Reconstruction of Transcription Control Networks in Mollicutes by High-Throughput Identification of Promoters

Bacteria of the class Mollicutes have significantly reduced genomes and gene expression control systems. They are also efficient pathogens that can colonize a broad range of hosts including plants and animals. Despite their simplicity, Mollicutes demonstrate complex transcriptional responses to various conditions, which contradicts their reduction in gene expression regulation mechanisms. We analyzed the conservation and distribution of transcription regulators across the 50 Mollicutes species. The majority of the transcription factors regulate transport and metabolism, and there are four transcription factors that demonstrate significant conservation across the analyzed bacteria. These factors include repressors of chaperone HrcA, cell cycle regulator MraZ and two regulators with unclear function from the WhiA and YebC/PmpR families. We then used three representative species of the major clades of Mollicutes (Acholeplasma laidlawii, Spiroplasma melliferum and Mycoplasma gallisepticum) to perform promoters mapping and activity quantitation. We revealed that Mollicutes evolved towards a promoter architecture simplification that correlates with a diminishing role of transcription regulation and an increase in transcriptional noise. Using the identified operons structure and a comparative genomics approach, we reconstructed the transcription control networks for these three species. The organization of the networks reflects the adaptation of bacteria to specific conditions and hosts

Photons Probe Entropic Potential Variation during Molecular Confinement in Nanocavities

In thin polymeric layers, external molecular analytes may well be confined within tiny surface nano/microcavities, or they may be attached to ligand adhesion binding sites via electrical dipole forces. Even though molecular trapping is followed by a variation of the entropic potential, the experimental evidence of entropic energy variation from molecular confinement is scarce because tiny thermodynamic energy density diverseness can be tracked only by sub-nm surface strain. Here, it is shown that water confinement within photon-induced nanocavities in Poly (2-hydroxyethyl methacrylate), (PHEMA) layers could be trailed by an entropic potential variation that competes with a thermodynamic potential from electric dipole attachment of molecular adsorbates in polymeric ligands. The nano/microcavities and the ligands were fabricated on a PHEMA matrix by vacuum ultraviolet laser photons at 157 nm. The entropic energy variation during confinement of water analytes on the photon processed PHEMA layer was monitored via sub-nm surface strain by applying white light reflectance spectroscopy, nanoindentation, contact angle measurements, Atomic Force Microscopy (AFM) imaging, and surface and fractal analysis. The methodology has the potency to identify entropic energy density variations less than 1 pJm−3 and to monitor dipole and entropic fields on biosurfaces

The Cyanotoxin BMAA Induces Heterocyst Specific Gene Expression in <i>Anabaena</i> sp. PCC 7120 under Repressive Conditions

Cyanobacteria synthesize neurotoxic &#946;-N-methylamino-l-alanine (BMAA). The roles of this non-protein amino acid in cyanobacterial cells are insufficiently studied. During diazotrophic growth, filamentous cyanobacteria form single differentiated cells, called heterocysts, which are separated by approximately 12&#8315;15 vegetative cells. When combined nitrogen is available, heterocyst formation is blocked and cyanobacterial filaments contain only vegetative cells. In the present study, we discovered that exogenous BMAA induces the process of heterocyst formation in filamentous cyanobacteria under nitrogen-replete conditions that normally repress cell differentiation. BMAA treated cyanobacteria form heterocyst-like dark non-fluorescent non-functional cells. It was found that glutamate eliminates the BMAA mediated derepression. Quantitative polymerase chain reaction (qPCR) permitted to detect the BMAA impact on the transcriptional activity of several genes that are implicated in nitrogen assimilation and heterocyst formation in Anabaena sp. PCC 7120. We demonstrated that the expression of several essential genes increases in the BMAA presence under repressive conditions

Tiny Rare-Earth Fluoride Nanoparticles Activate Tumour Cell Growth via Electrical Polar Interactions

