Project description:The advent of next generation sequencing (NGS) has greatly enriched the database of miRNAs. For plants so far 8455 miRNAs sequences from 73 species and 15401 miRNAs sequences from 150 species have been deposited in miRBase 22.0 and Plant Non-coding RNA Database, respectively. The occurrence of miRNAs in such a huge number, which is still increasing, is because of the fact that the profile of miRNAs expression differs greatly from species to species, both quantitatively and qualitatively. Besides, even within a species it is expected that the miRNA expression profile would differ from cultivar to cultivar depending on the trait with regard to which the two cultivars differ. Beises, the expression of a miRNA in a plant organ may differ depending upon it spatial location. The same is reflected in the NGS data of the apical and basal spikelets of the panicle of the rice cultivar Mahalaxmi.
Project description:The epiblast is the first cell type that forms apical-basal polarity de novo as the mouse embryo implants into the maternal uterus, while the extraembryonic neighbours of the epiblast - trophectoderm and primitive endoderm - retain their pre-established polarity beyond implantation [1]; however, it is still unclear how the epiblast establishes apical-basal polarity de novo. Here, we focused on Rap1 signaling pathway, which is activated during the transition of the epiblast from the naïve to primed state of pluripotency during implantation [2]. Through the preestablished in vitro three-dimensional culture system [3], genetic knockouts and proximity-biotinylation analyses, we found that Rap1 integrates multiple signals that contribute to de novo formation of apical-basal polarity. Importantly, formation of apical-basal polarity in the epiblast is essential for its correct patterning and proper communication with the extraembryonic lineages. Altogether, these results not only dissect molecular details of de novo apical-basal polarity formation, but also have broader implications for epithelial polarity and development.
Project description:Identification of genes regulated by apical auxin and basal cytokinin treatment of the nodal stem in cauline buds of Arabidopsis thaliana
Project description:After section, Hydra regenerate each missing part within 2 to 3 days. This study was designed to allow tracking of gene expression levels during apical and basal regeneration and to compare these different regenerative contexts systematically. We determine that transient early genetic events are generic, i.e. that modulations in gene expression have analogous directions, magnitudes and durations whatever the level along the central body column and orientation of the amputation plane. In turn, early modulated transcripts with sustained expression patterns during regeneration are generally distinct during apical and basal regeneration. Genes that were previously shown to be instrumental in defining the apical organizer (Wnt signalling pathway) are among the first genes to be expressed in the condition where Hydra regenerates its apical part, Wnt3 is actually the only detected transcript encoding a signalling protein already upregulated by 2h. Regarding basal regeneration, we identify a number of transcripts with sustained expression patterns already established by 4h, some of them encoding evolutionary conserved signalling proteins, which are almost exclusively consisting of agonists and antagonists of the BMP signalling pathway. The processed data deposited here are also accessible in a graphical manner from a blast-based web interface available at https://hydratlas.unige.ch
Project description:Laser Capture Microdissection (LCM) followed by RNA-seq of apical and basal domains of follicle cells from stage 9-10B Drosophila egg chambers. The experiment is composed of 5 Apical and 5 Basal biological replicates. Each biological replicate consists of a pool of 10 LCM fragments. Each fragment consists of 5-10 adjacent cell domains microdissected from either the apical half or the basal half of the follicular epithelium.
Project description:Cre recombinase-mediated conditional knockout of floxed Dicer1 alleles causes depletion of small RNAs including microRNAs, which function to repress target mRNA expression by inhibiting translation and/or stimulating mRNA degradation. We used microarrays to examine gene expression in apical versus basal organ of Corti from the cochleae of control and mutant mice in which Dicer1 was deleted and microRNAs were depleted specifically in sensory hair cells by Atoh1 promoter-driven Cre recombinase expression. Each biological replicate represents the combined apical or combined basal segments of organ of Corti from both cochleae of a single mouse. Two biological replicates for apical and basal organ of Corti from Dicer1 conditonal knockout and littermate controls were collected for RNA extraction and microarray analysis.
