Project description:Transcriptome sequencing of non-model organisms is valuable resource of the genetic basis of ecological-meaningful traits. The Royal Irises, Iris section Oncocyclus (Iris: Iridaceae, order Asparagales), are a Middle-East group of species in the course of speciation. The species are characterized with extremely large flowers, a huge range of flower colors and a unique pollination system. The Royal Irises, which are a symbol of conservation in the Middle-east, serve as a model for evolutionary processes of speciation and plant ecology. However, there are not sufficient transcriptomic and genomic data for molecular characterization. Thus, it is necessary to generate massive transcript sequences for functional characterization and molecular marker development for the Royal Irises. The Iris transcriptome sequencing provides valuable resource for studying adaptation-associated traits in this non-model plant. Although intensive eco-evolutionary studies, this is the first reported transcriptome for the Royal Irises. The data available from this study will facilitate gene discovery, functional genomic studies and development of molecular markers in irises, and will provide genetic tools for their conservation.
Project description:This study aims to investigate the binding DNA lesions of AIM2 in HaCaT cells exposed to 0Gy and 20Gy by ChIP-Seq. In this study, HaCaT cells were maintained in DMEM. All culture media were supplemented with 10% fetal bovine serum (FBS; Biological Industries, Kibbutz Beit-Haemek, Israel). Cells were grown at 37 °C in 5% CO2 incubators. Cells were exposed to 20Gy of ionizing radiation using X-ray linear accelerator (Rad Source, Suwanee, GA) at a fixed dose rate of 1.15 Gy/min.Four hours after irradiation, specific antibody against AIM2 was used to pull down AIM2 and the binding DNA lesions, which was then analyzed through ChIP-Seq.
Project description:Previous Genome-wide association studies (GWASs) have identified susceptibility loci of primary angle closure glaucoma (PACG), but applicating these findings is difficult. Although shallow anterior chamber depth (ACD) and short axial length (AL) are characteristic phenotypes of PACG, current GWAS variants do not show any correlation with these features, calling for the identification of more risk factors . Here, thicker and enlarged iris was identified as a significant independent risk factors. By employing allelic-specific STARR-seq and assay for transposase-accessible chromatin using sequencing (ATAC-seq), we screened disease-related variants in linkage disequilibrium and identified 2 causative variants in iris. Alterations in these variants may contribute to the pathogenic iris phenotype by upregulating the expression of PLEKHA7 and C10orf53, potentially regulating PACG development and progression. Our efforts nominate the important role of iris and identify pathogenic SNP-target gene interactions for PACG, providing a potentially powerful approach for interpreting noncoding variation of diseases.
Project description:Social caste determination in the honey bee is assumed to be determined by the dietary status of the young larvae and translated into physiological and epigenetic changes through nutrient-sensing pathways. We have employed Illumina/Solexa sequencing to examine the small RNA content in the bee larval food source, and show that worker jelly is enriched in miRNA complexity and abundance relative to royal jelly. The miRNA levels in worker jelly were 7-215 fold higher than in royal jelly, and both jellies showed dynamic changes in miRNA content during the 4th to 6th day of larval development. Adding specific miRNAs to royal jelly elicited significant changes in queen larval mRNA expression and in morphological characters of the emerging adult queen bee. We propose that miRNAs in the nurse bee secretions constitute an additional element in the regulatory control of caste determination in the honey bee.
Project description:Royal jelly has long been recognized as health food, with a high content of proteins. These proteins play important roles in honeybee caste and human health, but the proteomic analysis of those low-abundance proteins in royal jelly is always a challenge. Herein, we used the Osboren classification method to separate the royal jelly proteins of Xinjiang black bees, a sub-species of Apis mellifera mellifera, into various fractions. The globulin, ethanol-soluble protein and glutelin fractions were further separated by SDS-PAGE, and proteomic analysis was carried out by LC-MS/MS and searching against the NCBI database. A total of 63 proteins with definitive names were identified, in which 41 proteins were identified for the first time in royal jelly. The Osboren classification method combined with one-dimensional gel electrophoresis based proteomic analysis allows the identification of low-abundance proteins, and greatly extends the knowledge about the components and functions of royal jelly proteins.
