Synovial Tissue Infection with Burkholderia fungorum.
Ontology highlight
ABSTRACT:
SUBMITTER: Loong SK
PROVIDER: S-EPMC5038425 | biostudies-literature | 2016 Oct
REPOSITORIES: biostudies-literature
Publications
Synovial Tissue Infection with Burkholderia fungorum.
Loong Shih Keng SK Soh Yih Harng YH Mahfodz Nur Hidayana NH Johari Jefree J AbuBakar Sazaly S
Emerging infectious diseases 20161001 10
Similar Datasets
Project description:Burkholderia species are free-living bacteria with a versatile metabolic lifestyle. The genome of B. fungorum LB400 is predicted to encode three different pathways for formaldehyde oxidation: an NAD-linked, glutathione (GSH)-independent formaldehyde dehydrogenase; an NAD-linked, GSH-dependent formaldehyde oxidation system; and a tetrahydromethanopterin-methanofuran-dependent formaldehyde oxidation system. The other Burkholderia species for which genome sequences are available, B. mallei, B. pseudomallei, and B. cepacia, are predicted to contain only the first two of these pathways. The roles of the three putative formaldehyde oxidation pathways in B. fungorum LB400 have been assessed via knockout mutations in each of these pathways, as well as in all combinations of knockouts. The resulting mutants have the expected loss of enzyme activities and exhibit defects of varying degrees of severity during growth on choline, a formaldehyde-producing substrate. Our data suggest that all three pathways are involved in formaldehyde detoxification and are functionally redundant under the tested conditions.
| S-EPMC374398 | biostudies-literature
Project description:Burkholderia fungorum FLU100 simultaneously oxidized any mixture of toluene, benzene and mono-halogen benzenes to (3-substituted) catechols with a selectivity of nearly 100%. Further metabolism occurred via enzymes of ortho cleavage pathways with complete mineralization. During the transformation of 3-methylcatechol, 4-carboxymethyl-2-methylbut-2-en-4-olide (2-methyl-2-enelactone, 2-ML) accumulated transiently, being further mineralized only after a lag phase of 2 h in case of cells pre-grown on benzene or mono-halogen benzenes. No lag phase, however, occurred after growth on toluene. Cultures inhibited by chloramphenicol after growth on benzene or mono-halogen benzenes were unable to metabolize 2-ML supplied externally, even after prolonged incubation. A control culture grown with toluene did not show any lag phase and used 2-ML as a substrate. This means that 2-ML is an intermediate of toluene degradation and converted by specific enzymes. The conversion of 4-methylcatechol as a very minor by-product of toluene degradation in strain FLU100 resulted in the accumulation of 4-carboxymethyl-4-methylbut-2-en-4-olide (4-methyl-2-enelactone, 4-ML) as a dead-end product, excluding its nature as a possible intermediate. Thus, 3-methylcyclohexa-3,5-diene-1,2-diol, 3-methylcatechol, 2-methyl muconate and 2-ML were identified as central intermediates of productive ortho cleavage pathways for toluene metabolism in B. fungorum FLU100.
| S-EPMC4321380 | biostudies-literature
Project description:Phenanthrene (PHE) is a common pollutant of acidic and non-acidic environments that is recalcitrant to biodegradation. Herein, Burkholderia fungorum FM-2 (GenBank accession no. KM263605) was isolated from oil-contaminated soil in Xinjiang and characterized morphologically, physiologically, and phylogenetically. Environmental parameters including PHE concentration, pH, temperature, and salinity were optimized, and heavy metal tolerance was investigated. The MIC of strain FM-2 tolerant to Pb(II) and Cd(II) was 50 and 400 mg L-1, respectively, while the MIC of Zn(II) was >1,200 mg L-1. Atypically for a B. fungorum strain, FM-2 utilized PHE (300 mg L-1) as a sole carbon source over a wide pH range (between pH 3 and 9). PHE and heavy metal metabolism were assessed using gas chromatography (GC), inductively coupled plasma optical emission spectroscopy (ICP-OES), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), Fourier-transform infrared (FTIR) spectroscopy and ultraviolet (UV) absorption spectrometry. The effects of heavy metals on the bioremediation of PHE in soil were investigated, and the findings suggest that FM-2 has potential for combined bioremediation of soils co-contaminated with PHE and heavy metals.
