to analyze gene expression data. In terms of data selection, 1176 genes from the white mouse gene expression dataset under two experimental conditions were chosen, setting up two conditions: pneumococcal infection and no infection, and constructing a mixed-effects model. After preprocessing the gene chip information, the data were imported into the model, preliminary results were calculated, and permutation tests were performed to biologically validate the preliminary results using GSEA. The final dataset consists of 20 groups of gene expression data from pneumococcal infection, which categorizes functionally related genes based on the similarity of their expression profiles, facilitating the study of genes with unknown functions.展开更多
Glutathione-S-transferase(GST,EC2.5.1.18)multifunctional protease is important for detoxification,defense against biotic and abiotic stresses,and secondary metabolic material transport for plant growth and development...Glutathione-S-transferase(GST,EC2.5.1.18)multifunctional protease is important for detoxification,defense against biotic and abiotic stresses,and secondary metabolic material transport for plant growth and development.In this study,71 members of the BpGST family were identified from the entire Betula platyphylla Suk.genome.Most of the members encode proteins with amino acid lengths ranging from 101 to 875 and were localized to the cytoplasm by a prediction.BpGSTs can be divided into seven subfamilies,with a majority of birch U and F subfamily members according to gene structure,conserved motifs and evolutionary analysis.GST family genes showed collinearity with 22 genes in Oryza sativa L.,and three genes in Arabidopsis thaliana;promoter cis-acting elements predicted that the GST gene family is functional in growth,hormone regulation,and abiotic stress response.Most members of the F subfamily of GST(BpGSTFs)were expressed in roots,stems,leaves,and petioles,with the most expression observed in leaves.On the basis of the expression profiles of F subfamily genes(BpGSTF1 to BpGSTF13)during salt,mannitol and ABA stress,BpGSTF proteins seem to have multiple functions depending on the type of abiotic stress;for instance,BpGSTs may function at different times during abiotic stress.This study enhances understanding of the GST gene family and provides a basis for further exploration of their function in birch.展开更多
Heat stress causes overgrowth,leaf dryness and fruit malformation,which negatively impacts cucumber quality and yield.Yet,in spite of the devastating consequences of this abiotic stress,few genes for heat tolerance in...Heat stress causes overgrowth,leaf dryness and fruit malformation,which negatively impacts cucumber quality and yield.Yet,in spite of the devastating consequences of this abiotic stress,few genes for heat tolerance in cucumber have been identified.Here,the heat injury indices of 88 cucumber accessions representing diverse ecotypes were collected in two open-field environments,with naturally occurring high temperatures over two years.Seventeen of the 88 accessions were identified as highly heat-tolerant.Using a genome-wide association study,five loci(gHII3.1,gHII3.2,gHII3.3,gHII4.1 and gHII6.1)on three chromosomes associated with heat tolerance were detected.Pairwise linkage disequilibrium correlation,sequence polymorphisms,and qRT-PCR analyses at these loci,identified five candidate genes predicted to be casual for heat stress response in cucumber.CsaV3_3G04883,CsaV3_4G029050 and CsaV3_6G005370 each had nonsynonymous SNPs,and were significantly up-regulated by heat stress in the heat-tolerant genotypes.CsaV3_3G031890 was also induced by heat stress,but in the heatsensitive genotypes,and sequence polymorphism was only found in the promoter region.Identifying these candidate genes lays a foundation for understanding cucumber thermotolerance mechanisms.Our study is one of the few to examine heat stress in adult cucumber plants and it therefore fills a critical gap in knowledge.It is also an important first-step towards accelerating the breeding of robust heat-tolerant varieties.展开更多
Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is s...Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022).展开更多
The Chinese crested duck is a unique duck breed having a bulbous feather shape on its duck head.However,the mechanisms involved in its formation and development are unclear.In the present study,RNA sequencing analysis...The Chinese crested duck is a unique duck breed having a bulbous feather shape on its duck head.However,the mechanisms involved in its formation and development are unclear.In the present study,RNA sequencing analysis was performed on the crested tissues of 6 Chinese crested ducks and the scalp tissues of 6 cherry valley ducks(CVs)from 2 developmental stages.This study identified 261 differentially expressed genes(DEGs),122 upregulated and 139 downregulated,in the E28 stage and 361 DEGs,154 upregulated and 207 downregulated in the D42 stage between CC and CV ducks.The subsequent results of weighted gene co-expression network analysis(WGCNA)revealed that the turquoise and cyan modules were associated with the crest trait in the D42 stage,meanwhile,the green,brown,and pink modules were associated with the crest trait in the E28 stage.Venn analysis of the DEGs and WGCNA showed that 145 and 45 genes are associated between the D42 and E28 stages,respectively.The expression of WNT16,BMP2,SLC35F2,SLC6A15,APOBEC2,ABHD6,TNNC2,MYL1,and TNNI2 were verified by real-time quantitative PCR.This study provides an approach to reveal the molecular mechanisms underlying the crested trait development.展开更多
BACKGROUND Colon cancer is acknowledged as one of the most common malignancies worldwide,ranking third in United States regarding incidence and mortality.Notably,approximately 40%of colon cancer cases harbor oncogenic...BACKGROUND Colon cancer is acknowledged as one of the most common malignancies worldwide,ranking third in United States regarding incidence and mortality.Notably,approximately 40%of colon cancer cases harbor oncogenic KRAS mutations,resulting in the continuous activation of epidermal growth factor receptor signaling.AIM To investigate the key pathogenic genes in KRAS mutant colon cancer holds considerable importance.METHODS Weighted gene co-expression network analysis,in combination with additional bioinformatics analysis,were conducted to screen the key factors driving the progression of KRAS mutant colon cancer.Meanwhile,various in vitro experiments were also conducted to explore the biological function of transglutaminase 2(TGM2).RESULTS Integrated analysis demonstrated that TGM2 acted as an independent prognostic factor for progression-free survival.Immunohistochemical analysis on tissue microarrays revealed that TGM2 was associated with an elevated probability of perineural invasion in patients with KRAS mutant colon cancer.Additionally,biological roles of the key gene TGM2 was also assessed,suggesting that the downregulation of TGM2 attenuated the proliferation,invasion,and migration of the KRAS mutant colon cancer cell line.CONCLUSION This study underscores the potential significance of TGM2 in the progression of KRAS mutant colon cancer.This insight not only offers a theoretical foundation for therapeutic approaches but also highlights the need for additional clinical trials and fundamental research to support our preliminary findings.展开更多
