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The effect of HA on the bacterial toxicity of GNSs

ABSTRACT: Since its discovery in 2004, graphene nanosheets (GNSs) have been extensively studied for their unique properties that enabe multiple applications, including in electronics, catalysis, biomedicine, and environmental fields.The global graphene market is predicted to rise from $620 million in 2020 to $1.48 billion in 2025.3 However, with the increasing production and widespread application of GNSs, there is also an increased likelihood of GNSs-based waste entering the aquatic environment, raising cocners over potential environmental damage.

INSTRUMENT(S): 6520A Quadrupole Time-of-Flight LC/MS

ORGANISM(S): Escherichia Coli

TISSUE(S): Cell Culture, Electrically Active Cell

DISEASE(S): Disease Free

SUBMITTER: jin zeng

LAB HEAD: zeng jin

PROVIDER: PXD043749 | Pride | 2025-05-06

REPOSITORIES: Pride

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Publications

Mechanistic evaluation of enhanced graphene toxicity to Bacillus induced by humic acid adsorption.

Zhang Xuejiao X Zeng Jin J White Jason C JC Li Fangbai F Xiong Zhiqiang Z Zhang Siyu S Xu Yuze Y Yang Jingjing J Tang Weihao W Zhao Qing Q Wu Fengchang F Xing Baoshan B

Nature communications 20250103 1

The extensive application of graphene nanosheets (GNSs) has raised concerns over risks to sensitive species in the aquatic environment. The humic acid (HA) corona is traditionally considered to reduce GNSs toxicity. Here, we evaluate the effect of sorbed HA (GNSs-HA) on the toxicity of GNSs to Gram positive Bacillus tropicus. Contrary to previous data, GNSs-HA exhibits greater toxicity compared to GNSs. Multi-omics combined with sensitive bioassays and electrochemical methods reveals GNSs disrup ...[more]

PMID: 39753547

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The bacterial toxicity effect of HA on graphene

Project description:The bacterial toxicity effect and mechanism of HA on graphene

2025-05-07 | PXD056079 | Pride

RNA-seq of Clostridioides difficile ∆cwp66 mutant against wild-type control

Project description:The experiment intends to reveal the difference in gene expression profiles between the wild-type strain and the ∆cwp66 mutant of Clostridioides difficile. We first constructed the ∆cwp66 mutant, and the phenotypic changes of the ∆cwp66 mutant against the wild-type strain were studied. To further elucidate the mechanism of phenotypic changes of the ∆cwp66 mutant, RNA-sequencing experiments were carried out to reveal the underlying mechanism of phenotypic changes.

2022-03-01 | E-MTAB-11180 | biostudies-arrayexpress

Integrated proteomics and transcriptomics profiling reveals distinct aspects of kidney stone related genes in calculi rats

Project description:We conducted a calculi rat model, applied for an integrated proteomic and transcriptomic analysis to characterize the distinct gene expression profiles in calculi oxalate stone formation and its related kidney injury. Six distinct gene clusters were identified according to the consistency of transcriptome and proteome. Gene Ontology and KEGG pathway enrichment was performed to analyze the functions of each sub-group differentially expressed genes. Results showed that the calculi rat kidney was increased expression of injured & apoptotic markers and immune-molecules, and decreased expression of solute carriers & transporters and many metabolic related factors. The present proteotranscriptomic study provided a data resource and new insights for better understanding of the pathogenesis of nephrolithiasis, will hopefully facilitate the future development of new strategies for the recurrence prevention and treatment in patients with kidney stone disease.

2023-05-10 | PXD039169 | Pride

Extremely low frequency electromagnetic fields enhance neuronal differentiation of human mesenchymal stem cells on graphene-based substrate

Project description:Graphene-based substrate has efficient neuronal differentiation of hMSCs. Stimulatory effects of graphene on hMSCs neurogenesis can be enhanced by ELF-EMF exposure and it is mediated by enhancement of cell adhesion accompanied by intracellular signal pathway. We used microarrays to assess up-regulated genes in human gene expression profiles during neurogenesis induced by ELF-EMF exposure on graphene. 3 groups (HMSCs grown in neuronal medium on glass, graphene, graphene under ELF-EMF exposure) were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain total human gene expression. To that end, we hand-selected up-regulated gene involved in neurogenesis, extracellular matrix, and cell migration.

