Background A gap currently exists between genetic variants and the underlying cell and tissue biology of a trait,and expression quantitative trait loci(eQTL)studies provide important information to help close that gap...Background A gap currently exists between genetic variants and the underlying cell and tissue biology of a trait,and expression quantitative trait loci(eQTL)studies provide important information to help close that gap.However,two concerns that arise with eQTL analyses using RNA-sequencing data are normalization of data across samples and the data not following a normal distribution.Multiple pipelines have been suggested to address this.For instance,the most recent analysis of the human and farm Genotype-Tissue Expression(GTEx)project proposes using trimmed means of M-values(TMM)to normalize the data followed by an inverse normal transformation.Results In this study,we reasoned that eQTL analysis could be carried out using the same framework used for dif-ferential gene expression(DGE),which uses a negative binomial model,a statistical test feasible for count data.Using the GTEx framework,we identified 35 significant eQTLs(P<5×10^(–8))following the ANOVA model and 39 significant eQTLs(P<5×10^(–8))following the additive model.Using a differential gene expression framework,we identified 930 and six significant eQTLs(P<5×10^(–8))following an analytical framework equivalent to the ANOVA and additive model,respectively.When we compared the two approaches,there was no overlap of significant eQTLs between the two frameworks.Because we defined specific contrasts,we identified trans eQTLs that more closely resembled what we expect from genetic variants showing complete dominance between alleles.Yet,these were not identified by the GTEx framework.Conclusions Our results show that transforming RNA-sequencing data to fit a normal distribution prior to eQTL analysis is not required when the DGE framework is employed.Our proposed approach detected biologically relevant variants that otherwise would not have been identified due to data transformation to fit a normal distribution.展开更多
BACKGROUND The relationship between hepatitis B surface antigen(HBsAg)-positive carrier status and liver cancer has been extensively studied.However,the epigenetic changes that occur during progression from HBsAg-posi...BACKGROUND The relationship between hepatitis B surface antigen(HBsAg)-positive carrier status and liver cancer has been extensively studied.However,the epigenetic changes that occur during progression from HBsAg-positive carrier status or cirrhosis to liver cancer are unknown.The epigenetic modification of DNA hydroxymethylation is critical in tumor development.Further,5-hydroxymethylcytosine(5hmC)is an important base for DNA demethylation and epigenetic regulation.It is also involved in the assembly of chromosomes and the regulation of gene expression.However,the mechanism of action of 5hmC in HBsAgpositive carriers or patients with cirrhosis who develop liver cancer has not been fully elucidated.AIM To investigate the possible epigenetic mechanism of HBsAg-positive carriers and hepatocellular carcinoma(HCC)progression from cirrhosis.METHODS Forty HBsAg-positive carriers,forty patients with liver cirrhosis,and forty patients with liver cancer admitted to the First People's Hospital of Yongkang between March 2020 and November 2021 were selected as participants.Free DNA was extracted using a cf-DNA kit.cfDNA was extracted by 5hmC DNA sequencing for principal component analysis,the expression profiles of the three groups of samples were detected,and the differentially expressed genes(DEGs)modified by hydroxymethylation were screened.Bioinformatic analysis was used to enrich DEGs,such as in biological pathways.RESULTS A total of 16455 hydroxymethylated genes were identified.Sequencing results showed that 32 genes had significant 5hmC modification differences between HBsAg carriers and liver cancer patients,of which 30 were upregulated and 2 downregulated in patients with HCC compared with HBsAg-positive carriers.Significant 5hmC modification differences between liver cirrhosis and liver cancer patients were identified in 20 genes,of which 17 were upregulated and 3 were downregulated in patients with HCC compared with those with cirrhosis.These genes may have potential loci that are undiscovered or unelucidated,which contribute to the development and progression of liver cancer.Analysis of gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes showed that the major signaling pathways involved in the differential genes were biliary secretion and insulin secretion.The analysis of protein interactions showed that the important genes in the protein-protein interaction network were phosphoenolpyruvate carboxykinase and solute carrier family 2.CONCLUSION The occurrence and development of liver cancer involves multiple genes and pathways,which may be potential targets for preventing hepatitis B carriers from developing liver cancer.展开更多
[Objective] The paper was to study the temporal and spatial dynamics of Bt protein expression in transgenic Bt cotton and to determine the inner relationship of Bt protein expression and transgenic Bt cotton. [Method]...[Objective] The paper was to study the temporal and spatial dynamics of Bt protein expression in transgenic Bt cotton and to determine the inner relationship of Bt protein expression and transgenic Bt cotton. [Method] With transgenic cotton cultivar( GK19) as the test material,Bt protein contents in different organs,main stem functional leaves at different growth stages and different positions of main stem leaves at different growth stages were studied by enzyme-linked immunosorbent assay. [Result] There were differences in Bt protein content among different organs of transgenic Bt cotton; the Bt protein content of leaves at seedling stage was the highest,followed by flowers,bubs and bolls,and those of roots and stems were relatively low. The Bt protein content of main stem function leaves gradually decreased with the progressing development. There were great differences in Bt protein content among different positions of main stem leaves at different growth stages; the Bt protein content of the 1^(st)-7^(th) top leaves at seedling stage and full budding stage gradually decreased,while those at full flowering stage and full bolling stage first slowly increased then gradually stabilized. [Conclusion] Bt protein expression was found in all organs of transgenic cotton at all growth stages,and the expression level presented temporal and spatial dynamics.展开更多
Salinity resistance and differential gene expression associated with salinity in cotton germplasm were studied,because of the large scale area of salinity in China,and its significant negative effects
Background: Retinoblastoma, the most common intraocular pediatric cancer, presents complexities in its genetic landscape that necessitate a deeper understanding for improved therapeutic interventions. This study lever...Background: Retinoblastoma, the most common intraocular pediatric cancer, presents complexities in its genetic landscape that necessitate a deeper understanding for improved therapeutic interventions. This study leverages computational tools to dissect the differential gene expression profiles in retinoblastoma. Methods: Employing an in silico approach, we analyzed gene expression data from public repositories by applying rigorous statistical models, including limma and de seq 2, for identifying differentially expressed genes DEGs. Our findings were validated through cross-referencing with independent datasets and existing literature. We further employed functional annotation and pathway analysis to elucidate the biological significance of these DEGs. Results: Our computational analysis confirmed the dysregulation of key retinoblastoma-associated genes. In comparison to normal retinal tissue, RB1 exhibited a 2.5-fold increase in expression (adjusted p Conclusions: Our analysis reinforces the critical genetic alterations known in retinoblastoma and unveils new avenues for research into the disease’s molecular basis. The discovery of chemoresistance markers and immune-related genes opens potential pathways for personalized treatment strategies. The study’s outcomes emphasize the power of in silico analyses in unraveling complex cancer genomics.展开更多
Vascular etiology is the second most prevalent cause of cognitive impairment globally.Endothelin-1,which is produced and secreted by endothelial cells and astrocytes,is implicated in the pathogenesis of stroke.However...Vascular etiology is the second most prevalent cause of cognitive impairment globally.Endothelin-1,which is produced and secreted by endothelial cells and astrocytes,is implicated in the pathogenesis of stroke.However,the way in which changes in astrocytic endothelin-1 lead to poststroke cognitive deficits following transient middle cerebral artery occlusion is not well understood.Here,using mice in which astrocytic endothelin-1 was overexpressed,we found that the selective overexpression of endothelin-1 by astrocytic cells led to ischemic stroke-related dementia(1 hour of ischemia;7 days,28 days,or 3 months of reperfusion).We also revealed that astrocytic endothelin-1 overexpression contributed to the role of neural stem cell proliferation but impaired neurogenesis in the dentate gyrus of the hippocampus after middle cerebral artery occlusion.Comprehensive proteome profiles and western blot analysis confirmed that levels of glial fibrillary acidic protein and peroxiredoxin 6,which were differentially expressed in the brain,were significantly increased in mice with astrocytic endothelin-1 overexpression in comparison with wild-type mice 28 days after ischemic stroke.Moreover,the levels of the enriched differentially expressed proteins were closely related to lipid metabolism,as indicated by Kyoto Encyclopedia of Genes and Genomes pathway analysis.Liquid chromatography-mass spectrometry nontargeted metabolite profiling of brain tissues showed that astrocytic endothelin-1 overexpression altered lipid metabolism products such as glycerol phosphatidylcholine,sphingomyelin,and phosphatidic acid.Overall,this study demonstrates that astrocytic endothelin-1 overexpression can impair hippocampal neurogenesis and that it is correlated with lipid metabolism in poststroke cognitive dysfunction.展开更多
