Project description:The complete mitochondrial genome of the Critically Endangered Trinidad Piping Guan, Pipile pipile (Jacquin 1784) synonym Aburria pipile was sequenced for the first time in this study. The genome is 16,665 bp in length with overall base compositions of 30.1, 23.7, 32.3 and 13.9% for A, T, C, and G, respectively. Structurally, the P. pipile mitogenome is comparable to that of other Galliformes, thereby demonstrating typical avian gene organization. The mitogenome was subsequently used to produce a revised phylogenetic placement of P. pipile within the Galliforme order, positioning the Pipile genus basal within the Cracidae family. It is further envisaged that this novel genomic data will contribute to a wider understanding of genetic relationships within the genus Pipile and the analysis of the evolutionary relationships of the Galliforme order in a wider avian context.
Project description:This study aims to investigate the DNA methylation patterns at transcription factor binding regions and their evolutionary conservation with respect to binding activity divergence. We combined newly generated bisulfite-sequencing experiments in livers of five mammals (human, macaque, mouse, rat and dog) and matched publicly available ChIP-sequencing data for five transcription factors (CEBPA, HNF4a, CTCF, ONECUT1 and FOXA1). To study the chromatin contexts of TF binding subjected to distinct evolutionary pressures, we integrated publicly available active promoter, active enhancer and primed enhancer calls determined by profiling genome wide patterns of H3K27ac, H3K4me3 and H3K4me1.
Project description:Whole genome sequencing of the Arabidopsis thaliana dot5-1 transposon insertion line described in Petricka et al 2008 The Plant Journal 56(2): 251-263.
Project description:The analysis identifies differentially occupied genomic regions of H2Bub1, H3K79me3, and H3K27ac by RNF40 silencing in HCC1806 cells
Project description:This study aims to investigate the interactions of mutagenic lesions from diethylnitrosamine (DEN) treatment of mouse livers with such processes as replication, transcription, and interaction of DNA with proteins. Liver samples of 15-day old (P15) untreated C3H/HeOuJ mice were isolated and flash-frozen. ChIP-seq was performed to identify CTCF binding sites in livers of ten pooled individuals. The experiment was done with five biological replicates with a matched input library.
Project description:Because antibiotics have been widely used to prevent severe losses due to infectious fishery diseases, the liberal application and overuse of antibiotics has led to the spread and evolution of bacterial resistance, food safety hazards, and environmental issues. The use of some antibiotics, including florfenicol and enrofloxacin, is allowed in aquaculture in China. Accordingly, to better address the concerns and questions associated with the impact of administered enrofloxacin and florfenicol to grass carp, here we investigated the immune response, bacterial diversity, and transcriptome of the intestine of C. idella treated with these oral antibiotics. The aim of this study was to provide an in-depth evaluation of the antibiotic-induced patterns and dynamics of the microbiota grass carp and the potential mechanism involved.
