Project description:Wild-derived mice have contributed to mouse genetics by their genetic diversity that may increase the chance of identifying novel modifier genes responsible for specific phenotypes and diseases. However, gene-targeting using wild-derived mice has been unsuccessful due to the unavailability of stable embryonic stem cells. Here, we report that the CRISPR/Cas9-mediated gene-targeting can be applied to the Japanese wild-derived MSM/Ms strain. We targeted the nonagouti (a) gene encoding the agouti protein localized in hairs and the brain. We obtained three homozygous knockout mice as founders, all showing black coat color. While homozygous knockout offspring were physiologically indistinguishable from wild-type littermates, they showed specific domesticated behaviors; a high locomotion during the light period and a decline in the avoidance of a human hand. These phenotypes were consistent over the subsequent generations. Our findings support the empirical hypothesis that nonagouti is a domestication gene, which might repress aggressive behavior. Global gene expression patterns in the midbrain of wildtype and nonagouti (a) homogygous mutant MSM/Ms mice were analyzed by one-color Mouse Gene Expression 8x60K microarray. The midbrain tissues were manually isolated from 8-9 weeks old mice under dissecting microscope. Total RNA was purified from dissected midbrain using Trizol (Thermo Fisher Scientific). Purified total RNA was amplified and labeled with Cy3 using Low-Input QuickAmp Labeling Kit (Agilent Technologies). Cy3-labeled RNAs were hybridized to SurePrint G3 Mouse Gene Expression v2 8x60K Microarray Kit (Agilent Technologies) at 65 Â°C for 17h. After wash, the hybridized slides were scanned with DNA microarray scanner (Agilent Technologies). The scanned images were processed with Feature Extraction software (Agilent Technologies) to extract signal intensities of each probe. The extracted signal data were imported into the Gene Spring GX 13.1.1 software (Agilent Technologies) and normalized using the default settings. Two and six biological replicates were performed in wildtype and mutant group, respectively.

Project description:Gliadin triggers T-cell mediated immunity in celiac disease, and has cytotoxic effects on enterocytes mediated through obscure mechanisms. In addition, gliadin transport mechanisms, potential cell surface receptors and gliadin-activated downstream signaling pathways are not completely understood. In order to screen for novel downstream gliadin target genes we performed a systematic whole genome expression study on intestinal epithelial cells. Undifferentiated Caco-2 cells were exposed to pepsin- and trypsin- digested gliadin (PT-G), a blank pepsin-trypsin control (PT) and to a synthetic peptide corresponding to gliadin p31-43 peptide for six hours. RNA from four different experiments was used for hybridization on Agilent one color human whole genome DNA microarray chips. The microarray data were analyzed using the Bioconductor package LIMMA. Genes with nominal p < 0.01 were considered statistically significant. Compared to the untreated cells 1705, 1755 and 211 probes were affected by PT-G, PT and p31-43 respectively. 46 probes were significantly different between PT and PT-G treated cells. Among the p31-43 peptide affected probes, 10 and 21 probes were affected by PT-G and PT respectively. Only PT-G affected genes could be validated by quantitative real-time polymerase chain reaction. All the genes were, nonetheless, also affected to a comparable level by PT treated negative controls. In conclusion, we could not replicate previously reported direct effects of gliadin peptides on enterocytes. The PT-G affected genes in the microarray analysis were validated by qRT-PCR, however these genes were also affected by PT treated negative controls suggesting that certain epitopes derived from pepsin and trypsin may also affect epithelial cell gene transcription. Our study demonstrates novel non-enzymatic effects of pepsin and trypsin on cells and calls for proper controls in pepsin and trypsin digested gliadin experiments. It is conceivable that gliadin effects on enterocytes are secondary mediated through oxidative stress, NFkB activation and IL-15 up-regulation. In total, 16 samples were analyzed of which 4 were control (MED) samples, 4 samples of p31-43 treatment, 4 samples of PT treatmetn and 4 samples of PT-G treatment

Project description:Gliadin triggers T-cell mediated immunity in celiac disease, and has cytotoxic effects on enterocytes mediated through obscure mechanisms. In addition, gliadin transport mechanisms, potential cell surface receptors and gliadin-activated downstream signaling pathways are not completely understood. In order to screen for novel downstream gliadin target genes we performed a systematic whole genome expression study on intestinal epithelial cells. Undifferentiated Caco-2 cells were exposed to pepsin- and trypsin- digested gliadin (PT-G), a blank pepsin-trypsin control (PT) and to a synthetic peptide corresponding to gliadin p31-43 peptide for six hours. RNA from four different experiments was used for hybridization on Agilent one color human whole genome DNA microarray chips. The microarray data were analyzed using the Bioconductor package LIMMA. Genes with nominal p < 0.01 were considered statistically significant. Compared to the untreated cells 1705, 1755 and 211 probes were affected by PT-G, PT and p31-43 respectively. 46 probes were significantly different between PT and PT-G treated cells. Among the p31-43 peptide affected probes, 10 and 21 probes were affected by PT-G and PT respectively. Only PT-G affected genes could be validated by quantitative real-time polymerase chain reaction. All the genes were, nonetheless, also affected to a comparable level by PT treated negative controls. In conclusion, we could not replicate previously reported direct effects of gliadin peptides on enterocytes. The PT-G affected genes in the microarray analysis were validated by qRT-PCR, however these genes were also affected by PT treated negative controls suggesting that certain epitopes derived from pepsin and trypsin may also affect epithelial cell gene transcription. Our study demonstrates novel non-enzymatic effects of pepsin and trypsin on cells and calls for proper controls in pepsin and trypsin digested gliadin experiments. It is conceivable that gliadin effects on enterocytes are secondary mediated through oxidative stress, NFkB activation and IL-15 up-regulation.

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Global gene expression profiling of endothelial colony-forming cells from term and preterm neonates

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