BACKGROUND Gastric cancer(GC)has a high mortality rate worldwide.Despite significant progress in GC diagnosis and treatment,the prognosis for affected patients still remains unfavorable.AIM To identify important candi...BACKGROUND Gastric cancer(GC)has a high mortality rate worldwide.Despite significant progress in GC diagnosis and treatment,the prognosis for affected patients still remains unfavorable.AIM To identify important candidate genes related to the development of GC and iden-tify potential pathogenic mechanisms through comprehensive bioinformatics analysis.METHODS The Gene Expression Omnibus database was used to obtain the GSE183136 dataset,which includes a total of 135 GC samples.The limma package in R software was employed to identify differentially expressed genes(DEGs).Thereafter,enrichment analyses of Gene Ontology(GO)terms and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways were performed for the gene modules using the clusterProfile package in R software.The protein-protein interaction(PPI)networks of target genes were constructed using STRING and visualized by Cytoscape software.The common hub genes that emerged in the cohort of DEGs that was retrieved from the GEPIA database were then screened using a Venn Diagram.The expression levels of these overlapping genes in stomach adenocarcinoma samples and non-tumor samples and their association with prognosis in GC patients were also obtained from the GEPIA database and Kaplan-Meier curves.Moreover,real-time quantitative polymerase chain reaction(RT-qPCR)and western blotting were performed to determine the mRNA and protein levels of glutamic-pyruvic transaminase(GPT)in GC and normal immortalized cell lines.In addition,cell viability,cell cycle distribution,migration and invasion were evaluated by cell counting kit-8,flow cytometry and transwell assays.Furthermore,we also conducted a retrospective analysis on 70 GC patients diagnosed and surgically treated in Wenzhou Central Hospital,Dingli Clinical College of Wenzhou Medical University,The Second Affiliated Hospital of Shanghai University between January 2017 to December 2020.The tumor and adjacent normal samples were collected from the patients to determine the potential association between the expression level of GPT and the clinical as well as pathological features of GC patients.RESULTS We selected 19214 genes from the GSE183136 dataset,among which there were 250 downregulated genes and 401 upregulated genes in the tumor samples of stage III-IV in comparison to those in tumor samples of stage I-II with a P-value<0.05.In addition,GO and KEGG results revealed that the various upregulated DEGs were mainly enriched in plasma membrane and neuroactive ligand-receptor interaction,whereas the downregulated DEGs were primarily enriched in cytosol and pancreatic secretion,vascular smooth muscle contraction and biosynthesis of the different cofactors.Furthermore,PPI networks were constructed based on the various upregulated and downregulated genes,and there were a total 15 upregulated and 10 downregulated hub genes.After a comprehensive analysis,several hub genes,including runt-related transcription factor 2(RUNX2),salmonella pathogenicity island 1(SPI1),lysyl oxidase(LOX),fibrillin 1(FBN1)and GPT,displayed prognostic values.Interestingly,it was observed that GPT was downregulated in GC cells and its upregulation could suppress the malignant phenotypes of GC cells.Furthermore,the expression level of GPT was found to be associated with age,lymph node metastasis,pathological staging and distant metastasis(P<0.05).CONCLUSION RUNX2,SPI1,LOX,FBN1 and GPT were identified key hub genes in GC by bioinformatics analysis.GPT was significantly associated with the prognosis of GC,and its upregulation can effectively inhibit the proliferative,migrative and invasive capabilities of GC cells.展开更多
Kisspeptins and G protein coupled receptor(GPR54)play significant roles in regulating reproductive activity among seasonally reproductive animals;however,the mechanisms of KiSS-1 and GPR54 gene affecting the seasonal ...Kisspeptins and G protein coupled receptor(GPR54)play significant roles in regulating reproductive activity among seasonally reproductive animals;however,the mechanisms of KiSS-1 and GPR54 gene affecting the seasonal reproduction in striped hamster are still unknown.In this study,real-time quantitative polymerase chain reaction was employed to examine the expression profiles of KiSS-1 and GPR54 in the hypothalamus,ovaries,testes,uterus and epididymis of striped hamsters across 4 different seasons.Our results showed that,across different seasons,the KiSS-1 expression mode of male striped hamsters and the GPR54 expression mode of female striped hamsters were consistent with the seasonal photoperiod in the hypothalamus.Meanwhile,across different seasons,the expression profile of KiSS-1 in the testes and the GPR54 expression profile of male striped hamsters in the hypothalamus were consistent with the intensity of their seasonal reproductive activity.Among different tissues,the expression trend for GPR54 is consistent across 4 seasons,while that for KiSS-1 is tissue-dependent.The expression trend for GPR54 across 4 seasons is the same regardless of gender,while that for KiSS-1 is dramatically different and sex-dependent across different seasons.These results suggest that the expressions of KiSS-1 and GPR54 in the striped hamsters were regulated by complicated mechanisms,and the regulatory mechanisms in the striped hamsters are seasonal-dependent and sex-dependent.This research will provide a theoretical basis for studying how KiSS-1 and GPR54 affect seasonal reproduction and the mechanisms behind their influence.展开更多
Objective:To explore the function of cluster needling at scalp points therapy on regulating differential protein's expression at different time points in middle cerebral artery occlusion(MCAO)model rats.Methods:Fi...Objective:To explore the function of cluster needling at scalp points therapy on regulating differential protein's expression at different time points in middle cerebral artery occlusion(MCAO)model rats.Methods:Fifty-four rats were divided into three groups randomly and 18 rats in each group.The groups respectively were the model group(group M,n=18),cluster needling at scalp points group(group C,n=18),false operation group(group F,n=18).Each group was then assigned in three subgroups,including 24-h,7-day,and 14-day subgroups.Six rats in each subgroup.Acupuncture at Baihui(GV20)and 2 points beside Baihui,which was 3 e4 mm away from the midline.Longa score was used to evaluated neurological effects.Proteomics methods were used to identify differentially expression proteins with a standard of fold change greater than 1.5 and P<.05 at different times.Results:1.Nerve function scoring:The nerve function scores at 7 and 14 days decreased in group C,which showed better neural function than group M(P<.05).2.Fold change in proteins:Group M showed932 differentially expressed proteins compared with group F,and among them,414 proteins showed significant changes in expression after acupuncture.The expression levels of Cdc42 and GFAP were increased,and Mag,Shank2,and MBP levels were decreased.In the Gene Ontology analysis,the cellular component consisted of the terms cytoplasm,cytoskeleton,lysosome,and plasma membrane.The main related biological processes were cellecell signaling,protein transport,aging,and cell adhesion.Many synaptic and metabolic pathways were found by KEGG analysis.Conclusion:Cluster needling at scalp acupoints can improve the nerve function score and improve dyskinesia in MCAO model rats.Cluster needling at scalp acupoints can regulate the expression of 414 proteins,including Cdc42,GFAP,Mag,Shank2,and MBP,which are related to cerebral ischemia.The differential proteins are major concentration in cytoplasm,cytoskeleton,lysosomes,and plasma membrane,participate in cellecell signaling,protein transport,aging,and cell adhesion,and act through multiple synaptic and metabolic pathways to exert their biological functions.展开更多
BACKGROUND: The Glasgow Coma Scale,computer tomography,and nuclear magnetic reso-nance imaging have been frequently used to diagnose brain injury.However,these methods do not accurately and quantitatively evaluate inj...BACKGROUND: The Glasgow Coma Scale,computer tomography,and nuclear magnetic reso-nance imaging have been frequently used to diagnose brain injury.However,these methods do not accurately and quantitatively evaluate injury degree.However,proteomics displays some advan-tages.To date,there are few proteomics studies based on primary astrocyte cultures from a fluid percussion injury model.OBJECTIVE: To detect differential protein expression in rat cerebral cortical astrocytes following fluid percussion injury using two-dimensional gel electrophoresis and mass spectrum and to deter-mine specific biological markers of brain injury.DESIGN,TIME AND SETTING: Complete,randomized grouping and proteomics experiments were performed at the Molecular Pathological Laboratory,Central Laboratory and Tianjin Key Laboratory for Biomarkers of Occupational and Environmental Hazard of Medical College of Chinese People's Armed Police Force from October 2007 to May 2008.MATERIALS: Inverted phase-contrast microscope was purchased from Olympus,Japan.PRO-TEAN IEF Cell isoelectric focusing electrophoresis system and PROTEAN II Xi-Cell vertical elec-trophoresis system were purchased from Bio-Rad,USA.Autoflex MALDI-TOF mass spectrometer was purchased from Bruker,Germany.METHODS: A total of 90 culture dishes,fully coated with Sprague Dawley rat cortical astrocytes,were randomly divided into control (n = 30) and injury (n = 60) groups.Astrocytes in the injury group were subjected to fluid percussion and subdivided into 4-hour (n = 30) and 48-hour injury (n = 30) groups.MAIN OUTCOME MEASURES: Cell morphology was observed using inverted phase-contrast mi-croscopy.Cell total protein was extracted from each group,followed by two-dimensional gel elec-trophoresis and silver staining,and the differential protein expression was analyzed using PDQuest 7.0 software.Protein peptide mass fingerprinting of differential protein spots was obtained by matrix assisted laser desorption/ionization-time of flight mass spectrometry.The National Center for Bio-technology Information (NCBI) protein database was retrieved by Mascot to primarily identify protein type.Finally,differential protein expression was detected by Western blot analysis.RESULTS: Following fluid percussion injury,astrocytes displayed obvious swelling and increased intercellular space,with some cell detachment;the number of dead cells was significantly greater than the control group (P < 0.05).Expression intensity of 114 protein spots was significantly greater in the injury group compared with the control group (P < 0.05);9 of the 114 protein spots were iden-tified and peptide matching scores of 8 spots were > 61 (P < 0.05).Protein types were identified and included cellular retinol binding protein,brain fatty acid binding protein 7,S100 calcium binding protein A11,60S acidic ribosomal protein P2,calponin 3,breast carcinoma amplified sequence 2 homolog,eukaryotic translation initiation factor 1A,and hypothetical protein LOC685814.Western blot detection revealed brain fatty acid binding protein 7 expression in cortical astrocytes,which in-creased with injury time compared with the control group (P < 0.05).CONCLUSION: Results from this study showed morphological and proteomic changes in cortical astrocytes following fluid percussion injury.Brain fatty acid binding protein 7 was expressed in as-trocytes and possibly played an important role in injury repair.Mass-spectrum identified differentially expressed proteins that correlated with cell metabolism regulation,signal transduction,and transla-tion initiation,and could serve as specific biological markers of brain injury.展开更多
