Gene expressions specifically induced by the presence of SFB
ABSTRACT: To investigate SFB-host interactions and the host response to SFB, we compared gene expression profiles in terminal ileal mucosa collected from 5 SFB-positive and 5-negative age-matched patients identified from SFB PCR. We observed that 472 genes were different between the two groups (P < 0.05). Among them, 290 genes were up-regulated and 182 were down-regulated. GO biological pathway analysis of up-regulated genes revealed positive regulation of T-cell differentiation and activation pathways were enhanced (P < 0.001), suggesting that SFB colonization stimulated the human immune system, specifically T-cell maturation. Indeed, enhanced expression of Cd3e, Ifng, IL10, Foxp3 was observed in terminal ileal mucosa of 5 SFB-positive patients. To find immune-related genes significantly expressed (p < 0.05) between SFB-positive and -negative
Project description:To identify genes involved in the OsDIS1-mediated drought-responsive pathway, we performed microarray analysis of the OsDIS1 overexpression and wild-type plants under both normal and drought stress conditions using the Agilent rice Genechip. Seven-day-old plants of the OsDIS1 overexpression line 9-4-2 as well as the wild-type plants were used in the drought treatment. OsLEA3 was used as a positive control for the drought treatment. Genes with more than two-fold changes in the overexpression plants compared with the wild-type plants were selected. The expression pattern of some differentially expressed genes was further confirmed by real-time PCR. The OsDIS1 overexpression 9-4-2 plants and the wild-type plants were cultured on 1/2 MS medium plus 3% sucrose for seven days. About half of the plants were sampled as the untreated control for RNA isolation, and the rest were transferred with 1/2 MS medium onto filter papers to induce drought stress. When the leaves of the OsDIS1 overexpression plants began to show drought stress phenotypes, we collected leaves for RNA isolation. OsLEA3 was used as a positive control for the drought treatment.
Project description:To explore the molecular mechanism of the positive thermoregulation on Jinggangmycin A biosynthesis, the transcriptomes of S. hygroscopicus 5008 cultivated at 30℃ or 37℃ in liquid medium were compared by microarray analysis. Global gene expression in the strain 5008 was measured at 30℃ or 37℃, respectively. Three independent experiments were performed at each condition.
Project description:To explore the molecular mechanism of the positive thermoregulation on Jinggangmycin A biosynthesis, the transcriptomes of S. hygroscopicus 5008 cultivated at 30℃ or 37℃ in liquid medium were compared by microarray analysis. Additionally, the transcriptomes of S. avermitilis NRRL8165 cultivated at the same conditions were analyzed in parallel to filter transcriptional changes common to Streptomyces genus. Global gene expression in NRRL8165 was measured at 30℃ or 37℃, respectively. Three independent experiments were performed at each condition.
Project description:we characterized the rice alkaline tolerant mutant, alt1. Map-based cloning revealed that alt1 harbors a mutation in a putative chromatin remodeling ATPase gene. ALT1-RNAi transgenic plants mimicked the alt1 phenotype, exhibiting tolerance to alkali stress in a transcript dosage-dependent manner. We found that the predicted ALT1 protein belonged to the Ris1 subgroup of the Snf2 family and was localized in the nucleus. qRT-PCR analysis showed that ALT1 was predominantly expressed in leaf blades and sheaths, and that ALT1 transcription was rapidly suppressed after alkaline treatment. These results support the notion that ALT1 is a negative regulator of alkaline tolerance. Roots of two-leaf stage alt1 and WT seedlings grown under normal conditions were sampled for microarray analysis. The transcriptomic profiles were investigated using an Agilent-015241 Rice Gene Expression 4×44 K Microarray (Agilent Technology) containing 32,325 probes corresponding to cDNA, 6,934 probes corresponding to expressed sequence tags (ESTs), and 2,612 probes corresponding to gene predicted loci, respectively, with three independent biological replicates. Roots of two-leaf stage alt1 and WT seedlings grown under normal conditions were sampled for microarray analysis
Project description:To explore the molecular mechanisms and signal pathways induced by restoring tumor suppressor gene HIC-1 on breast cancer cells. We have employed whole genome microarray expression profiling as a discovery platform to identify the differential genes induced by HIC-1 gene activation. Small activating RNA (saRNA) that targeted promoter region was used, and MCF-7 breast cancer cell line was selected as cell model. After 96h for saRNA transfection, the cells were collected and the whole genome expression profiles were analyzed. Three independent experiments were repeated for different groups. With the treshold of p<0.01 and fold change >=2 or <-2, there were 1375 differential expression genes, which are related to cell cycle, apoptosis, cell migration, cell invasion and cell proliferation. SaRNA induced gene expression in human breast cancer cell MCF-7 was measured at 96 hours after transfection by 50 nM saRNA. Three independent experiments were performed for experimental group and control group.
