Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1072831 | ENA |
REPOSITORIES: ENA
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Project description:Protein aggregation in biotherapeutics can reduce their activity and effectiveness. It may also promote immune reactions responsible for severe adverse effects. The impact of plastic materials on protein destabilization is not totally understood. Here, we propose to deconvolve the effects of material surface, air/liquid interface, and agitation to decipher their respective role in protein destabilization and aggregation. We analyzed the effect of polypropylene, Teflon, glass and LoBindTM surfaces on the stability of purified proteins (BSA, hemoglobin and α-synuclein) and on a cell extract composed of 6,000 soluble proteins during agitation (P = 0.1-1.2 W/kg). Proteomic analysis revealed that chaperonins, intrinsically disordered proteins and ribosomes were more sensitive to the combined effect of material surfaces and agitation while small metabolic oligomers could be protected in the same conditions. Protein loss observations coupled to Raman microscopy, dynamic light scattering and proteomics allowed us to propose a mechanistic model of protein destabilization by plastics. Our results suggests that protein loss is not primarily due to the nucleation of small aggregates in solution, but to the destabilization of proteins exposed to material surfaces and their subsequent aggregation at the sheared air/liquid interface, an effect that cannot be prevented by using LoBind tubes. A guidance can be established on how to minimize these adverse effects. Remove one of the components of this combined stress – material, air (even partially), or agitation – and proteins will be preserved.
2023-03-11 | PXD038266 | Pride
Project description:For the studies of cell migration in various micro-environments, self-assembled monolayer surfaces presenting adhesive ligand, RGD peptide, were used for the assay. Presentation of RGD ligands was based on the immobilization reaction with alkanethiols on a gold surface. There were differences in cell morphology and migration according to the ligand affinity (linear vs. cyclic RGD) and manner of ligand presentation (dynamic vs. non-dynamic). In dynamic surface experiment, cells initially grown on the fibronectin-coated patterns were exposed to either linear or cyclic RGD while in non-dynamic surface experiment cells interacted with the immobilized RGD from the beginning. Goal was to compare how the affinity and spatio-temporal exposure of ligand affect the overall transcriptional profiling. Five conditioned surfaces were prepared by chemical treatment for cell culture: Fibronectin, Dynamic linear RGD, Dynamic cyclic RGD, Non-dynamic linear RGD, and Non-dynamic cyclic RGD surfaces. Reference: cells cultured in standard tissue culture flasks. Biological replicates: triplicates for each experiment (each surface was 1.25 cm x 1.25 cm and three surfaces were used for each condition). When reached 70-80% of confluency, cells from the triplicates were pooled and harvested for RNA extraction. Hybridization replicates: 4 replicates for each condition.
2014-10-15 | E-GEOD-62304 | biostudies-arrayexpress
Project description:The long-term resistance to desiccation on abiotic surfaces is a key determinant of the adaptive success of Acinetobacter baumannii as a healthcare-associated bacterial pathogen. Here, the cellular and molecular mechanisms enabling A. baumannii to resist desiccation and persist on abiotic surfaces were investigated. Experiments were set up to mimic the A. baumannii response to air-drying that would occur when bacterial cells contaminate fomites in hospitals. Resistance to desiccation and transition to the “viable but nonculturable” (VBNC) state were determined in the laboratory-adapted strain ATCC 19606T and the epidemic strain ACICU. Culturability, membrane integrity, metabolic activity, virulence, and gene expression profile were compared between the two strains at different stages of desiccation. Upon desiccation, ATCC 19606T and ACICU cells lose culturability and membrane integrity, lower their metabolism, and enter the VBNC state. However, desiccated A. baumannii cells fully recover culturability and virulence in an insect infection model following rehydration in physiological buffers or human biological fluids. Transcriptome and chemical analyses of A. baumannii cells during desiccation unveiled the production of protective metabolites (L-cysteine and L-glutamate) and decreased energetic metabolism consequent to activation of the glyoxylate shunt (GS) pathway, as confirmed by reduced resuscitation efficiency of aceA mutants, lacking the key enzyme of the GS pathway. VBNC cell formation and extensive metabolic reprogramming provide a biological basis for the response of A. baumannii to desiccation, with implications on environmental control measures aimed at preventing the transmission of A. baumannii infection in hospitals.
