Kadsura longipedunculata
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA476834 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:Kadsura spp. in the Schisandraceae family are woody vine plants, which produce edible red fruits that are rich in nutrients and antioxidant activities. Despite their valuable food applications, Kadsura spp. are only able to grow naturally in the forest, and reproduction handled by botanists is still in progress with a very low growth rate. Subsequently, Kadsura spp. were listed as endangered species by the International Union for Conservation of Nature and Natural Resources (IUCN) in 2011. Two different Kadsura spp., including Kadsura coccinea (Lem.) A.C. Sm. and Kadsura heteroclita (Roxb.) Craib, are mostly found in northern Thailand. These rare, wild fruits are unrecognizable to outsiders, and there have only been limited investigations into its biological properties. This study, therefore, aimed to comparatively investigate the phenolic profiles, antioxidant activities, and inhibitory activities against the key enzymes involved in diabetes (?-glucosidase and ?-amylase) and Alzheimer's disease (acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and beta-secretase 1 (BACE-1)) in different fruit parts (exocarp, mesocarp (edible part), seed, and core) of Kadsura coccinea (Lem.) A.C. Sm. and Kadsura heteroclita (Roxb.) Craib. The results suggested that Kadsura spp. extracts were rich in flavonol (quercetin), flavanone (naringenin), anthocyanidins (cyanidin and delphinidin), and anthocyanins (cyanidin 3-O-glucoside (kuromanin), cyanidin 3-O-galactoside (ideain), cyanidin 3-O-rutinoside (keracyanin), and cyanidin 3,5-di-O-glucoside (cyanin)). These flavonoids were found to be responsible for the high antioxidant activities and key enzyme inhibitions detected in Kadsura spp. extracts. The findings of the present study can support further development of Kadsura spp. as a potential source of phenolics and anti-oxidative agents with health benefits against diabetes and Alzheimer's disease. Besides, exocarp and the core of Kadsura spp. exhibited higher phenolic contents, antioxidant activities, and key enzyme inhibitory activities compared to the mesocarp and seeds, respectively. This information can promote the use of fruit parts other than the edible mesocarp for future food applications using Kadsura spp. rather than these being wasted.
| S-EPMC7555767 | biostudies-literature
Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
2022-06-27 | E-MTAB-11830 | biostudies-arrayexpress
Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
2022-06-27 | E-MTAB-11831 | biostudies-arrayexpress
Project description:Porcine 60K BeadChip genotyping arrays (Illumina) are increasingly being applied in pig genomics to validate SNPs identified by re-sequencing or assembly-versus-assembly method. Here we report that more than 98% SNPs identified from the porcine 60K BeadChip genotyping array (Illumina) were consistent with the SNPs identified from the assembly-based method. This result demonstrates that whole-genome de novo assembly is a reliable approach to deriving accurate maps of SNPs.
2016-07-05 | GSE83910 | GEO