Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Shedding Light on the African Enigma: In Vitro Testing of Homo Sapiens-Helicobacter Pylori Coevolution

ABSTRACT: We conducted the first in vitro coinfection assays with dual human- and bacterium-matched and -mismatched ancestries, in African and European backgrounds, to evaluate the genome wide gene expression host response to H. pylori.

PROVIDER: PRJEB42638 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR5241560.fastq.gz	Fastqsanger.gz
	ERR5241570.fastq.gz	Fastqsanger.gz
	ERR5241580.fastq.gz	Fastqsanger.gz
	ERR5241561.fastq.gz	Fastqsanger.gz
	ERR5241571.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 27

Similar Datasets

Shedding Light on the African Enigma: In Vitro Testing of Homo sapiens-Helicobacter pylori Coevolution.

Project description:The continuous characterization of genome-wide diversity in population and case-cohort samples, allied to the development of new algorithms, are shedding light on host ancestry impact and selection events on various infectious diseases. Especially interesting are the long-standing associations between humans and certain bacteria, such as the case of Helicobacter pylori, which could have been strong drivers of adaptation leading to coevolution. Some evidence on admixed gastric cancer cohorts have been suggested as supporting Homo-Helicobacter coevolution, but reliable experimental data that control both the bacterium and the host ancestries are lacking. Here, we conducted the first in vitro coinfection assays with dual human- and bacterium-matched and -mismatched ancestries, in African and European backgrounds, to evaluate the genome wide gene expression host response to H. pylori. Our results showed that: (1) the host response to H. pylori infection was greatly shaped by the human ancestry, with variability on innate immune system and metabolism; (2) African human ancestry showed signs of coevolution with H. pylori while European ancestry appeared to be maladapted; and (3) mismatched ancestry did not seem to be an important differentiator of gene expression at the initial stages of infection as assayed here.

| S-EPMC7912213 | biostudies-literature

Toxicity Testing in the 21st Century: An Integrated Approach to Genetic Safety Testing using the TGx-DDI Genomic Biomarker and High-Throughput CometChip® [NanoString]

Project description:The TGx-DDI is a transcriptomic biomarker used to predict the DNA damage-inducing (DDI) capability of chemicals by providing mechanistic information to aid in the interpretation of positive genotoxicity data. The biomarker was developed within the Health and Environmental Sciences Institute (HESI) and measures transcriptional changes in a set of primarily p53-responsive genes. We investigated three antibiotic drugs, nitrofurantoin (NIT), novobiocin sodium salt (NOV) and metronidazole (MTZ), with a long history of clinical use in human and/or veterinary applications. While all three drugs are considered safe, there is some evidence of chromosome damage with NIT and NOV. We conducted high-throughput CometChip and TGx-DDI assays to evaluate the drugs in a parallel test strategy to explore their toxicity using these newer mechanism-based tests. An extended concentration-response analysis was conducted in human TK6 cells (from 0 to 1 mM). The alkaline CometChip assay was used to measure DNA damage, while TGx-DDI was applied using TempO-Seq and NanoString technologies (in two different laboratories) to confirm reproducibility of the results. The CometChip was negative for all three drugs except at overtly cytotoxic concentrations, which were eliminated from the gene expression analysis. NIT and MTZ were classified as non-DDI by TGx-DDI at all concentrations tested. NOV classified as DDI at the highest concentrations tested. NOV is bacterial DNA-gyrase inhibitor that also acts as a topoisomerase II inhibitor at high concentrations. The TGx-DDI classification results were identical across laboratories/technologies. This case study demonstrates the utility of TGx-DDI to de-risk NIT and NOV, and the reproducibility of the biomarker.

