ABSTRACT: In this study we analyzed the effects of CRY2 over-expression on chloroplast genome transcription of tomato, by developing and using a tiling array. This array containing about 90,000 overlapping probes (5-nt resolution) is a versatile tool for global functional studies of tomato cp genome. We profiled transcription in leaves of wild-type (WT) and CRY2-overexpressing (CRY2-OX) plants grown in a diurnal cycle, to generate a comprehensive map of plastid transcription and to monitor potential specific modulations of chloroplast transcriptome induced by the overexpression of CRY2.
Project description:The red/far-red light photoreceptor phytochrome mediates photomorphological responses in plants. For light sensing and signaling, phytochromes need to associate with open-chain tetrapyrrole molecules as the chromophore. Biosynthesis of tetrapyrrole chromophores requires members of ferredoxin-dependent bilin reductases (FDBRs). There are two FDBRs in Physcomitrella patens, HY2 and PUBS. Knocking out both generates the phytochrome-deficient mutant. Datasets here provides the transcriptome profiling of Physcomitrella protonema grown in the dark and exposed to one hour red light. Wild type and the hy2 pubs double mutant were used to dissect the regulated genes of moss phytochromes. 4 samples, dark-grown wild-type and pubs hy2 protonema as time 0 control, followed by red light irradiation for one hour respectively
Project description:Kashin-Beck disease (KBD) is an endemic and chronic osteochondropathy with unknown etiology. The disease mostly occurs in children between the ages of 3 and 13 in a diagonal belt-like area ranging from Northeast to Southwest China. We carried out this microarray analysis to investigate the differences in gene expression levels between KBD patients and healthy controls. Total RNA was isolated from peripheral blood mononuclear cells (PBMCs).
Project description:In HLA-B27/human beta-2m transgenic rat (B27-rats), the spontaneous development of a chronic inflammatory disorder closely resembling spondyloarthritis (SpA) is strongly correlated with high levels of HLA-B27/human beta-2m transgene expression and with aberrant function of dendritic cells (DCs). To dissect the mechanisms that could be involved in DCs dysfunction, we investigated the genes expression by transcriptomic analysis in DCs from B27 versus controls rats
Project description:Comparing gene expression in a Bellringer overexpressor vs wild-type Col-0. 3 biological sample replicates were used for microarray analyses.<br> <br> In order to control against dye bias and dye specific artifacts the replicate arrays had a "dye swop" design:<br> <br> Array 1: cy5 Col-0 a; cy5 BLR-OX_Van a<br> Array 2: cy5 BLR-OX_Van b; cy5 Col-0 b<br> Array 3: cy5 Col-0 c; cy5 BLR-OX_Van c
Project description:In order to study possible effects of cryptochrome 2-mediated light signals on the global expression profiles of tomato genes, we performed large scale transcription comparisons in wt and CRY2-OX by using a DNA microarray of more than 90,000 tomato oligo-probes.<br>Tomato plants were grown under a daily light cycle of 16h light/8h darkness (LD) and leaves from both genotypes were sampled at presumptive dawn (Zeitgeber time (ZT) 0), eight hours after dawn (ZT8), at presumptive dusk (ZT16) and four hours after dusk (ZT20).
