Blueberry malvidin-3-galactoside modulated gut microbial dysbiosis and microbial TCA cycle KEGG pathway disrupted in a liver cancer model induced by HepG2 cells

HCC(Hepatocellular Carcinoma)is a critical health issue worldwide.Our previous animal experiment has confirmed that blueberry malvidin-3-galactoside(M3G)can regulate the progression of HCC.In this study,feces samples from the same batch of mice were collected to explore the regulatory mechanism of M3G on intestinal microbiota and microbial TCA cycle metabolism KEGG pathway in HCC mice based on 16S rRNA sequencing and metagenomics.Our results showed that blueberry M3G increased the microbial diversity and regulated the structure of intestinal microbiota in mice,such as increasing the abundance of Clostridia(butyric acid-producing bacteria),Oscillospira and Ruminococcus,and reducing the abundance of pathogenic Erysipelotrichi.Compared with the group of liver cancer and 5-fluorouracil,blueberry M3G significantly regulated microbial TCA cycle KEGG pathway via improving the expression of key proteins(porA,DLAT,aceE,PC and OGDH).Additionally,we found which the abundance of Muribaculum intestinale increased by blueberry M3G may be an important factor affecting the microbial TCA cycle KEGG pathway via the pearson correlation(R)analysis of protein and microbiota.Taken together,these results demonstrate that the blueberry M3G has the potential to be an intestinal microbiota regulator and an adjuvant to HCC therapy.

Screening ulcerative colitis key target gene and pathway based on KEGG pathway

Objective:To obtain the relevant information of pathway and gene by using the database of DAVID,analyze the function and distribution of important genes,screen out the target genes related to Ulcerative Colitis and promote the study of the pathogenesis of UC and the development of new drugs.Methods:The Ulcerative Colitis was used to search UC related genes in TTD,Drugbank,DisGeNET database.The obtained gene data was input to the database of Daved,and the data of gene enriched pathway was obtained 87 genes were Significant enriched in the first 20 KEGG pathways.The 87 genes were input to the string database to make the interaction network diagram,and the key genes enriched in the pathway were also made the network diagram,and the two network diagrams were compared.Results:RELA,TNF,IL1B,NFKB1,IL6 and IL10 were among the highest ranked genes in two network diagrams.Conclusion:The study of RELA,TNF,IL1B,NFKB1,IL6 and IL10 is necessary for us to study further.The pathogenesis of UC was associated with multiple pathways such as NF-kappa B signaling pathway,Jak-STAT signaling pathway,TNF signaling pathway and so on.It is helpful to understand the pathogenesis of disease and provide a reliable target for the development of new drugs by analyzing the pathway and the network diagram of the interaction between genes and disease related genes.

妊娠期糖尿病患者外周血长链非编码RNA表达谱的差异性分析

目的探讨妊娠期糖尿病(GDM)患者外周血中长链非编码RNA(lncRNAs)的差异表达谱及其功能。方法分别收集2020年7月至2021年12月在宣汉县人民医院妇产科入院治疗的妊娠期糖尿病患者(GDM组)、门诊健康体检孕妇(对照组)外周血标本各3例。使用高通量测序技术筛选获得差异表达的lncRNA,并通过GO富集分析和KEGG Pathway富集分析查明差异表达的lncRNAs靶向调控的m RNA转录本的生物信息学功能。结果与对照组比较,GDM组共筛选出差异表达的lncRNAs 333个,mRNA 2036个,其中上调的lncRNAs 169个,m RNA645个;下调的lncRNAs 164个,m RNA 1391个;GO生物学功能富集分析结果显示:差异表达的lncRNAs靶向调控的mRNA转录本主要富集在转录因子AP-1复合物、蛋白质复合物分解的调控、免疫系统调节、防御反应、细胞解剖实体、大分子代谢过程的调控、氮化合物代谢过程的调控、胞浆、代谢过程调节等;KEGG信号通路富集分析结果显示:差异表达的lncRNAs靶向调控的m RNA转录本参与的信号通路主要包括B细胞受体信号通路、泛素介导的蛋白质水解、破骨细胞分化、内质网中的蛋白质加工、人类T细胞白血病病毒1感染、雌激素信号通路、PD-L1和PD-1在癌症中的表达信号通路等。结论妊娠期糖尿病患者和门诊健康体检孕妇外周血中lncRNAs的表达存在较大差异,而差异表达的lncRNAs靶向调控的基因主要通过B细胞受体信号通路、泛素介导的蛋白质水解、破骨细胞分化、内质网中的蛋白质加工等信号通路参与GDM的发生发展。

