Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria.

Uranium is a naturally occurring radionuclide. Its redistribution, primarily due to human activities, can have adverse effects on human and non-human biota, which poses environmental concerns. The molecular mechanisms of uranium tolerance and the cellular response induced by uranium exposure in bacteria are not yet fully understood.

Melting transition of oriented Li-DNA fibers submerged in ethanol solutions.

The melting transition of Li-DNA fibers immersed in ethanol-water solutions has been studied using calorimetry and neutron diffraction techniques. The data have been analyzed using the Peyrard-Bishop-Dauxois model to determine the strengths of the intra- and inter-base pair potentials. The data and analysis show that the potentials are weaker than those for DNA in water.

Thermodynamics of force-induced B-DNA melting: Single-strand discreteness matters.

Overstretching of B-DNA is currently understood as force-induced melting. Depending on the geometry of the stretching experiment, the force threshold for the overstretching transition is around 65 or 110 pN. Although the mechanisms behind force-induced melting have been correctly described by Rouzina and Bloomfield [Biophys.

Melting Transition of Oriented DNA Fibers Submerged in Poly(ethylene glycol) Solutions Studied by Neutron Scattering and Calorimetry.

The influence of molecular confinement on the melting transition of oriented Na-DNA fibers submerged in poly(ethylene glycol) (PEG) solutions has been studied. The PEG solution exerts an osmotic pressure on the fibers which, in turn, is related to the DNA intermolecular distance. Calorimetry measurements show that the melting temperature increases and the width of the transition decreases with decreasing intermolecular distance.

Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes.

Agricultural productivity relies on a wide range of ecosystem services provided by the soil biota. Plowing is a fundamental component of conventional farming, but long-term detrimental effects such as soil erosion and loss of soil organic matter have been recognized. Moving towards more sustainable management practices such as reduced tillage or crop residue retention can reduce these detrimental effects, but will also influence structure and function of the soil microbiota with direct consequences for the associated ecosystem services.

Soil prokaryotic communities in Chernobyl waste disposal trench T22 are modulated by organic matter and radionuclide contamination.

After the Chernobyl nuclear power plant accident in 1986, contaminated soils, vegetation from the Red Forest and other radioactive debris were buried within trenches. In this area, trench T22 has long been a pilot site for the study of radionuclide migration in soil. Here, we used 454 pyrosequencing of 16S rRNA genes to obtain a comprehensive view of the bacterial and archaeal diversity in soils collected inside and in the vicinity of the trench T22 and to investigate the impact of radioactive waste disposal on prokaryotic communities.

Use of combined microscopic and spectroscopic techniques to reveal interactions between uranium and Microbacterium sp. A9, a strain isolated from the Chernobyl exclusion zone.

Although uranium (U) is naturally found in the environment, soil remediation programs will become increasingly important in light of certain human activities. This work aimed to identify U(VI) detoxification mechanisms employed by a bacteria strain isolated from a Chernobyl soil sample, and to distinguish its active from passive mechanisms of interaction. The ability of the Microbacterium sp.

Characterization of PPMUCL1/2/3, three members of a new oomycete-specific mucin-like protein family residing in Phytophthora parasitica biofilm.

The plant pathogen Phytophthora parasitica forms a biofilm on the host surface. The biofilm transcriptome is characterized by the expression of PPMUCL1/2/3 (PHYTOPHTHORA PARASITICA MUCIN-LIKE) genes, which we report here to be members of a new, large mucin-like gene family restricted to the oomycete lineage. These genes encode secreted proteins organized into two domains.

Temperature dependence of the DNA double helix at the nanoscale: structure, elasticity, and fluctuations.

Biological organisms exist over a broad temperature range of -15°C to +120°C, where many molecular processes involving DNA depend on the nanoscale properties of the double helix. Here, we present results of extensive molecular dynamics simulations of DNA oligomers at different temperatures. We show that internal basepair conformations are strongly temperature-dependent, particularly in the stretch and opening degrees of freedom whose harmonic fluctuations can be considered the initial steps of the DNA melting pathway.

Exploration of Deinococcus-Thermus molecular diversity by novel group-specific PCR primers.

The deeply branching Deinococcus-Thermus lineage is recognized as one of the most extremophilic phylum of bacteria. In previous studies, the presence of Deinococcus-related bacteria in the hot arid Tunisian desert of Tataouine was demonstrated through combined molecular and culture-based approaches. Similarly, Thermus-related bacteria have been detected in Tunisian geothermal springs.

