Transcriptomic and bioinformatics analysis of the mechanism by which erythropoietin promotes recovery from traumatic brain injury in mice

Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate traumatic brain injury in mice by intrape ritoneal injection of erythro poietin for 3 consecutive days.RNA sequencing detected a total of 4065 differentially expressed RNAs,including 1059 mRNAs,92 microRNAs,799 long non-coding RNAs,and 2115circular RNAs.Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed that the coding and non-coding RNAs that were differentially expressed after traumatic brain injury and treatment with erythropoietin play roles in the axon guidance pathway,Wnt pathway,and MAPK pathway.Constructing competing endogenous RNA networks showed that regulatory relationship between the differentially expressed non-coding RNAs and mRNAs.Because the axon guidance pathway was repeatedly enriched,the expression of Wnt5a and Ephb6,key factors in the axonal guidance pathway,was assessed.Ephb6 expression decreased and Wnt5a expression increased after traumatic brain injury,and these effects were reversed by treatment with erythro poietin.These findings suggest that erythro poietin can promote recove ry of nerve function after traumatic brain injury through the axon guidance pathway.

RNA sequencing of exosomes secreted by fibroblast and Schwann cells elucidates mechanisms underlying peripheral nerve regeneration

Exosomes exhibit complex biological functions and mediate a variety of biological processes,such as promoting axonal regeneration and functional recove ry after injury.Long non-coding RNAs(IncRNAs)have been reported to play a crucial role in axonal regeneration.Howeve r,the role of the IncRNA-microRNAmessenger RNA(mRNA)-competitive endogenous RNA(ceRNA)network in exosome-mediated axonal regeneration remains unclear.In this study,we performed RNA transcriptome sequencing analysis to assess mRNA expression patterns in exosomes produced by cultured fibroblasts(FC-EXOs)and Schwann cells(SCEXOs).Diffe rential gene expression analysis,Gene Ontology analysis,Kyoto Encyclopedia of Genes and Genomes analysis,and protein-protein intera ction network analysis were used to explo re the functions and related pathways of RNAs isolated from FC-EXOs and SC-EXOs.We found that the ribosome-related central gene Rps5 was enriched in FC-EXOs and SC-EXOs,which suggests that it may promote axonal regeneration.In addition,using the miRWalk and Starbase prediction databases,we constructed a regulatory network of ceRNAs targeting Rps5,including 27 microRNAs and five IncRNAs.The ceRNA regulatory network,which included Ftx and Miat,revealed that exsosome-derived Rps5 inhibits scar formation and promotes axonal regeneration and functional recovery after nerve injury.Our findings suggest that exosomes derived from fibro blast and Schwann cells could be used to treat injuries of peripheral nervous system.

Residue Return Effects Outweigh Tillage Effects on Soil Microbial Communities and Functional Genes in Black Soil Region of Northeast China

Conservation tillage as an effective alternative to mitigate soil degradation has attracted worldwide attention,but the influences of conservation tillage on soil microbial community and especially function remain unclear.Shotgun metagenomics sequencing was performed to examine the taxonomic and functional community variations of black soils under three tillage regimes,namely no-tillage with residue(maize straw)return(NTS),moldboard plow with residue return(MPS),and moldboard plow without residue return(MPN)in Northeast China.The results revealed:1)Soil bacterial and archaeal communities differed significantly under different tillage regimes in contrast to soil fungal community.2)The overlay of less tillage and residues return under NTS led to unique soil microbial community composition and functional composition.Specifically,in contrast to other treatments,NTS increased the relative abundances of some taxa such as Bradyrhizobium,Candidatus Solibacter,and Reyranella,along with the relative abundances of some taxa such as Sphingomonas,Unclassified Chloroflexi and Nitrososphaera decreased;NTS had a unique advantage of increasing the relative abundances of genes involved in‘ATP-binding cassette(ABC)transporters’and‘quorum sensing(QS)’pathways,while MPN favored the genes involved in‘flagellar assembly’pathway and some metabolic pathways such as‘carbon’and‘glyoxylate and dicarboxylate’and‘selenocompound’metabolisms.3)Significantly different soil bacterial phyla(Acidobacteria,Gemmatimonadetes,and Chloroflexi)and metabolic pathways existed between MPN and another two treatments(NTS and MPS),while did not exist between NTS and MPS.4)Dissolved organic carbon(DOC)and soil bulk density were significantly affected(P<0.05)by tillage and accounted for the variance both in microbial(bacterial)community structure and functional composition.These results indicated that a change in tillage regime from conventional to conservation tillage results in a shift of microbial community and functional genes,and we inferred that residue return played a more prominent role than less tillage in functional shifts in the microbial community of black soils.

