A Microarray approach for Identification of Candidate Genes Involved in Gyration of the Pig Cerebral Cortex
ABSTRACT: In this study we examined brain gyration using the pig brain as model. Pig cortical tissue from two time points in development representing a non-folded, lissencephalic, brain (embryonic day 60) and primary-folded, gyrencephalic, brain (embryonic day 80) were examined by whole genome expression microarray studies. Overall design: 3 samples from 3 litters mates representing the two time points E60 and E80 of the porcine gestation period
Project description:In this study we examined brain gyration using the pig brain as model. Pig cortical tissue from two time points in development representing a non-folded, lissencephalic, brain (embryonic day 60) and primary-folded, gyrencephalic, brain (embryonic day 80) were examined by whole genome expression microarray studies. Experiment Overall Design: 3 samples from 3 litters mates representing the two time points E60 and E80 of the porcine gestation period
Project description:The miRNAs expression profile of four typical stages of tooth development, embryonic day 35 (E35), E45, E50, and E60, which cover the major morphological and physiological changes in pig tooth germ growth and development throughout pregnancy, including the bud, cap, early bell, and late bell stages. Four-condition experiment: E35 vs. E45 vs. E50 vs. E60. Biological replicates: 3, independently removed under a microscope. Four replicates per array.
Project description:Background: DNA methylation is an important epigenetic modification critical to the regulation of gene expression during development. To date, little is known about the role of DNA methylation in tooth development in large animal models. Thus, we carried out a comparative genomic analysis of genome-wide DNA methylation profiles in E50 and E60 tooth germ from miniature pigs using methylated DNA immunoprecipitation-sequencing (MeDIP-seq).Results: We observed different DNA methylation patterns during the different developmental stages of pig tooth germ. A total of 2,469 differentially methylated genes were identified. Functional analysis identified several signaling pathways and 104 genes that may be potential key regulators of pig tooth development from E50 to E60.Conclusions: The present study provided a comprehensive analysis of the global DNA methylation pattern of tooth germ in miniature pigs and identified candidate genes that potentially regulate tooth development from E50 to E60. Overall design: genome-wide DNA methylation profiles in E50 and E60 tooth germ from miniature pigs using methylated DNA immunoprecipitation-sequencing (MeDIP-seq)
Project description:Cerebral malaria is a pathology involving inflammation in the brain. There are many immune cell types activated during this process, but there is little information on the contribution of microglia, the brain resident macrophages, to this severe complication. We have examined the responses of microglia in a model of experimental cerebral malaria (ECM), in which C57BL/6 mice are infected with Plasmodium berghei ANKA. Genome wide transcriptomic analysis of these cells revealed that thousands of transcripts were differentially expressed at two different time points during the infection. The analysis indicated that proliferation of microglia was a dominant feature before the onset of ECM, and supporting this, we observed an increase in numbers of these cells in the brain. When cerebral malaria symptoms were manifest, genes involved in immune responses and chemokine production were upregulated, which were possibly driven by Type I Interferon. Together, our data offer a unique insight into the responses of microglia in the brain during ECM. Overall design: Total RNA obtained from isolated microlgia from brains of Plasmodium berghei ANKA infected mice, 5 and 7 days post infection, compared to their uninfected controls
Project description:We using RNA sequences (from RNA-seq) from the prenatal muscle tissues of three pig breeds (Tibetan pig [TP], Wujin pig [WJ], and Large White pig [LW]) were analyzed to compare the differentially expressed genes related to embryonic myogenesis and to identify the genes related to postnatal growth rate and growth potential in pigs. We obtained 38.7-50.1 million clean data through the RNA-seq and detected that 19,626 genes were positively expressed and 13,660 of them were co-expressed in the muscle tissues of the four samples. The 3,626 unique DEGs in TP were mainly enriched in 76 GO terms and 35 KEGG pathways.The GO terms mainly included ATP binding, calcium ion binding, negative regulation of transcription from RNA polymerase II promoter, and cell components of cytoplasm, nucleus, and extracellular exosome . The top 20 KEGG pathways mainly included metabolic, insulin signaling, FoxO signaling, and AMPK signaling pathways that are mostly involved in muscle development and growth. Overall design: RNA sequences from the tissues of embryonic longissimus dorsi muscle of three pig breeds (Tibetan pig [TP], Wujin pig [WJ], and Large White pig [LW]) were examined using HiSeq 4000.
Project description:We identified the spatiotemporal pattern of cascade initiation of additional molars in miniature pig,where second molar (M2) initiated from the posterior-free end of the dental lamina over the first molar (M1) at E60 when M1 progressed to the late bell stage. Similarly, third molar (M3) budded off from the posterior-free end of the dental lamina over M2, which reached bell stage at PN20. However, the molecular mechanisms of the regulatory network during sequential formation of additional molars remain poorly characterized in diphyodont mammals. We performed microarrays on miniature pigs at three molar developmental stages to examine their differential gene expression profiles and potential regulatory networks during additional molar morphogenesis. Overall design: Miniature pigs' additional molar germs samples from early developmental stages at E50, E60 and E70 were selected for RNA extraction and hybridization on Affymetrix microarrays in biological triplicates. The differentially expressed genes between the 3 different stages were screened, then differentially expressed genes with significance were chosen for significant GO and pathway enriching. The differential genes and functions with significant expression tendencies were predicted using STC for further Path-Net, Signal-Net and Dynamic-Gene-Net analysis for Signal-Net to determine significant pathways and identify the key differentially expressed genes during early additional molars development. Additional molar germs from three key stages were chosen to determine the spatiotemporal control mechanisms of cascade initiation of these molars. The E50 stage corresponding to M1 at cap stage without M2 initiation and the E60 stage targeting M1 at bell stage followed by M2 initiation. The E70 stage as a control, when M1 progresses to late bell stage but M2 changes little.