Introduction:Verruca vulgaris is one of the most common low-risk HPV infections and is characterized by excessive proliferation of keratinocytes.Currently,very little genetic information is available regarding verruca...Introduction:Verruca vulgaris is one of the most common low-risk HPV infections and is characterized by excessive proliferation of keratinocytes.Currently,very little genetic information is available regarding verruca vulgaris in the Chinese population.This study aimed to obtain comprehensive transcript information of verruca vulgaris by RNA sequencing.Methods:High-throughput sequencing was performed on three fresh verruca vulgaris samples and adjacent normal skin on the Illumina sequencing platform.The transcriptomes were analyzed using bioinformatics and the differentially expressed genes(DEGs)were verified by immunohistochemistry.Verruca vulgaris exhibited a unique molecular signature.Results:In total,1,643 DEGs were identified in verruca vulgaris compared to normal skin.The functions of the DEGs were studies by Gene Ontology(GO)enrichment,Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis,DEGs Reactome analysis,disease annotation function,and STRING protein-protein interaction(PPI)network analysis.The results revealed 595 GO terms associated with the cell cycle,signal transduction,immune system,signaling molecules,and interaction.The Reactome analysis revealed enrichment in reversible hydration of carbon dioxide and BMP signaling,while the disease annotation function revealed that the enriched DEGs are involved in keratosis disorders.The STRING PPI network showed that the edges with the highest density mainly included the 2′-5′oligoadenylate synthase(OAS)family-related proteins.Furthermore,the M-code analysis found ISG15,IRF7,and OASL were scored as significant modules and their high expression compared to the control was verified by immunohistochemistry.Conclusion:These findings contribute to the genetic information of verruca vulgaris in the Chinese population,revealing that interferon-stimulated genes may play essential roles in verruca vulgaris.展开更多
Objective:To clarify the effect of endurance training on the expression profile of circRNA-lncRNA-miRNA-mRNA in myocardial tissues of mice after exhaustive exercise.Methods:A total of 45 male C57BL/6 mice were randoml...Objective:To clarify the effect of endurance training on the expression profile of circRNA-lncRNA-miRNA-mRNA in myocardial tissues of mice after exhaustive exercise.Methods:A total of 45 male C57BL/6 mice were randomly divided into control(C),low-strength endurance training(LSET)and high-strength endurance training(HSET)groups(n=15).The mice in the control group were not conducted to platform training.The mice in the LSET and HSET groups were conducted to platform training at 30%and 60%of exhaustive exercise once a day for 5 days a week,respectively.The exhaustion exercise was performed after 5 weeks of platform training.Total RNA was extracted from myocardial tissues,and the expression profile of circRNA-lncRNA-miRNA-mRNA in myocardial tissues was analyzed using Illimina transcriptome sequencing.Results:The distance and time of exhaustive exercise were longer in the LSET and HSET groups than in the control group,and the distance and time of exhaustive exercise were longer in the HSET group than in the LSET group(P<0.05).A total of 54 differentially expressed circRNAs(28 down-regulated and 26 up-regulated),7 differentially expressed lncRNAs(all down-regulated),3 differentially expressed miRNAs(1 down-regulated and 2 up-regulated)and 99 differentially expressed mRNAs(81 down-regulated and 18 up-regulated)were identified by transcriptome sequencing(P<0.05).Interaction network analysis revealed that ENSMUSG00000113041,MSTRG.79740,mmu-miR-374c-5p,18 down-regulated mRNAs and 3 up-regulated mRNAs formed a regulatory network.GO functional analysis revealed that the differentially expressed mRNAs were mainly enriched in primary metabolic processes and macromolecular synthesis and metabolic processes.KEGG pathway analysis revealed that the differentially expressed mRNAs were mainly enriched in complement and coagulation cascade pathways,estrogen signaling pathway and glucagon signaling pathway.Conclusion:Endurance training could alter the expression profile of circRNA-lncRNA-miRNA-mRNA in myocardial tissues of mice after exhaustive exercise,and these differentially expressed RNAs form a regulatory network that affects cardiomyocyte synthesis and metabolism and thus participates in the regulation of myocardial injury.展开更多
The term “microgravity” is used to describe the “weightlessness” or “zero-g” circumstances that can only be found in space beyond earth’s atmosphere. Rhodobacter sphaeroides is a gram-negative purple phototroph...The term “microgravity” is used to describe the “weightlessness” or “zero-g” circumstances that can only be found in space beyond earth’s atmosphere. Rhodobacter sphaeroides is a gram-negative purple phototroph, used as a model organism for this study due to its genomic complexity and metabolic versatility. Its genome has been completely sequenced, and profiles of the differential gene expression under aerobic, semi-aerobic, and photosynthetic conditions were examined. In this study, we hypothesized that R. sphaeroides will show altered growth characteristics, morphological properties, and gene expression patterns when grown under simulated microgravity. To test that, we measured the optical density and colony-forming units of cell cultures grown under both microgravity and normal gravity conditions. Differences in the cell morphology were observed using scanning electron microscopy (SEM) images by measuring the length and the surface area of the cells under both conditions. Furthermore, we also identified homologous genes of R. spheroides using the differential gene expression study of Acidovorax under microgravity in our laboratory. Growth kinetics results showed that R. sphaeroides cells grown under microgravity experience a shorter log phase and early stationary phase compared to the cells growing under normal gravity conditions. The length and surface area of the cells under microgravity were significantly higher confirming that bacterial cells experience altered morphological features when grown under microgravity conditions. Differentially expressed homologous gene analysis indicated that genes coding for several COG and GO functions, such as metabolism, signal-transduction, transcription, translation, chemotaxis, and cell motility are differentially expressed to adapt and survive microgravity.展开更多
Objective To investigate the value of BT-H3 in expressed prostatic secretions ( EPS) in differential diagnosis of patients with inflammatory elevation of PSA in t - PSA gray zone ( 4 - 10 ng /ml) . Methods One hundred...Objective To investigate the value of BT-H3 in expressed prostatic secretions ( EPS) in differential diagnosis of patients with inflammatory elevation of PSA in t - PSA gray zone ( 4 - 10 ng /ml) . Methods One hundred and sixteen patients from ages of 19 to 80 years ( mean,40 years) were studied. In the group there展开更多
Complex pathological changes occur during the development of spinal cord injury(SCI),and determining the underlying molecular events that occur during SCI is necessary for the development of promising molecular target...Complex pathological changes occur during the development of spinal cord injury(SCI),and determining the underlying molecular events that occur during SCI is necessary for the development of promising molecular targets and therapeutic strategies.This study was designed to explore differentially expressed genes(DEGs)associated with the acute and chronic stages of SCI using bioinformatics analysis.Gene expression profiles(GSE45006,GSE93249,and GSE45550)were downloaded from the Gene Expression Omnibus database.SCI-associated DEGs from rat samples were identified,and Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed.In addition,a protein-protein interaction network was constructed.Approximately 66 DEGs were identified in GSE45550 between 3–14 days after SCI,whereas 2418 DEGs were identified in GSE450061–56 days after SCI.Moreover,1263,195,and 75 overlapping DEGs were identified between these two expression profiles,3,7/8,and 14 days after SCI,respectively.Additionally,16 overlapping DEGs were obtained in GSE450061–14 days after SCI,including Pank1,Hn1,Tmem150c,Rgd1309676,Lpl,Mdh1,Nnt,Loc100912219,Large1,Baiap2,Slc24a2,Fundc2,Mrps14,Slc16a7,Obfc1,and Alpk3.Importantly,3882 overlapping DEGs were identified in GSE932491–6 months after SCI,including 3316 protein-coding genes and 567 long non-coding RNA genes.A comparative analysis between GSE93249 and GSE45006 resulted in the enrichment of 1135 overlapping DEGs.The significant functions of these 1135 genes were correlated with the response to the immune effector process,the innate immune response,and cytokine production.Moreover,the biological processes and KEGG pathways of the overlapping DEGs were significantly enriched in immune system-related pathways,osteoclast differentiation,the nuclear factor-κB signaling pathway,and the chemokine signaling pathway.Finally,an analysis of the overlapping DEGs associated with both acute and chronic SCI,assessed using the expression profiles GSE93249 and GSE45006,identified four overlapping DEGs:Slc16a7,Alpk3,Lpl and Nnt.These findings may be useful for revealing the biological processes associated with SCI and the development of targeted intervention strategies.展开更多