Bioinformatic identification of key candidate genes and pathways in axon regeneration after spinal cord injury in zebrafish

Zebrafish and human genomes are highly homologous;however,despite this genomic similarity,adult zebrafish can achieve neuronal proliferation,regeneration and functional restoration within 6–8 weeks after spinal cord injury,whereas humans cannot.To analyze differentially expressed zebrafish genes between axon-regenerated neurons and axon-non-regenerated neurons after spinal cord injury,and to explore the key genes and pathways of axonal regeneration after spinal cord injury,microarray GSE56842 was analyzed using the online tool,GEO2R,in the Gene Expression Omnibus database.Gene ontology and protein-protein interaction networks were used to analyze the identified differentially expressed genes.Finally,we screened for genes and pathways that may play a role in spinal cord injury repair in zebrafish and mammals.A total of 636 differentially expressed genes were obtained,including 255 up-regulated and 381 down-regulated differentially expressed genes in axon-regenerated neurons.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment results were also obtained.A protein-protein interaction network contained 480 node genes and 1976 node connections.We also obtained the 10 hub genes with the highest correlation and the two modules with the highest score.The results showed that spectrin may promote axonal regeneration after spinal cord injury in zebrafish.Transforming growth factor beta signaling may inhibit repair after spinal cord injury in zebrafish.Focal adhesion or tight junctions may play an important role in the migration and proliferation of some cells,such as Schwann cells or neural progenitor cells,after spinal cord injury in zebrafish.Bioinformatic analysis identified key candidate genes and pathways in axonal regeneration after spinal cord injury in zebrafish,providing targets for treatment of spinal cord injury in mammals.

Bioinformatics analysis of ferroptosis in spinal cord injury

Ferroptosis plays a key role in aggravating the progression of spinal cord injury(SCI),but the specific mechanism remains unknown.In this study,we constructed a rat model of T10 SCI using a modified Allen method.We identified 48,44,and 27 ferroptosis genes that were differentially expressed at 1,3,and 7 days after SCI induction.Compared with the sham group and other SCI subgroups,the subgroup at 1 day after SCI showed increased expression of the ferroptosis marker acyl-CoA synthetase long-chain family member 4 and the oxidative stress marker malondialdehyde in the injured spinal cord while glutathione in the injured spinal cord was lower.These findings with our bioinformatics results suggested that 1 day after SCI was the important period of ferroptosis progression.Bioinformatics analysis identified the following top ten hub ferroptosis genes in the subgroup at 1 day after SCI:STAT3,JUN,TLR4,ATF3,HMOX1,MAPK1,MAPK9,PTGS2,VEGFA,and RELA.Real-time polymerase chain reaction on rat spinal cord tissue confirmed that STAT3,JUN,TLR4,ATF3,HMOX1,PTGS2,and RELA mRNA levels were up-regulated and VEGFA,MAPK1 and MAPK9 mRNA levels were down-regulated.Ten potential compounds were predicted using the DSigDB database as potential drugs or molecules targeting ferroptosis to repair SCI.We also constructed a ferroptosis-related mRNA-miRNA-lncRNA network in SCI that included 66 lncRNAs,10 miRNAs,and 12 genes.Our results help further the understanding of the mechanism underlying ferroptosis in SCI.