Transcriptome Analysis of a Wild Eggplant Germplasm M239 in Response to Verticillium dahliae Infection

In this study,wild eggplant germplasm No.M239,which is highly susceptible to Verticillium wilt,was used as the experimental material.The physiological and biochemical indices(SOD,PAL,MDA and soluble protein)of M239 roots were measured at different times(0,12,24,36,48,60 and 72 h)post inoculation with Verticillium dahliae,and the key time points for the M239 response to Verticillium wilt infection were screened.Then,RNA-Seq technology was used to screen the differentially expressed genes(DEGs)in M239 roots at 0,12 and 48 h post-inoculation(hpi).The transcriptional results of M239 were also compared with those resistance genes from some reported wild relative Solanum species(S.sisymbriifolium and S.aculeatissimum).Then some DEGs were chosen for validation by qRT–PCR.The results showed that 12 and 48 hpi were the turning points in the changes in all physiological and biochemical indices.A total of 6,783 DEGs were identified by RNA-Seq,including 6,141 DEGs(3,046 upregulated and 3,095 downregulated)at the M_12 h vs.M_0 h,1,903 DEGs(792 upregulated and 1,111 downregulated)at M_48 h vs.M_12 h,and 1,261 DEGs that appeared simultaneously in both stages.KEGG enrichment analysis showed that there were 5 metabolic pathways enriched from DEGs,which were mostly related to primary metabolism,such as glycolysis,amino acid and ribosome biogenesis.Compared with the NCBI non-redundant protein(NR)database,one Ve2 homologous gene and 8 PR protein-related genes were screened.Transcription factor analysis showed that there were a large number of DEGs,such as MYB,AP2-EREBP,bHLH,NAC and Orphans in the two stages.Compared with the reported Verticillium wilt-resistant wild eggplant species,it was found that there were fewer genes and enriched metabolic pathways in the M239 response to Verticillium wilt infection,and it also lacked the response of some known key resistance genes.These results proved that the above resistance genes and metabolic pathways played a key role in the wild eggplant response to V.dahliae infection.

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.

MicroRNAs: a novel promising therapeutic target for cerebral ischemia/reperfusion injury?

To determine the molecular mechanism of cerebral ischemia/reperfusion injury, we examined the micro RNA（mi RNA） expression profile in rat cortex after focal cerebral ischemia/reperfusion injury using mi RNA microarrays and bioinformatic tools to systematically analyze Gene Ontology（GO） function classifications, as well as the signaling pathways of genes targeted by these differentially expressed mi RNAs. Our results show significantly changed mi RNA expression profiles in the reperfusion period after focal cerebral ischemia, with a total of 15 mi RNAs up-regulated and 44 mi RNAs down-regulated. Target genes of these differentially expressed mi RNAs were mainly involved in metabolic and cellular processes, which were identified as hub nodes of a mi RNA-GO-network. The most correlated pathways included D-glutamine and D-glutamate metabolism, the renin-angiotensin system, peroxisomes, the PPAR signaling pathway, SNARE interactions in vesicular transport, and the calcium signaling pathway. Our study suggests that mi RNAs play an important role in the pathological process of cerebral ischemia/reperfusion injury. Understanding mi RNA expression and function may shed light on the molecular mechanism of cerebral ischemia/reperfusion injury.

Differential mRNA expression profiling of oral squamous cell carcinoma by high-throughput RNA sequencing

Differentially expressed genes are thought to regulate the development and progression of oral squamous cell carcinomas （OSCC）. The purpose of this study was to screen differentially expressed mRNAs in OSCC and matched paraneoplastic normal tissues, and to explore the intrinsic mechanism of OSCC development and progres- sion. We obtained the differentially expressed mRNA expression profiles in 10 pairs of fresh-frozen OSCC tissue specimens and matched paraneoplastic normal tissue specimens by high-throughput RNA sequencing. By using Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment analyses, the functional significance of the differentially expressed genes were analyzed. We identified 1,120 sig- nificantly up-regulated mRNAs and 178 significantly down-regulated mRNAs in OSCC, compared to normal tissue. The differentially expressed mRNAs were involved in 20 biological processes and 68 signal pathways. Compared to adjacent normal tissue, the expression of MAGEAll was up-regulated; TCHH was down-regulated. These find- ings were verified by real-time PCR. These differentially expressed mRNAs may function as oncogenes or tumor suppressors in the development and progression of OSCC. This study provides novel insights into OSCC. However, further work is needed to determine if these differentially expressed mRNAs have potential roles as diagnostic bio- markers and candidate therapeutic targets for OSCC.