| S-EPMC6427951 | biostudies-literature
Project description:Paraburkholderia fungorum is an opportunistic bacteria infrequently associated with human infections. Here, we report the draft genome sequence of P. fungorum strain BF370, recovered from the synovial tissue of a patient in Malaysia. The P. fungorum genome contains a 8,950,957 bp chromosome with a G+C content of 61.8%. Colicin and heavy metal resistant genes were also present in the genome. Conserved sequence indels unique to P. fungorum were observed in the genome. The draft genome was deposited at the European Nucleotide Archive under the sample accession number ERS1776561 and study accession number PRJEB17921.
| S-EPMC6610667 | biostudies-literature
Project description:To investigate the effect of Burkholderia fungorum (BF) on cholangiocarcinoma cells, we treated the cell lines with bacterial supernatant and performed transcriptome sequencing. By transcriptome sequencing, we quantified the differentially expressed genes in control and experimental groups. The results of GO and KEGG functional enrichment analysis showed that the differentially expressed genes were mainly involved in some biological processes of metabolism and amino acid synthesis. We inferred that the transcriptome characterization can help us understand the relationship between bacterium and tumor cell metabolism.
2022-12-31 | GSE182319 | GEO
Project description:The analysis of synovial tissue offers the potential for the comprehensive characterization of cell types involved in arthritis pathogenesis. The studies performed to date in synovial tissue have made it possible to define synovial pathotypes, which relate to disease severity and response to treatment. Lipidomics is the branch of metabolomics that allows the quantification and identification of lipids in different biological samples. Studies in animal models of arthritis and in serum/plasma from patients with arthritis suggest the involvement of different types of lipids (glycerophospholipids, glycerolipids, sphingolipids, oxylipins, fatty acids) in the pathogenesis of arthritis. We reviewed studies that quantified lipids in different types of tissues and their relationship with inflammation. We propose that combining lipidomics with currently used "omics" techniques can improve the information obtained from the analysis of synovial tissue, for a better understanding of pathogenesis and the development of new therapeutic strategies.
| S-EPMC9051397 | biostudies-literature
Project description:Two distinct defense strategies can protect the host from infection: resistance is the ability to destroy the infectious agent, and tolerance is the ability to withstand infection by minimizing the negative impact it has on the host's health without directly affecting pathogen burden. Burkholderia pseudomallei is a Gram-negative bacterium that infects macrophages and causes melioidosis. We have recently shown that inflammasome-triggered pyroptosis and IL-18 are equally important for resistance to B. pseudomallei, whereas IL-1β is deleterious. Here we show that the detrimental role of IL-1β during infection with B. pseudomallei (and closely related B. thailandensis) is due to excessive recruitment of neutrophils to the lung and consequent tissue damage. Mice deficient in the potentially damaging enzyme neutrophil elastase were less susceptible than the wild type C57BL/6J mice to infection, although the bacterial burdens in organs and the extent of inflammation were comparable between C57BL/6J and elastase-deficient mice. In contrast, lung tissue damage and vascular leakage were drastically reduced in elastase-deficient mice compared to controls. Bradykinin levels were higher in C57BL/6 than in elastase-deficient mice; administration of a bradykinin antagonist protected mice from infection, suggesting that increased vascular permeability mediated by bradykinin is one of the mechanisms through which elastase decreases host tolerance to melioidosis. Collectively, these results demonstrate that absence of neutrophil elastase increases host tolerance, rather than resistance, to infection by minimizing host tissue damage.
