Ontology highlight
ABSTRACT:
PROVIDER: PRJNA389564 | ENA |
REPOSITORIES: ENA
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Project description:The aim of this study was to complete and fully characterize the proteome of rainbow trout coelomic fluid (CF). Furthermore, we intended to identify the proteins responsible for the extension of egg viability in salmonids coelomic fluid. For this, the proteomic composition of different salmonids CF and non-salmonids CF were compared to identify proteins specifically present in salmonids CF. Those proteins could be responsible for the egg conservation property of the salmonids CF. In parallel, rainbow trout CF has been fractionated using HPLC coupled to gel filtration or ion exchange columns. We have then tested the egg conservation properties of the different fractions obtained. Proteins present in the fractions allowing egg quality preservation were identified. Identifying the CF components involved in egg viability would have important applied outputs with various biotechnological applications for aquaculture. It could help understanding egg quality preservation mechanisms, and consequently improving egg storage condition.
2024-05-21 | PXD034989 | Pride
Project description:Improving methods for human embryonic stem cell differentiation represents a challenge in modern regenerative medicine research. Using drug repurposing approaches, we discover small molecules that regulate the formation of definitive endoderm. Among them are inhibitors of known processes involved in endoderm differentiation (mTOR, PI3K, and JNK pathways) and a new compound, with an unknown mechanism of action, capable of inducing endoderm formation in the absence of growth factors in the media. Optimization of the classical protocol by including this compound achieves the same differentiation efficiency with a 90% cost reduction. The gene expression profile induced by the compound suggests that it is an inhibitor of the MYC pathway. The proposed in silico procedure for candidate molecule selection has broad potential for improving stem cell differentiation protocols.
2023-02-15 | GSE185628 | GEO
Project description:The filamentous fungus Aspergillus oryzae is an important microbial cell factory for industrial production of useful enzymes, such as α-amylase. In order to optimize the industrial enzyme production process, there is a need to understand fundamental processes underlying protein production, here under how protein production links to metabolism through global regulatory structures. In this study, two α-amylase-producing strains of A. oryzae, a wild type strain and a transformant strain containing additional copies of the α-amylase gene, were characterized at a systematic level. Based on integrated analysis of ome-data together with genome-scale metabolic network and flux calculation, we identified key genes, key enzymes, key proteins, and key metabolites involved in the processes of protein synthesis and secretion, nucleotide metabolism, and amino acid metabolism that can be the potential targets for improving industrial protein production. Keywords: Two Aspergillus oryzae strains and two different carbon sources Two carbon sources (glucose, maltose) with three biological replicates for A. oryzae strain A1560 and strain CF1.1
2012-02-12 | E-GEOD-22566 | biostudies-arrayexpress
Project description:Large genes including several CRISPR-Cas modules, such as gene activators (CRISPRa), require dual adeno-associated viral (AAV) vectors for efficient in vivo delivery and expression. Current dual AAV vector approaches have important limitations, e.g., low reconstitution efficiency, production of alien proteins, or low flexibility in split site selection. Here, we present a dual AAV vector technology based on reconstitution via mRNA trans-splicing (REVeRT). REVeRT is flexible in split site selection and can efficiently reconstitute different split genes in numerous in vitro models, in human organoids and in vivo. Furthermore, REVeRT can functionally reconstitute a CRISPRa module targeting genes in various mouse tissues and organs in single or multiplexed approaches upon different routes of administration. Finally, supplementation of ABCA4 (6.8 kb) via REVeRT improves retinal degeneration and function in a mouse model of inherited blindness. Due to its flexibility and efficiency REVeRT harbors great potential for basic research and clinical applications.
2023-03-18 | GSE198863 | GEO
Project description:Large genes including several CRISPR-Cas modules, such as gene activators (CRISPRa), require dual adeno-associated viral (AAV) vectors for efficient in vivo delivery and expression. Current dual AAV vector approaches have important limitations, e.g., low reconstitution efficiency, production of alien proteins, or low flexibility in split site selection. Here, we present a dual AAV vector technology based on reconstitution via mRNA trans-splicing (REVeRT). REVeRT is flexible in split site selection and can efficiently reconstitute different split genes in numerous in vitro models, in human organoids and in vivo. Furthermore, REVeRT can functionally reconstitute a CRISPRa module targeting genes in various mouse tissues and organs in single or multiplexed approaches upon different routes of administration. Finally, supplementation of ABCA4 (6.8 kb) via REVeRT improves retinal degeneration and function in a mouse model of inherited blindness. Due to its flexibility and efficiency REVeRT harbors great potential for basic research and clinical applications.
2023-09-06 | GSE198893 | GEO
Project description:Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) are advancing cardiovascular development and disease modeling, drug testing, and regenerative therapies. However, hPSC-CM production is hindered by significant variability in the differentiation process. Establishment of early quality markers to monitor lineage progression and predict terminal differentiation outcomes would address this robustness and reproducibility roadblock in hPSC-CM production. We performed an integrated transcriptomic and epigenomic analysis to assess how attributes of the cardiac progenitor cell (CPC) affect CM differentiation outcome. Our analysis identified predictive markers of CPCs that give rise to high purity CM batches, including TTN, TRIM55, DUSP5, DUSP6, GIPR, RHOBTB3, CRIP2, SLC7A11, MAB21L2, and CALD1. We also gained insight into mechanisms of batch failure and dominant non-CM cell types generated in failed batches. This study demonstrates how integrated multi-omic analysis of progenitor cells can identify quality attributes of that progenitor and predict differentiation outcomes, thereby improving differentiation protocols and increasing process robustness.
2024-09-05 | GSE254294 | GEO