Project description:Differentially expressed genes in the skin tissue of newborn Hu sheep were screened using an Agilent gene chip and RT-PCR. Differential expression analysis revealed 3 groups of large waves and small waves; 1067, 2071, and 3879 differentially expressed genes; and 137 genes common to all 3 groups. Differentially expressed genes were classified using gene ontology. They were found to be mainly involved in cell differentiation, proliferation, apoptosis, growth, immune response, and ion transport. RT-PCR results of 4 differentially expressed genes were consistent with gene chip results. Combined with related literature, our results suggest that BMP7, MMP2, SNAI1, SFXN1, CDKNIC, MT3, and POU1F1 may have important effects on the formation of large-wave and small-wave hair follicles. The samples collected with three full-sib individual and they borned at two days, what's more they were from the same paternal, each pair of big wave and small wave individuals from the same female parent.
Project description:Purpose: We aimed to investigate the effect of several anti-leukemia drugs in combination with decitabine (DAC) on the proliferation of myeloid leukemia cells in vitro and in vivo, to select the most efficient combination group and explore associated mechanisms of these combination therapies. Experimental Design: After comparing with five anti-leukemia drugs in several different kinds of cell lines, the combination effect of idarubicin (IDA) with DAC was best. In vivo, by using microPET, TUNEL, and transmission electron microscopy, the inhibitory effects obtained by sequentially combining DAC with IDA, evidenced by evaluating tumor cell proliferation and cell apoptosis. Molecular studies were conducted using gene chip, which was used to explore associated pathways, and real-time quantitative reverse transcription-PCR, western blot and immunohistochemistry (IHC), used to assess regulation of Wnt/β-catenin pathway. Results: The sequential combination of DAC and IDA showed synergistic induction of cell death in U937, HEL, SKM-1 and cells isolated from AML patients. Importantly, the inhibition of tumor growth in the sequential combination group was found to be significantly higher than that of single drug group or control group in vivo. Moreover, sequential treatment with DAC and IDA induced apoptosis and depression of the Wnt/β-catenin pathway in both culture and animal studies. Conclusions: Our findings showed that sequentially combining decitabine with idarubicin had a synergistic anti-leukemia effect. These findings were attributed to demethylation of Wnt pathway inhibitors and downregulation of Wnt pathway nuclear targets observed in vitro and in vivo. After comparing with five anti-leukemia drugs in several different kinds of cell lines, the combination effect of idarubicin (IDA) with DAC was best. In vivo, by using microPET, TUNEL, and transmission electron microscopy, the inhibitory effects obtained by sequentially combining DAC with IDA, evidenced by evaluating tumor cell proliferation and cell apoptosis. Molecular studies were conducted using gene chip, which was used to explore associated pathways, and real-time quantitative reverse transcription-PCR, western blot and immunohistochemistry (IHC), used to assess regulation of Wnt/β-catenin pathway.
Project description:To identify miRNAs differentially expressed in cholangiocarcinoma,3 human cholangiocarcinoma and their corresponding normal bile duct tissues were obtained from 3 patients after operation with postoperative pathological diagnosed perihilar or distal biliary cholangiocarcinoma miRNAs expression in human cholangiocarcinoma/normal bile duct samples was measured after operation.Three independent experiments were performed using different patients for each experiment.
Project description:Global expression profiles in Huh7 after infection with Lv-shMEF2D and Lv-scrambled, as well as transfection with siRNA-MEF2D and siRNA-control, were compared to investigate the molecular mechanisms involved in MEF2D-mediated regulation of cell cycle. In order to investigate the molecular mechanisms involved in MEF2D-mediated regulation of cell cycle, we assessed gene expression profiles in Huh7 cells after infection with Lv-shMEF2D and Lv-scrambled, as well as transfection with siRNA-MEF2D and siRNA-control, by cDNA microarray. Analysis of global mRNA expression profile indicated a shift toward G2/M arrest in the cells after downregulating MEF2D expression. The genes that inhibit G2/M transition were found to be expressed in high level in MEF2D-downregulated group, as compared with control group. Meanwhile, mRNA abundance of G2/M transition-promoting genes, except CDC2 and CDC25C, was reduced when MEF2D expression was depressed in Huh7 cells
Project description:To exploring the difference of mRNA expression between IA and MMA, we have employed mRNA array expression profiling as a discovery platform to identify genes between the IA and MMA. It's a compensate experiment after microRNA array, we paired the mRNA data with miRNA targets, finally, these data were used for the functional analysis. 2 IA and 2 MMA tissue were used for the microarray