Mature oligodendrocytes form myelin sheaths that are crucial for the insulation of axons and efficient signal transmission in the central nervous system.Recent evidence has challenged the classical view of the functio...Mature oligodendrocytes form myelin sheaths that are crucial for the insulation of axons and efficient signal transmission in the central nervous system.Recent evidence has challenged the classical view of the functionally static mature oligodendrocyte and revealed a gamut of dynamic functions such as the ability to modulate neuronal circuitry and provide metabolic support to axons.Despite the recognition of potential heterogeneity in mature oligodendrocyte function,a comprehensive summary of mature oligodendrocyte diversity is lacking.We delve into early 20th-century studies by Robertson and Río-Hortega that laid the foundation for the modern identification of regional and morphological heterogeneity in mature oligodendrocytes.Indeed,recent morphologic and functional studies call into question the long-assumed homogeneity of mature oligodendrocyte function through the identification of distinct subtypes with varying myelination preferences.Furthermore,modern molecular investigations,employing techniques such as single cell/nucleus RNA sequencing,consistently unveil at least six mature oligodendrocyte subpopulations in the human central nervous system that are highly transcriptomically diverse and vary with central nervous system region.Age and disease related mature oligodendrocyte variation denotes the impact of pathological conditions such as multiple sclerosis,Alzheimer's disease,and psychiatric disorders.Nevertheless,caution is warranted when subclassifying mature oligodendrocytes because of the simplification needed to make conclusions about cell identity from temporally confined investigations.Future studies leveraging advanced techniques like spatial transcriptomics and single-cell proteomics promise a more nuanced understanding of mature oligodendrocyte heterogeneity.Such research avenues that precisely evaluate mature oligodendrocyte heterogeneity with care to understand the mitigating influence of species,sex,central nervous system region,age,and disease,hold promise for the development of therapeutic interventions targeting varied central nervous system pathology.展开更多
Degenerative cervical myelopathy is a common cause of spinal cord injury,with longer symptom duration and higher myelopathy severity indicating a worse prognosis.While numerous studies have investigated serological bi...Degenerative cervical myelopathy is a common cause of spinal cord injury,with longer symptom duration and higher myelopathy severity indicating a worse prognosis.While numerous studies have investigated serological biomarkers for acute spinal cord injury,few studies have explored such biomarkers for diagnosing degenerative cervical myelopathy.This study involved 30 patients with degenerative cervical myelopathy(51.3±7.3 years old,12 women and 18 men),seven healthy controls(25.7±1.7 years old,one woman and six men),and nine patients with cervical spondylotic radiculopathy(51.9±8.6 years old,three women and six men).Analysis of blood samples from the three groups showed clear differences in transcriptomic characteristics.Enrichment analysis identified 128 differentially expressed genes that were enriched in patients with neurological disabilities.Using least absolute shrinkage and selection operator analysis,we constructed a five-gene model(TBCD,TPM2,PNKD,EIF4G2,and AP5Z1)to diagnose degenerative cervical myelopathy with an accuracy of 93.5%.One-gene models(TCAP and SDHA)identified mild and severe degenerative cervical myelopathy with accuracies of 83.3%and 76.7%,respectively.Signatures of two immune cell types(memory B cells and memory-activated CD4^(+)T cells)predicted levels of lesions in degenerative cervical myelopathy with 80%accuracy.Our results suggest that peripheral blood RNA biomarkers could be used to predict lesion severity in degenerative cervical myelopathy.展开更多
BACKGROUND Colorectal cancer(CRC)remains a major global health burden due to its high incidence and mortality,with treatment efficacy often hindered by tumor hetero-geneity,drug resistance,and a complex tumor microenv...BACKGROUND Colorectal cancer(CRC)remains a major global health burden due to its high incidence and mortality,with treatment efficacy often hindered by tumor hetero-geneity,drug resistance,and a complex tumor microenvironment(TME).Lactate metabolism plays a pivotal role in reshaping the TME,promoting immune eva-sion and epithelial-mesenchymal transition,making it a promising target for novel therapeutic strategies and prognostic modeling in CRC.AIM To offer an in-depth analysis of the role of lactate metabolism in CRC,high-lighting its significance in the TME and therapeutic response.METHODS Utilizing single-cell and transcriptomic data from the Gene Expression Omnibus and The Cancer Genome Atlas,we identified key lactate metabolic activities,particularly in the monocyte/macrophage subpopulation.RESULTS Seven lactate metabolism-associated genes were significantly linked to CRC prognosis and used to construct a predictive model.This model accurately forecasts patient outcomes and reveals notable distinct patterns of immune infiltration and transcriptomic profiles mutation profiles between high-and low-risk groups.High-risk patients demonstrated elevated immune cell infiltration,increased mutation frequencies,and heightened sensitivity to specific drugs(AZD6482,tozasertib,and SB216763),providing a foundation for personalized treatment approaches.Additionally,a nomogram integrating clinical and metabolic data effectively predicted 1-,3-,and 5-year survival rates.CONCLUSION This report underscored the pivotal mechanism of lactate metabolism in CRC prognosis and suggest novel avenues for therapeutic intervention.展开更多
Objective:To identify promising biomarkers for the pathogenesis of major depressive disorder(MDD).Methods:Microarray chips of MDD patients,including the GSE98793,GSE52790,and GSE39653 datasets,were obtained from the G...Objective:To identify promising biomarkers for the pathogenesis of major depressive disorder(MDD).Methods:Microarray chips of MDD patients,including the GSE98793,GSE52790,and GSE39653 datasets,were obtained from the Gene Expression Omnibus database.The biological processes and pathways related to MDD were investigated using the GO and KEGG pathway tools.Weighted gene coexpression network analysis was conducted to identify modules related to MDD.The hub genes associated with MDD were obtained via protein-protein interaction analysis.Finally,the expression of hub genes in the hippocampal tissues of depression-like rats was detected by reverse transcription-polymerase chain reaction and Western blotting.Results:A total of 658 differentially expressed genes were identified from the Gene Expression Omnibus datasets;thus,these genes and the GSE98793 dataset were used to conduct weighted gene coexpression network analysis.A total of 244 module-related genes were identified and these genes were highly correlated with MDD.These genes were involved in the Ras signaling pathway,regulation of the actin cytoskeleton,and axon guidance according to the KEGG analysis.Hub genes,including MAPK14,SOCS1,TLR2,PTK2B,and GRB2,were obtained via protein-protein interaction analysis.All these hub genes showed better diagnostic efficiency in the GSE52790,GSE39653,and GSE98793 datasets.In vivo experiments revealed that compared with those in control rats,SOCS1 and MAPK14 expression was significantly decreased;while GRB2,TLR2,and PTK2B expression was increased in the hippocampi of depression-like rats.Conclusions:Our study demonstrates that GRB2,TLR2,SOCS1,PTK2B,and MAPK14 are promising hub genes,and targeting these five genes may be an effective treatment strategy for MDD.展开更多
