Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete Genome Sequence of a Bacterium Representing a Deep Uncultivated Lineage within the Gammaproteobacteria Associated with the Degradation of Polycyclic Aromatic Hydrocarbons.

ABSTRACT: The bacterial strain TR3.2, representing a novel deeply branching lineage within the Gammaproteobacteria, was isolated and its genome sequenced. This isolate is the first cultivated representative of the previously described "Pyrene Group 2" (PG2) and represents a variety of environmental sequences primarily associated with petrochemical contamination and aromatic hydrocarbon degradation.

SUBMITTER: Singleton DR

PROVIDER: S-EPMC5054325 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete Genome Sequence of a Bacterium Representing a Deep Uncultivated Lineage within the Gammaproteobacteria Associated with the Degradation of Polycyclic Aromatic Hydrocarbons.

Singleton David R DR Dickey Allison N AN Scholl Elizabeth H EH Wright Fred A FA Aitken Michael D MD

Genome announcements 20161006 5

The bacterial strain TR3.2, representing a novel deeply branching lineage within the Gammaproteobacteria, was isolated and its genome sequenced. This isolate is the first cultivated representative of the previously described "Pyrene Group 2" (PG2) and represents a variety of environmental sequences primarily associated with petrochemical contamination and aromatic hydrocarbon degradation. ...[more]

PMID: 27795254

Similar Datasets

Degradation of polycyclic aromatic hydrocarbons by a newly discovered enteric bacterium, Leclercia adecarboxylata.

Project description:A bacterial strain, PS4040, capable of degrading polycyclic aromatic hydrocarbons for use as the sole carbon source was isolated from oily-sludge-contaminated soil. The 16S rRNA gene showed 98.8% homology to that of Leclercia adecarboxylata. Comparative molecular typing with the clinical strain of L. adecarboxylata revealed that there were few comigrating and few distinct amplimers among them.

| S-EPMC404440 | biostudies-literature

Microbial degradation of petrochemical waste-polycyclic aromatic hydrocarbons.

Project description:BackgroundPetrochemical industry is one of the fastest growing industries. This industry has immense importance in the growth of economy and manufacture of large varieties of chemicals. The petrochemical industry is a hazardous group of industry generating hazardous waste containing organic and inorganic compounds. In spite of the present treatment process, the hazardous waste compounds are found untreated to the acceptable level and found discharged at soil-water environment resulting into the persistent organic-inorganic pollutant into the environment. The bioremediation will be the innovative techniques to remove the persistent pollutants in the environment.ResultPetrochemical contaminated site was found to be a rich source of microbial consortium degrading polycyclic aromatic hydrocarbons. Indigenous microbial consortiums were identified and used for bioremediation of polycyclic aromatic hydrocarbons (naphthalene and anthracene) at the concentrations of 250, 500, and 750 ppm. The potential microorganism was also identified for naphthalene and anthracene, and their bioremediation was studied at varying concentrations. The bioremediation with consortium was found to be comparatively more effective than the potential microorganism used for bioremediation of each compound. Pseudomonas aeruginosa a potential organism was identified by 16S rRNA and further studied for the gene responsible for the PAH compounds.ConclusionIndigenous microorganism as a consortium has been found effective and efficient source for remediation of organic compound-Polycyclic aromatic hydrocarbon and this will also be applicable to remediate the toxic compounds to clean up the environment.

| S-EPMC5493705 | biostudies-literature

HepG2 treated with Polycyclic Aromatic Hydrocarbons (PAHs)

2012-04-18 | GSE37326 | GEO

Polycyclic aromatic hydrocarbons degraders

Project description:Polycyclic aromatic hydrocarbons degraders Raw sequence reads

| PRJNA590550 | ENA

HepG2 treated with Polycyclic Aromatic Hydrocarbons (PAHs)

Project description:Assessing the potential carcinogenicity of human toxins represents an ongoing challenge. Chronic rodent bioassays predict human cancer risk with limited reliability, and are expensive and time-consuming. To identify alternative prediction methods, we evaluated a transcriptomics-based human in vitro model to classify carcinogens by their modes of action. The aim of this study was to determine the transcriptomic response and identify specific molecular signatures of polycyclic aromatic hydrocarbons (PAHs), which can be used as predictors of carcinogenicity of environmental toxins in human in vitro systems. We found that characteristic molecular signatures facilitate identification and prediction of carcinogens. To evaluate the change in gene expression levels, human hepatocellular carcinoma (HepG2) cells were exposed to nine different PAHs (benzo[a]pyrene, dibenzo[a,h]anthracene, 3-methylcholanthrene, naphthalene, chrysene, phenanthrene, benzo[a]anthracene, benzo[k]fluoranthene, and indeno[1,2,3-c,d]pyrene) for 48 h. Gene expression analysis was conducted using a 44K whole human genome microarray (Agilent Technologies, USA).

