Ambient Light Alters Gene Expression Pattern of Enzymes and Transcription Factors Involved in Phenylpropanoid Metabolic Pathway in Potato under Chilling Stress

[Objective] Expressions of key enzymatic genes involved in phenyl-propanoid metabolic pathway in potato and StR2R3-MYB and StTGA transcripters were investigated in the present study. [Method] The primitive cultivar Yan was the materials for replicated trials and total RNA extracted from tissues of seedlings. Re-al-time florescent quantification PCR, multiple intervals of air temperature, light-il umi-nation and time-duration were factors of treatments in the experiment. Data on gene expressions were obtained and proceed to asses and compare effects based on statistical analysis. [Result] The results showed negative correlations between tem-perature degrees and expressions of StPAL, StDFR and StR2R3-MYB genes but not StTGA. Positive correlations, however, were derived between those of StCHS, StDFR and StR2R3-MYB and light-intensity. Significant interactive effects between expressions of StPAL and StDFR and treatments, light intensity and temperature degree, along the phenylpropanoid pathway were observed. Transcription regulator of StR2R3-MYB showed significant positive effect on the expression of StCHS of potato. StTGA transcription factor, on the other hand, gave significant negative ef-fects on the expression of StDFR. [Conclusion] Results from present study reveal the role of environmental factors and complicate interactions between such condi-tions as temperature-light il umination and mRNA function of target genes.

Relationships between cell cycle pathway gene polymorphisms and risk of hepatocellular carcinoma

AIM: To investigate the associations between the polymorphisms of cell cycle pathway genes and the risk of hepatocellular carcinoma(HCC). METHODS: We enrolled 1127 cases newly diagnosed with HCC from the Tumor Hospital of Guangxi Medical University and 1200 non-tumor patients from the First Affiliated Hospital of Guangxi Medical University. General demographic characteristics, behavioral information, and hematological indices were collected by unified questionnaires. Genomic DNA was isolatedfrom peripheral venous blood using Phenol-Chloroform. The genotyping was performed using the Sequenom Mass ARRAY i PLEX genotyping method. The association between genetic polymorphisms and risk of HCC was shown by P-value and the odd ratio(OR) with 95% confidence interval(CI) using the unconditional logistic regression after adjusting for age, sex, nationality, smoking, drinking, family history of HCC, and hepatitis B virus(HBV) infection. Moreover, stratified analysis was conducted on the basis of the status of HBV infection, smoking, and alcohol drinking.RESULTS: The HCC risk was lower in patients with the MCM4 rs2305952 CC(OR = 0.22, 95%CI: 0.08-0.63, P = 0.01) and with the CHEK1 rs515255 TC, TT, TC/TT(OR = 0.73, 95%CI: 0.56-0.96, P = 0.02; OR = 0.67, 95%CI: 0.46-0.97, P = 0.04; OR = 0.72, 95%CI: 0.56-0.92, P = 0.01, respectively). Conversely, the HCC risk was higher in patients with the KAT2 B rs17006625 GG(OR = 1.64, 95%CI: 1.01-2.64, P = 0.04). In addition, the risk was markedly lower for those who were carriers of MCM4 rs2305952 CC and were also HBs Ag-positive and non-drinking and nonsmoking(P < 0.05, respectively) and for those who were carriers of CHEK1 rs515255 TC, TT, TC/TT and were also HBs Ag-negative and non-drinking(P < 0.05, respectively). Moreover, the risk was higher for those who were carriers of KAT2 B rs17006625 GG and were also HBs Ag-negative(P < 0.05).CONCLUSION: Of 12 cell cycle pathway genes, MCM4, CHEK1 and KAT2 B polymorphisms may be associated with the risk of HCC.

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.