BACKGROUND Lotus plumule and its active components have demonstrated inhibitory effects on gastric cancer(GC).However,the molecular mechanism of lotus plumule against GC remains unclear and requires further investigat...BACKGROUND Lotus plumule and its active components have demonstrated inhibitory effects on gastric cancer(GC).However,the molecular mechanism of lotus plumule against GC remains unclear and requires further investigation.AIM To identify the key hub genes associated with the anti-GC effects of lotus plumule.METHODS This study investigated the potential targets of traditional Chinese medicine for inhibiting GC using weighted gene co-expression network analysis and bio-informatics.Initially,the active components and targets of the lotus plumule and the differentially expressed genes associated with GC were identified.Sub-sequently,a protein-protein interaction network was constructed to elucidate the interactions between drug targets and disease-related genes,facilitating the identification of hub genes within the network.The clinical significance of these hub genes was evaluated,and their upstream transcription factors and down-stream targets were identified.The binding ability of a hub gene with its down-stream targets was verified using molecular docking technology.Finally,molecular docking was performed to evaluate the binding affinity between the active ingredients of lotus plumule and the hub gene.RESULTS This study identified 26 genes closely associated with GC.Machine learning analysis and external validation narrowed the list to four genes:Aldo-keto reductase family 1 member B10,fructose-bisphosphatase 1,protein arginine methyltransferase 1,and carbonic anhydrase 9.These genes indicated a strong correlation with anti-GC activity.CONCLUSION Lotus plumule exhibits anti-GC effects.This study identified four hub genes with potential as novel targets for diagnosing and treating GC,providing innovative perspectives for its clinical management.展开更多
Background:Tetralogy of Fallot(TOF),the predominant cyanotic congenital heart defect,arisesfrom multifactorial gene-envirorment interactions disrup ting cardiac developmental networks.This studyinvestiga ted TOF-speci...Background:Tetralogy of Fallot(TOF),the predominant cyanotic congenital heart defect,arisesfrom multifactorial gene-envirorment interactions disrup ting cardiac developmental networks.This studyinvestiga ted TOF-specific transcriptional alterations and identified high-confidence candidate genes.Methods:Based on GSE36761 transcriptome data,a weighted gene co-exp ression network analysis(WGCNA)andprotein-protein interaction(PPI)network were conducted to identify TOF-related sub-netrwork and Hub genes.The potentialbiological functions among these genes were revealed by enrichment analysis.Genetic,epigeneticand transcriptional alteration in the Fub genes were analyzed with leveraged public resources:a methylationdataset(CSE62629)and two single-cell datasets(EGAS00001003996 and GSE126128),Results:Eight Hub geneswere identified using the WGCNA network and PPl network,and functional errichment analysis revealedthatGJA1,RUNX2,FTK7,PRICKLE1,and SPRP1 were involved in the morphogenesis of an epithelium,anddysregulation of the signaling were also found in the other two TOF datasets,Furthermore,the study foundthat the promoters of GJA1,RUNX2,FTK7,and PRICKLE1 genes were hypermethylated and that GJA1 andSFRP1 are highly expressed in mouse second heart field cells and neural crest cells,and the la tter is expressedin human embry onic outflow tract cells.Since RUNX2 was not expressed in human and mouse embryonichearts,GJA1,FTK7,PRICKLE1,and SPRP1 were ultimately identified as TOF candidate genes.Conclusion:Based on the WGCNA network and various bioinformatics analysis approaches,we screened 4 TOF candidatepathogenic genes,and found that the signaling pathways related to the morphogenesis of an epithelium maybe involved in the pathogenesis of TOF.展开更多
Plant height is one of the important agronomic traits of rice. Over higher plant would easily result in plant lodging and output reducing. On the other hand, the dwarf varieties with proper plant height had higher lod...Plant height is one of the important agronomic traits of rice. Over higher plant would easily result in plant lodging and output reducing. On the other hand, the dwarf varieties with proper plant height had higher lodging resistance and a greater harvest index, allowing for the increased use of nitrogen fertilizer. Dwarf breeding had made a great breakthrough in the rice breeding. The breeding and extension of excellent dwarf varieties remarkably improved the yield potential of rice. Therefore, the plant height is still one of the focuses in rice genetic research.展开更多
Stripe rust,caused by Puccinia striiformis f.sp.tritici(Pst),is a devastating disease in wheat worldwide.Discovering and characterizing new resistance genes/QTL is crucial for wheat breeding programs.In this study,we ...Stripe rust,caused by Puccinia striiformis f.sp.tritici(Pst),is a devastating disease in wheat worldwide.Discovering and characterizing new resistance genes/QTL is crucial for wheat breeding programs.In this study,we fine-mapped and characterized a stripe rust resistance gene,YRAYH,on chromosome arm 5BL in the Chinese wheat landrace Anyuehong(AYH).Evaluations of stripe rust response to prevalent Chinese Pst races in near-isogenic lines derived from a cross of Anyuehong and Taichung 29 showed that YrAYH conferred a high level of resistance at all growth stages.Fine mapping using a large segregating population of 9748 plants,narrowed the YRAYH locus to a 3.7 Mb interval on chromosome arm 5BL that included 61 annotated genes.Transcriptome analysis of two NIL pairs identified 64 upregulated differentially expressed genes(DEGs)in the resistant NILs(NILs-R).Annotations indicated that many of these genes have roles in plant disease resistance pathways.Through a combined approach of fine-mapping and transcriptome sequencing,we identified a serine/threonine-protein kinase SRPK as a candidate gene underlying YrAYH.A unique 25 bp insertion was identified in the NILs-R compared to the NILs-S and previously published wheat genomes.An InDel marker was developed and co-segregated with YrAYH.Agronomic trait evaluation of the NILs suggested that YrAYH not only reduces the impact of stripe rust but was also associated with a gene that increases plant height and spike length.展开更多
