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).
Project description:36 Yucatan minipigs underwent anterior cruciate ligament (ACL) transection and were randomly assigned in equal numbers to no further treatment, reconstruction or ligament repair. Cartilage was harvested at 1 and 4 weeks post-operatively and histology and RNA-sequencing performed. The generated data served to identify the molecular pathophysiology present in early post-traumatic osteoarthritis (PTOA), as well as differences between surgical treatments.
Project description:Experimental screening of a compound library identified a molecule that potently inhibits the growth of the obligate intracellular bacterial pathogen Chlamydia trachomatis in human cells. To identify the molecular target of the compound, three mutant bacterial strains resistant to its inhibitory action were generated by long-term passage in the presence of initially low but increasing concentrations of the molecule. Subsequently, genomic DNA of the three mutant and the wildtype bacteria was isolated and subjected to whole genome sequencing to identify resistance-promoting mutations.
Project description:36 Yucatan minipigs underwent anterior cruciate ligament (ACL) transection and were randomly assigned in equal numbers to no further treatment, reconstruction or ligament repair. Peri-meniscal synovium was harvested at 1 and 4 weeks post-operatively and histology and RNA-sequencing performed. The generated data served to identify the molecular pathophysiology present in inflamed synovium during the early development of post-traumatic osteoarthritis (PTOA), as well as differences between surgical treatments.
Project description:Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.
Project description:Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.
Project description:In this research, Pseudomonas aeruginosa underwent evolution in the supernatant of either S. aureus (SA) or K. pneumoniae (KP). Through this evolution process, we enriched a sufficient number of bacterial cells along with their corresponding proteins. Following 15 cultivation cycles, notable changes were observed in the phenotypes of P. aeruginosa, with a series of mutations identified through whole-genome sequencing (WGS). Proteomics analysis unveiled that the supernatant-evolved mutants displayed distinct regulation patterns in crucial pathways (including the type VI secretion system, biofilm formation, phenazine biosynthesis, translation, beta-lactam resistance, and O-antigen biosynthesis) in comparison to both the ancestral strain and the unmodified medium-evolved (UmMd-evolved) strain.
2025-05-21 | PXD059669 | Pride
Project description:Mangrove sediment Yucatan
| PRJNA1039151 | ENA
Project description:Metataxonomic Bacterial Diversity of Cave Roots in the Yucatan Cenotes
Project description:Whole-genome sequencing is an important way to understand the genetic information, gene function, biological characteristics, and living mechanisms of organisms. There is no difficulty to have mega-level genomes sequenced at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. The shotgun sequencing method failed to dissect this genome. After insisting for 10 years and going over 3 generations of sequencing techniques, we successfully dissected the PaP1 genome with 91,715 bp in length. Single-molecule sequencing revealed that this genome contains lots of modified bases, including 51 N6-methyladenines (m6A) and 152 N4-methylcytosines (m4C). At the same time, further investigations revealed a novel immune mechanism of bacteria, by which the host bacteria can recognize and repel the modified bases containing inserts in large scale, and this led to the failure of the shotgun method in PaP1 genome sequencing. Strategy of resolving this problem is use of non-library dependent sequencing techniques or use of the nfi- mutant of E. coli DH5M-NM-1 as the host bacteria to construct the shotgun library. In conclusion, we unlock the mystery of phage PaP1 genome hard to be sequenced, and discover a new mechanism of bacterial immunity in present study. Methylation profiling of Pseudomonas aeruginosa phage PaP1 using kinetic data generated by single-molecule, real-time (SMRT) sequencing on the PacBio RS.
