Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Antibiotic Resistance Profile and Genomic Characteristics of Multidrug-Resistant Bacteria from the Sludge of a Pharmaceutical Wastewater Treatment Plant

ABSTRACT: Incomplete antibiotic removal in pharmaceutical wastewater treatment plants (PWWTPs) could lead to the development and spread of antibiotic-resistant bacteria (ARBs) and genes (ARGs) in the environment, posing a growing public health threat. In this study, two multiantibiotic-resistant bacteria, Ochrobactrum intermedium (N1) and Stenotrophomonas acidaminiphila (N2), were isolated from the sludge of a PWWTP in Guangzhou, China. The N1 strain was highly resistant to ampicillin, cefazolin, chloramphenicol, tetracycline, and norfloxacin, while the N2 strain exhibited high resistance to ampicillin, chloramphenicol, and cefazolin. Whole-genome sequencing revealed that N1 and N2 had genome sizes of 0.52 Mb and 0.37 Mb, respectively, and harbored 33 and 24 ARGs, respectively. The main resistance mechanism in the identified ARGs included efflux pumps, enzymatic degradation, and target bypass, with the N1 strain possessing more multidrug-resistant efflux pumps than the N2 strain (22 vs 12). This also accounts for the broader resistance spectrum of N1 than of N2 in antimicrobial susceptibility tests. Additionally, both genomes contain numerous mobile genetic elements (89 and 21 genes, respectively) and virulence factors (276 and 250 factors, respectively), suggesting their potential for horizontal transfer and pathogenicity. Overall, this research provides insights into the potential risks posed by ARBs in pharmaceutical wastewater and emphasizes the need for further studies on their impact and mitigation strategies.

INSTRUMENT(S): Complete Genomics

ORGANISM(S): mixed sample

SUBMITTER: Ningyu Sun

PROVIDER: E-MTAB-14497 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Antibiotic Resistance Profile and Genomic Characteristics of Multidrug-Resistant Bacteria from the Sludge of a Pharmaceutical Wastewater Treatment Plant

Project description:In this study, two multiantibiotic-resistant bacteria, Ochrobactrum intermedium (N1) and Stenotrophomonas acidaminiphila (N2), were isolated from the sludge of a PWWTP in Guangzhou, China. Whole-genome sequencing revealed that N1 and N2 had genome sizes of 0.52 Mb and 0.37 Mb, respectively, and harbored 33 and 24 ARGs, respectively. The main resistance mechanism in the identified ARGs included efflux pumps, enzymatic degradation, and target bypass, with the N1 strain possessing more multidrug-resistant efflux pumps than the N2 strain (22 vs 12). This also accounts for the broader resistance spectrum of N1 than of N2 in antimicrobial susceptibility tests. Additionally, both genomes contain numerous mobile genetic elements (89 and 21 genes, respectively) and virulence factors (276 and 250 factors, respectively), suggesting their potential for horizontal transfer and pathogenicity.

2024-10-20 | E-MTAB-14496 | biostudies-arrayexpress

The Effect of Calcium on Activity, Immunogenicity and Efficacy of a Recombinant N1/N2 Neuraminidase Vaccine

Project description:Despite the importance of immunity against neuraminidase (NA), NA content and immunogenicity is neglected in current influenza vaccines. To address this, a novel recombinant N1/N2 NA vaccine (NAV) was developed. Stability assays were used to determine optimal temperature and buffer conditions for vaccine storage. The effect of calcium-related enhancement of NA stability and activity on N1 and N2 immunogenicity and efficacy against viral challenge was assessed. Differences in activity between N1 and N2 and calcium-related activity enhancement did not translate into differences in immunogenicity or efficacy. NAV vaccinated mice showed robust antibody titers against N1 and N2, decreased viral titers, and decreased antiviral and inflammatory responses by transcriptomic analysis.