A strain of gram-positive bacillus was isolated from suppurative lung organs of nursery pigs in a pig farm, which was further characterized by morphological observation, cultivation test, biochemical test, drug sensit...A strain of gram-positive bacillus was isolated from suppurative lung organs of nursery pigs in a pig farm, which was further characterized by morphological observation, cultivation test, biochemical test, drug sensitivity test, pathogenicity test and 16S rDNA gene cloning and sequence analysis. The results showed that the isolate grew well in rabbit blood agar plate and horse serum tryptone soybean agar （TSA） plate under aerobic condition, which could lead to mortality of mice and were susceptible to cephalosporin antibiotics and fluoroquinolone antibiotics. Phylogenetic analysis showed that the isolate had close genetic evolutionary relationships with Corynebacterium bacteria, and the sequence of 16S rRNA gene shared the homology of 91.7% -98.3% with the representative strain of coryne- bacteria, indicating the isolated strain was eorynebactefium.展开更多
Many eukaryotic genes are members of multi-gene families due to gene duplications, which generate new copies that allow functional divergence. However, the relationship between
AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression lev...AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study.METHODS: Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus(GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes.The function of the genes were annotated by gene ontology(GO).RESULTS: In this study, we identified four co-expression modules significantly correlated with clinictraits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location(sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter(LTD). Additionally, we identified the hug gene(top connectivity with other genes) in each module. The hub gene RPS15 A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma.CONCLUSION: From WGCNA analysis and hub gene calculation, we identified RPS15 A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma.展开更多
Study of gene expression has been arguably the most active research field in functional genomics.Over the last two decades,various high-throughput technologies,from gene expression microarray to RNA-seq,have been wide...Study of gene expression has been arguably the most active research field in functional genomics.Over the last two decades,various high-throughput technologies,from gene expression microarray to RNA-seq,have been widely applied to the wholegenome profiling of gene expression.The commonality of these experiments is that they measure the gene expression levels of"bulk"sample,which pools a large number(often in the scale of millions)of cells,and thus the measurements reflect the average expression展开更多
Objective： In this study, we aimed to expand current knowledge of head and neck squamous cell carcinoma （HNSCC）-associated long noncoding RNAs （IncRNAs）, and to discover potential IncRNA prognostic biomarkers for...Objective： In this study, we aimed to expand current knowledge of head and neck squamous cell carcinoma （HNSCC）-associated long noncoding RNAs （IncRNAs）, and to discover potential IncRNA prognostic biomarkers for HNSCC based on next-generation RNA-seq. Methods： RNA-seq data of 546 samples from patients with HNSCC were downloaded from The Cancer Genome Atlas （TCGA）, including 43 paired samples of tumor tissue and adjacent normal tissue. An integrated analysis incorporating differential expression, weighted gene co-expression networks, functional enrichment, clinical parameters, and survival analysis was conducted to discover HNSCC-associated IncRNAs. The function of CYTOR was verified by cell-based experiments. To further identify IncRNAs with prognostic significance, a multivariate Cox proportional hazard regression analysis was performed. The identified IncRNAs were validated with an independent cohort using clinical feature relevance analysis and multivariate Cox regression analysis. Results： We identified nine HNSCC-relevant IncRNAs likely to play pivotal roles in HNSCC onset and development. By functional enrichment analysis, we revealed that CYTOR might participate in the multistep pathological processes of cancer, such as ribosome biogenesis and maintenance of genomic stability. CY-I-OR was identified to be positively correlated with lymph node metastasis, and significantly negatively correlated with overall survival （OS） and disease free survival （DFS） of HNSCC patients. Moreover, CYTOR inhibited cell apoptosis following treatment with the chemotherapeutic drug diamminedichloroplatinum （DDP）. HCG22, the most dramatically down-regulated IncRNA in tumor tissue, may function in epidermis differentiation. It was also significantly associated with several clinical features of patients with HNSCC, and positively correlated with patient survival. CYTOR and HCG22 maintained their prognostic values in- dependent of several clinical features in multivariate Cox hazards analysis. Notably, validation either based on an independent HNSCC cohort or by laboratory experiments confirmed these findings. Conclusions： Our transcriptomic analysis suggested that dysregulation of these HNSCC-associated IncRNAs might be involved in HNSCC oncogenesis and progression. Moreover, CYTOR and HCG22 were confirmed as two independent prognostic factors for HNSCC patient survival, providing new insights into the roles of these IncRNAs in HNSCC as well as clinical applications.展开更多
基金supported by grants from the Project of Creating High Quality,Disease Resistance and High Combining Ability CMS Lines(Grant No.cstc2018jscx-msybX0250)Chongqing Technology Innovation and Application Demonstration Project and the Project of High Photosynthetic Efficiency Rice Breeding Technology System(Grant No.2017YFD0100201)the National Key Research and Development Program“Seven Crops Breeding”.
文摘Leaf color mutants are ideal materials for studying many plant physiological and metabolic processes such as photosynthesis,photomorphogenesis,hormone physiology and disease resistance.In this study,the genetically stable yellow-green leaf mutant ygl16 was identified from mutated“Xinong 1B”.Compared with the wild type,the pigment concentration and photosynthetic capacity of the ygl16 decreased significantly.The ultrastructural observation showed that the distribution of thylakoid lamellae was irregular in ygl16 chloroplasts,and the grana and matrix lamellae were blurred and loose in varied degrees,and the chloroplast structure was disordered,while the osmiophilic corpuscles increased.The results of the genetic analysis and mapping showed that the phenotype of ygl16 was controlled by a pair of recessive nuclear gene.The gene located in the 56Kb interval between RM25654 and R3 on the long arm of chromosome 10.The sequencing results showed that the 121st base of the first intron of the candidate gene OsPORB/FGL changed from A to T in the interval.qRT-PCR results showed that the expression of chlorophyll synthase-related genes in the mutant decreased.
