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:We acquired the largest bacterial proteomic resource, covering 303 species, 119 genera, and five phyla. The proteome coverage is, on average, over 50%. Additionally, we acquired further datasets for bacterial identification algorithm validation: i) 303 species at a 30-minute gradient (38 samples per day throughput), ii) 303 species at a 10-minute gradient (80 samples per day throughput), iii) reproducibility dataset, iv) genus-specific Pseudomonas spp. dataset (94 Pseudomonas spp. strains), v) genus-specific Bacillus spp. dataset (28 Bacillus cereus s.l. strains), vi) food routine dataset (60 dairy product isolates), and vii) clinical routine dataset (570 clinical isolates).
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:Whole genome enrichment sequencing of Cryptosporidium spp. directly from clinical samples
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:Whole genome sequencing of SYBARIS Aspergillus spp. known to be multi-drug resistant and difficult to treat. Aim of this experiment is to investigate the genetic basis of susceptibility to disease and elucidate molecular mechanisms of drug resistance in these strains.
Project description:Pseudomonas aeruginosa is a major cause of infection in hospitalised patients, with a large genome which makes it highly versatile and resistant to most antimicrobial agents. Ceftazidime-avibactam (CZA) offers an alternative treatment, but resistance is quickly evolving. There is limited knowledge on the exact resistance mechanisms to this drug, or on cross-resistance to meropenem (MEM). This laboratory experiment aimed to decipher these mechanisms in order to provide guidance for the best treatment choice in meropenem pre-treated P. aeruginosa infections. Six clinical isolates of P. aeruginosa were subjected to multistep resistance selection in sub inhibitory concentrations of CZA and MEM. MICs were also determined in the presence of the efflux pump inhibitor phenyl-Arginine-β-Naphthylamide (PAβN). Molecular analyses were performed by whole genome sequencing, whole -gene- and -protein expression profiles. CRISPR/Cas9 genome editing was performed using a two-plasmid method for selected mutations
Project description:Pseudomonas aeruginosa, the type species of the Pseudomonas genus, is an environmental Gram negative bacterium, well-known for its ability to produce toxins, resist antibiotics, and opportunistically colonize various niches, including invertebrate and vertebrate hosts. P. aeruginosa produces redox active secondary metabolites called phenazines involved in quorum sensing, biofilm formation, virulence, and iron acquisition. Moreover, these colorful pigmented virulence factors act as ligands for the highly conserved aryl hydrocarbon receptor (AhR) thereby regulating antibacterial defenses in vertebrates. Pseudomonas spp. are some of the most frequently identified bacteria in larval and adult stages of wild mosquito populations. Here we investigated global transcriptional changes induced in A. coluzzii third instar larvae incubated with a sublethal concentration (50 µM) of 1-hydroxyphenazine (1-HP) or pyocyanin (Pyo) at 4 h and 8 h of continuous incubation by whole-genome DNA microarrays.