2014-12-23 | E-GEOD-64416 | biostudies-arrayexpress

Investigating the Regulation of Hypopharyngeal Gland Activity in Honeybees Under Nutrition and Brood Pheromone Conditions through RNA-seq Transcriptomics

Project description:The hypopharyngeal gland (HG) is the main site of the synthesis and secretion of royal jelly protein (RJP), and shows high plasticity. To identify differentially expressed genes (DEGs) that affect the development of HG and the synthesis and secretion of RJP, we performed a digital gene expression analysis of 9 d Apis mellifera under different conditions of nutrition and exposure to brood pheromone.Six RNA-seq libraries were generated using RNA extracted from 9 d bee HGs. A total of 2801 DEGs were identified on the basis of at least one pairwise comparison, among which 205, 1617 and 2328 genes were differentially expressed in comparisons between the Pollen group and the Honey group, the Brood group and Pollen group and the Brood group and Honey group respectively. The Brood group exhibited the highest number of DEGs, suggesting that brood pheromone plays a key role in the HG ontogeny. A total of 1991 genes were mapped to 129 canonical signaling pathways found in the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the pathways associated with ribosome function and protein processing were significantly enriched. Hypopharyngeal gland mRNA profiles of 9-day old honeybees under three conditions (one control and two treatments) were generated by deep sequencing, in duplicate, using Illumina Hiseq 2500 platform.

2015-08-06 | E-GEOD-71750 | biostudies-arrayexpress

Characterization of clumpy adhesion of Escherichia coli to human cells and associated factors influencing antibiotic sensitivity

Project description:Escherichia coli intestinal infection pathotypes are characterized by distinct adhesion patterns including the recently described clumpy adhesion phenotype. Here we identify and characterize genetic factors contributing to clumpy adhesion of E. coli strain 4972. In this strain, the transcriptome and proteome of adhered bacteria were found distinct from planktonic bacteria in supernatant. A total of 622 genes in the transcriptome were differentially expressed in bacteria present in clumps relative to the planktonic bacteria. Seven genes targeted for disruption had variable distribution in different pathotypes and nonpathogenic E. coli with pilV and spnT genes being the least frequent or absent from most groups. Deletion (Δ) of five differentially expressed genes, flgH, ffp, pilV, spnT and yggT affected motility, adhesion or antibiotic stress. ΔflgH exhibited 80 % decrease and ΔyggT depicted 145.5 % increase in adhesion, and upon complementation, adhesion significantly reduced to 13 %. ΔflgH lost motility and was regenerated when complemented whereas Δffp had significantly increased motility and reintroduction of the same gene reduced it to the wild-type level. The clumps produced by of Δffp and ΔspnT were more resistant and protected the bacteria with ΔspnT showing the best clump formation in terms of ampicillin stress protection. ΔyggT had the lowest tolerance to gentamicin where the antibiotic stress completely eliminated the bacteria. Overall, we were able to investigate the influence of clump formation on the cell surface adhesion and antimicrobial tolerance with the contribution of several factors crucial to clump formation on susceptibility to the selected antibiotics.

2024-04-09 | PXD042731 | Pride

E14RNA-seq

Project description:Ctbp2 regulates exit from pluripotency via silencing of embryonic stem cell active genes during differentiation. Gene expression profiles were analyzed for wild-type and Ctbp2-knockdown ESCs at both fferentiated(+LIF) and undifferentiated(-LIF) state.