文摘DNA microarray technology is an extremely effective technique for studying gene expression patterns in cells, and the main challenge currently faced by this technology is how to analyze the large amount of gene expression data generated. To address this, this paper employs a mixed-effects model to analyze gene expression data. In terms of data selection, 1176 genes from the white mouse gene expression dataset under two experimental conditions were chosen, setting up two conditions: pneumococcal infection and no infection, and constructing a mixed-effects model. After preprocessing the gene chip information, the data were imported into the model, preliminary results were calculated, and permutation tests were performed to biologically validate the preliminary results using GSEA. The final dataset consists of 20 groups of gene expression data from pneumococcal infection, which categorizes functionally related genes based on the similarity of their expression profiles, facilitating the study of genes with unknown functions.
基金supported by the National Key Research and Development Program of China(No.2021YFD2200304)FundamentalResearch Funds for the Central Universities(2572022DQ08)the National Natural Science Foundation of China(No32171738).
文摘Glutathione-S-transferase(GST,EC2.5.1.18)multifunctional protease is important for detoxification,defense against biotic and abiotic stresses,and secondary metabolic material transport for plant growth and development.In this study,71 members of the BpGST family were identified from the entire Betula platyphylla Suk.genome.Most of the members encode proteins with amino acid lengths ranging from 101 to 875 and were localized to the cytoplasm by a prediction.BpGSTs can be divided into seven subfamilies,with a majority of birch U and F subfamily members according to gene structure,conserved motifs and evolutionary analysis.GST family genes showed collinearity with 22 genes in Oryza sativa L.,and three genes in Arabidopsis thaliana;promoter cis-acting elements predicted that the GST gene family is functional in growth,hormone regulation,and abiotic stress response.Most members of the F subfamily of GST(BpGSTFs)were expressed in roots,stems,leaves,and petioles,with the most expression observed in leaves.On the basis of the expression profiles of F subfamily genes(BpGSTF1 to BpGSTF13)during salt,mannitol and ABA stress,BpGSTF proteins seem to have multiple functions depending on the type of abiotic stress;for instance,BpGSTs may function at different times during abiotic stress.This study enhances understanding of the GST gene family and provides a basis for further exploration of their function in birch.
基金supported by Beijing Joint Research Program for Germplasm Innovation and New Variety Breeding(Grant No.G20220628003-03)Chongqing Municipal People's Government and Chinese Academy of Agricultural Sciences strategic cooperation project,Key-Area Research and Development Program of Guangdong Province(Grant No.2020B020220001)+3 种基金the Earmarked Fund for Modern Agro-industry Technology Research System(Grant No.CARS-23)Science and Technology Innovation Program of the Chinese Academy of Agricultural Science(Grant No.CAAS-ASTIP-IVFCAAS)Central public-interest Scientific Institution Basal Research Fund(Grant No.Y2017PT52)the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops,Ministry of Agriculture,P.R.China。
文摘Heat stress causes overgrowth,leaf dryness and fruit malformation,which negatively impacts cucumber quality and yield.Yet,in spite of the devastating consequences of this abiotic stress,few genes for heat tolerance in cucumber have been identified.Here,the heat injury indices of 88 cucumber accessions representing diverse ecotypes were collected in two open-field environments,with naturally occurring high temperatures over two years.Seventeen of the 88 accessions were identified as highly heat-tolerant.Using a genome-wide association study,five loci(gHII3.1,gHII3.2,gHII3.3,gHII4.1 and gHII6.1)on three chromosomes associated with heat tolerance were detected.Pairwise linkage disequilibrium correlation,sequence polymorphisms,and qRT-PCR analyses at these loci,identified five candidate genes predicted to be casual for heat stress response in cucumber.CsaV3_3G04883,CsaV3_4G029050 and CsaV3_6G005370 each had nonsynonymous SNPs,and were significantly up-regulated by heat stress in the heat-tolerant genotypes.CsaV3_3G031890 was also induced by heat stress,but in the heatsensitive genotypes,and sequence polymorphism was only found in the promoter region.Identifying these candidate genes lays a foundation for understanding cucumber thermotolerance mechanisms.Our study is one of the few to examine heat stress in adult cucumber plants and it therefore fills a critical gap in knowledge.It is also an important first-step towards accelerating the breeding of robust heat-tolerant varieties.
基金supported by the Notional Natural Science Foundation of China,No.81960417 (to JX)Guangxi Key Research and Development Program,No.GuiKeA B20159027 (to JX)the Natural Science Foundation of Guangxi Zhuang Autonomous Region,No.2022GXNSFBA035545 (to YG)。
文摘Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022).
基金supported by the earmarked fund for CARS,China(CARS-42)the earmarked fund for Jiangsu Agricultural Industry Technology System,China(JATS(2022)331)the Jiangsu Key Research and Development Program,China(BE2021332)。
文摘The Chinese crested duck is a unique duck breed having a bulbous feather shape on its duck head.However,the mechanisms involved in its formation and development are unclear.In the present study,RNA sequencing analysis was performed on the crested tissues of 6 Chinese crested ducks and the scalp tissues of 6 cherry valley ducks(CVs)from 2 developmental stages.This study identified 261 differentially expressed genes(DEGs),122 upregulated and 139 downregulated,in the E28 stage and 361 DEGs,154 upregulated and 207 downregulated in the D42 stage between CC and CV ducks.The subsequent results of weighted gene co-expression network analysis(WGCNA)revealed that the turquoise and cyan modules were associated with the crest trait in the D42 stage,meanwhile,the green,brown,and pink modules were associated with the crest trait in the E28 stage.Venn analysis of the DEGs and WGCNA showed that 145 and 45 genes are associated between the D42 and E28 stages,respectively.The expression of WNT16,BMP2,SLC35F2,SLC6A15,APOBEC2,ABHD6,TNNC2,MYL1,and TNNI2 were verified by real-time quantitative PCR.This study provides an approach to reveal the molecular mechanisms underlying the crested trait development.
基金Supported by National Nature Science Foundation of China,No.82100195China Postdoctoral Science Foundation,No.2021M700777Medical Research Project of Foshan Municipal Health Bureau,No.20230349.