Project description:Blood consists of different cell populations with distinct functions and correspondingly, distinct gene expression profiles. In this study, global miRNA expression profiling was performed across a panel of nine human immune cell subsets (neutrophils, eosinophils, monocytes, B cells, NK cells, CD4 T cells, CD8 T cells, mDCs and pDCs) to identify cell-type specific miRNAs. mRNA expression profiling was performed on the same samples, to determine if miRNAs specific to certain cell types down-regulated expression levels of their target genes. Six cell-type specific miRNAs (miR-143; neutrophil specific, miR-125; T cells and neutrophil specific, miR-500; monocytes and pDC specific, miR-150; lymphoid cells specific, miR-652 and miR-223; both myeloid cells specific) were negatively correlated with expression of their predicted target genes. These results were further validated using an independent cohort where similar immune cell subsets were isolated and profiled for both miRNA and mRNA expression. miRNAs negatively correlated with target gene expression in both cohorts were identified as candidates for miRNA-mRNA regulatory pairs and were used to construct a cell-type specific regulatory network. miRNA-mRNA pairs formed two distinct clusters in the network corresponding to myeloid (nine miRNAs) and lymphoid lineages (two miRNAs). Several myeloid specific miRNAs targeted common genes including ABL2, EIF4A2, EPC1 and INO80D; these common targets were enriched for genes involved in the regulation of gene expression (p < 9.0E-7). Those miRNA might therefore have significant further effect on gene expression by repressing the expression of genes involved in transcriptional regulation. The miRNA and mRNA expression profiles reported in this study form a comprehensive transcriptome database of various human blood cells and serve as a valuable resource for elucidating the role of miRNA mediated regulation in the establishment of immune cell identity. Nine cell subsets (CD16+CD66b+ Neutrophils, CD16-CD66b+ Eosinophils, CD14+ Monocytes, CD4+ T cells, CD8+ T cells, CD56+ NK cells, CD19+ B cells, CD123+ pDCs and CD11c+ mDCs) were isolated from healthy human blood and assessed for cell type purity by flow cytometry. Cell types were isolated from 5 pools of 5 healthy donors each, with the exception for monocytes, where 10 pools were used. RNA obtained from these purified populations were subsequently used for miRNA and mRNA expression profiling by Affymetrix GeneChip miRNA and HG-U133Plus2.0 microarrays.
Project description:Blood consists of different cell populations with distinct functions and correspondingly, distinct gene expression profiles. In this study, global miRNA expression profiling was performed across a panel of nine human immune cell subsets (neutrophils, eosinophils, monocytes, B cells, NK cells, CD4 T cells, CD8 T cells, mDCs and pDCs) to identify cell-type specific miRNAs. mRNA expression profiling was performed on the same samples, to determine if miRNAs specific to certain cell types down-regulated expression levels of their target genes. Six cell-type specific miRNAs (miR-143; neutrophil specific, miR-125; T cells and neutrophil specific, miR-500; monocytes and pDC specific, miR-150; lymphoid cells specific, miR-652 and miR-223; both myeloid cells specific) were negatively correlated with expression of their predicted target genes. These results were further validated using an independent cohort where similar immune cell subsets were isolated and profiled for both miRNA and mRNA expression. miRNAs negatively correlated with target gene expression in both cohorts were identified as candidates for miRNA-mRNA regulatory pairs and were used to construct a cell-type specific regulatory network. miRNA-mRNA pairs formed two distinct clusters in the network corresponding to myeloid (nine miRNAs) and lymphoid lineages (two miRNAs). Several myeloid specific miRNAs targeted common genes including ABL2, EIF4A2, EPC1 and INO80D; these common targets were enriched for genes involved in the regulation of gene expression (p < 9.0E-7). Those miRNA might therefore have significant further effect on gene expression by repressing the expression of genes involved in transcriptional regulation. The miRNA and mRNA expression profiles reported in this study form a comprehensive transcriptome database of various human blood cells and serve as a valuable resource for elucidating the role of miRNA mediated regulation in the establishment of immune cell identity. Nine cell subsets (CD16+CD66b+ Neutrophils, CD16-CD66b+ Eosinophils, CD14+ Monocytes, CD4+ T cells, CD8+ T cells, CD56+ NK cells, CD19+ B cells, CD123+ pDCs and CD11c+ mDCs) were isolated from healthy human blood and assessed for cell type purity by flow cytometry. Cell types were isolated from 5 pools of 5 healthy donors each, with the exception for monocytes, where 10 pools were used. RNA obtained from these purified populations were subsequently used for miRNA and mRNA expression profiling by Affymetrix GeneChip miRNA and HG-U133Plus2.0 microarrays.