2012-04-17 | E-GEOD-37326 | biostudies-arrayexpress

Polycyclic aromatic hydrocarbons-Polluted Soil

Project description:Polycyclic aromatic hydrocarbons-Polluted Soil Metagenome

| PRJNA656884 | ENA

Zirconacyclopentadiene-Annulated Polycyclic Aromatic Hydrocarbons.

Project description:Syntheses of large polycyclic aromatic hydrocarbons (PAHs) and graphene nanostructures demand methods that are capable of selectively and efficiently fusing large numbers of aromatic rings, yet such methods remain scarce. Herein, we report a new approach that is based on the quantitative intramolecular reductive cyclization of an oligo(diyne) with a low-valent zirconocene reagent, which gives a PAH with one or more annulated zirconacyclopentadienes (ZrPAHs). The efficiency of this process is demonstrated by a high-yielding fivefold intramolecular coupling to form a helical ZrPAH with 16?fused rings (from a precursor with no fused rings). Several other PAH topologies are also reported. Protodemetalation of the ZrPAHs allowed full characterization (including by X-ray crystallography) of PAHs containing one or more appended dienes with the ortho-quinodimethane (o-QDM) structure, which are usually too reactive for isolation and are potentially valuable for the fusion of additional rings by Diels-Alder reactions.

| S-EPMC5671771 | biostudies-literature

Extended O-Doped Polycyclic Aromatic Hydrocarbons.

Project description:The synthesis of O-doped benzorylenes, in which peripheral carbon atoms have been replaced by oxygen atoms, has been achieved for the first time. This includes key high-yielding ring-closure steps which, through intramolecular C-O bond formation, allow stepwise planarization of oligonaphthalenes. Single-crystal X-ray diffraction showed that the tetraoxa derivative forms remarkable face-to-face ?-? stacks in the solid state, a favorable solid-state arrangement for organic electronics.

| S-EPMC5071652 | biostudies-literature

Enhanced degradation of polycyclic aromatic hydrocarbons by indigenous microbes combined with chemical oxidation.

Project description:In this study, the removal efficiency PAHs by chemical oxidation combined with microbe remediation was evaluated in two contaminated soils. The number of indigenous soil microbes decreased after the addition of chemical oxidants and then increased by nutrients addition. The total removal efficiencies of PAHs by chemical oxidation and nutrient addition followed the order: activated persulfate > potassium permanganate > modified Fenton reagent > Fenton reagent. There are 24.29-27.97%, 22.00-23.67%, 10.24-13.74% and 1.9-2.5% contributions separately due to nutrient treatment in Fenton, modified Fenton, activated persulfate and potassium permanganate treatment, which show significantly difference. The different chemical oxidants exhibited 78-90% removal efficiency for 5-6 rings PAHs, while 52-85% removal efficiency for 2-4 rings PAHs. With the addition of nutrients, the growth of indigenous microbes was enhanced significantly, and the contents of 2-4 rings PAHs in the soil were further decreased. Furthermore, the removal efficiencies of NAP and ANY were increased by more than 45%, while the removal efficiencies of ANE, FLE and PHE were about 30% at Fenton system. There was a complementary enhancing effect of microbial remediation for PAHs degradation after chemical oxidation.

| S-EPMC6775777 | biostudies-literature

Classifying polycyclic aromatic hydrocarbons by carcinogenic potency using in vitro biosignatures

Project description:In this study, we compare genomic signature safter treatment ofprimary human bronchial epithelial cells (HBEC) cultured in 3D with polycyclic aromatic hydrocarbons (PAHs) and identify genesets predictive of cancer risk.

2020-10-28 | GSE156147 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data