Neuroprotective effects of long noncoding RNAs involved in ischemic postconditioning after ischemic stroke

During acute reperfusion,the expression profiles of long noncoding RNAs in adult rats with focal cerebral ischemia undergo broad changes.However,whether long noncoding RNAs are involved in neuroprotective effects following focal ischemic stroke in rats remains unclear.In this study,RNA isolation and library preparation was performed for long noncoding RNA sequencing,followed by determining the coding potential of identified long noncoding RNAs and target gene prediction.Differential expression analysis,long noncoding RNA functional enrichment analysis,and co-expression network analysis were performed comparing ischemic rats with and without ischemic postconditioning rats.Rats were subjected to ischemic postconditioning via the brief and repeated occlusion of the middle cerebral artery or femoral artery.Quantitative real-time reverse transcription-polymerase chain reaction was used to detect the expression levels of differentially expressed long noncoding RNAs after ischemic postconditioning in a rat model of ischemic stroke.The results showed that ischemic postconditioning greatly affected the expression profile of long noncoding RNAs and mRNAs in the brains of rats that underwent ischemic stroke.The predicted target genes of some of the identified long noncoding RNAs(cis targets)were related to the cellular response to ischemia and stress,cytokine signal transduction,inflammation,and apoptosis signal transduction pathways.In addition,15 significantly differentially expressed long noncoding RNAs were identified in the brains of rats subjected to ischemic postconditioning.Nine candidate long noncoding RNAs that may be related to ischemic postconditioning were identified by a long noncoding RNA expression profile and long noncoding RNA-mRNA co-expression network analysis.Expression levels were verified by quantitative real-time reverse transcription-polymerase chain reaction.These results suggested that the identified long noncoding RNAs may be involved in the neuroprotective effects associated with ischemic postconditioning following ischemic stroke.The experimental animal procedures were approved by the Animal Experiment Ethics Committee of Kunming Medical University(approval No.KMMU2018018)in January 2018.

柴芩承气汤潜在作用的生物信息学预测

目的:通过分析柴芩承气汤所含中药成分的相关基因富集性、信号通路富集性及病种富集性,预测其潜在的作用机制。方法:对柴芩承气汤中所含中药成分采用生物信息学技术中的KEGG pathway/GO terms/TTD disease/OMIM disease等方法分析其相关基因富集性、信号通路富集性及病种富集性。结果:预测得出柴芩承气汤除在重症急性胰腺炎方面可能通过清除炎症因子、预防发生炎症反应综合征以及通过峻下热结改善肠道动力功能而起到预防多脏器功能衰竭的作用外,还在分子和基因水平方面对诸多疾病有潜在作用。结论:对于该预测结果可从实验室开始,同时结合临床中医辨证论治过程判定其适应症及其安全性和确切性。

Mechanism of Wumei Pill in the Treatment of Non-Erosive reflux disease from the Perspective of Network Pharmacology and Molecular docking

Objective:Based on network pharmacology and molecular docking to explore the mechanism of Wumei Pill in the treatment of non-erosive reflux disease(NERD).Method:We collected the active ingredients and targets of Wumei Pill by Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP),and collected NERD related targets through Genecards,PharmGKB,Drugbank,DisGeNET,OMIM,CTD and TTD databases.Intersection targets of Wumei Pill targets and NERD related targets were the potential targets of Wumei Pill in the treatment of NERD.We imported the intersection targets into the STRING database to obtain the PPI network,and obtained the hub targets.The network diagram of"Drugs-Potential active ingredients-Potential targets"was constructed by Cytoscape 3.7.2 software.We used R software to perform Gene Ontology function enrichment analysis(GO)and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis(KEGG)on hub targets,and then performed molecular docking verification.Results:There were 129 active ingredients and 213 drug targets of Wumei Pill of which 114 were the intersection targets.1587 GO enrichment items were identified(P<0.05),including 1,491 biological processes,11 cell components,and 85 molecular functions.143 KEGG pathways(P<0.05),mainly related to Kaposi sarcoma-associated herpesvirus infection,IL-17 signaling pathway,the TNF signaling pathway,MAPK signaling pathway.Results of molecular docking showed that the potential active ingredients in Wumei Pill had relatively stable binding activity to the key targets.Conclusion:Wumei pill for the treatment of non-erosive reflux disease are main active ingredients quercetin,kaempferol,beta sitosterol,Isocorypalmine,Stigmasterol,rutaecarpine,etc,the main targets is JUN,TP53,AKT1,may inhibit excessive inflammation,antioxidant therapy effect into full play.This provided a certain theoretical basis for clinical application.

