Project description:Here we present the first whole-genome assemblies of Arabidopsis thaliana strains since the release of the 125 Mb reference genome sequence a decade ago. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone.
Project description:The goal was to examine gene expression after in vivo activation by different vaccine strains of Listeria monocytogenes. Heat killed LM, irradiated LM and live actA- LM were used to immunize mice after transfer of OT-I cells
Project description:We adapted the widely used digestion of chromatin with micrococcal nuclease (MNase) followed by deep sequencing to the parasite Trypanosoma cruzi, which presents numerous singularities. In this work, we use the hybrid CL Brener strain carrying two set of chromosomes from two substantially different parental strains. The hybrid strain CL Brener is composed of the Esmeraldo-like and non Esmeraldo-like haplotypes. Additionally, part of the genome was not assembled into any of the haplotypes. Sometimes the community working in the field uses just one haplotype as reference genome for simplicity. In this work, we emphasize the importance of using its whole genome as a reference. Moreover, we extended our analysis to a clonal strain, Sylvio-X10.
Project description:A Saccharomyces cerevisiae mutant with extended chronological life span was obtained by using an evolutionary engineering strategy, based on successive batch cultivation under gradually enhanced caloric restriction. The mutant strain SRM11 was selected which had about 50% longer life span than the reference strain. Whole-genome transcriptomic analysis of SRM11 with respect to the reference strain was performed to identify differences in gene expression levels between the two strains.
Project description:A propolis-resistant Saccharomyces cerevisiae mutant strain was obtained using an evolutionary engineering strategy based on successive batch cultivation under gradually increasing propolis levels. The mutant strain FD 11 was selected at a propolis concentration that the reference strain could not grow at all. Whole-genome transcriptomic analysis of FD11 was performed with respect to its reference strain to determine differences in gene expression levels between the two strains. Saccharomyces cerevisiae
Project description:A Saccharomyces cerevisiae mutant with improved coniferyl aldehyde resistance was obtained by using an evolutionary engineering strategy, based on successive batch cultivation under gradually increased coniferyl aldehyde concentration. The mutant strain BH13 was selected which could grow at a coniferyl aldehyde concentration that the reference strain could not grow at all. Whole-genome transcriptomic analysis of BH13 with respect to the reference strain was performed to identify differences in gene expression levels between the two strains.
Project description:Uterine leiomyomas (LM) affect up to 80% of all reproductive-age women. LM growth requires progesterone, progesterone receptor (PGR), and the maintenance and proliferation of a small (5%) stem cell population. Stem cell activation and differentiation are driven by DNA methylation and nuclear hormone receptor action, but crosstalk between these mechanisms remains unclear. We performed an integrated analysis of the transcriptome and epigenetic landscape of LM cells at three differentiation stages and the PGR cistrome of whole LM tissue. The PGR-deficient stem cell population harbored a unique methylation landscape, with hypermethylation at the PGR gene locus and PGR-binding regions, which suppressed stem cell responsiveness to progesterone. The DNA methylation inhibitor 5’-Aza upregulated the expression of PGR and its target genes by stimulating PGR recruitment to the targeted gene loci, and significantly depleted the LM stem cell population and its tumor-initiating capacity. We herein provided mechanistic insights via therapeutically accelerating the stem cell differentiation process of a hormone-sensitive tumor.