Sweet potato leaf tips have high nutritional value,and exploring the differences in the metabolic profiles of leaf tips among different sweet potato varieties can provide information to improve their qualities.In this...Sweet potato leaf tips have high nutritional value,and exploring the differences in the metabolic profiles of leaf tips among different sweet potato varieties can provide information to improve their qualities.In this study,a UPLC-Q-Exactive Orbitrap/MS-based untargeted metabolomics method was used to evaluate the metabolites in leaf tips of 32 sweet potato varieties.Three varieties with distinct overall metabolic profiles(A01,A02,and A03),two varieties with distinct profiles of phenolic acids(A20 and A18),and three varieties with distinct profiles of flavonoids(A05,A12,and A16)were identified.In addition,a total of 163 and 29 differentially expressed metabolites correlated with the color and leaf shape of sweet potato leaf tips,respectively,were identified through morphological characterization.Group comparison analysis of the phenotypic traits and a metabolite-phenotypic trait correlation analysis indicated that the color differences of sweet potato leaf tips were markedly associated with flavonoids.Also,the level of polyphenols was correlated with the leaf shape of sweet potato leaf tips,with lobed leaf types having higher levels of polyphenols than the entire leaf types.The findings on the metabolic profiles and differentially expressed metabolites associated with the morphology of sweet potato leaf tips can provide useful information for breeding sweet potato varieties with higher nutritional value.展开更多
Coastal and estuarine protists are frequently exposed to salinity undulation.While the tolerance and stress responses of microalgae to salinity have been extensively studied,there have been scarce studies on the physi...Coastal and estuarine protists are frequently exposed to salinity undulation.While the tolerance and stress responses of microalgae to salinity have been extensively studied,there have been scarce studies on the physiological response of heterotrophic protists to salinity stressing.In this study,we investigated the physiological response of the heterotrophic ciliate Gastrostyla setifera to a salinity of 3,via a transcriptomic approach.The first transcriptome of genus Gastrostyla was obtained utilizing a group of manually isolated ciliate individuals(cells)and RNA-seq technique.The completeness of the transcriptome was verified.Differentially expressed gene(DEG)analysis was performed among the transcriptomes of G.setifera acclimated in saline water(salinity 3)and those cultured in fresh water.The results demonstrated a significant alternation in gene transcription,in which the ciliate exhibits a transcripttomic acclimation in responding salinity stressing.The up-regulated DEGs were enriched in the pathways of cytoskeleton proteins,membrane trafficking,protein kinases and protein phosphatases.These may represent enhanced functions of ion transport,stress response and cell protections.Pathways involved in energy metabolism and biosynthesis were markedly down-regulated,reflecting decreased cell activity.Particularly,we detected significantly down-regulated genes involved in several pathways of amino acid catabolism,which may lead to accumulation of amino acids in the ciliate cell.Amino acid could act as compatible solutes in the cytoplasm to maintain the osmotic balance in saline water.Overall,this work is an initial exploration to the molecular basis of the heterotrophic protist responding to salinity stressing.The result sheds light on the mechanisms of enhancement of cell protection,reduction of cell activity,and osmotic pressure regulation in ciliates acclimated to salinity.展开更多
Turbot Scophthalmus maximus is an important mariculture fish species with high economic value.However,the bacterial diseases caused by Vibrio anguillarum infection bring huge economic losses to the turbot aquaculture ...Turbot Scophthalmus maximus is an important mariculture fish species with high economic value.However,the bacterial diseases caused by Vibrio anguillarum infection bring huge economic losses to the turbot aquaculture industry.To understand the immune response of the turbot against V.anguillarum infection and to explore novel immune-related genes,the transcriptome analysis of turbot spleen and gills were conducted after V.anguillarum infection.Differentially expressed genes(DEGs)were identified in spleen and gill of the turbot amounted to 17261 and 16436,respectively.A large number of immunerelated DEGs were enriched in cytokine-cytokine receptor interaction signaling pathway,and the others by the kyoto encyclopedia of genes and genomes(KEGG)enrichment.The gene ontology(GO)classification analysis revealed that V.anguillarum infection had the greatest effect on biological processes and cellular components.Twelve immune-related DEGs were identified in the spleen(cstl.1,egfl6,lamb21,v2rx4,calcr,and gpr78a)and gills(ghra,sh3gl2a,cst12,inhbaa,cxcl8,and il-1b)by heat map.The proteinprotein interaction(PPI)networks were constructed to analyze the immune mechanism.The results demonstrate that the maturation and antigen processing of major histocompatibility complex(MHC)class II molecule,and calcitonin-or adrenomedullin-regulated physiological activity were important events in the immunity of turbot against V.anguillarum infection.In the gills,the protein interactions in TGF-βsignaling pathway,production of inflammatory factors,and endocytosis regulation were most significant.Our research laid a foundation for discovering novel immune-related genes and enriching the knowledge of immune mechanisms of turbot against V.anguillarum infection.展开更多
BACKGROUND A growing number of clinical examples suggest that coronavirus disease 2019(COVID-19)appears to have an impact on the treatment of patients with liver cancer compared to the normal population,and the preval...BACKGROUND A growing number of clinical examples suggest that coronavirus disease 2019(COVID-19)appears to have an impact on the treatment of patients with liver cancer compared to the normal population,and the prevalence of COVID-19 is significantly higher in patients with liver cancer.However,this mechanism of action has not been clarified.Gene sets for COVID-19(GSE180226)and liver cancer(GSE87630)were obtained from the Gene Expression Omnibus database.After identifying the common differentially expressed genes(DEGs)of COVID-19 and liver cancer,functional enrichment analysis,protein-protein interaction network construction and scree-ning and analysis of hub genes were performed.Subsequently,the validation of the differential expression of hub genes in the disease was performed and the regulatory network of transcription factors and hub genes was constructed.RESULTS Of 518 common DEGs were obtained by screening for functional analysis.Fifteen hub genes including aurora kinase B,cyclin B2,cell division cycle 20,cell division cycle associated 8,nucleolar and spindle associated protein 1,etc.,were further identified from DEGs using the“cytoHubba”plugin.Functional enrichment analysis of hub genes showed that these hub genes are associated with P53 signalling pathway regulation,cell cycle and other functions,and they may serve as potential molecular markers for COVID-19 and liver cancer.Finally,we selected 10 of the hub genes for in vitro expression validation in liver cancer cells.CONCLUSION Our study reveals a common pathogenesis of liver cancer and COVID-19.These common pathways and key genes may provide new ideas for further mechanistic studies.展开更多
基金partially funded by the Virginia Cattle Industry Board and the Virginia Agriculture CouncilVT Open Access Subvention Fund for the partial support of the publication fees
文摘Background A gap currently exists between genetic variants and the underlying cell and tissue biology of a trait,and expression quantitative trait loci(eQTL)studies provide important information to help close that gap.However,two concerns that arise with eQTL analyses using RNA-sequencing data are normalization of data across samples and the data not following a normal distribution.Multiple pipelines have been suggested to address this.For instance,the most recent analysis of the human and farm Genotype-Tissue Expression(GTEx)project proposes using trimmed means of M-values(TMM)to normalize the data followed by an inverse normal transformation.Results In this study,we reasoned that eQTL analysis could be carried out using the same framework used for dif-ferential gene expression(DGE),which uses a negative binomial model,a statistical test feasible for count data.Using the GTEx framework,we identified 35 significant eQTLs(P<5×10^(–8))following the ANOVA model and 39 significant eQTLs(P<5×10^(–8))following the additive model.Using a differential gene expression framework,we identified 930 and six significant eQTLs(P<5×10^(–8))following an analytical framework equivalent to the ANOVA and additive model,respectively.When we compared the two approaches,there was no overlap of significant eQTLs between the two frameworks.Because we defined specific contrasts,we identified trans eQTLs that more closely resembled what we expect from genetic variants showing complete dominance between alleles.Yet,these were not identified by the GTEx framework.Conclusions Our results show that transforming RNA-sequencing data to fit a normal distribution prior to eQTL analysis is not required when the DGE framework is employed.Our proposed approach detected biologically relevant variants that otherwise would not have been identified due to data transformation to fit a normal distribution.
