Project description:The dataset includes SNP genotypes and CNP signals for 40 individuals from the capital region of Finland representing general population (IDs as FIN_#) and 41 individuals from the population sub-isolate Late-settlement area (IDs as LSFIN_#).
Project description:To assess how larvae of different ages vary in their responses to different settlement cues, we induced individual Amphimedon queenslandica larvae with one of three different settlement cues at 1.5, 3, 5, and 8 hours post emergence (hpe) from the adult sponge. The settlement cues were (1) the articulated coralline algae Amphiroa fragilissima, (2) the crustose coralline algae Mesophyllum sp., and (3) the filtered seawater (FSW) negative control. We used CEL-Seq2, an RNA-Sequencing approach (Hashimshony et al., 2016), to generate transcriptome data for a total of 144 individuals (larvae and settled post-larvae) at 2 hours post induction (hpi) to the different settlement cues.
Project description:Two known settlement/metamorphosis inducing stimuli (crustose coralline algae, and ethanolic extract of crustose coralline algae) and one stimulus which just induces metamorphosis (LWamide) were used to stimulate competent planula larvae of the coral Acropora millepora. Samples were taken 0.5h, 4h and 12h post induction isolate the genes controlling settlement and metamorphosis in this coral.
Project description:Bariatric surgical techniques are known to cause weight loss and diabetes remission to varying degrees in severly obese patients. However, the mechanisms involved in the restoration of beta-cell function remain to be uncovered. In this study, the leptin-deficient ob/ob mouse was used as a model to investigate the effect of EGA bariactric surgery on pancreatic islet miRNA expression.
2020-08-05 | GSE133569 | GEO
Project description:Comparison of biofilm on different substrate used for oyster larvae settlement
Project description:Reprogramming of the gamete into a developmentally competent embryo identity is a fundamental aspect of preimplantation development. One of the most important processes of this reprogramming is the transcriptional awakening during embryonic genome activation (EGA), which robustly occurs in fertilized embryos but is defective in most somatic cell nuclear transfer (SCNT) embryos. However, little is known about the genome-wide underlying chromatin landscape during EGA in SCNT embryos and how it differs from a fertilized embryo. By profiling open chromatin genome-wide in both types of bovine embryos, we find that SCNT embryos fail to reprogram a subset of the EGA gene targets that are normally activated in fertilized embryos. Importantly, a small number of transcription factor (TF) motifs explain most chromatin regions that fail to open in SCNT embryos suggesting that over-expression of a limited number of TFs may provide more robust reprogramming. One such TF, the zygotically-expressed bovine gene DUXC which is a homologue of EGA factors DUX/DUX4 in mouse/human, is alone capable of activating ~84% of all EGA transcripts that fail to activate normally in SCNT embryos. Additionally, single-cell chromatin profiling revealed low intra-embryo heterogeneity but high inter-embryo heterogeneity in SCNT embryos and an uncoupling of cell division and open chromatin reprogramming during EGA. Surprisingly, our data also indicate that transcriptional defects may arise downstream of promoter chromatin opening in SCNT embryos, suggesting additional mechanistic insights into how and why transcription at EGA is dysregulated. We anticipate that our work will lead to altered SCNT protocols to increase the developmental competency of bovine SCNT embryos.
Project description:Reprogramming of the gamete into a developmentally competent embryo identity is a fundamental aspect of preimplantation development. One of the most important processes of this reprogramming is the transcriptional awakening during embryonic genome activation (EGA), which robustly occurs in fertilized embryos but is defective in most somatic cell nuclear transfer (SCNT) embryos. However, little is known about the genome-wide underlying chromatin landscape during EGA in SCNT embryos and how it differs from a fertilized embryo. By profiling open chromatin genome-wide in both types of bovine embryos, we find that SCNT embryos fail to reprogram a subset of the EGA gene targets that are normally activated in fertilized embryos. Importantly, a small number of transcription factor (TF) motifs explain most chromatin regions that fail to open in SCNT embryos suggesting that over-expression of a limited number of TFs may provide more robust reprogramming. One such TF, the zygotically-expressed bovine gene DUXC which is a homologue of EGA factors DUX/DUX4 in mouse/human, is alone capable of activating ~84% of all EGA transcripts that fail to activate normally in SCNT embryos. Additionally, single-cell chromatin profiling revealed low intra-embryo heterogeneity but high inter-embryo heterogeneity in SCNT embryos and an uncoupling of cell division and open chromatin reprogramming during EGA. Surprisingly, our data also indicate that transcriptional defects may arise downstream of promoter chromatin opening in SCNT embryos, suggesting additional mechanistic insights into how and why transcription at EGA is dysregulated. We anticipate that our work will lead to altered SCNT protocols to increase the developmental competency of bovine SCNT embryos.
Project description:Bariatric surgical techniques are known to cause weight loss and diabetes remission to varying degrees in severly obese patients. However, the mechanisms involved in the restoration of beta-cell function remain to be uncovered. In this study, the leptin-deficient ob/ob mouse was used as a model to investigate the effect of EGA bariactric surgery on pancreatic islet gene expression.
Project description:Microbe associated molecular pattern (MAMP)-responsive genes were identified in leaves of four different genotypes. The genotypes used in this study were: LD0-2817P; LDX01-1-65; Ripley and EF59. Leaves from three-weeks old plants were used in this study We used microarray to identified the MAMP-responsive genes in leaves of four soybean genotypes trated with 1 uM flg22 and 50 ug/ml chitin for 30 minutes
Project description:Characterization of the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here, we reconstruct the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. We find that the His3 fitness landscape is dominated by synergistic epistasis, such that the cumulative effect of amino acid substitutions causes a dramatic decline in fitness. Furthermore, in 63% of sites substitutions were strongly positive in one genetic background and strongly negative in another, with 41% of sites showing reciprocal sign epistasis. This sign epistasis, present in proportionally few genotypes, was caused by simultaneous interaction of multiple sites with demonstrating a complex multidimensional nature of the His3 fitness landscape.
