EX VIVO EVALUATION OF ANTIBIOTIC SENSITIVITY IN SAMPLES FROM ENDODONTIC INFECTIONS
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA873285 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21460500_1.fastq.gz | Fastqsanger.gz | |||
| SRR21460500_2.fastq.gz | Fastqsanger.gz | |||
| SRR21460600_1.fastq.gz | Fastqsanger.gz | |||
| SRR21460600_2.fastq.gz | Fastqsanger.gz | |||
| SRR21460501_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 262 |
Similar Datasets
Project description:ObjectiveTo develop an in vitro model for real-time monitoring of endodontic biofilm growth and evaluate the ex vivo effect of antibiotics on biofilm growth.Material and methodsRoot canal samples were taken from 40 patients and inoculated into 96-well plates in a system that measures biofilm growth through electrical impedance. Biofilm bacterial composition at the genus and species level was analyzed by Illumina sequencing. ANCOM-BC corrected data were used to compare bacterial composition after antibiotic treatment through compositional analysis, and to compare microbiological with clinical data.ResultsThe stationary phase was reached at 8 hours. The biofilm formed had a similar bacterial composition to the inoculum, and Enterococcus faecalis was virtually absent from the samples. The bacterial composition and the effect of antibiotics were sample-dependent. Metronidazole was the antibiotic that most inhibited biofilm formation and azithromycin the one that inhibited it in the highest percentage of cases. The antibiotic effect could not be related to the biofilm original bacterial composition.ConclusionsThe impedance system allowed real-time monitoring of endodontic biofilm formation, and we propose it as a model for ex vivo evaluation of the whole biofilm susceptibility to antimicrobials, as opposed to evaluating antibiotic sensitivity of specific bacterial isolates.
| S-EPMC9793940 | biostudies-literature
Project description:Background: Understanding individual patient host-response to viruses is key to designing optimal personalized therapy. Indeed, a subjectM-bM-^@M-^Ys epigenetic, transcriptomic and proteomic profiles dynamically respond to environmental challenges according to their intrinsic specific genetics. Unsurprisingly, in vivo human experimentation to understand individualized dynamic response of the transcriptome to viruses are rarely studied because of the obviously limitations stemming from ethical considerations of the clinical risk. In this rhinovirus study, we first establish that ex vivo human cells response to virus can serve as proxy for otherwise controversial in vivo human experimentation of viral infection. We further demonstrate that the N-of-1-pathways framework, that we previously validated for single patient M-bM-^@M-^Xomics analyses in cancer, can be utilized to understand individualized ex vivo response to viral stress and inform clinicians involved in personalized therapeutics. Method: N-of-1-pathways, validated retrospectively in whole tumors and experimentally in cancer cell lines, is a framework designed for identifying deregulated pathways at the single patient level between two M-bM-^@M-^Xomics profiles. It computes a significance score for a list of given genesets, using the M-bM-^@M-^Xomics profiles of a mere two samples as input (e.g. normal/tumoral, pre/post-treatment). We hypothesized that its usage could be extended to virus exposed cells. Additionally, we developed the Similarity Venn Diagram, an efficient and deceptively simple method for comparing results expressed in an ontology organized as a directed acyclic graph. We extracted the peripheral blood of four human subjects, with and without an ex vivo infection to rhinovirus. Their deregulated pathways were compared to those of 9 human subjects prior and after intranasal inoculation M-bM-^@M-^\in vivoM-bM-^@M-^] with rhinovirus. Results: We compared the N-of-1-pathways results using two established cohort-level methodologies: GSEA and enrichment of differentially expressed genes. Results are significantly and biologically similar between in vivo and ex vivo studies, both at the genes and enriched pathways levels. ROC curves demonstrate that deregulated pathways identified by N-of-1-pathways in cells each single subject infected ex vivo recapitulate the biologically relevant pathways observed in vivo in a whole cohort. Conclusion: In the context of less than five published transcriptomes of human viral infections in vivo and one ex vivo, the latter can be supplemented by 2-sample analyses yielding increased insight in individualized response without clinical risks. PBMCs incubated with viruses: The live PBMCs had been isolated from blood samples collected from four human subjects under a protocol approved by The University of Arizona Internal Review Board. Whole blood was obtained from donors and placed in heparin tubes that were centrifuged according to standard protocols to obtain PBMCs, then each aliquoted in two paired samples. Each sample of the pair was subsequently exposed to and incubated with either (i) Human Rhinovirus serotype 16 obtained from the American Type Culture Collection (RV; ATCCM-BM-. VR-283; ex vivo infected sample), or to (ii) sterile medium (control ex vivo non-infected sample) and incubated at 35M-BM-0C. This protocol resulted in 4 ex vivo infected + 4 ex vivo controls = 8 paired samples. RNA was extracted from these samples, amplified, tagged and hybridized on Affymetrix Human Gene 1.0 ST microarrays according to standard operating procedures. Dataset and preprocessing: Robust Multiple-array Average (RMA) normalization was applied on each patient data independently (2 paired samples at a time, to avoid bias in the single-patient experiments) using Affymetrix Power Tools (APT)
2014-08-07 | E-GEOD-60153 | biostudies-arrayexpress
Project description:Multiple myeloma (MM) is a plasma cell malignancy defined by complex genetics and extensive patient heterogeneity. Despite a growing arsenal of approved therapies, MM remains incurable and in need of guidelines to identify effective personalized treatments. Here, we survey the ex vivo drug and immunotherapy sensitivities across 101 bone marrow (BM) samples from 70 MM patients using multiplexed immunofluorescence, automated microscopy and deep learning-based single-cell phenotyping. Combined with sample-matched genetics, proteotyping, and cytokine profiling, we map the molecular regulatory network of drug sensitivity, implicating the DNA-repair pathway and EYA3 expression in proteasome inhibitor sensitivity, and MHC class II expression in the response to Elotuzumab. Globally, ex vivo drug sensitivity associated with BM microenvironmental signatures reflecting treatment stage, clonality, and inflammation. Furthermore, ex vivo drug sensitivity significantly stratified clinical treatment responses, including to immunotherapy. Taken together, our study provides molecular and actionable insights into diverse treatment strategies for multiple myeloma patients.