基金Supported by Science and Technology Planning Project of Zhejiang Province,No.LGF20H160001.
文摘BACKGROUND The relationship between hepatitis B surface antigen(HBsAg)-positive carrier status and liver cancer has been extensively studied.However,the epigenetic changes that occur during progression from HBsAg-positive carrier status or cirrhosis to liver cancer are unknown.The epigenetic modification of DNA hydroxymethylation is critical in tumor development.Further,5-hydroxymethylcytosine(5hmC)is an important base for DNA demethylation and epigenetic regulation.It is also involved in the assembly of chromosomes and the regulation of gene expression.However,the mechanism of action of 5hmC in HBsAgpositive carriers or patients with cirrhosis who develop liver cancer has not been fully elucidated.AIM To investigate the possible epigenetic mechanism of HBsAg-positive carriers and hepatocellular carcinoma(HCC)progression from cirrhosis.METHODS Forty HBsAg-positive carriers,forty patients with liver cirrhosis,and forty patients with liver cancer admitted to the First People's Hospital of Yongkang between March 2020 and November 2021 were selected as participants.Free DNA was extracted using a cf-DNA kit.cfDNA was extracted by 5hmC DNA sequencing for principal component analysis,the expression profiles of the three groups of samples were detected,and the differentially expressed genes(DEGs)modified by hydroxymethylation were screened.Bioinformatic analysis was used to enrich DEGs,such as in biological pathways.RESULTS A total of 16455 hydroxymethylated genes were identified.Sequencing results showed that 32 genes had significant 5hmC modification differences between HBsAg carriers and liver cancer patients,of which 30 were upregulated and 2 downregulated in patients with HCC compared with HBsAg-positive carriers.Significant 5hmC modification differences between liver cirrhosis and liver cancer patients were identified in 20 genes,of which 17 were upregulated and 3 were downregulated in patients with HCC compared with those with cirrhosis.These genes may have potential loci that are undiscovered or unelucidated,which contribute to the development and progression of liver cancer.Analysis of gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes showed that the major signaling pathways involved in the differential genes were biliary secretion and insulin secretion.The analysis of protein interactions showed that the important genes in the protein-protein interaction network were phosphoenolpyruvate carboxykinase and solute carrier family 2.CONCLUSION The occurrence and development of liver cancer involves multiple genes and pathways,which may be potential targets for preventing hepatitis B carriers from developing liver cancer.
基金Supported by Genetic Engineering Project of Sichuan Province(2014LWJJ-011)
文摘[Objective] The paper was to study the temporal and spatial dynamics of Bt protein expression in transgenic Bt cotton and to determine the inner relationship of Bt protein expression and transgenic Bt cotton. [Method] With transgenic cotton cultivar( GK19) as the test material,Bt protein contents in different organs,main stem functional leaves at different growth stages and different positions of main stem leaves at different growth stages were studied by enzyme-linked immunosorbent assay. [Result] There were differences in Bt protein content among different organs of transgenic Bt cotton; the Bt protein content of leaves at seedling stage was the highest,followed by flowers,bubs and bolls,and those of roots and stems were relatively low. The Bt protein content of main stem function leaves gradually decreased with the progressing development. There were great differences in Bt protein content among different positions of main stem leaves at different growth stages; the Bt protein content of the 1^(st)-7^(th) top leaves at seedling stage and full budding stage gradually decreased,while those at full flowering stage and full bolling stage first slowly increased then gradually stabilized. [Conclusion] Bt protein expression was found in all organs of transgenic cotton at all growth stages,and the expression level presented temporal and spatial dynamics.
文摘Salinity resistance and differential gene expression associated with salinity in cotton germplasm were studied,because of the large scale area of salinity in China,and its significant negative effects
文摘Background: Retinoblastoma, the most common intraocular pediatric cancer, presents complexities in its genetic landscape that necessitate a deeper understanding for improved therapeutic interventions. This study leverages computational tools to dissect the differential gene expression profiles in retinoblastoma. Methods: Employing an in silico approach, we analyzed gene expression data from public repositories by applying rigorous statistical models, including limma and de seq 2, for identifying differentially expressed genes DEGs. Our findings were validated through cross-referencing with independent datasets and existing literature. We further employed functional annotation and pathway analysis to elucidate the biological significance of these DEGs. Results: Our computational analysis confirmed the dysregulation of key retinoblastoma-associated genes. In comparison to normal retinal tissue, RB1 exhibited a 2.5-fold increase in expression (adjusted p Conclusions: Our analysis reinforces the critical genetic alterations known in retinoblastoma and unveils new avenues for research into the disease’s molecular basis. The discovery of chemoresistance markers and immune-related genes opens potential pathways for personalized treatment strategies. The study’s outcomes emphasize the power of in silico analyses in unraveling complex cancer genomics.
基金financially supported by the National Natural Science Foundation of China,No.81303115,81774042 (both to XC)the Pearl River S&T Nova Program of Guangzhou,No.201806010025 (to XC)+3 种基金the Specialty Program of Guangdong Province Hospital of Chinese Medicine of China,No.YN2018ZD07 (to XC)the Natural Science Foundatior of Guangdong Province of China,No.2023A1515012174 (to JL)the Science and Technology Program of Guangzhou of China,No.20210201 0268 (to XC),20210201 0339 (to JS)Guangdong Provincial Key Laboratory of Research on Emergency in TCM,Nos.2018-75,2019-140 (to JS)
文摘Vascular etiology is the second most prevalent cause of cognitive impairment globally.Endothelin-1,which is produced and secreted by endothelial cells and astrocytes,is implicated in the pathogenesis of stroke.However,the way in which changes in astrocytic endothelin-1 lead to poststroke cognitive deficits following transient middle cerebral artery occlusion is not well understood.Here,using mice in which astrocytic endothelin-1 was overexpressed,we found that the selective overexpression of endothelin-1 by astrocytic cells led to ischemic stroke-related dementia(1 hour of ischemia;7 days,28 days,or 3 months of reperfusion).We also revealed that astrocytic endothelin-1 overexpression contributed to the role of neural stem cell proliferation but impaired neurogenesis in the dentate gyrus of the hippocampus after middle cerebral artery occlusion.Comprehensive proteome profiles and western blot analysis confirmed that levels of glial fibrillary acidic protein and peroxiredoxin 6,which were differentially expressed in the brain,were significantly increased in mice with astrocytic endothelin-1 overexpression in comparison with wild-type mice 28 days after ischemic stroke.Moreover,the levels of the enriched differentially expressed proteins were closely related to lipid metabolism,as indicated by Kyoto Encyclopedia of Genes and Genomes pathway analysis.Liquid chromatography-mass spectrometry nontargeted metabolite profiling of brain tissues showed that astrocytic endothelin-1 overexpression altered lipid metabolism products such as glycerol phosphatidylcholine,sphingomyelin,and phosphatidic acid.Overall,this study demonstrates that astrocytic endothelin-1 overexpression can impair hippocampal neurogenesis and that it is correlated with lipid metabolism in poststroke cognitive dysfunction.