文摘BACKGROUND Colon cancer is acknowledged as one of the most common malignancies worldwide,ranking third in United States regarding incidence and mortality.Notably,approximately 40%of colon cancer cases harbor oncogenic KRAS mutations,resulting in the continuous activation of epidermal growth factor receptor signaling.AIM To investigate the key pathogenic genes in KRAS mutant colon cancer holds considerable importance.METHODS Weighted gene co-expression network analysis,in combination with additional bioinformatics analysis,were conducted to screen the key factors driving the progression of KRAS mutant colon cancer.Meanwhile,various in vitro experiments were also conducted to explore the biological function of transglutaminase 2(TGM2).RESULTS Integrated analysis demonstrated that TGM2 acted as an independent prognostic factor for progression-free survival.Immunohistochemical analysis on tissue microarrays revealed that TGM2 was associated with an elevated probability of perineural invasion in patients with KRAS mutant colon cancer.Additionally,biological roles of the key gene TGM2 was also assessed,suggesting that the downregulation of TGM2 attenuated the proliferation,invasion,and migration of the KRAS mutant colon cancer cell line.CONCLUSION This study underscores the potential significance of TGM2 in the progression of KRAS mutant colon cancer.This insight not only offers a theoretical foundation for therapeutic approaches but also highlights the need for additional clinical trials and fundamental research to support our preliminary findings.
基金supported by a grant from the Progressive MS Alliance(BRAVE in MS)Le Grand Portage Fund。
文摘Mature oligodendrocytes form myelin sheaths that are crucial for the insulation of axons and efficient signal transmission in the central nervous system.Recent evidence has challenged the classical view of the functionally static mature oligodendrocyte and revealed a gamut of dynamic functions such as the ability to modulate neuronal circuitry and provide metabolic support to axons.Despite the recognition of potential heterogeneity in mature oligodendrocyte function,a comprehensive summary of mature oligodendrocyte diversity is lacking.We delve into early 20th-century studies by Robertson and Río-Hortega that laid the foundation for the modern identification of regional and morphological heterogeneity in mature oligodendrocytes.Indeed,recent morphologic and functional studies call into question the long-assumed homogeneity of mature oligodendrocyte function through the identification of distinct subtypes with varying myelination preferences.Furthermore,modern molecular investigations,employing techniques such as single cell/nucleus RNA sequencing,consistently unveil at least six mature oligodendrocyte subpopulations in the human central nervous system that are highly transcriptomically diverse and vary with central nervous system region.Age and disease related mature oligodendrocyte variation denotes the impact of pathological conditions such as multiple sclerosis,Alzheimer's disease,and psychiatric disorders.Nevertheless,caution is warranted when subclassifying mature oligodendrocytes because of the simplification needed to make conclusions about cell identity from temporally confined investigations.Future studies leveraging advanced techniques like spatial transcriptomics and single-cell proteomics promise a more nuanced understanding of mature oligodendrocyte heterogeneity.Such research avenues that precisely evaluate mature oligodendrocyte heterogeneity with care to understand the mitigating influence of species,sex,central nervous system region,age,and disease,hold promise for the development of therapeutic interventions targeting varied central nervous system pathology.
基金supported by Hunan Provincial Key Research and Development Program,No.2021SK2002(to BW)the Natural Science Foundation of Hunan Province of China(General Program),No.2021JJ30938(to YL)。
文摘Degenerative cervical myelopathy is a common cause of spinal cord injury,with longer symptom duration and higher myelopathy severity indicating a worse prognosis.While numerous studies have investigated serological biomarkers for acute spinal cord injury,few studies have explored such biomarkers for diagnosing degenerative cervical myelopathy.This study involved 30 patients with degenerative cervical myelopathy(51.3±7.3 years old,12 women and 18 men),seven healthy controls(25.7±1.7 years old,one woman and six men),and nine patients with cervical spondylotic radiculopathy(51.9±8.6 years old,three women and six men).Analysis of blood samples from the three groups showed clear differences in transcriptomic characteristics.Enrichment analysis identified 128 differentially expressed genes that were enriched in patients with neurological disabilities.Using least absolute shrinkage and selection operator analysis,we constructed a five-gene model(TBCD,TPM2,PNKD,EIF4G2,and AP5Z1)to diagnose degenerative cervical myelopathy with an accuracy of 93.5%.One-gene models(TCAP and SDHA)identified mild and severe degenerative cervical myelopathy with accuracies of 83.3%and 76.7%,respectively.Signatures of two immune cell types(memory B cells and memory-activated CD4^(+)T cells)predicted levels of lesions in degenerative cervical myelopathy with 80%accuracy.Our results suggest that peripheral blood RNA biomarkers could be used to predict lesion severity in degenerative cervical myelopathy.
基金Supported by Henan Province Science and Technology Research Project,No.232102310043Henan Provincial Science and Technology Research and Development Plan Joint Fund,No.222103810047Key Scientific Research Project Plan of Colleges and Universities in Henan Province,No.22A320033.
文摘BACKGROUND Colorectal cancer(CRC)remains a major global health burden due to its high incidence and mortality,with treatment efficacy often hindered by tumor hetero-geneity,drug resistance,and a complex tumor microenvironment(TME).Lactate metabolism plays a pivotal role in reshaping the TME,promoting immune eva-sion and epithelial-mesenchymal transition,making it a promising target for novel therapeutic strategies and prognostic modeling in CRC.AIM To offer an in-depth analysis of the role of lactate metabolism in CRC,high-lighting its significance in the TME and therapeutic response.METHODS Utilizing single-cell and transcriptomic data from the Gene Expression Omnibus and The Cancer Genome Atlas,we identified key lactate metabolic activities,particularly in the monocyte/macrophage subpopulation.RESULTS Seven lactate metabolism-associated genes were significantly linked to CRC prognosis and used to construct a predictive model.This model accurately forecasts patient outcomes and reveals notable distinct patterns of immune infiltration and transcriptomic profiles mutation profiles between high-and low-risk groups.High-risk patients demonstrated elevated immune cell infiltration,increased mutation frequencies,and heightened sensitivity to specific drugs(AZD6482,tozasertib,and SB216763),providing a foundation for personalized treatment approaches.Additionally,a nomogram integrating clinical and metabolic data effectively predicted 1-,3-,and 5-year survival rates.CONCLUSION This report underscored the pivotal mechanism of lactate metabolism in CRC prognosis and suggest novel avenues for therapeutic intervention.
