Thalamus and hypothalamus response to visual input deprivation
Ontology highlight
ABSTRACT: Analysis of thalamus and hypothalamus under conditions of visual deprivation by dark-rearing (DR). Animals subjected to DR from birth till postnatal day (P) 14. Results provide insight into the role of visual inputs in the regulation of gene expression in thalamus and hypothalamus during development. RNA sample was taken from thalamus and hypothalamus of 14-day-old mouse reared in standard or dark condition. Comparisons among groups were made by one-color method with normalized data from Cy3 channels for data analysis.
Project description:Gliomas arising in the brainstem and thalamus are devastating tumors that are difficult to surgically resect due to their proximity to eloquent brain structures. Here, we performed a comprehesive genomic and epigenomic study, using gene expression and methylation microarrays, to research on th different genomic and epigenetic signatures between brainstem, thalamic, and supratentorial gliomas. Comparison of brainstem, thalamic and supratentorial gliomas
Project description:Tumor formation constitutes a major obstacle to the clinical application of embryonic stem cells (ESCs). As P-RPCs could successfully integrate into host eyes without development of teratomas or NOG, we sought to identify differentially expressed genes between P-RPCs and ESC-RPCs through genome-wide transcript profiling. Inhibition of Wnt signaling by DKK1 promotes the commitment of ESC-RPCs to more mature retinal cells and reduces the occurrence of NOG to 3%. DKK1-treated ESC-RPCs efficiently integrate to the host retina, form synaptic connections and restore visual function. Here, we report that further differentiation of ESC-derived neural progenitors into retinal progenitor cells (ESC-RPCs) completely eliminates teratomas in ocular transplantation. However, tumor-like neural overgrowth (NOG) occurs in 61% of transplanted eyes. ESC-RPCs were divided into two groups according to the differentiation stages for RNA extraction and hybridization on Affymetrix microarrays. Normal control ESC-RPCs (N) were represented the homogeneous populations of early stage expression profiles of immature ESC-RPCs. DKK1 treated ESC-RPCs (D) were represented the homogeneous populations of late stage expression profiles of further differetiated mature ESC-RPCs. To sought the pathways involved in the proliferation and oncogenesis of ESC-RPCs, the newborn C57 mice reitinal progenitor cells (R) were applied as negative control. Each group above had three independent biological repeats.
Project description:Analysis of thalamus and hypothalamus under conditions of visual deprivation by dark-rearing (DR). Animals subjected to DR from birth till postnatal day (P) 14. Results provide insight into the role of visual inputs in the regulation of gene expression in thalamus and hypothalamus during development.
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: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: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 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: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: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: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.