Analysis of the autophagy gene expression profile of pancreatic cancer based on autophagy-related protein microtubule-associated protein 1A/1B-light chain 3

BACKGROUND Pancreatic cancer is a highly invasive malignant tumor. Expression levels of the autophagy-related protein microtubule-associated protein 1 A/1 B-light chain 3(LC3) and perineural invasion(PNI) are closely related to its occurrence and development. Our previous results showed that the high expression of LC3 was positively correlated with PNI in the patients with pancreatic cancer. In this study, we further searched for differential genes involved in autophagy of pancreatic cancer by gene expression profiling and analyzed their biological functions in pancreatic cancer, which provides a theoretical basis for elucidating the pathophysiological mechanism of autophagy in pancreatic cancer and PNI.AIM To identify differentially expressed genes involved in pancreatic cancer autophagy and explore the pathogenesis at the molecular level.METHODS Two sets of gene expression profiles of pancreatic cancer/normal tissue(GSE16515 and GSE15471) were collected from the Gene Expression Omnibus.Significance analysis of microarrays algorithm was used to screen differentially expressed genes related to pancreatic cancer. Gene Ontology(GO) analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis were used to analyze the functional enrichment of the differentially expressed genes. Protein interaction data containing only differentially expressed genes was downloaded from String database and screened. Module mining was carried out by Cytoscape software and ClusterOne plug-in. The interaction relationship between the modules was analyzed and the pivot nodes between the functional modules were determined according to the information of the functional modules and the data of reliable protein interaction network.RESULTS Based on the above two data sets of pancreatic tissue total gene expression, 6098 and 12928 differentially expressed genes were obtained by analysis of genes with higher phenotypic correlation. After extracting the intersection of the two differential gene sets, 4870 genes were determined. GO analysis showed that 14 significant functional items including negative regulation of protein ubiquitination were closely related to autophagy. A total of 986 differentially expressed genes were enriched in these functional items. After eliminating the autophagy related genes of human cancer cells which had been defined, 347 differentially expressed genes were obtained. KEGG pathway analysis showed that the pathways hsa04144 and hsa04020 were related to autophagy. In addition,65 clustering modules were screened after the protein interaction network was constructed based on String database, and module 32 contains the LC3 gene,which interacts with multiple autophagy-related genes. Moreover, ubiquitin C acts as a pivot node in functional modules to connect multiple modules related to pancreatic cancer and autophagy.CONCLUSION Three hundred and forty-seven genes associated with autophagy in human pancreatic cancer were concentrated, and a key gene ubiquitin C which is closely related to the occurrence of PNI was determined, suggesting that LC3 may influence the PNI and prognosis of pancreatic cancer through ubiquitin C.

Bioinformatics analyses of differentially expressed genes associated with spinal cord injury:a microarray-based analysis in a mouse model

Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new opportunity for investigating diagnosis,treatment,and prognosis of spinal cord injury.However,differentially expressed genes are not consistent among studies,and many key genes and signaling pathways have not yet been accurately studied.GSE5296 was retrieved from the Gene Expression Omnibus DataSet.Differentially expressed genes were obtained using R/Bioconductor software(expression changed at least two-fold;P < 0.05).Database for Annotation,Visualization and Integrated Discovery was used for functional annotation of differentially expressed genes and Animal Transcription Factor Database for predicting potential transcription factors.The resulting transcription regulatory protein interaction network was mapped to screen representative genes and investigate their diagnostic and therapeutic value for disease.In total,this study identified 109 genes that were upregulated and 30 that were downregulated at 0.5,4,and 24 hours,and 3,7,and 28 days after spinal cord injury.The number of downregulated genes was smaller than the number of upregulated genes at each time point.Database for Annotation,Visualization and Integrated Discovery analysis found that many inflammation-related pathways were upregulated in injured spinal cord.Additionally,expression levels of these inflammation-related genes were maintained for at least 28 days.Moreover,399 regulation modes and 77 nodes were shown in the protein-protein interaction network of upregulated differentially expressed genes.Among the 10 upregulated differentially expressed genes with the highest degrees of distribution,six genes were transcription factors.Among these transcription factors,ATF3 showed the greatest change.ATF3 was upregulated within 30 minutes,and its expression levels remained high at28 days after spinal cord injury.These key genes screened by bioinformatics tools can be used as biological markers to diagnose diseases and provide a reference for identifying therapeutic targets.