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.

应用基因芯片技术分析甘草酸改善大鼠酒精性肝损伤的作用机制

目的运用基因芯片技术检测甘草酸对大鼠酒精性肝损伤保护作用的分子机制。方法 45只大鼠随机分为3组:模型组、甘草酸组、正常对照组,连续灌服56度白酒8周,处理动物,测定血清谷丙转氨酶(ALT)和谷草转氨酶(AST)水平;抽提肝脏RNA,全基因组表达谱芯片检测,运用GO和KEGG Pathway富集分析。结果与正常对照组比较,模型组血清AST和ALT含量显著升高,差异有统计学意义(t=7.784,P<0.05;t=11.366,P<0.05),肝组织出现显著的肝损伤;与模型组相比,甘草酸组能显著改善肝组织病变,降低血清AST和ALT含量,差异有统计学意义(t=6.448,P<0.05;t=7.526,P<0.05)。芯片结果分析显示,甘草酸组与模型组共筛选出7 482条差异可变剪切RNA(Splicing Index<-3或>3,P<0.05),其中差异可变剪切编码RNA为6 512条。对差异可变剪切编码RNA进行GO和Pathway富集分析,结果显示,主要与乙醇分解代谢、肝星状细胞活化、氧化还原酶活性、氨基酸合成代谢、脂肪酸的生物合成、Notch信号通路等功能或通路有关。结论甘草酸在改善大鼠酒精性肝损伤病变过程中存在大量差异可变剪切编码RNA,提示甘草酸可通过调节多基因可变剪切改善酒精性肝损伤病变。

斑块型银屑病患者外周血SLC35E2B基因的表达及其变异研究

目的通过检测斑块型银屑病患者外周血中SLC35E2B的表达情况,并利用数据库分析基因富集的功能和参与的通路,探讨SLC35E2B在银屑病发病机制中的作用。方法收集斑块型银屑病47例、正常对照14例的外周静脉血,提取样本基因组DNA,用外显子捕获-高通量测序(exon-capture high-throughput sequencing,EC-HTS)技术进行检测,数据经过Calling、数据库比对、软件分析得到最终SLC35E2B基因病理性突变位点,利用GO和KEGG pathway数据库分析基因富集的功能和参与的通路。结果对61例样本所得数据进行生物信息学分析得到致病性突变位点1个:SLC35E2Bc.833C>T(p.T278M),仅见于斑块型银屑病组,正常组未见;GO富集提示SLC35E2B生物学过程主要涉及调节IL-12家族细胞因子、IL-17家族细胞因子、调节对生物刺激的细胞应答、TNF的合成、调节Th1细胞相关的免疫应答以及抵抗病原微生物等多细胞生物过程;KEGG通路分析提示SLC35E2B基因主要与结核病、1型糖尿病、弓形虫病、哮喘、类风湿性关节炎等疾病相关。结论SLC35E2B可能参与银屑病发病的病理过程。

Identification of micro RNAs and their target genes in Alport syndrome using deep sequencing of iPSCs samples

MicroRNAs （miRNAs） are a class of small RNA molecules that are implicated in post-transcriptional reg- ulation of gene expression during development. The discovery and understanding of miRNAs has revolutionized the traditional view of gene expression. Alport syndrome （AS） is an inherited disorder of type IV collagen, which most commonly leads to glomerulonephritis and kidney failure. Patients with AS inevitably reach end-stage renal disease and require renal replacement therapy, starting in young adulthood. In this study, Solexa sequencing was used to identify and quantitatively profile small RNAs from an AS family. We identified 30 known miRNAs that showed a sig- nificant change in expression between two individuals. Nineteen miRNAs were up-regulated and eleven were down-regulated. Forty-nine novel miRNAs showed significantly different levels of expression between two individuals. Gene target predictions for the miRNAs revealed that high ranking target genes were implicated in cell, cell part and cellular process categories. The purine metabolism pathway and mitogen-activated protein kinase （MAPK） signaling pathway were enriched by the largest number of target genes. These results strengthen the notion that miRNAs and their target genes are involved in AS and the data advance our understanding of miRNA function in the patho- genesis of AS.