基金supported by the National Natural Science Foundation of China(No.81774281 and No.82474303)the Natural Science Foundation of Hunan Province(2023JJ30888)the leading national joint discipline of Chinese and Western medicines to the Chinese Medicine Department,Xiangya Hospital,CSU.
文摘Objective:To identify promising biomarkers for the pathogenesis of major depressive disorder(MDD).Methods:Microarray chips of MDD patients,including the GSE98793,GSE52790,and GSE39653 datasets,were obtained from the Gene Expression Omnibus database.The biological processes and pathways related to MDD were investigated using the GO and KEGG pathway tools.Weighted gene coexpression network analysis was conducted to identify modules related to MDD.The hub genes associated with MDD were obtained via protein-protein interaction analysis.Finally,the expression of hub genes in the hippocampal tissues of depression-like rats was detected by reverse transcription-polymerase chain reaction and Western blotting.Results:A total of 658 differentially expressed genes were identified from the Gene Expression Omnibus datasets;thus,these genes and the GSE98793 dataset were used to conduct weighted gene coexpression network analysis.A total of 244 module-related genes were identified and these genes were highly correlated with MDD.These genes were involved in the Ras signaling pathway,regulation of the actin cytoskeleton,and axon guidance according to the KEGG analysis.Hub genes,including MAPK14,SOCS1,TLR2,PTK2B,and GRB2,were obtained via protein-protein interaction analysis.All these hub genes showed better diagnostic efficiency in the GSE52790,GSE39653,and GSE98793 datasets.In vivo experiments revealed that compared with those in control rats,SOCS1 and MAPK14 expression was significantly decreased;while GRB2,TLR2,and PTK2B expression was increased in the hippocampi of depression-like rats.Conclusions:Our study demonstrates that GRB2,TLR2,SOCS1,PTK2B,and MAPK14 are promising hub genes,and targeting these five genes may be an effective treatment strategy for MDD.
基金Supported by Ningxia Key Research and Development Program,No.2023BEG02015Talent Development Projects of Young Qihuang of National Administration of Traditional Chinese Medicine(2020).
文摘BACKGROUND Lotus plumule and its active components have demonstrated inhibitory effects on gastric cancer(GC).However,the molecular mechanism of lotus plumule against GC remains unclear and requires further investigation.AIM To identify the key hub genes associated with the anti-GC effects of lotus plumule.METHODS This study investigated the potential targets of traditional Chinese medicine for inhibiting GC using weighted gene co-expression network analysis and bio-informatics.Initially,the active components and targets of the lotus plumule and the differentially expressed genes associated with GC were identified.Sub-sequently,a protein-protein interaction network was constructed to elucidate the interactions between drug targets and disease-related genes,facilitating the identification of hub genes within the network.The clinical significance of these hub genes was evaluated,and their upstream transcription factors and down-stream targets were identified.The binding ability of a hub gene with its down-stream targets was verified using molecular docking technology.Finally,molecular docking was performed to evaluate the binding affinity between the active ingredients of lotus plumule and the hub gene.RESULTS This study identified 26 genes closely associated with GC.Machine learning analysis and external validation narrowed the list to four genes:Aldo-keto reductase family 1 member B10,fructose-bisphosphatase 1,protein arginine methyltransferase 1,and carbonic anhydrase 9.These genes indicated a strong correlation with anti-GC activity.CONCLUSION Lotus plumule exhibits anti-GC effects.This study identified four hub genes with potential as novel targets for diagnosing and treating GC,providing innovative perspectives for its clinical management.
基金supported by the National Natural Science Found ation of China(No.8230045i for Zhen Wang,82302230 for jiawei Shi,82202194 for Jing Wang and 82171961 for Haiyan Cao).
文摘Background:Tetralogy of Fallot(TOF),the predominant cyanotic congenital heart defect,arisesfrom multifactorial gene-envirorment interactions disrup ting cardiac developmental networks.This studyinvestiga ted TOF-specific transcriptional alterations and identified high-confidence candidate genes.Methods:Based on GSE36761 transcriptome data,a weighted gene co-exp ression network analysis(WGCNA)andprotein-protein interaction(PPI)network were conducted to identify TOF-related sub-netrwork and Hub genes.The potentialbiological functions among these genes were revealed by enrichment analysis.Genetic,epigeneticand transcriptional alteration in the Fub genes were analyzed with leveraged public resources:a methylationdataset(CSE62629)and two single-cell datasets(EGAS00001003996 and GSE126128),Results:Eight Hub geneswere identified using the WGCNA network and PPl network,and functional errichment analysis revealedthatGJA1,RUNX2,FTK7,PRICKLE1,and SPRP1 were involved in the morphogenesis of an epithelium,anddysregulation of the signaling were also found in the other two TOF datasets,Furthermore,the study foundthat the promoters of GJA1,RUNX2,FTK7,and PRICKLE1 genes were hypermethylated and that GJA1 andSFRP1 are highly expressed in mouse second heart field cells and neural crest cells,and the la tter is expressedin human embry onic outflow tract cells.Since RUNX2 was not expressed in human and mouse embryonichearts,GJA1,FTK7,PRICKLE1,and SPRP1 were ultimately identified as TOF candidate genes.Conclusion:Based on the WGCNA network and various bioinformatics analysis approaches,we screened 4 TOF candidatepathogenic genes,and found that the signaling pathways related to the morphogenesis of an epithelium maybe involved in the pathogenesis of TOF.
文摘Plant height is one of the important agronomic traits of rice. Over higher plant would easily result in plant lodging and output reducing. On the other hand, the dwarf varieties with proper plant height had higher lodging resistance and a greater harvest index, allowing for the increased use of nitrogen fertilizer. Dwarf breeding had made a great breakthrough in the rice breeding. The breeding and extension of excellent dwarf varieties remarkably improved the yield potential of rice. Therefore, the plant height is still one of the focuses in rice genetic research.