Abstract Localised extracellular interactions between nanoparticles and transmembrane signal receptors may well activate cancer cell growth. Herein, tiny LaF3 and PrF3 nanoparticles in DMEM+FBS suspensions stimulated tumour cell growth in three different human cell lines (A549, SW837 and MCF7). Size distribution of nanoparticles, activation of AKT and ERK signalling pathways and viability tests pointed to mechanical stimulation of ligand adhesion binding sites of integrins and EGFR via a synergistic action of an ensemble of tiny size nanoparticles (< 10 nm). While tiny size nanoparticles may be well associated with the activation of EGFR, integrin interplay with nanoparticles remains a multifaceted issue. A theoretical motif shows that, within the requisite pN force scale, each ligand adhesion binding site can be activated by a tiny size dielectric nanoparticle via electrical dipole interaction. The size of the active nanoparticle stayed specified by the amount of the surface charges on the ligand adhesion binding site and the nanoparticle, and also by the separating distance between them. The polar component of the electrical dipole force remained inversely proportional to the second power of nanoparticle’s size, evincing that only tiny size dielectric nanoparticles might stimulate cancer cell growth via electrical dipole interactions. The work contributes towards recognising different cytoskeletal stressing modes of cancer cells

Optical Properties of LiGdF₄ Single Crystal in the Terahertz and Infrared Ranges

The basic mechanisms of absorption of THz range radiation in optically perfect LiGdF4 single crystals were studied using the broadband experimental data and the dielectric response function analysis within the harmonic oscillator model. The polarized IR reflection spectra have allowed one to determine the phonon contribution in the absorption coefficient in the THz range, while transmission spectra in the THz range were used to obtain the birefringence value and the effects of various mulitparticle processes. Additionally, we established the optical and electrodynamic parameters of the LiGdF4 single crystal, which are necessary for the design of nonlinear optical devices

Physical Background for Luminescence Thermometry Sensors Based on Pr3+:LaF3 Crystalline Particles

The main goal of this study was creating multifunctional nanoparticles based on rare-earth doped LaF3 nanocrystals, which can be used as fluorescence thermal sensors operating over the 80–320 K temperature range including physiological temperature range (10–50°C). The Pr3+:LaF3 (CPr = 1%) microcrystalline powder and the Pr3+:LaF3 (CPr = 12%, 20%) nanoparticles were studied. It was proved that all the samples were capable of thermal sensing into the temperature range from 80 to 320 K. It was revealed that the mechanisms of temperature sensitivity for the microcrystalline powder and the nanoparticles are different. In the powder, the 3P1 and 3P0 states of Pr3+ ion share their electronic populations according to the Boltzmann and thermalization of the 3P1 state takes place. In the nanoparticles, two temperature dependent mechanisms were suggested: energy migration within 3P0 state in the temperature range from 80 K to 200 K followed by quenching of 3P0 state by OH groups at higher temperatures. The values of the relative sensitivities for the Pr3+:LaF3 (CPr = 1%) microcrystalline powder and the Pr3+:LaF3 (CPr = 12%, 20%) nanoparticles into the physiological temperature range (at 45°C) were 1, 0.5, and 0.3% °C−1, respectively

Coprecipitation Method of Synthesis, Characterization, and Cytotoxicity of Pr 3+

The Pr3+:LaF3 (CPr = 3, 7, 12, 20, 30%) nanoparticles were characterized by means of high-resolution transmission electron microscopy, X-ray diffraction, optical spectroscopy, energy dispersive X-ray spectroscopy, dynamic light scattering, and MTT assay. It was revealed that the average diameter of all the NPs is around 14–18 nm. The hydrodynamic radius of the Pr3+:LaF3 (CPr = 7%) nanoparticles strongly depends on the medium. It was revealed that hydrodynamic radii of the Pr3+:LaF3 (CPr = 7%) nanoparticles in water, DMEM, and RPMI-1640 biological mediums were 18 ± 5, 41 ± 6, and 186 ± 8 nm, respectively. The Pr3+:LaF3 (CPr = 7%) nanoparticles were nontoxic at micromolar concentrations toward COLO-320 cell line. The lifetime curves were fitted biexponentially, and for the Pr3+:LaF3 (CPr = 7%) NPs, the luminescence lifetimes of Pr3+ ions were 480 ± 2 and 53 ± 5 nanosec

Draft genome of the nitrogen-fixing bacterium Pseudomonas stutzeri strain KOS6 isolated from industrial hydrocarbon sludge

© 2013 Grigoryeva et al. Here we present a draft genome of Pseudomonas stutzeri strain KOS6. This strain was isolated from industrial hydrocarbon sludge as a diazotrophic microorganism. It represents one of the major parts of the culturable community of the waste and has potential importance for phytoremediation technology.Ministry of Science and Education of the Russian Federatio