Spatiotemporal microRNA profile in peripheral nerve regeneration:miR-138 targets vimentin and inhibits Schwann cell migration and proliferation

While the peripheral nervous system has regenerative ability,restoration of sufficient function remains a challenge.Vimentin has been shown to be localized in axonal growth fronts and associated with nerve regeneration,including myelination,neuroplasticity,kinase signaling in nerve axoplasm,and cell migration;however,the mechanisms regulating its expression within Schwann cell（SC） remain unexplored.The aim of this study was to profile the spatial and temporal expression profile of micro RNA（mi RNA） in a regenerating rat sciatic nerve after transection,and explore the potential role of mi R-138-5 p targeting vimentin in SC proliferation and migration.A rat sciatic nerve transection model,utilizing a polyethylene nerve guide,was used to investigate mi RNA expression at 7,14,30,60,and 90 days during nerve regeneration.Relative levels of mi RNA expression were determined using microarray analysis and subsequently validated with quantitative real-time polymerase chain reaction.In vitro assays were conducted with cultured Schwann cells transfected with mi RNA mimics and assessed for migratory and proliferative potential.The top seven dysregulated mi RNAs reported in this study have been implicated in cell migration elsewhere,and GO and KEGG analyses predicted activities essential to wound healing.Transfection of one of these,mi RNA-138-5 p,into SCs reduced cell migration and proliferation.mi R-138-5 p has been shown to directly target vimentin in cancer cells,and the luciferase assay performed here in rat Schwann cells confirmed it.These results detail a role of mi R-138-5 p in rat peripheral nerve regeneration and expand on reports of it as an important regulator in the peripheral nervous system.

Identification of microRNA-mRNA regulatory networks and pathways related to retinoblastoma across human and mouse

AIM: To explore the m RNA and pathways related to retinoblastoma(RB) genesis and development.METHODS: Microarray datasets GSE29683(human) and GSE29685(mouse) were downloaded from NCBI GEO database. Homologous genes between the two species were identified using WGCNA, followed by protein-protein interaction(PPI) network construction and gene enrichment analysis. Disease-related mi RNAs and pathways were retrieved from mi R2 Disease database and Comparative Toxicogenomics Database(CTD), respectively.RESULTS: A total of 352 homologous genes were identified. Two pathways including "cell cycle" and "pathway in cancer" in CTD and enrichment analysis were identified and seven mi RNAs(including hsa-mi R-373, hsa-mi R-34 a, hsami R-129, hsa-mi R-494, hsa-mi R-503, hsa-let-7 and hsami R-518 c) were associated with RB. mi RNAs modulate "cell cycle" and "pathway in cancer" pathways via regulating 13 genes(including CCND1, CDC25 C, E2 F2, CDKN2 D and TGFB2).CONCLUSION: These results suggest that these mi RNAs play crucial roles in RB genesis through "cell cycle" and "pathway in cancer" pathways by regulating their targets including CCND1, CDC25 C, E2 F2 and CDKN2 D.

Transcriptomic Analysis of Aflatoxin B1-Regulated Genes in Rat Hepatic Epithelial Cells

Aflatoxins are the most popular hepatotoxicants. Chronic exposure to aflatoxins leads to a wide variety ofliver diseases, such as hepatocellular carcinoma. In this study, we analyzed the genome wide expression profiles ofaflatoxin B1-induced rat hepatic epithelial cells. The expression of 325, 184 and 199 special genes was altered whenexposed to 0.03, 0.1 and 0.2 μmol/L aflatoxin B1 respectively, and 239 genes were commonly expressed. After thefunctional analysis on these dose-special genes, we determined several key pathways related to hepatotoxicity, such asTGF-beta signaling pathway, tight junction, adherens junction, the regulation of actin cytoskeleton, ErbB signalingpathway, p53 signaling pathway, pathways in cancer and axon guidance. Common genes were mainly associated withfocal adhesion, ECM-receptor interaction, and cell adhesion molecules. Gene ontology annotations showed a goodconcordance with these pathways. The quantitative real-time polymerase chain reaction（PCR） analysis of selectedgenes showed similar patterns in microarrays. The toxicogenomic study provides a better understanding of molecularmechanisms of aflatoxins.