Project description:Within a spike of wheat, the central spikelets usually generate three to four fertile florets, while the basal spikelets hardly achieve this. The physiological and transcriptional mechanism behind the difference in fertility between the basal and central spikelets is unclear. This study reports a high temporal-resolution investigation of transcriptomes, number and morphology of floret primordia, and physiological traits. The W6.5–W7.5 stage was regarded as the boundary to distinguish between fertile and abortive floret primordia; those floret primordia reaching the W6.5–W7.5 stage during the differentiation phase (3–9 d after terminal spikelet stage) usually developed into fertile florets in the next, dimorphism phase (12–27 d after terminal spikelet stage), whereas the others aborted. The central spikelets had a greater number of fertile florets than the basal spikelets, which was associated with more floret primordia reaching the W6.5–W7.5 stage. Physiological and transcriptional results demonstrated that the central spikelets had a higher sucrose content and lower abscisic acid (ABA) and jasmonic acid (JA) accumulation than the basal spikelets due to down-regulation of genes involved in ABA and JA synthesis. Collectively, we propose a model in which ABA and JA accumulation is induced under limiting sucrose availability (basal spikelet) through up-regulating genes involved in ABA and JA synthesis; this leads to floret primordia in the basal spikelets being hardly able to reach their fertile potential (W6.5–W7.5 stage) during the differentiation phase and then aborting. This fertility repression module may also regulate spikelet fertility in other cereal crops and potentially provides genetic resources to improve spikelet fertility.
Project description:Clostridioides difficile (C. difficile) toxins A (TcdA) and B (TcdB) cause antibiotic-associated colitis, increasing morbidity and mortality. Accurate in vitro models are necessary to detect early toxicity kinetics, investigate disease etiology, and develop preclinical models for new therapies. Properties of cancer cell lines and organoids inherently limit these efforts. We developed adult stem cell-derived monolayers of differentiated human colonic epithelium (hCE) with barrier function, investigated the impact of toxin application to apical/basal aspects of monolayers, and evaluated whether a leaky epithelial barrier enhances toxicity. Single-cell RNA-sequencing (scRNAseq) mapped C. difficile-relevant genes to human gut epithelial lineages. Transcriptomics informed timing of stem cell differentiation to achieve in vitro colonocyte maturation like that observed in vivo. Transepithelial electrical resistance (TEER) and fluorescent dextran permeability assays measured cytotoxicity as barrier loss post-toxin exposure. Leaky epithelial barriers were induced with diclofenac. scRNAseq demonstrated broad and variable toxin receptor expression across human gut lineages. Absorptive colonocytes displayed generally enhanced toxin receptor, Rho GTPase, and cell junction expression. 22-day differentiated Caco-2 cells remained immature whereas hCE monolayers were similar to mature colonocytes. hCE monolayers exhibited high barrier function after 1-day differentiation. Basal TcdA/B application to monolayers caused greater toxicity and apoptosis. Diclofenac induced leaky hCE monolayers and enhanced toxicity of apical TcdB exposure. Apical/basal toxicities are uncoupled with more rapid onset and increased magnitude of basal toxicity. Leaky paracellular junctions enhance toxicity of apical TcdB exposure. hCE monolayers represent a physiologically relevant and sensitive culture system to evaluate the impact of microbial toxins on gut epithelium.
Project description:We analyzed the transcriptomes of 30 isolated apical OHCs and basal OHCs from rat cochlea, and the results showed that more than 50 genes were differentially expressed and 20 genes were uniquely expressed among these populations. We analyzed these genes with a focus on their functions related to cellular structure and transmembrane channels and their vulnerability to and involvement in hereditary deafness caused by OHC defects. Our results could serve as a guideline for exploring the molecular mechanisms underlying the biological properties of OHCs.