Stochastic Ratchet Mechanisms for Replacement of Proteins Bound to DNA

Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multi-step replacement of DNA-bound proteins by solution-phase proteins. For four different kinetic scenarios we calculate the depen- dence of protein unbinding and replacement rates on solution protein concentration. We find (1) strong effects of progressive 'rezipping' of the solution-phase protein onto DNA sites liberated by 'unzipping' of the originally bound protein; (2) that a model in which solution-phase proteins bind non-specifically to DNA can describe experiments on exchanges between the non specific DNA- binding proteins Fis-Fis and Fis-HU; (3) that a binding specific model describes experiments on the exchange of CueR proteins on specific binding sites.Comment: \`a paraitre en PHys. Rev. Lett. june 201

Thermodynamics of beta-amyloid fibril formation

Amyloid fibers are aggregates of proteins. They are built out of a peptide called $\beta$--amyloid (A$\beta$) containing between 41 and 43 residues, produced by the action of an enzyme which cleaves a much larger protein known as the Amyloid Precursor Protein (APP). X-ray diffraction experiments have shown that these fibrils are rich in $\beta$--structures, whereas the shape of the peptide displays an $\alpha$--helix structure within the APP in its biologically active conformation. A realistic model of fibril formation is developed based on the seventeen residues A$\beta$12--28 amyloid peptide, which has been shown to form fibrils structurally similar to those of the whole A$\beta$ peptide. With the help of physical arguments and in keeping with experimental findings, the A$\beta$12--28 monomer is assumed to be in four possible states (i.e., native helix conformation, $\beta$--hairpin, globular low--energy state and unfolded state). Making use of these monomeric states, oligomers (dimers, tertramers and octamers) were constructed. With the help of short, detailed Molecular Dynamics (MD) calculations of the three monomers and of a variety of oligomers, energies for these structures were obtained. Making use of these results within the framework of a simple yet realistic model to describe the entropic terms associated with the variety of amyloid conformations, a phase diagram can be calculated of the whole many--body system, leading to a thermodynamical picture in overall agreement with the experimental findings. In particular, the existence of micellar metastable states seem to be a key issue to determine the thermodynamical properties of the system

Understanding the determinants of stability and folding of small globular proteins from their energetics

The results of minimal model calculations suggest that the stability and the kinetic accessibility of the native state of small globular proteins are controlled by few "hot" sites. By mean of molecular dynamics simulations around the native conformation, which simulate the protein and the surrounding solvent at full--atom level, we generate an energetic map of the equilibrium state of the protein and simplify it with an Eigenvalue decomposition. The components of the Eigenvector associated with the lowest Eigenvalue indicate which are the "hot" sites responsible for the stability and for the fast folding of the protein. Comparison of these predictions with the results of mutatgenesis experiments, performed for five small proteins, provide an excellent agreement

Fine frequency shift of sigle vortex entrance and exit in superconducting loops

The heat capacity $C_{p}$ of an array of independent aluminum rings has been measured under an external magnetic field $\vec{H}$ using highly sensitive ac-calorimetry based on a silicon membrane sensor. Each superconducting vortex entrance induces a phase transition and a heat capacity jump and hence $C_{p}$ oscillates with $\vec{H}$. This oscillatory and non-stationary behaviour measured versus the magnetic field has been studied using the Wigner-Ville distribution (a time-frequency representation). It is found that the periodicity of the heat capacity oscillations varies significantly with the magnetic field; the evolution of the period also depends on the sweeping direction of the field. This can be attributed to a different behavior between expulsion and penetration of vortices into the rings. A variation of more than 15% of the periodicity of the heat capacity jumps is observed as the magnetic field is varied. A description of this phenomenon is given using an analytical solution of the Ginzburg-Landau equations of superconductivity

Model adaptation enriched with an anisotropic mesh spacing for nonlinear equations: application to environmental and CFD problems

Goal of this paper is to suitably combine a model with an anisotropic mesh adaptation for the numerical simulation of nonlinear advection-diffusion-reaction systems and incompressible flows in ecological and environmental applications. Using the reduced-basis method terminology, the proposed approach leads to a noticeable computational saving of the online phase with respect to the resolution of the reference model on nonadapted grids. The search of a suitable adapted model/mesh pair is to be meant, instead, in an offline fashion

Tadalafil modulates aromatase activity and androgen receptor expression in a human osteoblastic cell in vitro model