2022-08-02 | GSE196369 | GEO

Toxicity Testing in the 21st Century: An Integrated Approach to Genetic Safety Testing using the TGx-DDI Genomic Biomarker and High-Throughput CometChip® [Sequencing]

2022-08-02 | GSE196372 | GEO

Bioinformatics-based selection of a model cell type for in vitro biomaterial testing

Project description:Biomaterial properties can be tailored for specific applications via systematic and high-throughput screening of biomaterial–cell interactions. However, progress in material development is often hampered by the lack of adequate in vitro testing methods, frequently due to incomplete understanding of involved in vivo mechanisms. In line with drug discovery in pharmacology, a crucial step in assay development for biomaterial screening is the identification of a target to direct the screen against. Herein, the cell type to be used for screening is of essential importance and has to be carefully chosen. So far, few attention has been put on selecting a cell type specifically suitable for in vitro testing of materials for predefined applications. In this manuscript, we describe an approach to define a suitable cell type for screening assays, for which biomaterials for bone regeneration served as example. Using a bioinformatics methodology, different cell lines are compared on three well-characterized model materials. The transcriptional profiles of MG63, iMSC, SV-HFO, hPPCT, hBPCT and SW480 cells are assessed on 3 calcium phosphate-based materials to evaluate their potential application in a screening assay. We show that MG63 is the most suitable cell line to evaluate biomaterials for bone regeneration applications, evidenced by their robust gene expression differences between the 3 model materials. The gene expression differences between the cell lines were assessed based on the overall gene expression profiles and specific subsets of genes and pathways related to osteogenesis and bone homeostasis in response to the 3 materials tested. In the next phase, this cell line will be used to identify a target correlating with in vivo biomaterial performance and henceforth to develop an in vitro screening system.

2018-08-12 | E-MTAB-7057 | biostudies-arrayexpress

Higher self renewal and oncogenic potential of keratinocytes from Black versus White populations linked to the hydroxysteroid dehydrogenase HSD17B7 gene.

Project description:Genotyping of 62 foreskin-derived human primary fibroblasts from individuals of Black African versus Caucasian ancestries.

2021-05-12 | GSE156977 | GEO

Coinfection of monocyte derived dendritic cells with HSV2 and HIV

Project description:Coinfection of monocyte derived dendritic cells with HSV2 and HIV

2019-11-19 | GSE140612 | GEO

Phage coevolution

Project description:Experimental evolution of rhizobia and phages

| PRJEB83638 | ENA

Higher self renewal and oncogenic potential of keratinocytes from Black versus White populations linked to the hydroxysteroid dehydrogenase HSD17B7 gene

Project description:Transcriptomic profiling of 54 foreskin-derived human primary keratinocytes from individuals of Black African versus Caucasian ancestries.

2021-05-12 | GSE156011 | GEO

Phenotypic modifications of bacteria-plasmid coevolution facilitate gut colonization

Project description:Purpose: We investigate the evolutionary footprints of a bacteria-plasmid association consisting of Escherichia coli K-12 MG1655 and plasmid RP4 undergoing a long-term sub-MIC antibiotic stress. Methods: Bacterial mRNA profiles of evolved RP4-carrying strains (E:H:p) and ancestral RP4-carrying strains (A:H:p) were generated by deep sequencing on an Illumina Hiseq platform. The sequence reads that passed quality filters were analyzed by Burrows–Wheeler Aligner (BWA), followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 15 million sequence reads of E:H:p and 12 million sequence reads of A:H:p to the E. coli MG1655 genome (GCF_000801205.1) and differential expressed genes were identified with TopHat workflow. RNA-seq data showed that approximately 15% of the transcripts showed differential expression between the E:H:p and A:H:p strains, with a fold change ≥1 and p value <0.005. Altered expression of 26 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Data analysis with bowtie and TopHat workflows provided complementary insights in transcriptome profiling. Conclusions: Our study showed the coevolved bacteria-plasmid pairs has colonization traits superior to the wild-type parent strain. Antibiotic stress was necessary for bacterial evolution and evolved strains mostly employed transcriptional modifications to reduce plasmid-related cost in evolutionary adaptations. Several genes related to chromosome-encoded efflux pumps were transcriptionally upregulated, while most plasmid-harboring genes were downregulated based on RNA gene sequencing. These transcriptional modifications endowed evolved strains with resistant phenotype modifications, including the enhanced bacterial growth and biofilm formation.

2020-09-24 | GSE158461 | GEO

Wool shedding

Project description:Study of natural wool shedding

| PRJEB31930 | ENA