2021-03-30 | GSE160010 | GEO

Radiogenomics reveals significant correlation between quantitative texture radiomic features of biparametric MRI and hypoxia related gene expression in men with localised prostate cancer

Project description:The aim of this study was to perform the multiscale correlation between quantitative texture features phenotype of pre-biopsy biparametric MRI (bpMRI) and targeted sequence-based RNA expression for hypoxia-related genes. Images from pre-biopsy 3T bpMRI scans in clinically localised prostate cancer (PCa) patients of various risk categories (n=15) were used to extract textural features. The genomic landscape of hypoxia-related genes expression was obtained using post-radical prostatectomy tissue for targeted RNA expression profiling using the TempO-sequence method. The nonparametric Games Howell test was used to correlate the differential expression of the three important hypoxia-related genes with 28 radiomic texture features. Following this, cBioportal was accessed and a gene-oriented query was conducted to extract Oncoprint genomic output graph of the selected hypoxia-related genes from The Cancer Genome Atlas (TCGA). Correlation analysis using Pearson's coefficients calculated against each selected gene profile; survival analysis using Kaplan-Meier estimators were carried out. We found the quantitative bpMR imaging textural features, including histogram and grey level co-occurrence matrix (GLCM), correlated with hypoxia related genes (ANGPTL4, VEGFA, and P4HA1) seen on RNA sequencing using TempO-Seq method. Further radiogenomic analysis, including data accessed on cBioportal genomic database, confirmed that overexpressed hypoxia-related genes significantly correlated with a poor survival outcome, with a median survival of 81.11: 133.00 months in those with and without alterations of genes respectively. In summary, radiomic texture features of bpMRI in localised PCa correlate with the expression of hypoxia-related genes expression in prostate cancer. The expression data analysis showed that hypoxia-related genes are associated with poor survival.

2023-01-29 | E-MTAB-12593 | biostudies-arrayexpress

Genomic Counter-Stress Changes Induced by Mind-Body Practice

Project description:Mind-body practices that elicit the relaxation response (RR) have been used worldwide for millennia to prevent and treat disease. The RR is believed to be the counterpart to stress response and is characterized by decreased oxygen consumption, increased exhaled nitric oxide, and reduced psychological distress. Individuals experiencing chronic psychological stress have the opposite pattern of physiology and a characteristic transcriptional profile. We hypothesized that consistent, long-term practice of RR techniques results in characteristic changes in gene expression. We tested this hypothesis by assessing the transcriptional profile of whole blood in healthy, long-term practitioners of daily RR practice (group M) in comparison to healthy controls (group N1). The signature obtained has been validated on new subject data. Experiment Overall Design: In the study, the gene expression profiling was performed on individuals with a long-term RR practice (group M; n=19) or those with no prior RR experience; novice (group N1; n=19). Group N1 novices, furthermore, underwent 8-weeks of RR training (Group N2; n=20) for the prospective analysis.As a validation of results , we developed an independent validation sets that includes gene expression profiling on 4 N1, 4 N2 and 6 M subjects.

2008-10-21 | E-GEOD-10041 | biostudies-arrayexpress

RNA-seq of mouse neutrophils polarized to proinflammatory N1 by lipopolysaccharide and interferon-γ or anti-inflammatory N2 by interleukin-4 versus control

Project description:Gene expression profiling for mouse N1 and N2 neutrophils. Neutrphils were isolated form the bone marrow of C57BL/6J mice between 12-16 weeks old. Approximately 8x10^7 neutrophils were used per condition and were split into 3 biological replicates. Freshly isolated neutrophils were cultured for 2h in RPMI medium, in the presence of 100 ng/ml lipopolysaccharide (LPS) and 20 ng/ml interferon gamma (IFNγ) or 20 ng/ml interleukin 4 (IL-4). Total RNA was isolated with TRIzol reagent and Phasemaker tubes. A sample from the LPS+IFNγ polarization did not pass the quality control test and was excluded from the downstream analysis.

2021-07-29 | E-MTAB-10508 | biostudies-arrayexpress

Defining the Roles and Regulation of the GATA-factor ELT-2 in the C. elegans Endoderm

Project description:We identified genome-wide sites of occupancy for the intestine-specific transcription factor ELT-2 in L3-staged N2 worm by performing ELT-2 ChIP-seq on whole worms; we performed RNA-seq on L3-staged N2 whole worms To identify DNA regions of direct ELT-2 occupancy, we performed the following ChIP-seq assays 1) ELT-2 ChIP-seq on L3 staged N2 C. elegans worms; 2) H3K4me3 ChIP-seq on matched L3 staged N2 worms; 3) Mock IgG-only ChIP-seq negative control on L3 stage N2 worms. Input DNA was also sequenced for each replicate. In addition, we performed RNA-seq on two replicates of L3 N2 C. elegans worms.