2024-09-23 | GSE249021 | GEO
Project description:Compensation is a physiological response that occurs during chemical exposure to maintain homeostasis. Because compensatory responses are not usually considered adverse effects, it is important to understand compensatory mechanisms for chemical risk assessment. Although the kidney is a major target organ for toxicity, there is controversy over whether hyperplasia or hypertrophy contributes to the compensatory mechanism, and there is limited information to apply for chemical risk assessment. In the current study, compensatory mechanisms of the kidney were investigated in a unilateral nephrectomy (UNx) model using adult male and female rats. In residual kidneys of male and female rats after UNx, 5-bromo-2'-deoxyuridine-labeling indices and mRNA expression of cell cycle-related genes were increased, although there were no fluctuations in mRNA expression of transforming growth factor-β1, which contributes to hypertrophy in renal tubules. Pathway analysis using mRNA expression data from a cDNA microarray revealed that canonical pathways related to cell proliferation were mainly activated and that forkhead box M1 (FOXM1) was an upstream regulator of compensatory cell proliferation in residual kidneys of male and female rats. cDNA microarray for microRNAs (miRNAs) demonstrated that 9 miRNAs were downregulated in residual kidneys, and mRNA/miRNA integrated analysis indicated that miRNAs were associated with the expression of factors downstream of FOXM1. Overall, these results suggested that FOXM1-mediated hyperplasia rather than hypertrophy contributed to compensatory mechanisms in the kidney and that miRNAs regulated downstream FOXM1 signaling. These results will be beneficial for evaluating nephrotoxicity in chemical risk assessment and for developing new biomarkers to predict nephrotoxicity.
2020-04-01 | GSE144261 | GEO
Project description:Neuronal repair is promoted after a nerve injury by chemical and physical stimuli from their environment. Among them, local adhesion energy gradients generated on surfaces trigger cone formation and neurite outgrowth without any nerve growth factor (NGF) addition. In this study, the molecu- lar mechanisms leading to neuronal differentiation after stimulation via energy gradients are inves- tigated. For this purpose, PC12 cells are cultured on n-[3-(trimethoxysilyl)propyl] ethylendiamine (EDA) and n-hexyl trimethoxysilane (HTMS), two functionalized surfaces possessing local energy gradients but chemically different. These surfaces similarly trigger neurite and growth cone forma- tion after 3 days in culture. The gene expression analysis of a microarray reveals the activation of the PI3/Akt signaling pathway from these surfaces in the same way than NGF does after binding on its TrkA receptor. The biological downstream effectors of this signaling pathway are also upreg- ulated, thereby promoting cell survival, growth cone formation and neurite outgrowth. EDA and HTMS surfaces act as an ongoing stimulus of the TrkA receptor as the addition of 100 nM K252a, its specific inhibitor, leads to the inhibition of neurite growth. Taken together, these results show that functionalized surface with energy surface gradients could be useful to promote nerve repair after an injury.
2022-08-26 | GSE208126 | GEO
Project description:A genomic expression comparison was done among neural progenitor cells cultured on 2D substrates, 3D porous polystyrene scaffolds, and as 3D neural spheres (in vivo surrogate), with the goal of assessing the feasibility of establishing the meaning of 3D and associated physiological relevance at the molecular level Neural progenitor cells were cultured on 2D surfaces, in 3D scaffolds and as 3D neural spheres. Chemical cues are controlled by coating. Only spacial properties of the culture systems were compared.
2009-12-22 | E-GEOD-13715 | biostudies-arrayexpress
Project description:Analytes, from sample preparation, until entering an analytical instrument, are prone to adsorb to surfaces, driven by the chemical properties of the surface and the liquids they are dissolved in. This problem can be addressed with internal standards when a single or few known analytes are quantified that are usually not available in omics. However, minimal to no loss of analytes is the aim. Here, we present a novel assay for qualifying and quantifying interactions responsible for adsorption of molecules to surfaces (APS) by using LC-MS/MS-based differential quantitative analysis. To reflect a broad range of chemical interactions with surfaces, a reference mixture of thousands of tryptic peptides, with known compositions was selected, representing a variety of different chemical characteristics. The assay was tested by investigating the adsorption properties of several different vials with different surface chemistries. A significant number of hydrophobic peptides adsorbed to conventional polypropylene vials. In contrast, only few peptides adsorbed to polypropylene vials, assigned as low-protein-binding. The highest number of peptides adsorbed to glass vials driven by electrostatic interactions. In summary, the new assay is suitable to characterize adsorption properties of different surfaces and to approximate the loss of analytes during sample preparation.
2024-08-30 | PXD044268 | Pride
Project description:This experiment was conducted to study the short-term (12h) transcriptional responses in Daphnia magna after exposure to the anti-sea lice chemical emamectin benzoate (EMB). The microarray results were further vefiried using qPCR. The gene exression responses were linked to adverse effects after 48h exposure, in order to supply knowledge for environmental hazard assessment of this chemical in non-target crustaceans.
2016-06-30 | GSE83859 | GEO
Project description:Genetic polymorphism of Oryzias latipes for chemical substance impact assessment
| PRJDB17117 | ENA