Insilico Identification of Genes and Molecular Pathways during Aging in <i>Drosophila</i>Brain

The regulation of gene expression in brain vicissitudes during aging is still not much known and explored. Differential gene expression and regulation is a key factor involved to identify the important landmarks within the brain transcriptome to study neuronal aging. Recently, transcriptomic studies are highly explored to understand and depict diseased versus normal as next generation sequencing enables to capture the complete biological context to the entire genome. Study of gene expression during aging compared to young flies provides a signature and scenario of gene expression and regulation during aging. In this study, we took advantage of NGS raw data of young and old flies head from SRA database of NCBI and decrypted the gene expression regulation during normal aging in drosophila model. We identified 350 genes with significant differential expression between young and old flies having 0.01% FDR. Various pathways in context to identified genes which are involved in aging include autophagy i.e. cell death and apoptosis, proteolysis, oxidative stress, declination grey and white matter and neurotransmitter levels, mitochondrial discrepancy, electron transport chain, sugar degradation pathways, activation of transcription factors involved in epigenetic changes, regulators involved in negative and positive regulation WNT signaling pathways, G protein coupled receptor etc. as all these factors contribute to neurodegeneration and possibly dementia in normal aging. So, to find the specific genes and regulators which are differentially expressed in normal aging, we investigate brain transcriptome of normal aging flies compared to young flies which offer a repertoire of genes, regulators and factors involved in network of neurodegeneration to establish direct correlation between aging and dementia. We also identified the pathways which are involved in aging and corresponding gene regulation in these pathways in aging flies brain. It is found that there are some common pathways whose genes and regulators are highly differentially regulated in both aging and dementia.

Advances in Single Nucleotide Polymorphisms of Vitamin D Metabolic Pathway Genes and Respiratory Diseases

Vitamin D is a fat-soluble vitamin.It is an essential vitamin for human body.It has a classical effect on regulating calcium and phosphorus metabolism.Participate in cellular and humoral immune processes by regulating the growth,differentiation and metabolism of immune cells.A large number of studies in recent years have shown that vitamin D deficiency increases the incidence of respiratory diseases.Respiratory diseases mainly include bronchial asthma,chronic obstructive pulmonary disease,tuberculosis,acute upper respiratory tract infection and pneumonia.Vitamin D metabolic pathway genes play a very important regulatory role in the transformation of vitamin D into active vitamin D,including CYP2R1,CYP27B1,CYP24A1,VDBP,VDR five genes.Genetic polymorphism of genes is the molecular basis of individual differences and disease development.Therefore,this paper summarizes the research on single nucleotide polymorphism of vitamin D metabolic pathway gene and respiratory diseases.In order to provide a new idea for future treatment.

Expression Profile Analysis of Genes Involved in Brassinosteroid Biosynthesis Pathway in Cotton Fiber Development

Cotton(Gossypium hirsutum L.) is the leading fiber crop and one of the mainstays of the economy in the world.Cotton fibers,as the main product of cotton plants,are unicellular,linear

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.

Predicting Arabidopsis thaliana Gene Function by Transitiving Co-expression in Shortest-path

The present paper predicted the function of unknow genes by analyzing the co-expression data of Arabidopsis thaliana from biological pathway based on the shortest-path algorithm. This paper proposed that transitive co-expression among genes can be used as an important attribute to link genes of the same biological pathway. The genes from the same biological pathway with similar functions are strongly correlated in expression. Moreover,the function of unknown genes can be predicted by the known genes where they are strongly correlated in expression lying on the same shortest-path from the biological pathway. Analyzing the Arabidopsis thaliana from the biological pathway,this study showed that this method can reliably reveal function of the unknown Arabidopsis thaliana genes and the approach of predicting gene function by transitiving co-expression in shortest-path is feasible and effective.

Identification of a potential tumor suppressor gene, UBL3, in non-small cell lung cancer

Objective: Oncogenes have been shown to be drivers of non-small cell lung cancer(NSCLC), yet the tumor suppressing genes involved in lung carcinogenesis remain to be systematically investigated. This study aimed to identify tumor suppressing ubiquitin pathway genes(UPGs) that were critical to lung tumorigenesis.Methods: The 696 UPGs were silenced by an siRNA screening in NSCLC cells;the potential tumor suppressing UPGs were analyzed, and their clinical significance was investigated.Results: We reported that silencing of 11 UPGs resulted in enhanced proliferation of NSCLC cells, and four UPGs(UBL3, TRIM22, UBE2 G2, and MARCH1) were significantly downregulated in tumor samples compared to that in normal lung tissues and their expression levels were positively associated with overall survival(OS) of NSCLC patients. Among these genes, UBL3 was the most significant one. UBL3 expression was decreased in tumor samples compared to that in paired normal lung tissues in 59/86(68.6%) NSCLCs, was correlated with TNM stage and sex of NSCLC patients, and was significantly higher in non-smoking patients than in smoking patients. Silencing UBL3 accelerated cell proliferation and ectopic expression of UBL3 suppressed NSCLC in vitro and in vivo.Conclusions: These results showed that UBL3 represented a tumor suppressor in NSCLC and may have potential for use in therapeutics and for the prediction of clinical outcome of patients.