文摘BACKGROUND Gastric cancer(GC)has a high mortality rate worldwide.Despite significant progress in GC diagnosis and treatment,the prognosis for affected patients still remains unfavorable.AIM To identify important candidate genes related to the development of GC and iden-tify potential pathogenic mechanisms through comprehensive bioinformatics analysis.METHODS The Gene Expression Omnibus database was used to obtain the GSE183136 dataset,which includes a total of 135 GC samples.The limma package in R software was employed to identify differentially expressed genes(DEGs).Thereafter,enrichment analyses of Gene Ontology(GO)terms and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways were performed for the gene modules using the clusterProfile package in R software.The protein-protein interaction(PPI)networks of target genes were constructed using STRING and visualized by Cytoscape software.The common hub genes that emerged in the cohort of DEGs that was retrieved from the GEPIA database were then screened using a Venn Diagram.The expression levels of these overlapping genes in stomach adenocarcinoma samples and non-tumor samples and their association with prognosis in GC patients were also obtained from the GEPIA database and Kaplan-Meier curves.Moreover,real-time quantitative polymerase chain reaction(RT-qPCR)and western blotting were performed to determine the mRNA and protein levels of glutamic-pyruvic transaminase(GPT)in GC and normal immortalized cell lines.In addition,cell viability,cell cycle distribution,migration and invasion were evaluated by cell counting kit-8,flow cytometry and transwell assays.Furthermore,we also conducted a retrospective analysis on 70 GC patients diagnosed and surgically treated in Wenzhou Central Hospital,Dingli Clinical College of Wenzhou Medical University,The Second Affiliated Hospital of Shanghai University between January 2017 to December 2020.The tumor and adjacent normal samples were collected from the patients to determine the potential association between the expression level of GPT and the clinical as well as pathological features of GC patients.RESULTS We selected 19214 genes from the GSE183136 dataset,among which there were 250 downregulated genes and 401 upregulated genes in the tumor samples of stage III-IV in comparison to those in tumor samples of stage I-II with a P-value<0.05.In addition,GO and KEGG results revealed that the various upregulated DEGs were mainly enriched in plasma membrane and neuroactive ligand-receptor interaction,whereas the downregulated DEGs were primarily enriched in cytosol and pancreatic secretion,vascular smooth muscle contraction and biosynthesis of the different cofactors.Furthermore,PPI networks were constructed based on the various upregulated and downregulated genes,and there were a total 15 upregulated and 10 downregulated hub genes.After a comprehensive analysis,several hub genes,including runt-related transcription factor 2(RUNX2),salmonella pathogenicity island 1(SPI1),lysyl oxidase(LOX),fibrillin 1(FBN1)and GPT,displayed prognostic values.Interestingly,it was observed that GPT was downregulated in GC cells and its upregulation could suppress the malignant phenotypes of GC cells.Furthermore,the expression level of GPT was found to be associated with age,lymph node metastasis,pathological staging and distant metastasis(P<0.05).CONCLUSION RUNX2,SPI1,LOX,FBN1 and GPT were identified key hub genes in GC by bioinformatics analysis.GPT was significantly associated with the prognosis of GC,and its upregulation can effectively inhibit the proliferative,migrative and invasive capabilities of GC cells.
基金supported by the National Science Foundation of China(31270417,31300304,31670385,31570377)the Provincial Key Construction Project the“twelfth five-year”plan for Qufu Normal University.
文摘Kisspeptins and G protein coupled receptor(GPR54)play significant roles in regulating reproductive activity among seasonally reproductive animals;however,the mechanisms of KiSS-1 and GPR54 gene affecting the seasonal reproduction in striped hamster are still unknown.In this study,real-time quantitative polymerase chain reaction was employed to examine the expression profiles of KiSS-1 and GPR54 in the hypothalamus,ovaries,testes,uterus and epididymis of striped hamsters across 4 different seasons.Our results showed that,across different seasons,the KiSS-1 expression mode of male striped hamsters and the GPR54 expression mode of female striped hamsters were consistent with the seasonal photoperiod in the hypothalamus.Meanwhile,across different seasons,the expression profile of KiSS-1 in the testes and the GPR54 expression profile of male striped hamsters in the hypothalamus were consistent with the intensity of their seasonal reproductive activity.Among different tissues,the expression trend for GPR54 is consistent across 4 seasons,while that for KiSS-1 is tissue-dependent.The expression trend for GPR54 across 4 seasons is the same regardless of gender,while that for KiSS-1 is dramatically different and sex-dependent across different seasons.These results suggest that the expressions of KiSS-1 and GPR54 in the striped hamsters were regulated by complicated mechanisms,and the regulatory mechanisms in the striped hamsters are seasonal-dependent and sex-dependent.This research will provide a theoretical basis for studying how KiSS-1 and GPR54 affect seasonal reproduction and the mechanisms behind their influence.
基金National Natural Science Foundation of China(No.81473775)。
文摘Objective:To explore the function of cluster needling at scalp points therapy on regulating differential protein's expression at different time points in middle cerebral artery occlusion(MCAO)model rats.Methods:Fifty-four rats were divided into three groups randomly and 18 rats in each group.The groups respectively were the model group(group M,n=18),cluster needling at scalp points group(group C,n=18),false operation group(group F,n=18).Each group was then assigned in three subgroups,including 24-h,7-day,and 14-day subgroups.Six rats in each subgroup.Acupuncture at Baihui(GV20)and 2 points beside Baihui,which was 3 e4 mm away from the midline.Longa score was used to evaluated neurological effects.Proteomics methods were used to identify differentially expression proteins with a standard of fold change greater than 1.5 and P<.05 at different times.Results:1.Nerve function scoring:The nerve function scores at 7 and 14 days decreased in group C,which showed better neural function than group M(P<.05).2.Fold change in proteins:Group M showed932 differentially expressed proteins compared with group F,and among them,414 proteins showed significant changes in expression after acupuncture.The expression levels of Cdc42 and GFAP were increased,and Mag,Shank2,and MBP levels were decreased.In the Gene Ontology analysis,the cellular component consisted of the terms cytoplasm,cytoskeleton,lysosome,and plasma membrane.The main related biological processes were cellecell signaling,protein transport,aging,and cell adhesion.Many synaptic and metabolic pathways were found by KEGG analysis.Conclusion:Cluster needling at scalp acupoints can improve the nerve function score and improve dyskinesia in MCAO model rats.Cluster needling at scalp acupoints can regulate the expression of 414 proteins,including Cdc42,GFAP,Mag,Shank2,and MBP,which are related to cerebral ischemia.The differential proteins are major concentration in cytoplasm,cytoskeleton,lysosomes,and plasma membrane,participate in cellecell signaling,protein transport,aging,and cell adhesion,and act through multiple synaptic and metabolic pathways to exert their biological functions.