Bioinformatic analysis of cytokine expression in the proximal and distal nerve stumps after peripheral nerve injury

In our previous study,we investigated the dynamic expression of cytokines in the distal nerve stumps after peripheral nerve injury using microarray analysis,which can characterize the dynamic expression of proteins.In the present study,we used a rat model of right sciatic nerve transection to examine changes in the expression of cytokines at 1,7,14 and 28 days after injury using protein microarray analysis.Interleukins were increased in the distal nerve stumps at 1–14 days post nerve transection.However,growth factors and growth factor-related proteins were mainly upregulated in the proximal nerve stumps.The P-values of the inflammatory response,apoptotic response and cell-cell adhesion in the distal stumps were higher than those in the proximal nerve stumps,but the opposite was observed for angiogenesis.The number of cytokines related to axons in the distal stumps was greater than that in the proximal stumps,while the percentage of cytokines related to axons in the distal stumps was lower than that in the proximal nerve stumps.Visualization of the results revealed the specific expression patterns and differences in cytokines in and between the proximal and distal nerve stumps.Our findings offer potential therapeutic targets and should help advance the development of clinical treatments for peripheral nerve injury.Approval for animal use in this study was obtained from the Animal Ethics Committee of the Chinese PLA General Hospital on September 7,2016(approval No.2016-x9-07).

Role of ESR Pathway Genes in Breast Cancer: A Review

Breast cancer is the leading cause of death in women. Prognosis of breast cancer is often pessimistic because the tumors are prone to metastasizing to the bone, brain, and lung. The estrogen signaling receptor (ESR) pathway contains 39 main genes and proteins which makes it one of the larger signaling pathways. Predominately this pathway and the proteins within are involved in breast growth and development, making it a prospective area of study for breast cancer. While the healthy ESR pathway has been constructed and is well established, a mechanistic model of mutated genes of ESR pathway has not been delved upon. Such mutated models could be utilized for selecting combinational targets for drug therapies, as well as elucidating crosstalk between other pathways and feedback mechanisms. To construct the mutated models of the ESR pathway it is imperative to assess what is currently understood in the literature and what inconsistencies exist in order to resolve them. Without this information, a model of the ESR pathway will be unreliable and likely unproductive. This review is the detailed literature survey of the biological studies performed on ESR pathways genes, and their respective roles in breast cancer. Furthermore, the details mentioned in the review can be beneficial for the integrated study of the ESR pathway genes, which includes, structural and dynamics study of the genes products, to have a holistic understanding of the cancer mechanism.

Protein microarray analysis of cytokine expression changes in distal stumps after sciatic nerve transection

A large number of chemokines,cytokines,other trophic factors and the extracellular matrix molecules form a favorable microenvironment for peripheral nerve regeneration.This microenvironment is one of the major factors for regenerative success.Therefore,it is important to investigate the key molecules and regulators affecting nerve regeneration after peripheral nerve injury.However,the identities of specific cytokines at various time points after sciatic nerve injury have not been determined.The study was performed by transecting the sciatic nerve to establish a model of peripheral nerve injury and to analyze,by protein microarray,the expression of different cytokines in the distal nerve after injury.Results showed a large number of cytokines were up-regulated at different time points post injury and several cytokines,e.g.,ciliary neurotrophic factor,were downregulated.The construction of a protein-protein interaction network was used to screen how the proteins interacted with differentially expressed cytokines.Kyoto Encyclopedia of Genes and Genomes pathway and Gene ontology analyses indicated that the differentially expressed cytokines were significantly associated with chemokine signaling pathways,Janus kinase/signal transducers and activators of transcription,phosphoinositide 3-kinase/protein kinase B,and notch signaling pathway.The cytokines involved in inflammation,immune response and cell chemotaxis were up-regulated initially and the cytokines involved in neuronal apoptotic processes,cell-cell adhesion,and cell proliferation were up-regulated at 28 days after injury.Western blot analysis showed that the expression and changes of hepatocyte growth factor,glial cell line-derived neurotrophic factor and ciliary neurotrophic factor were consistent with the results of protein microarray analysis.The results provide a comprehensive understanding of changes in cytokine expression and changes in these cytokines and classical signaling pathways and biological functions during Wallerian degeneration,as well as a basis for potential treatments of peripheral nerve injury.The study was approved by the Institutional Animal Care and Use Committee of the Chinese PLA General Hospital,China(approval number:2016-x9-07)in September 2016.