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.

Role of microRNA in liver regeneration

BACKGROUND： Liver regeneration is a complex process. micro RNAs（mi RNAs） are short, single-stranded RNAs that modify gene expression at the post-transcriptional level. Recent investigations have revealed that mi RNAs are closely linked to liver regeneration.DATA SOURCES： All included studies were obtained from Pub Med, Embase, the Science Direct databases and Web of Science, with no limitation on publication year. Only studies published in English were considered.RESULTS： We grouped studies that involved mi RNA and liver regeneration into two groups： mi RNAs as promoters and as inhibitors of liver regeneration. We summarized the relevant mi RNAs separately from the related pathways.CONCLUSIONS： Blocking or stimulating the pathways of mi RNAs in liver regeneration may be novel therapeutic strategies in future regeneration-related liver managements. We may discover additional chemotherapy targets of mi RNA.

Differential Expression of Genes in HepG2 Cells Caused by UC001kfo RNAi as Shown by RNA-seq

The differential expression of genes in HepG2 cells caused by UC001 kfo RNAi was investigated using RNA-seq. HepG2 cells were infected by Lenti-sh UC001 kfo lentivirus particles. The expression of UC001 kfo m RNA in the HepG2-sh UC001 kfo cell line was detected by real-time PCR. RNA-seq technology was used to identify the difference in the expression of genes regulated by lnc RNA UC001 kfo in the HepG2 cell line. Gene ontology and signaling pathway analysis were performed to reveal the biological functions of the genes encoding of significantly different m RNAs. The results showed that m RNAs were differentially expressed between the HepG2-sh UC001 kfo cell line and the HepG2 cell line. The UC001 kfo m RNA was significantly down-regulated in the stable cell line HepG2-sh UC001kfo（P〈0.001）. Additionally, we found 19 signaling pathways or functional classifications encompassing 30 genes that played a role in cancer characteristics, cell adhesion, invasion and migration. The results also showed that the expression of many genes associated with cancer cell invasion and metastasis was decreased with the down-regulation of the lnc RNA UC001 kfo. Lnc RNA UC001 kfo may play a role in regulating cancer cell invasion and metastasis. It was suggested that m RNAs were differentially expressed in the HepG2 cell line after the down-regulation of lnc RNA-UC001 kfo. Some took part in the extracellular matrix, cell adhesion, motility, growth, and localization. The genes encoding of differentially expressed m RNAs may participate in cell invasion and metastasis.

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.

Literature-based knowledgebase of pancreatic cancer gene to prioritize the key genes and pathways

Pancreatic cancer （PC） occurs when malignant cells develop in the part of the pancreas, a glandular organ behind the stomach. For 2015, there are about 40,560 people dead of pancreatic cancer （20,710 men and 19,850 women） in the US （Siegel et al., 2015）. Though PC accounts for about 3% of all cancers in the US, it can cause about 7% of cancer deaths. This is mainly because that the early stages of this cancer do not usually produce symptoms, and thus the cancer is almost always fatal when it is diagnosed.

Metagenomic Analysis of Mangshan Pit Viper (Protobothrops mangshanensis) Gut Microbiota Reveals Differences among Wild and Captive Individuals Linked to Hibernating Behaviors

Gut microbiota play important roles in the immunity,digestion,and energy meta bolism of their reptile hosts.Mangshan pit viper(Protobothrops mangshanensis)is a critically endangered snake species that is a Class I national protected species in China.Little is known regarding the relationship between P.mangshanensis and their gut microbial communities.In this study,the gut microbiota of wild P.mangshanensis individuals,artificially hiberna ting captive individuals,and non-hibernating captive individuals were compared across nine samples.Comparative shotgun metagenomic analysis was used to investigate the taxonomic composition,diversity,and function of P.mangshanensis gut microbial communities and assess whether their gut microbiomes were affected by their living environments and captivity conditions.The dominant phyla within P.mangshanensis gut microbial communities were Proteobacteria(65.55%),Bacteroidetes(15.97%),and Firmicutes(8.11%).Enriched functional pathways within the gut microbiota included meta bolism(54.9%),environmental information processing(9.67%),and genetic information processing(9.37%).Wild snake gut communities exhibited higher microbial diversity than the other two groups.The gut microbiomes of wild and hibernating captive snakes may be more reflective of healthy intestinal homeostasis than that in nonhibernating snakes.Specifically,non-hibernating snakes exhibited increased levelsof potentially pathogenic populations and functional specialization within gut microbial communities.Thus,different livingenvironments and captivitymethodsmay correspond to major shifts in microbiota composition,diversity,and function within P.mangshanensis.This study provides important insights to help guide the conservation of P.mangshanensis,while also carrying broad implications for our understanding of the effects of living environments and non-hibernating captivity conditions on the gut microbiota of snakes.