Base pair openings and temperature dependence of DNA flexibility.

The relationship of base pair openings to DNA flexibility is examined. Published experimental data on the temperature dependence of the persistence length by two different groups are well described in terms of an inhomogeneous Kratky-Porot model with soft and hard joints, corresponding to open and closed base pairs, and sequence-dependent statistical information about the state of each pair provided by a Peyrard-Bishop-Dauxois (PBD) model calculation with no freely adjustable parameters.

Structural correlations and melting of B-DNA fibers.

Despite numerous attempts, understanding the thermal denaturation of DNA is still a challenge due to the lack of structural data on the transition since standard experimental approaches to DNA melting are made in solution and do not provide spatial information. We report a measurement using neutron scattering from oriented DNA fibers to determine the size of the regions that stay in the double-helix conformation as the melting temperature is approached from below. A Bragg peak from the B form of DNA is observed as a function of temperature and its width and integrated intensity are measured.

Thermal denaturation of DNA studied with neutron scattering.

The melting transition of DNA, whereby the strands of the double-helix structure completely separate at a certain temperature, has been characterized using neutron scattering. A Bragg peak from B-form fiber DNA has been measured as a function of temperature, and its widths and integrated intensities have been interpreted using the Peyrard-Bishop-Dauxois model with only one free parameter. The experiment is unique, as it gives spatial correlation along the molecule through the melting transition where other techniques cannot.

Melting of genomic DNA: Predictive modeling by nonlinear lattice dynamics.

The melting behavior of long, heterogeneous DNA chains is examined within the framework of the nonlinear lattice dynamics based Peyrard-Bishop-Dauxois (PBD) model. Data for the pBR322 plasmid and the complete T7 phage have been used to obtain model fits and determine parameter dependence on salt content. Melting curves predicted for the complete fd phage and the Y1 and Y2 fragments of the ϕX174 phage without any adjustable parameters are in good agreement with experiment.

DNA denaturation bubbles at criticality.

The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of nonlinear base-stacking interactions. Small bubbles extending over fewer than ten base pairs are associated with much larger free energies of formation per site than larger bubbles.

Modeling DNA beacons at the mesoscopic scale.

We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer models; alternative calculations performed using the freely rotating chain and the discrete Kratky-Porod models are reported.

Nonlinear structures and thermodynamic instabilities in a one-dimensional lattice system.

The equilibrium states of the discrete Peyrard-Bishop Hamiltonian with one end fixed are computed exactly from the two-dimensional nonlinear Morse map. These exact nonlinear structures are interpreted as domain walls, interpolating between bound and unbound segments of the chain. Their free energy is calculated to leading order beyond the Gaussian approximation.

Thermal denaturation of a helicoidal DNA model.

We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e., the separation of the two strands upon heating.

Thermodynamic instabilities in one-dimensional particle lattices: a finite-size scaling approach.

One-dimensional thermodynamic instabilities are phase transitions, not prohibited by Landau's argument because the energy of the domain wall which separates the two phases is infinite. Whether they actually occur in a given system of particles must be demonstrated on a case-by-case basis by examining the properties of the corresponding singular transfer integral (TI) equation. The present work deals with the generic Peyrard-Bishop model of DNA denaturation.

Order of the phase transition in models of DNA thermal denaturation.

We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness parameter, it is shown to have either (i) a second-order transition with nu( perpendicular) = -beta = 1,nu(||) = gamma/2 = 2 (characteristic of short-range attractive part of the Morse potential) or (ii) a first-order transition with finite melting entropy, discontinuous fraction of bound pairs, divergent correlation lengths, and critical exponents nu( perpendicular) = -beta = 1/2,nu(||) = gamma/2 = 1.

Biomonitoring human exposure to environmental carcinogenic chemicals.

A coordinated study was carried out on the development, evaluation and application of biomonitoring procedures for populations exposed to environmental genotoxic pollutants. The procedures used involved both direct measurement of DNA or protein damage (adducts) and assessment of second biological effects (mutation and cytogenetic damage). Adduct detection at the level of DNA or protein (haemoglobin) was carried out by 32P-postlabelling, immunochemical, HPLC or mass spectrometric methods.