Expression and regulatory network of long noncoding RNA in rats after spinal cord hemisection injury

Long noncoding RNAs(lncRNAs)participate in a variety of biological processes and diseases.However,the expression and function of lncRNAs after spinal cord injury has not been extensively analyzed.In this study of right side hemisection of the spinal cord at T10,we detected the expression of lncRNAs in the proximal tissue of T10 lamina at different time points and found 445 lncRNAs and 6522 mRNA were differentially expressed.We divided the differentially expressed lncRNAs into 26 expression trends and analyzed Profile 25 and Profile 2,the two expression trends with the most significant difference.Our results showed that the expression of 68 lncRNAs in Profile 25 rose first and remained high 3 days post-injury.There were 387 mRNAs co-expressed with the 68 lncRNAs in Profile 25.The co-expression network showed that the co-expressed genes were mainly enriched in cell division,inflammatory response,FcγR-mediated cell phagocytosis signaling pathway,cell cycle and apoptosis.The expression of 56 lncRNAs in Profile2 first declined and remained low after 3 days post-injury.There were 387 mRNAs co-expressed with the 56 lncRNAs in Profile 2.The co-expression network showed that the co-expressed genes were mainly enriched in the chemical synaptic transmission process and in the signaling pathway of neuroactive ligand-receptor interaction.The results provided the expression and regulatory network of the main lncRNAs after spinal cord injury and clarified their co-expressed gene enriched biological processes and signaling pathways.These findings provide a new direction for the clinical treatment of spinal cord injury.

Global Profiles of Acetylated Proteins in Brains of Scrapie Agents 139A- and ME7-Infected Mice Collected at Mid-Early, Mid-Late, and Terminal Stages

Objective To describe the global profiles of acetylated proteins in the brains of scrapie agents 139Aand ME7-infected mice collected at mid-early,mid-late,and terminal stages.Methods The acetylated proteins from the cortex regions of scrapie agent(139A-and ME7)-infected mice collected at mid-early(80 days postinfection,dpi),mid-late(120 dpi),and terminal(180 dpi) stages were extracted,and the global profiles of brain acetylated proteins were assayed with proteomic mass spectrometry.The proteins in the infected mice showing 1.5-fold higher or lower levels than that of agematched normal controls were considered as differentially expressed acetylated peptides(DEAPs).Results A total of 118,42,and 51 DEAPs were found in the brains of 139A-80,139A-120,and 139A-180dpi mice,respectively.Meanwhile,390,227,and 75 DEAPs were detected in the brains of ME7-80,ME7-120,and ME7-180 dpi mice,respectively.The overwhelming majority of DEAPs in the mid-early stage were down-regulated,and more portions of DEAPs in the mid-late and late stages were up-regulated.Approximately 22.1%(328/1,485) of acetylated peptides mapped to 74 different proteins were mitochondrial associated.Kyoto Encyclopedia of Genes and Genomes pathway analysis identified 39(80dpi),13(120 dpi),and 10(180 dpi) significantly changed pathways in 139A-infected mice.Meanwhile,55,25,and 18 significantly changed pathways were observed in the 80,120,and 180 dpi samples of139A-and ME7-infected mice(P < 0.05),respectively.Six pathways were commonly involved in all tested samples.Moreover,many steps in the citrate cycle(tricarboxylic acid cycle) were affected,represented by down-regulated acetylation for relevant enzymes in the mid-early stage and upregulated acetylation in the mid-late and late stages.Conclusion Our data here illustrated the changes in the global profiles for brain acetylated proteins during prion infection,showing remarkably inhibited acetylation in the early stage and relatively enhanced acetylation in the late stage.