Purpose Phosphodiesterase type-5 inhibitor (PDE5i) tadalafil administration in men with erectile dysfunction is associated with increased testosterone/estradiol ratio, leading to hypothesize a potential increased effect of androgen action on target tissues. We aimed to characterize, in a cellular model system in vitro, the potential modulation of aromatase and sex steroid hormone receptors upon exposure to tadalafil (TAD). Methods Human osteoblast-like cells SAOS-2 were chosen as an in vitro model system since osteoblasts are target of steroid hormones. Cells were tested for viability upon TAD exposure, which increased cell proliferation. Then, cells were treated with/without TAD for several times to evaluate potential modulation in PDE5, aromatase (ARO), androgen (AR) and estrogen (ER) receptor expression. Results Osteoblasts express significant levels of both PDE5 mRNA and protein. Exposure of cells to increasing concentrations of TAD (10−8–10−7 M) decreased PDE5 mRNA and protein expression. Also, TAD inhibited ARO mRNA and protein expression leading to an increase in testosterone levels in the supernatants. Interestingly, TAD increased total AR mRNA and protein expression and decreased ERα, with an increased ratio of AR/ER, suggesting preferential androgenic vs estrogenic pathway activation. Conclusions Our results demonstrate for the first time that TAD decreases ARO expression and increases AR protein expression in human SAOS-2, strongly suggesting a new control of steroid hormones pathway by PDE5i. These findings might represent the first evidence of translational actions of PDE5i on AR, which leads to hypothesize a growing relevance of this molecule in men with prostate cancer long-term treated with TAD for sexual rehabilitation. Keywords Tadalafil · Osteoblasts · Aromatase · Androgen receptor · Estrogen recepto

A characterization of four B16 murine melanoma cell sublines molecular fingerprint and proliferation behavior

Background: One of the most popular and versatile model of murine melanoma is by inoculating B16 cells in the syngeneic C57BL6J mouse strain. A characterization of different B16 modified cell sub-lines will be of real practical interest. For this aim, modern analytical tools like surface enhanced Raman spectroscopy/scattering (SERS) and MTT were employed to characterize both chemical composition and proliferation behavior of the selected cells. Methods: High quality SERS signal was recorded from each of the four types of B16 cell sub-lines: B164A5, B16GMCSF, B16FLT3, B16F10, in order to observe the differences between a parent cell line (B164A5) and other derived B16 cell sub-lines. Cells were incubated with silver nanoparticles of 50–100 nm diameter and the nanoparticles uptake inside the cells cytoplasm was proved by transmission electron microscopy (TEM) investigations. In order to characterize proliferation, growth curves of the four B16 cell lines, using different cell numbers and FCS concentration were obtained employing the MTT proliferation assay. For correlations doubling time were calculated. Results: SERS bands allowed the identification inside the cells of the main bio-molecular components such as: proteins, nucleic acids, and lipids. An "on and off" SERS effect was constantly present, which may be explained in terms of the employed laser power, as well as the possible different orientations of the adsorbed species in the cells in respect to the Ag nanoparticles. MTT results showed that among the four tested cell sub-lines B16 F10 is the most proliferative and B164A5 has the lower growth capacity. Regarding B16FLT3 cells and B16GMCSF cells, they present proliferation ability in between with slight slower potency for B16GMCSF cells. Conclusion: Molecular fingerprint and proliferation behavior of four B16 melanoma cell sub-lines were elucidated by associating SERS investigations with MTT proliferation assay

Development and reproduction of Cataclysta lemnata, a potential natural enemy of the invasive alien duckweed Lemna minuta in Italy

Life cycle of the aquatic moth Cataclysta lemnata (Lepidoptera: Crambidae) was studied in laboratory conditions to obtain a basic biological knowledge useful for predicting the possible success of the herbivorous larvae of this insect as potential control agents in limiting the spread of the invasive American duckweed Lemna minuta (Alismatales: Araceae) in Italy. The multivoltinism of C. lemnata, as well as the high overall emergence from the pupal stage (85%), the high success in mating among the formed couples (>90%), and the high number of larvae born from each egg laying (on average 310 individuals), suggest that the insect can be successfully bred in the laboratory for the purposes of an augmentative biological control. Under experimental conditions, larvae developed in 23 days (through six larval instars, distinguishable by cephalic capsule dimensions) and pupae in 10, with no difference in duration between females and males. The larval phase resulted longer than the adult one (23 vs 10 days), therefore it can be considered the most suitable stage for releasing the insect in field for biocontrol purposes. Indeed, the larvae having a herbivorous diet might consume large amount of the invasive plant, contrarily to the adult phase which is focused exclusively on reproduction. The results emerged not only allow to contribute to the knowledge on aquatic lepidoptera that are scarcely known, but also support the effectiveness of a possible protocol for an augmentative biological control of the invasive alien duckweed L. minuta