2016-03-30 | E-GEOD-71720 | biostudies-arrayexpress

10x Single-cell Sequencing for Smad3 wild-type and knockout neutrophils

Project description:The role of neutrophils in tumor is still controversial and largely unknown. We previously identified an anticancer tumor microenvironment from mice lacking Smad3, but the underlying mechanism is still largely unclear. Interestingly, depletion of neutrophils largely suppressed the anticancer phenotype of Smad3-KO mice against syngeneic murine Lewis lung carcinoma (LLC). Here, we discovered that Smad3 is essential for promoting N1/N2 polarization of the tumor_x0002_associated neutrophils (TANs) in lung carcinoma. We found that Smad3 deficiency dramatically increased N1 TANs associated with an anticancer phenotype in mice and detected a negative correlation between Smad3 activation and anticancer N1 associated with a higher mortality of NSCLC. By conducting a neutrophil-specific single-cell RNA-sequencing, we uncovered that Smad3 is essential for completing the N1/N2 polarization of TANs, whereas N1 will be the dominated phenotype in the Smad3-KO TME by analyzing the developmental pathways of TANs with pseudo-time at transcriptome level. Mechanistically, direct binding of Smad3 on the developmental genes in neutrophils under cancer condition was evidenced by ChIP-sequencing at genomic level. Importantly, both neutrophil-specific and pharmaceutical inhibition of Smad3 effectively enhanced the anticancer activity of human and murine TANs, thereby suppressing the progression of lung carcinoma in vivo. Thus, Smad3 may represent a precision therapeutic target for enhancing the anticancer activity of TANs via blocking N1/N2 polarization in NSCLC. in C57BL6 (wild-type) and Smad3-deficient (Smad3-/- ) mice and submitted for cell encapsulation and library construction by Chromium controller with 5’ expression kit (10x genomics)

2023-03-16 | GSE186530 | GEO

Genome-wide comparative analysis of digital gene expression tag profiles during maize ear development

Project description:The present study profiled and analyzed gene expression of the maize ear at four key developmental stages. Based on genome-wide profile analysis, we detected differential mRNA of maize genes. Some of the differentially expressed genes (DEGs) were predicted to be potential candidates of maize ear development. Several well-known genes were found with reported mutants analyses, such as, compact plant2 (ct2), zea AGAMOUS homolog1 (zag1), bearded ear (bde), and silky1 (si1). MicroRNAs such as microRNA156 were predicted to target genes involved in maize ear development. Antisense transcripts were widespread throughout all the four stages, and are suspected to play important roles in maize ear development. Thus, identification and characterization of important genes and regulators at all the four developmental stages will contribute to an improved understanding of the molecular mechanisms responsible for maize ear development. Seeds of the maize inbred line 18-599 (Maize Research Institute, Sichuan Agricultural University, Chengdu, China) were grown in a growth chamber at 24°C/18°C (day/night) with 12 h illumination per day. Ears were collected as described previously [10] at four developmental stages: the growth point elongation, spikelet differentiation, floret primordium differentiation, and the floret organ differentiation phases. In brief, ears were manually collected at the four developmental stages. All the samples were harvested and immediately frozen in liquid nitrogen, and stored at -80°C until used for RNA isolation.

2015-04-30 | E-GEOD-49805 | biostudies-arrayexpress

The IclR-family regulator BapR controls biofilms formation in B. cenocepacia H111

Project description:In Burkholderia cenocepacia H111, the large surface protein BapA plays a crucial role in the formation of highly structured communities, known as biofilms. We have recently demonstrated that Quorum sensing (QS) is necessary for the maximal expression of bapA. In this study we identify a protein from the IclR family of transcriptional regulators that, in conjunction with QS, controls biofilm formation by affecting the expression of bapA. We present evidence that, in addition to BapA, BapR influences the expression of extracellular protease, swimming motility and has a profound impact in the abundance of persister cells, making this regulator an interesting target for persister and biofilm eradication. Identification of a new regulator BapR controlling biofilm formation

2014-03-26 | E-GEOD-52769 | biostudies-arrayexpress

sdg25 and sdg26-Functional characterization of Arabidopsis NAP1/SET genes

Project description:rs05-12_setii - sdg25 and sdg26 - Differential transcriptome in mutant plants - seeds were sown in vitro and plantlets (Col0 wild type ,and n1, n2, n3, x123, sdg8, vip4,sdg25 and sdg26 mutants)were cultivated during 6 days (1.02 boyes stadge) Keywords: gene knock out

2007-07-20 | GSE8429 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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