On microbial community of Pyropia haitanensis by metagenomic analysis

Microorganisms plays an important role in the growth of Pyropia haitanensis.To understand the structural and functional diversity of the microorganism community of P.haitanensis(PH40),the associated metabolic pathway network in cluster of orthologous groups(COG)and Kyoto Encyclopedia of Genes and Genomes(KEGG),and carbohydrate-active enzymes(CAZymes)were explored in metagenomic analysis.DNA extraction from gametophytes of P.haitanensis was performed first,followed by library construction,sequencing,preprocessing of sequencing data,taxonomy assignment,gene prediction,and functional annotation.The results show that the predominant microorganisms of P.haitanensis were bacteria(98.98%),and the phylum with the highest abundance was Proteobacteria(54.64%),followed by Bacteroidetes(37.92%).Erythrobacter(3.98%)and Hyunsoonleella jejuensis(1.56%)were the genera and species with the highest abundance of bacteria,respectively.The COG annotation demonstrated that genes associated with microbial metabolism was the predominant category.The results of metabolic pathway annotation show that the ABC transport system and two-component system were the main pathways in the microbial community.Plant growth hormone biosynthesis pathway and multi-vitamin biosynthesis functional units(modules)were the other important pathways.The CAZyme annotation revealed that the starch might be an important carbon source for microorganisms.Glycosyl transferase family 2(GT2)and glycosyl transferase family 3(GT3)were the highly abundant families in glucoside transferase superfamily.Six metagenome-assembled genomes containing enzymes involved in the biosynthesis of cobalamin(vitamin B 12)and indole-3-acetic acid were obtained by binning method.They were confirmed to belong to Rhodobacterales and Rhizobiales,respectively.Our findings provide comprehensive insights into the microorganism community of Pyropia.

酒精性肝炎自噬关键基因的筛选及生物信息学分析

目的筛选酒精性肝炎(AH)的自噬关键基因,探讨AH潜在的生物标志物和治疗靶点。方法采用基因表达综合数据库(GEO)中的2个AH基因芯片和从MSigDB、GeneCards数据库中获得的自噬相关数据集,通过加权基因共表达网络分析(WGCNA)获取关键基因。对筛选的关键基因进行基因本体(GO)、京都基因和基因组百科全书(KEGG)功能富集分析,蛋白质相互作用(PPI)分析,免疫浸润分析,构建信使RNA(mRNA)-微小RNA(miRNA)网络,进行酒精性肝病不同分期的自噬相关关键基因的表达差异分析,并进一步通过实时荧光定量逆转录聚合酶链反应(RT-qPCR)在AH患者和小鼠肝脏组织中验证。结果本研究筛选得到了11个与AH自噬相关的基因(EEF1A2、CFTR、SOX4、TREM2、CTHRC1、HSPB8、TUBB3、PRKAA2、RNASE1、MTCL1、HGF),均为上调基因。在AH患者和小鼠肝脏组织中,SOX4、TREM2、HSPB8、PRKAA2在AH组中的相对表达量均高于对照组。结论SOX4、TREM2、HSPB8、PRKAA2可能是AH潜在的生物标志物和治疗靶点。

高尿酸血症状态下低度炎症的病理特点研究

目的:探讨高尿酸血症(HUA)状态下低度炎症的病理特点。方法:根据体质量随机将迪法克鹌鹑分为正常组、模型组,每组10只。以普通饲料:酵母浸膏粉=4∶1制备食饵,并以该食饵喂养模型组鹌鹑,正常组鹌鹑则自由饮食饮水。分别于造模第10、20、30天检测血清尿酸,血清炎症介质白细胞介素-1β(IL-1β)、IL-33、IL-2、IL-13、IL-8、IL-17、IL-6、IL-10、IL-12/P40、IL-16、IL-21、C反应蛋白(CRP)、粒细胞巨噬细胞集落刺激因子(GM-CSF)、肿瘤坏死因子-α(TNF-α)、趋化因子CC配体2(CCL2)及γ干扰素(IFN-γ)、神经突起生长导向因子2(Netrin-2)、五聚蛋白3(Pentraxin 3),观察各炎症介质强度变化;造模第30天,取鹌鹑肝、回肠、肾各脏器组织,进行HE染色后观察组织病理形态变化;造模第20天,用基因本体(GO)和京都基因与基因组百科全书(KEGG)富集分析差异炎症介质功能及相关信号通路;用Pearson相关性分析方法分析差异炎症介质与血清尿酸水平的相关性。结果:与正常组比较,模型组鹌鹑血清尿酸水平高(P<0.05),以血清IL-17、IL-6、IL-33等为主的白细胞介素类,以IL-8、CCL2为主的趋化因子类,IFN-γ、TNF-α、CRP及GM-CSF水平均升高(P<0.05),而IL-13、IL-10水平降低(P<0.05)。造模第20天,GO/KEGG富集分析结果显示,HUA状态下的低度炎症可能是尿酸代谢靶点群,通过IL-17、Janus激酶信号转导和转录激活因子(JAK-STAT)等信号通路激活、细胞因子-细胞因子间相互作用,从而诱导IL-6、TNF-α等炎症介质产生。2组组织病理变化结果显示,与正常组相比,模型组回肠组织黏膜下层可见炎性细胞浸润,肝、肾组织未见明显差异。差异炎症介质与血清尿酸水平的相关性分析结果显示,鹌鹑血清中IL-6、TNF-α、CRP、IL-33、IL-17、IL-8、IFN-γ、CCL2、GM-CSF、IL-1β、IL-2、IL-6水平均与血清尿酸水平正相关,IL-10、IL-13水平与血清尿酸水平负相关。结论:HUA鹌鹑模型存在低度炎症,该低度炎症可能与尿酸代谢靶点群通过IL-17、JAK-STAT等信号通路的激活以及细胞因子间的相互作用,从而调控IL-6、TNF-α等炎症介质的产生有关。