2022-03-06 | MSV000088992 | MassIVE
Project description:Microbial diversity in secondary endodontic infections
| PRJNA217469 | ENA
Project description:BackgroundHuman intestines contain a heterogeneous collection of cells that include immune, neural and epithelial elements interacting in a highly complex physiology that is challenging to maintain ex vivo. There is an extreme oxygen gradient across the intestinal wall due in part to microbiota in the lumen and close to the gut wall, which complicates the design of tissue culture systems. The current study established the use of an organotypic slice model of human intestinal tissue derived from colonoscopy biopsies to study host-microbial interactions after antibiotic treatment, and the influence of oxygen concentration on gut wall function.MethodsOrganotypic slices from human colon biopsies collected during routine colonoscopy provided three-dimensional environments that maintained cellular morphology ex vivo. Biopsy slices were used to study impacts of oxygen concentrations and antibiotic treatments on epithelial proliferation rates, and metabolites from tissue culture supernatants.ResultsImmune function was validated via demonstration of a T lymphocyte response to Salmonella enterica serovar Typhimurium. Following 24 h of Salmonella exposure there was a significant increase in CD3+ T-lymphocytes in biopsy slices. Metabolite profiling of tissue culture supernatants validated the influence of antibiotic treatment under varied oxygen culture conditions on both host and microbiome-mediated metabolism. Epithelial health was influenced by oxygen and antibiotic. Increased epithelial proliferation was measured in lowered oxygen conditions (1% = 5.9 mmHg) compared to atmospheric conditions standard at 5000 feet above sea level in Colorado (~17% = 100 mmHg). Antibiotic treatment reduced epithelial proliferation only in 5.9 mmHg oxygen cultured slices.ConclusionsA human colon organotypic slice model was established for applications ranging from gut epithelial proliferation to enteric pathogen influence on mucosal immune functions ex vivo. The results further support the need to account for oxygen concentration in primary tissue cultures, and that antibiotic use impacts gut-microbe-immune interactions.
| S-EPMC6522050 | biostudies-literature
Project description:Ex vivo drug sensitivity screening predicts response to temozolomide in glioblastoma patients and identifies candidate biomarkers
| PRJNA971167 | ENA
Project description:Cationic antimicrobial peptides (CAPs) are promising novel alternatives to conventional antibacterial agents, but the overlap in resistance mechanisms between small-molecule antibiotics and CAPs is unknown. Does evolution of antibiotic resistance decrease (cross-resistance) or increase (collateral sensitivity) susceptibility to CAPs? We systematically addressed this issue by studying the susceptibilities of a comprehensive set of antibiotic resistant Escherichia coli strains towards 24 antimicrobial peptides. Strikingly, antibiotic resistant bacteria frequently showed collateral sensitivity to CAPs, while cross-resistance was relatively rare. We identified clinically relevant multidrug resistance mutations that simultaneously elevate susceptibility to certain CAPs. Transcriptome and chemogenomic analysis revealed that such mutations frequently alter the lipopolysaccharide composition of the outer cell membrane and thereby increase the killing efficiency of membrane-interacting antimicrobial peptides. Furthermore, we identified CAP-antibiotic combinations that rescue the activity of existing antibiotics and slow down the evolution of resistance to antibiotics. Our work provides a proof of principle for the development of peptide based antibiotic adjuvants that enhance antibiotic action and block evolution of resistance.
2018-03-29 | GSE96706 | GEO
Project description:Ascites or solid tumour samples from patients with ovarian cancer were collected and grown in culture as ex vivo models of purified tumour cells. RNA-seq was performed on these models to establish gene expression profiles, which allow identification of genes that are differentially expressed between patients with differing tumour intrinsic properties. These samples have been interrogated for the presence of a gene expression signature indicative of sensitivity to an inhibitor of poly(ADP-ribose) glycohydrolase (PARG). These samples are processed in the same manner as previous studies: “E-MTAB-7223 - RNA-seq of human ex vivo ovarian cancer models with matched stromal cells” and “E-MTAB-10801 - RNA-seq of human ex vivo ovarian cancer models with matched stromal cells - part II” with no stromal counterparts included in this current sequencing batch.
2021-10-10 | E-MTAB-11000 | biostudies-arrayexpress
Project description:Evaluation of the evolution of aged vs young lung tumor cells derived from ex vivo transformation
| PRJNA1161417 | ENA