基金the National Natural Science Foundation of China, No. 30471934
文摘BACKGROUND: The Glasgow Coma Scale,computer tomography,and nuclear magnetic reso-nance imaging have been frequently used to diagnose brain injury.However,these methods do not accurately and quantitatively evaluate injury degree.However,proteomics displays some advan-tages.To date,there are few proteomics studies based on primary astrocyte cultures from a fluid percussion injury model.OBJECTIVE: To detect differential protein expression in rat cerebral cortical astrocytes following fluid percussion injury using two-dimensional gel electrophoresis and mass spectrum and to deter-mine specific biological markers of brain injury.DESIGN,TIME AND SETTING: Complete,randomized grouping and proteomics experiments were performed at the Molecular Pathological Laboratory,Central Laboratory and Tianjin Key Laboratory for Biomarkers of Occupational and Environmental Hazard of Medical College of Chinese People's Armed Police Force from October 2007 to May 2008.MATERIALS: Inverted phase-contrast microscope was purchased from Olympus,Japan.PRO-TEAN IEF Cell isoelectric focusing electrophoresis system and PROTEAN II Xi-Cell vertical elec-trophoresis system were purchased from Bio-Rad,USA.Autoflex MALDI-TOF mass spectrometer was purchased from Bruker,Germany.METHODS: A total of 90 culture dishes,fully coated with Sprague Dawley rat cortical astrocytes,were randomly divided into control (n = 30) and injury (n = 60) groups.Astrocytes in the injury group were subjected to fluid percussion and subdivided into 4-hour (n = 30) and 48-hour injury (n = 30) groups.MAIN OUTCOME MEASURES: Cell morphology was observed using inverted phase-contrast mi-croscopy.Cell total protein was extracted from each group,followed by two-dimensional gel elec-trophoresis and silver staining,and the differential protein expression was analyzed using PDQuest 7.0 software.Protein peptide mass fingerprinting of differential protein spots was obtained by matrix assisted laser desorption/ionization-time of flight mass spectrometry.The National Center for Bio-technology Information (NCBI) protein database was retrieved by Mascot to primarily identify protein type.Finally,differential protein expression was detected by Western blot analysis.RESULTS: Following fluid percussion injury,astrocytes displayed obvious swelling and increased intercellular space,with some cell detachment;the number of dead cells was significantly greater than the control group (P < 0.05).Expression intensity of 114 protein spots was significantly greater in the injury group compared with the control group (P < 0.05);9 of the 114 protein spots were iden-tified and peptide matching scores of 8 spots were > 61 (P < 0.05).Protein types were identified and included cellular retinol binding protein,brain fatty acid binding protein 7,S100 calcium binding protein A11,60S acidic ribosomal protein P2,calponin 3,breast carcinoma amplified sequence 2 homolog,eukaryotic translation initiation factor 1A,and hypothetical protein LOC685814.Western blot detection revealed brain fatty acid binding protein 7 expression in cortical astrocytes,which in-creased with injury time compared with the control group (P < 0.05).CONCLUSION: Results from this study showed morphological and proteomic changes in cortical astrocytes following fluid percussion injury.Brain fatty acid binding protein 7 was expressed in as-trocytes and possibly played an important role in injury repair.Mass-spectrum identified differentially expressed proteins that correlated with cell metabolism regulation,signal transduction,and transla-tion initiation,and could serve as specific biological markers of brain injury.
基金The National Natural Science Foundation of China(Grant No.81903227)supported our study.
文摘Introduction:Verruca vulgaris is one of the most common low-risk HPV infections and is characterized by excessive proliferation of keratinocytes.Currently,very little genetic information is available regarding verruca vulgaris in the Chinese population.This study aimed to obtain comprehensive transcript information of verruca vulgaris by RNA sequencing.Methods:High-throughput sequencing was performed on three fresh verruca vulgaris samples and adjacent normal skin on the Illumina sequencing platform.The transcriptomes were analyzed using bioinformatics and the differentially expressed genes(DEGs)were verified by immunohistochemistry.Verruca vulgaris exhibited a unique molecular signature.Results:In total,1,643 DEGs were identified in verruca vulgaris compared to normal skin.The functions of the DEGs were studies by Gene Ontology(GO)enrichment,Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis,DEGs Reactome analysis,disease annotation function,and STRING protein-protein interaction(PPI)network analysis.The results revealed 595 GO terms associated with the cell cycle,signal transduction,immune system,signaling molecules,and interaction.The Reactome analysis revealed enrichment in reversible hydration of carbon dioxide and BMP signaling,while the disease annotation function revealed that the enriched DEGs are involved in keratosis disorders.The STRING PPI network showed that the edges with the highest density mainly included the 2′-5′oligoadenylate synthase(OAS)family-related proteins.Furthermore,the M-code analysis found ISG15,IRF7,and OASL were scored as significant modules and their high expression compared to the control was verified by immunohistochemistry.Conclusion:These findings contribute to the genetic information of verruca vulgaris in the Chinese population,revealing that interferon-stimulated genes may play essential roles in verruca vulgaris.
基金The Medical and Health Science and Technology Development Planning Project of Shandong Province(202103011061)。
文摘Objective:To clarify the effect of endurance training on the expression profile of circRNA-lncRNA-miRNA-mRNA in myocardial tissues of mice after exhaustive exercise.Methods:A total of 45 male C57BL/6 mice were randomly divided into control(C),low-strength endurance training(LSET)and high-strength endurance training(HSET)groups(n=15).The mice in the control group were not conducted to platform training.The mice in the LSET and HSET groups were conducted to platform training at 30%and 60%of exhaustive exercise once a day for 5 days a week,respectively.The exhaustion exercise was performed after 5 weeks of platform training.Total RNA was extracted from myocardial tissues,and the expression profile of circRNA-lncRNA-miRNA-mRNA in myocardial tissues was analyzed using Illimina transcriptome sequencing.Results:The distance and time of exhaustive exercise were longer in the LSET and HSET groups than in the control group,and the distance and time of exhaustive exercise were longer in the HSET group than in the LSET group(P<0.05).A total of 54 differentially expressed circRNAs(28 down-regulated and 26 up-regulated),7 differentially expressed lncRNAs(all down-regulated),3 differentially expressed miRNAs(1 down-regulated and 2 up-regulated)and 99 differentially expressed mRNAs(81 down-regulated and 18 up-regulated)were identified by transcriptome sequencing(P<0.05).Interaction network analysis revealed that ENSMUSG00000113041,MSTRG.79740,mmu-miR-374c-5p,18 down-regulated mRNAs and 3 up-regulated mRNAs formed a regulatory network.GO functional analysis revealed that the differentially expressed mRNAs were mainly enriched in primary metabolic processes and macromolecular synthesis and metabolic processes.KEGG pathway analysis revealed that the differentially expressed mRNAs were mainly enriched in complement and coagulation cascade pathways,estrogen signaling pathway and glucagon signaling pathway.Conclusion:Endurance training could alter the expression profile of circRNA-lncRNA-miRNA-mRNA in myocardial tissues of mice after exhaustive exercise,and these differentially expressed RNAs form a regulatory network that affects cardiomyocyte synthesis and metabolism and thus participates in the regulation of myocardial injury.
文摘The term “microgravity” is used to describe the “weightlessness” or “zero-g” circumstances that can only be found in space beyond earth’s atmosphere. Rhodobacter sphaeroides is a gram-negative purple phototroph, used as a model organism for this study due to its genomic complexity and metabolic versatility. Its genome has been completely sequenced, and profiles of the differential gene expression under aerobic, semi-aerobic, and photosynthetic conditions were examined. In this study, we hypothesized that R. sphaeroides will show altered growth characteristics, morphological properties, and gene expression patterns when grown under simulated microgravity. To test that, we measured the optical density and colony-forming units of cell cultures grown under both microgravity and normal gravity conditions. Differences in the cell morphology were observed using scanning electron microscopy (SEM) images by measuring the length and the surface area of the cells under both conditions. Furthermore, we also identified homologous genes of R. spheroides using the differential gene expression study of Acidovorax under microgravity in our laboratory. Growth kinetics results showed that R. sphaeroides cells grown under microgravity experience a shorter log phase and early stationary phase compared to the cells growing under normal gravity conditions. The length and surface area of the cells under microgravity were significantly higher confirming that bacterial cells experience altered morphological features when grown under microgravity conditions. Differentially expressed homologous gene analysis indicated that genes coding for several COG and GO functions, such as metabolism, signal-transduction, transcription, translation, chemotaxis, and cell motility are differentially expressed to adapt and survive microgravity.
文摘Objective To investigate the value of BT-H3 in expressed prostatic secretions ( EPS) in differential diagnosis of patients with inflammatory elevation of PSA in t - PSA gray zone ( 4 - 10 ng /ml) . Methods One hundred and sixteen patients from ages of 19 to 80 years ( mean,40 years) were studied. In the group there
基金This study was supported by the National Natural Science Foundation of China,No.31571236(to YHK)Science and Technology Planning Project of Beijing of China,No D161100002816001+1 种基金the National Key Research and Development Program of China,No.2016YFC1101604(to DYZ)the Ministry of Education Innovation Program of China,No.IRT_16R01.