| S-EPMC4148436 | biostudies-literature
Project description:ObjectiveInflammatory responses are associated with changes in tissue metabolism. Prior studies find altered metabolomic profiles in both the synovial fluid (SF) and serum of osteoarthritis subjects. Our study determined the metabolomic profile of synovial tissue (ST) and SF of individuals with osteoarthritis (OA) and its association with synovial inflammation.Design37 OA ST samples were collected during joint replacement, 21 also had SF. ST samples were fixed in formalin for histological analysis, cultured (explants) for cytokine analysis by enzyme-linked immunosorbent assay, or snap-frozen for metabolomic analysis. ST samples were categorized by Krenn synovitis score and picrosirius red. CD68 and vimentin expression was assessed by immunohistochemistry and semi-quantified using Image J. Proton-nuclear magnetic resonance (1H NMR) was used to acquire a spectrum from ST and SF samples. Chenomx NMR suite 8.5 was used for metabolite identification and quantification. Metaboanalyst 5.0, SPSS v26, and R (v4.1.2) were used for statistical analysis.Results42 and 29 metabolites were detected in the ST and SF respectively by 1H NMR. Only 3 metabolites, lactate, dimethylamine, and creatine positively correlated between SF and ST. ST concentrations of several metabolites (lactate, alanine, fumarate, glutamine, glycine, leucine, lysine, methionine, trimethylamine N-oxide, tryptophan and valine) were associated with synovitis score, mostly to the lining score. IL-6, acetoacetate, and tyrosine in SF predicted high Krenn synovitis scores in ST.ConclusionMetabolomic profiling of ST identified metabolic changes associated with inflammation. Further studies are needed to determine whether metabolomic profiling of synovial tissue can identify new therapeutic targets in osteoarthritis.
| S-EPMC9718344 | biostudies-literature
Project description:Osteoarthritis (OA) and rheumatoid arthritis (RA) are the most common forms of arthritis. The synovial tissue is the major site of inflammation of OA and RA and consists of diverse cells. Synovial tissue cell composition changes during arthritis pathogenesis and progression have not been systematically characterized and may provide critical insights into disease processes. In this study we aimed at systematically examining cellular changes in synovial tissue. Publicly available synovial tissue transcriptomic data sets were used. We computationally estimated cell compositions in synovial tissue based on transcriptomic data and compared cell compositions in different diseases or at different disease stages. Synovial fibroblasts, macrophages, adipocytes, and immune cells were the major cell types in all synovial tissue. Both OA and RA patients had a significantly lower adipocyte fraction compared with healthy controls. The decrease trend was also observed during OA and RA progression. The fraction of monocytes was also increased in both OA and RA arthritis patients, consistent with the observations that inflammation involved in both OA and RA. But the monocyte fraction in RAs was much higher than the ones in healthy controls and OAs. The M2 macrophage fraction was reduced in RA compared with OA, the reduction trend continued during RA progression from the early- to the late-stage. There were consistent cell composition differences between different types or stages of arthritis. Both in RA and OA, the new discovery of changes in the adipocyte and M2 macrophage fractions has potential leading to novel therapeutic development.
| S-EPMC6620645 | biostudies-literature
Project description:ObjectiveTo improve the fidelity of the cellular transcriptome of disaggregated synovial tissue for applications such as single-cell RNA sequencing (scRNAseq) by modifying the disaggregation technique.MethodsOsteoarthritis (OA) and rheumatoid arthritis (RA) synovia were collected at arthroplasty. RNA was extracted from intact or disaggregated replicate pools of tissue fragments. Disaggregation was performed with either a proprietary protease, Liberase TL (Lib) as a reference method, Liberase TL with an RNA polymerase inhibitor flavopyridol (Flavo), or a cold digestion with subtilisin A (SubA). qPCR on selected markers and RNAseq were used to compare disaggregation methods using the original intact tissue as reference.ResultsDisaggregated cell yield and viability were similar for all three methods with some viability improved (SubA). Candidate gene analysis showed that Lib alone dramatically increased expression of several genes involved in inflammation and immunity compared with intact tissue and was unable to differentiate RA from OA. Both alternative methods reduced the disaggregation induced changes. Unbiased analysis using bulk RNAseq and the 3 protocols confirmed the candidate gene studies and showed that disaggregation-induced changes were largely prevented. The resultant data improved the ability to distinguish RA from OA synovial transcriptomes.ConclusionsDisaggregation of connective tissues such as synovia has complex and selective effects on the transcriptome. We found that disaggregation with an RNA polymerase inhibitor or using a cold enzyme tended to limit induction of some relevant transcripts during tissue processing. The resultant data in the disaggregated transcriptome better represented the in situ transcriptome. The specific method chosen can be tailored to the genes of interest and the hypotheses being tested in order to optimize the fidelity of technique for applications based on cell suspensions such as sorted populations or scRNAseq.
| S-EPMC9400013 | biostudies-literature