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).

Survival-associated alternative splicing events interact with the immune microenvironment in stomach adenocarcinoma

BACKGROUND Alternative splicing(AS)increases the diversity of mRNA during transcription;it might play a role in alteration of the immune microenvironment,which could influence the development of immunotherapeutic strategies against cancer.AIM To obtain the transcriptomic and clinical features and AS events in stomach adenocarcinoma(STAD)from the database.The overall survival data associated with AS events were used to construct a signature prognostic model for STAD.METHODS Differentially expressed immune-related genes were identified between subtypes on the basis of the prognostic model.In STAD,2042 overall-survival-related AS events were significantly enriched in various pathways and influenced several cellular functions.Furthermore,the network of splicing factors and overallsurvival-associated AS events indicated potential regulatory mechanisms underlying the AS events in STAD.RESULTS An eleven-AS-signature prognostic model(CD44|14986|ES,PPHLN1|21214|AT,RASSF4|11351|ES,KIAA1147|82046|AP,PPP2R5D|76200|ES,LOH12CR1|20507|ES,CDKN3|27569|AP,UBA52|48486|AD,CADPS|65499|AT,SRSF7|53276|RI,and WEE1|14328|AP)was constructed and significantly related to STAD overall survival,immune cells,and cancer-related pathways.The differentially expressed immune-related genes between the high-and low-risk score groups were significantly enriched in cancer-related pathways.CONCLUSION This study provided an AS-related prognostic model,potential mechanisms for AS,and alterations in the immune microenvironment(immune cells,genes,and pathways)for future research in STAD.

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.

Effect of electroacupuncture on gene expression in calcium signaling pathway in hippocampal cells in mice with cerebral ischemia reperfusion

OBJECTIVE:To observe the regulation of electroacupuncture on gene expression at calcium signaling pathways in mice with cerebral ischemia reperfusion.METHODS:Sixty male, inbred Kunming mice were randomly assigned to three groups:repeated cerebral ischemia reperfusion group(RG, n = 24),sham-operated group(SG, n = 12), and electroacupuncture group(EG, n = 24).Mice in RG and EGgroups were modeled by repeated cerebral ischemia reperfusion surgery, and EG mice were treated with electroacupuncture for 30 min after recovery from anesthesia.Changes in gene expression profile of mice hippocampi were analyzed by global expression profile microarray.Genes that were up-regulated or down-regulated greater than 1.5folds were considered to be biologically meaningful.Real-time quantitative polymerase chain reaction(q-PCR) method was used to verify the expression of selected genes based on the algorithm [2^(ΔΔCt)].RESULTS:Compared with SG mice, 242 genes showed different in expressions in RG mice:107down-regulated and 135 up-regulated.Compared with RG mice, 609 genes showed a difference of expression in EG mice:315 down-regulated and 375up-regulated.Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses indicated two pathways:calcium signaling and long-term potentiation in which 11 differentially expressed genes selected.Six of the 11 genes in the calcium signaling pathway were verified after real-time q-PCR testing.CONCLUSION:Electroacupuncture treatment of cerebral ischemia reperfusion appears to regulate Atp2a2, Cacna1 e, Camk2 a, Gnas, Grm1, Rapgef3 genes in the calcium signaling pathway.

Bioinformatics research of CD44 and epithelial cell adhesion molecule related genes and pathways in colorectal cancer

Objective To investigate genes and involved biological processes closely associated with stem cell markers of colorectal cancer-epithelial cell adhesion molecule(EpCAM)+and CD44+.Methods By the bioinformatics method,with microarray data of colorectal cancer from gene expression omnibus(GEO)database and R2 platform,the genes significantly related with CD44 and Ep-