Project description:Pancreatic cancer is characterized by a high frequency of cachexia, pain and neural invasion (N-inv). Neural damage is occurred by N-inv and modulates pain and muscle atrophy via the activation of astrocyte in the connected spine. The activated astrocyte by N-inv, thus, may affect cachexia in pancreatic cancer. Clinical studies in patients and autopsy cases with pancreatic cancer have revealed that N-inv is related to cachexia and astrocytic activation. We established a novel murine model of cancer cachexia using N-inv of human pancreatic cancer cells. Mice with N-inv showed a loss of body weight, skeletal muscle, and fat mass without appetite loss, which are compatible with an animal model of cancer cachexia. Activation of astrocytes in the spinal cord connected with N-inv was observed in our model. Experimental cachexia was suppressed by disrupting neural routes or inhibiting the activation of astrocytes. These data provide the first evidence that N-inv induces cachexia via astrocytic activation of neural route in pancreatic cancer. We produced neural invasion (N-inv) model using intraneural injection of Capan-1 cells to left sciatic nerve of male SCID mouse. For controls, subcutaneous model (SC) and PBS model were produced. Microarray analysis was performed using the first lumbar cord (L1) from PBS, SC, and N-inv mice at 6 w (n = 2 each).
Project description:Skeletal muscle has remarkable capacity to regenerate upon injury due to the presence of satellite cells. The maintenance and function of satellite cells are regulated by circadian clock. Cryptocrhome 2 (CRY2) is a key component of the circadian clock and its role in skeletal muscle regeneration remains controversial. Here, we report that CRY2 is down-regulated during muscle regeneration. Using the satellite cell specific CRY2 knockout mice (CRY2scko), we show that deletion of CRY2 enhances muscle regeneration. Single myofiber analysis showed that deletion of CRY2 enhances satellite cell self-renewal. In the absence of CRY2, the ERK1/2 and JNK1/2 signaling pathways become activated, which phosphorylates the transcription factor ETS1, which in turn binds to the promoter of PAX7 to induce its transcription. CRY2 deficient myoblasts survived better in ischemic muscle. Deletion of CRY2 also alleviated myopathy in mdx mice. Therefore, CRY2 plays an essential role in regulating satellite cell function and skeletal muscle regeneration.
Project description:The spaceflight experiment was carried out using male C57BL/10J mice (8 weeks old at launch). Wild type mice (n=3) were launched by Space Shuttle Discovery and housed on the International Space Station (ISS) for 91 days. They returned to the Earth by Space Shuttle Atlantis. But only one mouse returned to the Earth alive. Whole brain was sampled from the mouse killed by inhalation of carbon dioxide at the Life Sciences Support Facility of Kennedy Space Center within 3-4 hours after landing. After the spaceflight experiment, the on-ground experiment was also carried out at the Advanced Biotechnology Center in Genova, Italy. A mouse with the same species, sex, and age was housed in mice drawer system (MDS), which was utilized for the spaceflight (SF) mice, for 3 months as the ground control (GC). Another mouse was housed in normal vivarium cage as the laboratory control (LC). Amount of food and water supplementation and environmental conditions were simulated as the flight group. After 3 months, brain was sampled from one mouse in group GC and LC, respectively. Comprehensive analyses of gene expression were performed in the right brain. Total of 4,000 genes were analyzed. The expression levels of 60 genes significantly changed in response to SF compared with LC and/or GC. The 15 and 16 genes were up- (> 2 folds) and down-regulated (< 0.5 folds), respectively, following SF vs. GC. The levels of 58 genes were significantly altered by housing in MDS in space and/or on the ground. Forty seven and 11 genes were significantly up- and down-regulated vs. LC. Twenty seven out of these genes responded to caging in MDS both in space and on the ground. Further, 31 genes were influenced by housing in MDS on the Earth. Responses of the characteristics of brain to long-term gravitational unloading were investigated in mice.