基金supported by grants from the Major Program of National Agricultural Science and Technology of China(NK20220607)the National Natural Science Foundation of China(32272059 and 31971883)the Science and Technology Department of Sichuan Province(2021YFYZ0002,2022ZDZX0014,and 2023NSFSC1995)。
文摘Stripe rust,caused by Puccinia striiformis f.sp.tritici(Pst),is a devastating disease in wheat worldwide.Discovering and characterizing new resistance genes/QTL is crucial for wheat breeding programs.In this study,we fine-mapped and characterized a stripe rust resistance gene,YRAYH,on chromosome arm 5BL in the Chinese wheat landrace Anyuehong(AYH).Evaluations of stripe rust response to prevalent Chinese Pst races in near-isogenic lines derived from a cross of Anyuehong and Taichung 29 showed that YrAYH conferred a high level of resistance at all growth stages.Fine mapping using a large segregating population of 9748 plants,narrowed the YRAYH locus to a 3.7 Mb interval on chromosome arm 5BL that included 61 annotated genes.Transcriptome analysis of two NIL pairs identified 64 upregulated differentially expressed genes(DEGs)in the resistant NILs(NILs-R).Annotations indicated that many of these genes have roles in plant disease resistance pathways.Through a combined approach of fine-mapping and transcriptome sequencing,we identified a serine/threonine-protein kinase SRPK as a candidate gene underlying YrAYH.A unique 25 bp insertion was identified in the NILs-R compared to the NILs-S and previously published wheat genomes.An InDel marker was developed and co-segregated with YrAYH.Agronomic trait evaluation of the NILs suggested that YrAYH not only reduces the impact of stripe rust but was also associated with a gene that increases plant height and spike length.
基金Supported by Research Project of Guangxi Bureau of Fishery Sciences and Animal Husbandry and Veterinary(GYMK 12049031,1304522)Research Project of Xixiangtang District in Nanning City(2014304,2014302)Systematic Research Project for Key Laboratory of Livestock and Poultry Vaccine New Technology in Guangxi Province(12-071-28-A-5)
文摘A strain of gram-positive bacillus was isolated from suppurative lung organs of nursery pigs in a pig farm, which was further characterized by morphological observation, cultivation test, biochemical test, drug sensitivity test, pathogenicity test and 16S rDNA gene cloning and sequence analysis. The results showed that the isolate grew well in rabbit blood agar plate and horse serum tryptone soybean agar （TSA） plate under aerobic condition, which could lead to mortality of mice and were susceptible to cephalosporin antibiotics and fluoroquinolone antibiotics. Phylogenetic analysis showed that the isolate had close genetic evolutionary relationships with Corynebacterium bacteria, and the sequence of 16S rRNA gene shared the homology of 91.7% -98.3% with the representative strain of coryne- bacteria, indicating the isolated strain was eorynebactefium.
文摘Many eukaryotic genes are members of multi-gene families due to gene duplications, which generate new copies that allow functional divergence. However, the relationship between
基金Supported by the National Natural Science Foundation of China(No.81271019No.61463046)Gansu Province Science Foundation for Youths(No.145RJYA282)
文摘AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study.METHODS: Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus(GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes.The function of the genes were annotated by gene ontology(GO).RESULTS: In this study, we identified four co-expression modules significantly correlated with clinictraits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location(sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter(LTD). Additionally, we identified the hug gene(top connectivity with other genes) in each module. The hub gene RPS15 A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma.CONCLUSION: From WGCNA analysis and hub gene calculation, we identified RPS15 A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma.
基金partially supported by NIH grants (2U19AI090023,5P30AI50409,and R01GM122083)
文摘Study of gene expression has been arguably the most active research field in functional genomics.Over the last two decades,various high-throughput technologies,from gene expression microarray to RNA-seq,have been widely applied to the wholegenome profiling of gene expression.The commonality of these experiments is that they measure the gene expression levels of"bulk"sample,which pools a large number(often in the scale of millions)of cells,and thus the measurements reflect the average expression
基金Project supported by the National Natural Science Foundation of China(Nos.31471226 and 91440108)the Fundamental Research Funds for the Central Universities(Nos.WK2070000044 and WK2070000034),China
文摘Objective： In this study, we aimed to expand current knowledge of head and neck squamous cell carcinoma （HNSCC）-associated long noncoding RNAs （IncRNAs）, and to discover potential IncRNA prognostic biomarkers for HNSCC based on next-generation RNA-seq. Methods： RNA-seq data of 546 samples from patients with HNSCC were downloaded from The Cancer Genome Atlas （TCGA）, including 43 paired samples of tumor tissue and adjacent normal tissue. An integrated analysis incorporating differential expression, weighted gene co-expression networks, functional enrichment, clinical parameters, and survival analysis was conducted to discover HNSCC-associated IncRNAs. The function of CYTOR was verified by cell-based experiments. To further identify IncRNAs with prognostic significance, a multivariate Cox proportional hazard regression analysis was performed. The identified IncRNAs were validated with an independent cohort using clinical feature relevance analysis and multivariate Cox regression analysis. Results： We identified nine HNSCC-relevant IncRNAs likely to play pivotal roles in HNSCC onset and development. By functional enrichment analysis, we revealed that CYTOR might participate in the multistep pathological processes of cancer, such as ribosome biogenesis and maintenance of genomic stability. CY-I-OR was identified to be positively correlated with lymph node metastasis, and significantly negatively correlated with overall survival （OS） and disease free survival （DFS） of HNSCC patients. Moreover, CYTOR inhibited cell apoptosis following treatment with the chemotherapeutic drug diamminedichloroplatinum （DDP）. HCG22, the most dramatically down-regulated IncRNA in tumor tissue, may function in epidermis differentiation. It was also significantly associated with several clinical features of patients with HNSCC, and positively correlated with patient survival. CYTOR and HCG22 maintained their prognostic values in- dependent of several clinical features in multivariate Cox hazards analysis. Notably, validation either based on an independent HNSCC cohort or by laboratory experiments confirmed these findings. Conclusions： Our transcriptomic analysis suggested that dysregulation of these HNSCC-associated IncRNAs might be involved in HNSCC oncogenesis and progression. Moreover, CYTOR and HCG22 were confirmed as two independent prognostic factors for HNSCC patient survival, providing new insights into the roles of these IncRNAs in HNSCC as well as clinical applications.