文摘Complex pathological changes occur during the development of spinal cord injury(SCI),and determining the underlying molecular events that occur during SCI is necessary for the development of promising molecular targets and therapeutic strategies.This study was designed to explore differentially expressed genes(DEGs)associated with the acute and chronic stages of SCI using bioinformatics analysis.Gene expression profiles(GSE45006,GSE93249,and GSE45550)were downloaded from the Gene Expression Omnibus database.SCI-associated DEGs from rat samples were identified,and Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed.In addition,a protein-protein interaction network was constructed.Approximately 66 DEGs were identified in GSE45550 between 3–14 days after SCI,whereas 2418 DEGs were identified in GSE450061–56 days after SCI.Moreover,1263,195,and 75 overlapping DEGs were identified between these two expression profiles,3,7/8,and 14 days after SCI,respectively.Additionally,16 overlapping DEGs were obtained in GSE450061–14 days after SCI,including Pank1,Hn1,Tmem150c,Rgd1309676,Lpl,Mdh1,Nnt,Loc100912219,Large1,Baiap2,Slc24a2,Fundc2,Mrps14,Slc16a7,Obfc1,and Alpk3.Importantly,3882 overlapping DEGs were identified in GSE932491–6 months after SCI,including 3316 protein-coding genes and 567 long non-coding RNA genes.A comparative analysis between GSE93249 and GSE45006 resulted in the enrichment of 1135 overlapping DEGs.The significant functions of these 1135 genes were correlated with the response to the immune effector process,the innate immune response,and cytokine production.Moreover,the biological processes and KEGG pathways of the overlapping DEGs were significantly enriched in immune system-related pathways,osteoclast differentiation,the nuclear factor-κB signaling pathway,and the chemokine signaling pathway.Finally,an analysis of the overlapping DEGs associated with both acute and chronic SCI,assessed using the expression profiles GSE93249 and GSE45006,identified four overlapping DEGs:Slc16a7,Alpk3,Lpl and Nnt.These findings may be useful for revealing the biological processes associated with SCI and the development of targeted intervention strategies.
基金This work was supported by grants from the construction and operation of the Food Nutrition and Health Research Center of Guangdong Academy of Agricultural Sciences,China(XTXM 202205)the earmarked fund for CARS-10Sweetpotato,and the Guangdong Modern Agro-industry Technology Research System,China(2022KJ111).
文摘Sweet potato leaf tips have high nutritional value,and exploring the differences in the metabolic profiles of leaf tips among different sweet potato varieties can provide information to improve their qualities.In this study,a UPLC-Q-Exactive Orbitrap/MS-based untargeted metabolomics method was used to evaluate the metabolites in leaf tips of 32 sweet potato varieties.Three varieties with distinct overall metabolic profiles(A01,A02,and A03),two varieties with distinct profiles of phenolic acids(A20 and A18),and three varieties with distinct profiles of flavonoids(A05,A12,and A16)were identified.In addition,a total of 163 and 29 differentially expressed metabolites correlated with the color and leaf shape of sweet potato leaf tips,respectively,were identified through morphological characterization.Group comparison analysis of the phenotypic traits and a metabolite-phenotypic trait correlation analysis indicated that the color differences of sweet potato leaf tips were markedly associated with flavonoids.Also,the level of polyphenols was correlated with the leaf shape of sweet potato leaf tips,with lobed leaf types having higher levels of polyphenols than the entire leaf types.The findings on the metabolic profiles and differentially expressed metabolites associated with the morphology of sweet potato leaf tips can provide useful information for breeding sweet potato varieties with higher nutritional value.
基金supported by the National Natural Science Foundation of China(Nos.32370488,42176163,31970398 and 31672251)the Youth Innovation Promotion Association of CAS(Nos.2019216 and 2022211).
文摘Coastal and estuarine protists are frequently exposed to salinity undulation.While the tolerance and stress responses of microalgae to salinity have been extensively studied,there have been scarce studies on the physiological response of heterotrophic protists to salinity stressing.In this study,we investigated the physiological response of the heterotrophic ciliate Gastrostyla setifera to a salinity of 3,via a transcriptomic approach.The first transcriptome of genus Gastrostyla was obtained utilizing a group of manually isolated ciliate individuals(cells)and RNA-seq technique.The completeness of the transcriptome was verified.Differentially expressed gene(DEG)analysis was performed among the transcriptomes of G.setifera acclimated in saline water(salinity 3)and those cultured in fresh water.The results demonstrated a significant alternation in gene transcription,in which the ciliate exhibits a transcripttomic acclimation in responding salinity stressing.The up-regulated DEGs were enriched in the pathways of cytoskeleton proteins,membrane trafficking,protein kinases and protein phosphatases.These may represent enhanced functions of ion transport,stress response and cell protections.Pathways involved in energy metabolism and biosynthesis were markedly down-regulated,reflecting decreased cell activity.Particularly,we detected significantly down-regulated genes involved in several pathways of amino acid catabolism,which may lead to accumulation of amino acids in the ciliate cell.Amino acid could act as compatible solutes in the cytoplasm to maintain the osmotic balance in saline water.Overall,this work is an initial exploration to the molecular basis of the heterotrophic protist responding to salinity stressing.The result sheds light on the mechanisms of enhancement of cell protection,reduction of cell activity,and osmotic pressure regulation in ciliates acclimated to salinity.
基金the National Key Research and Development Program of the Ministry of Science and Technology(CN)(No.2022YFD2400401)the Key Research and Development Plan of Shandong Province(CN)(for Academician Team in Shandong)(No.2023ZLYS02)+1 种基金the Fundamental Research Funds for the Central Universities(No.202261029)the Enterprise Authorized Project(No.20200025)。
文摘Turbot Scophthalmus maximus is an important mariculture fish species with high economic value.However,the bacterial diseases caused by Vibrio anguillarum infection bring huge economic losses to the turbot aquaculture industry.To understand the immune response of the turbot against V.anguillarum infection and to explore novel immune-related genes,the transcriptome analysis of turbot spleen and gills were conducted after V.anguillarum infection.Differentially expressed genes(DEGs)were identified in spleen and gill of the turbot amounted to 17261 and 16436,respectively.A large number of immunerelated DEGs were enriched in cytokine-cytokine receptor interaction signaling pathway,and the others by the kyoto encyclopedia of genes and genomes(KEGG)enrichment.The gene ontology(GO)classification analysis revealed that V.anguillarum infection had the greatest effect on biological processes and cellular components.Twelve immune-related DEGs were identified in the spleen(cstl.1,egfl6,lamb21,v2rx4,calcr,and gpr78a)and gills(ghra,sh3gl2a,cst12,inhbaa,cxcl8,and il-1b)by heat map.The proteinprotein interaction(PPI)networks were constructed to analyze the immune mechanism.The results demonstrate that the maturation and antigen processing of major histocompatibility complex(MHC)class II molecule,and calcitonin-or adrenomedullin-regulated physiological activity were important events in the immunity of turbot against V.anguillarum infection.In the gills,the protein interactions in TGF-βsignaling pathway,production of inflammatory factors,and endocytosis regulation were most significant.Our research laid a foundation for discovering novel immune-related genes and enriching the knowledge of immune mechanisms of turbot against V.anguillarum infection.
文摘BACKGROUND A growing number of clinical examples suggest that coronavirus disease 2019(COVID-19)appears to have an impact on the treatment of patients with liver cancer compared to the normal population,and the prevalence of COVID-19 is significantly higher in patients with liver cancer.However,this mechanism of action has not been clarified.Gene sets for COVID-19(GSE180226)and liver cancer(GSE87630)were obtained from the Gene Expression Omnibus database.After identifying the common differentially expressed genes(DEGs)of COVID-19 and liver cancer,functional enrichment analysis,protein-protein interaction network construction and scree-ning and analysis of hub genes were performed.Subsequently,the validation of the differential expression of hub genes in the disease was performed and the regulatory network of transcription factors and hub genes was constructed.RESULTS Of 518 common DEGs were obtained by screening for functional analysis.Fifteen hub genes including aurora kinase B,cyclin B2,cell division cycle 20,cell division cycle associated 8,nucleolar and spindle associated protein 1,etc.,were further identified from DEGs using the“cytoHubba”plugin.Functional enrichment analysis of hub genes showed that these hub genes are associated with P53 signalling pathway regulation,cell cycle and other functions,and they may serve as potential molecular markers for COVID-19 and liver cancer.Finally,we selected 10 of the hub genes for in vitro expression validation in liver cancer cells.CONCLUSION Our study reveals a common pathogenesis of liver cancer and COVID-19.These common pathways and key genes may provide new ideas for further mechanistic studies.