2014-12-31 | E-MTAB-2030 | biostudies-arrayexpress

EZH2 controls mammary differentiation independently of its methyltransferase activity through controlling genomic STAT5 access

Project description:Mammary development is characterized by the proliferation and progressive differentiation of alveolar epithelium during pregnancy, culminating in lactation. These processes are largely controlled by hormones through transcription factors. We now explore the contributions of histone methyltransferases, which establish H3K27me3 marks, in the temporally-regulated differentiation of mammary epithelium. Loss of EZH2, but not EZH1, resulted in precocious mammary differentiation, which was facilitated by STAT5 binding to specific target genes and their activation. Mammary stem cells were not compromised in the absence of EZH2. Genome-wide H3K27me3 patterns remained intact in the absence of EZH2. Mammary-specific loci were devoid of H3K27me3 marks in mammary progenitor and mature cells, suggesting no regulatory role for this repressive mark. Lastly, the combined absence of EZH1 and EZH2 inhibited the formation of alveoli. Taken together, EZH2 controls temporally-restricted differentiation of mammary epithelium through H3K27me3-independent mechanisms. mRNA-seq and ChIP-seq in MMTV-Cre (Control), E1-/- (E1KO), E1+/-;E2f/f;control (E1+/-E2KO) and Ezh2f/f;control (E2KO) mammary gland tissues or MECs (purified mammary epithelial cells). H3K27me3 and STAT5 ChIP-seqs in mammary tissues at p13; H3K4me3 ChIP-seq in MECs (mammary epithelial cells) at p13; RNA-seqs at mature virgin (with/without prolactin injection), p13 and p18 mammary tissues.

2013-12-31 | E-GEOD-52016 | biostudies-arrayexpress

Exposure of C. elegans to AOBr-containing surface water samples and to a M. aeruginosa batch culture

Project description:Elevated levels of adsorbable organic bromine compounds (AOBr) have been detected in German lakes, and cyanobacteria like Microcystis, which are known for the synthesis of microcystins, are one of the main producers of natural organobromines. However, very little is known about how environmental realistic concentrations of organobromines impact invertebrates. Here, the nematode C. elegans was exposed to AOBr-containing surface water samples and to a Microcystis aeruginosa enriched batch culture (MC-BA) and compared to single organobromines and microcystin-LR exposures. Stimulatory effects were observed in certain life trait variables, which were particularly pronounced in nematodes exposed to MC-BA. A whole genome DNA-microarray revealed that MC-BA led to the differential expression of more than 2000 genes, many of which are known to be involved in metabolic, neurologic, and morphologic processes. Moreover, the up-regulation of cyp- and the down-regulation of abu-genes suggested the presence of chronic stress. However, the nematodes were not marked by negative phenotypic responses. The observed difference in MC-BA and microcystin-LR (which impacted lifespan, growth and reproduction) exposed nematodes was hypothesized to be likely due to other compounds within the batch culture. Most likely the exposure to low concentrations of organobromines appears to buffer the effects of toxic substances, like microcystin-LR. Nematodes were exposed to filtrated samples of Lake Stößensee Berlin (August and October) and compared to the control-group (exposure to water). Furthermore, nematodes were exposed to filtrated M. aeruinosa batch culture samples and compared to another control-group (exposure to Z-Medium). Three samples (biological replicates) were prepared for each group.

2015-05-12 | E-GEOD-68709 | biostudies-arrayexpress

A multi-condition inter-strain transcriptomic compendium identifies phenotypic differences between European and African Salmonella pathovariants (C4PR_LIV)

Project description:Salmonella Typhimurium ST313 is associated with invasive nontyphoidal salmonellosis (iNTS) disease in sub-Saharan Africa. Using ST313 isolate, D23580, and the well-characterized ST19 isolate 4/74, that causes gastroenteritis across Europe, we generated transcriptomic data from sixteen infection-relevant in vitro conditions and during infection of murine macrophages (http://bioinf.gen.tcd.ie/cgi-bin/jay/salcom_v2.pl?db=salcom_africa_new_HL). The transcriptional response of the two S. Typhimurium pathovariants to environmental stress was broadly similar. Comparative gene expression analysis identified virulence and metabolic genes that were up/down-regulated in D23580 versus 4/74. Findings were backed up by proteomic analysis, with12 genes being differentially-expressed at both the transcriptional and protein levels including melA and cysS. The data led us to discover that the ablation of melibiose utilization was caused by 3 SNP mutations in D23580 and to identify a novel plasmid-maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase. Our functional transcriptomic analysis represents a powerful tool for identification of key phenotypic differences between bacterial pathovariants.

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