Browse
Submit Data
Databases
API
Help

Dataset Information

7 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Influence of Bacterial Physiology on Processing of Selenite, Biogenesis of Nanomaterials and Their Thermodynamic Stability.

ABSTRACT: We explored how Ochrobactrum sp. MPV1 can convert up to 2.5 mM selenite within 120 h, surviving the challenge posed by high oxyanion concentrations. The data show that thiol-based biotic chemical reaction(s) occur upon bacterial exposure to low selenite concentrations, whereas enzymatic systems account for oxyanion removal when 2 mM oxyanion is exceeded. The selenite bioprocessing produces selenium nanomaterials, whose size and morphology depend on the bacterial physiology. Selenium nanoparticles were always produced by MPV1 cells, featuring an average diameter ranging between 90 and 140 nm, which we conclude constitutes the thermodynamic stability range for these nanostructures. Alternatively, selenium nanorods were observed for bacterial cells exposed to high selenite concentration or under controlled metabolism. Biogenic nanomaterials were enclosed by an organic material in part composed of amphiphilic biomolecules, which could form nanosized structures independently. Bacterial physiology influences the surface charge characterizing the organic material, suggesting its diverse biomolecular composition and its involvement in the tuning of the nanomaterial morphology. Finally, the organic material is in thermodynamic equilibrium with nanomaterials and responsible for their electrosteric stabilization, as changes in the temperature slightly influence the stability of biogenic compared to chemogenic nanomaterials.

SUBMITTER: Piacenza E

PROVIDER: S-EPMC6681009 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Relationship between digital information and thermodynamic stability in bacterial genomes.

Project description:Ever since the introduction of the Watson-Crick model, numerous efforts have been made to fully characterize the digital information content of the DNA. However, it became increasingly evident that variations of DNA configuration also provide an "analog" type of information related to the physicochemical properties of the DNA, such as thermodynamic stability and supercoiling. Hence, the parallel investigation of the digital information contained in the base sequence with associated analog parameters is very important for understanding the coding capacity of the DNA. In this paper, we represented analog information by its thermodynamic stability and compare it with digital information using Shannon and Gibbs entropy measures on the complete genome sequences of several bacteria, including Escherichia coli (E. coli), Bacillus subtilis (B. subtilis), Streptomyces coelicolor (S. coelicolor), and Salmonella typhimurium (S. typhimurium). Furthermore, the link to the broader classes of functional gene groups (anabolic and catabolic) is examined. Obtained results demonstrate the couplings between thermodynamic stability and digital sequence organization in the bacterial genomes. In addition, our data suggest a determinative role of the genome-wide distribution of DNA thermodynamic stability in the spatial organization of functional gene groups.

| S-EPMC4740571 | biostudies-literature

Synthetic Biogenesis of Bacterial Amyloid Nanomaterials with Tunable Inorganic-Organic Interfaces and Electrical Conductivity.

Project description:Amyloids are highly ordered, hierarchal protein nanoassemblies. Functional amyloids in bacterial biofilms, such as Escherichia coli curli fibers, are formed by the polymerization of monomeric proteins secreted into the extracellular space. Curli is synthesized by living cells, is primarily composed of the major curlin subunit CsgA, and forms biological nanofibers with high aspect ratios. Here, we explore the application of curli fibers for nanotechnology by engineering curli to mediate tunable biological interfaces with inorganic materials and to controllably form gold nanoparticles and gold nanowires. Specifically, we used cell-synthesized curli fibers as templates for nucleating and growing gold nanoparticles and showed that nanoparticle size could be modulated as a function of curli fiber gold-binding affinity. Furthermore, we demonstrated that gold nanoparticles can be preseeded onto curli fibers and followed by gold enhancement to form nanowires. Using these two approaches, we created artificial cellular systems that integrate inorganic-organic materials to achieve tunable electrical conductivity. We envision that cell-synthesized amyloid nanofibers will be useful for interfacing abiotic and biotic systems to create living functional materials..

| S-EPMC6422533 | biostudies-literature

Influence of 5-N-carboxamide modifications on the thermodynamic stability of oligonucleotides.

Project description:We have recently shown that the incorporation of modified nucleotides such as 5-N-carboxamide-deoxyuridines into random nucleic acid libraries improves success rates in SELEX experiments and facilitates the identification of ligands with slow off-rates. Here we report the impact of these modifications on the thermodynamic stability of both duplexes and intramolecular 'single-stranded' structures. Within duplexes, large, hydrophobic naphthyl groups were destabilizing relative to the all natural DNA duplex, while the hydrophilic groups exhibited somewhat improved duplex stability. All of the significant changes in stability were driven by opposing contributions from the enthalpic and entropic terms. In contrast, both benzyl and naphthyl modifications stabilized intramolecular single-stranded structures relative to their natural DNA analogs, consistent with the notion that intramolecular folding allows formation of novel, stabilizing hydrophobic interactions. Imino proton NMR data provided evidence that elements of the folded structure form at temperatures well below the Tm, with a melting transition that is distinctly less cooperative when compared to duplex DNA. Although there are no data to suggest that the unmodified DNA sequences fold into structures similar to their modified analogs, this still represents clear evidence that these modifications impart thermodynamic stability to the folded structure not achievable with unmodified DNA.

| S-EPMC4627095 | biostudies-literature

Widespread Influence of 3′-end Structures on Mammalian mRNA Processing and Stability

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-03-12 | GSE95468 | GEO

Beyond the Nanomaterials Approach: Influence of Culture Conditions on the Stability and Antimicrobial Activity of Silver Nanoparticles.