基于网络药理学探讨派特灵治疗尖锐湿疣的作用机制

目的基于网络药理学研究外用派特灵治疗尖锐湿疣(CA)的作用机制。方法基于网络药理学的方法,经研究表明派特灵是主要由金银花、苦参、白花蛇舌草、鸦胆子、五倍子、蛇床子和大青叶等组成的中药复方制剂,通过中药系统药理学数据库与分析平台(TCMSP)数据库获取派特灵主要组成中药的活性成分与相应靶点;通过GeneCards数据库获得与CA相关的疾病靶点,取其基因与靶点交集制作韦恩图;通过STRING数据库和Cytoscape3.7.1软件共同构建蛋白互作网络(PPI),应用R语言下载安装Bioconductor数据库中的相关R包对交集得到的核心靶点进行相应的基因本体(GO)和京都基因与基因组百科全书(KEGG)富集分析。结果在TCMSP数据库共获取109个活性化合物,主要为β谷甾醇、鸦胆甙、槲皮素等,GeneCards数据库共获取疾病靶点74个,PPI网络分析显示共涉及前列腺素内过氧化物合酶-2(PTGS-2)、B细胞淋巴瘤/白血病-2(BCL-2)、过氧化物酶体增殖物激活受体-γ(PPAR-γ)、血管内皮生长因子-A(VEGF-A)、同期蛋白D1(CCND1)等15个核心蛋白,GO、KEGG富集分析显示派特灵可以通过各类癌症通路、人乳头状瘤病毒(HPV)感染、磷脂酰肌醇3激酶-蛋白激酶B(PI3K-Akt)、人巨细胞病毒感染信号通路等多途径、多靶点作用于CA。结论派特灵通过抗HPV病毒、调节免疫等方面达到治疗CA的目的。

基于咽部分泌物蛋白质组学分析的术后咽痛机制研究

目的 筛选术后咽痛(postoperative sore throat, POST)病理过程中的差异表达的蛋白质,探讨POST的发生机制。方法 收集山西医科大学第一医院择期手术行全身麻醉气管插管患者的咽部分泌物20例,根据其术后24 h是否发生咽痛将其分为咽痛组(POST组)和非咽痛组(对照组),各10例,并进行蛋白定量分析,筛选出样本中的差异蛋白谱,对差异蛋白进行基因本体论(gene ontology, GO)注释及京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes, KEGG)通路分析。结果 POST组和对照组共同鉴定到3 419个蛋白,显著上调的蛋白有190个,显著下调的蛋白有16个。GO注释提示差异蛋白主要参与细胞的代谢、生物调节过程、应激反应及免疫过程。KEGG富集分析提示差异蛋白主要富集于Wnt、泛素介导的蛋白水解及氧化磷酸化等信号通路。结论 POST涉及的生物学过程较多,其中Wnt信号通路与疼痛关系密切,因此POST可能是通过该通路介导的结果。