Project description:Silver nanoparticles (AgNPs) as antimicrobial agents have been extensively studied. It is generally assumed that their inhibitory activity heavily depends on their physicochemical features. Yet, other parameters may affect the AgNP traits and activity, such as culture medium composition, pH, and temperature, among others. In this work, we evaluated the effect of the culture medium physicochemical traits on both the stability and antibacterial activity of AgNPs. We found that culture media impact the physicochemical traits of AgNPs, such as hydrodynamic size, surface charge, aggregation, and the availability of ionic silver release rate. As a consequence, culture media play a major role in AgNP stability and antimicrobial potency. The AgNP minimal inhibitory concentration (MIC) values changed up to 2 orders of magnitude by the influence of culture media alone when single-stock AgNPs were tested on the same strain of Escherichia coli. Furthermore, a meta-analysis of the AgNP MIC values confirms that the "chemical complexity" of culture media influences the AgNP activity. Studies that address only the antimicrobial activities of nanoparticles on common bacterial models should be performed by standardized susceptibility assays, thus generating replicable, comparable reports regarding the antimicrobial potency of nanomaterials.

| S-EPMC7658933 | biostudies-literature

Widespread Influence of 3'-End Structures on Mammalian mRNA Processing and Stability.

Project description:The physiological relevance of structures within mammalian mRNAs has been elusive, as these mRNAs are less folded in cells than in vitro and have predicted secondary structures no more stable than those of random sequences. Here, we investigate the possibility that mRNA structures facilitate the 3'-end processing of thousands of human mRNAs by juxtaposing poly(A) signals (PASs) and cleavage sites that are otherwise too far apart. We find that RNA structures are predicted to be more prevalent within these extended 3'-end regions than within PAS-upstream regions and indeed are substantially more folded within cells, as determined by intracellular probing. Analyses of thousands of ectopically expressed variants demonstrate that this folding both enhances processing and increases mRNA metabolic stability. Even folds with predicted stabilities resembling those of random sequences can enhance processing. Structure-controlled processing can also regulate neighboring gene expression. Thus, RNA structure has widespread roles in mammalian mRNA biogenesis and metabolism.

| S-EPMC5546744 | biostudies-literature

Thermodynamic Stability of Fenclorim and Clopyralid.

Project description:The present work reports an experimental thermodynamic study of two nitrogen heterocyclic organic compounds, fenclorim and clopyralid, that have been used as herbicides. The sublimation vapor pressures of fenclorim (4,6-dichloro-2-phenylpyrimidine) and of clopyralid (3,6-dichloro-2-pyridinecarboxylic acid) were measured, at different temperatures, using a Knudsen mass-loss effusion technique. The vapor pressures of both crystalline and liquid (including supercooled liquid) phases of fenclorim were also determined using a static method based on capacitance diaphragm manometers. The experimental results enabled accurate determination of the standard molar enthalpies, entropies and Gibbs energies of sublimation for both compounds and of vaporization for fenclorim, allowing a phase diagram representation of the (p,T) results, in the neighborhood of the triple point of this compound. The temperatures and molar enthalpies of fusion of the two compounds studied were determined using differential scanning calorimetry. The standard isobaric molar heat capacities of the two crystalline compounds were determined at 298.15 K, using drop calorimetry. The gas phase thermodynamic properties of the two compounds were estimated through ab initio calculations, at the G3(MP2)//B3LYP level, and their thermodynamic stability was evaluated in the gaseous and crystalline phases, considering the calculated values of the standard Gibbs energies of formation, at 298.15 K. All these data, together with other physical and chemical properties, will be useful to predict the mobility and environmental distribution of these two compounds.

| S-EPMC8746602 | biostudies-literature

Widespread Influence of 3′-end Structures on Mammalian mRNA Processing and Stability [Artificial-3'-end]

Project description:Understanding the physiological relevance of structures in mammalian mRNAs remains elusive, especially considering the global unfolding of mRNA structures in eukaryotic organisms recently examined, as well as the decade-long observation that mRNAs generally seem no more likely than random sequences to be stably folded. Here we show that RNA secondary structures, mostly weak and close-to-random, facilitate the 3′-end processing of thousands of human mRNAs by juxtaposing poly(A) signals (PASs) and cleavage sites that are otherwise too far apart. Folding of these 3′-end structures also enhances mRNA stability. Global structure probing shows that 3′-end regions are indeed folded in cells despite substantial unfolding of PAS-upstream regions. Analyses of thousands of ectopically expressed variants prove that folding both enhances processing and increases stability. Mutagenesis of a genomic locus further implicates structure-controlled processing in regulating neighboring gene expression. These results reveal widespread roles for RNA structure in mammalian mRNA biogenesis and metabolism.

2017-03-12 | GSE95467 | GEO

Widespread Influence of 3′-end Structures on Mammalian mRNA Processing and Stability [DIM-2P-seq]

2017-03-12 | GSE95465 | GEO

Widespread Influence of 3′-end Structures on Mammalian mRNA Processing and Stability [4sU-2P-seq]

2017-03-12 | GSE95464 | GEO