Extraction methods of red blood cell membrane proteins for Multidimensional Protein Identification Technology (MudPIT) analysis

Since red blood cells (RBCs) lack nuclei and organelles, cell membrane is their main load-bearing component and, according to a dynamic interaction with the cytoskeleton compartment, plays a pivotal role in their functioning. Even if erythrocyte membranes are available in large quantities, the low abundance and the hydrophobic nature of cell membrane proteins complicate their purification and detection by conventional 2D gel-based proteomic approaches. So, in order to increase the efficiency of RBC membrane proteome identification, here we took advantage of a simple and reproducible membrane sub-fractionation method coupled to Multidimensional Protein Identification Technology (MudPIT). In addition, the adoption of a stringent RBC filtration strategy from the whole blood, permitted to remove exhaustively contaminants, such as platelets and white blood cells, and to identify a total of 275 proteins in the three RBC membrane fractions collected and analysed. Finally, by means of software for the elaboration of the great quantity of data obtained and programs for statistical analysis and protein classification, it was possible to determine the validity of the entire system workflow and to assign the proper sub-cellular localization and function for the greatest number of the identified proteins.     

Diverse population-bursting modes of adapting spiking neurons

We study the dynamics of a noisy network of spiking neurons with spike-frequency adaptation (SFA), using a mean-field approach, in terms of a two-dimensional Fokker-Planck equation for the membrane potential of the neurons and the calcium concentration gating SFA. The long time scales of SFA allow us to use an adiabatic approximation and to describe the network as an effective nonlinear two-dimensional system. The phase diagram is computed for varying levels of SFA and synaptic coupling. Two different population-bursting regimes emerge, depending on the level of SFA in networks with noisy emission rate, due to the finite number of neurons.     

Structural-dynamical investigation of the ZnuA histidine-rich loop: involvement in zinc management and transport

Comparative homology modelling techniques have been used to model the protein ZnuA from Salmonella enterica serovar Typhimurium using the 3D structure of the homologous protein from Escherichia coli. These two-domain proteins bind one Zn²⁺ atom, with high affinity, in the inter-domain cleft and possess a histidine-rich loop in the N-terminal domain. Alternative structures of the ZnuA histidine-rich loop, never resolved by the X-ray diffraction method, have been modelled. A model of the apo form, one with the histidine-rich loop deleted and two alternative structures with a second zinc ion bound to the histidine-rich loop, have been generated. In all the modelled proteins, investigated through molecular dynamics simulation, the histidine-rich loop is highly mobile and its fluctuations are correlated to the ligand stability observed in the zinc sites. Based on the plasticity of the histidine-rich loop and its significant effects on protein mobility a possible role in the capture and/or transfer of the zinc ions has been suggested.     

Supramolecular engineering through temperature-induced chemical modification of 2H-tetraphenylporphyrin on Ag(111): flat phenyl conformation and possible dehydrogenation reactions

Scratching the surface: Formation of a monolayer of 2H-tetraphenylporphyrins (2H-TPP) on Ag(111), either by sublimation of a multilayer in the range 525-600?K or by annealing (at the same temperature) a monolayer deposited at room temperature, induces a chemical modification of the molecules. Rotation of the phenyl rings into a flat conformation is observed and tentatively explained, by using DFT calculations, as a peculiar reaction due to molecular dehydrogenation.     

A Chaotic Circuit with Ferroelectric Nonlinearity

In this paper, the possibility of observing strange attractors in an electronic circuit including a nonlinear ferroelectric component has been investigated. The ferroelectric constitutes the medium interposed between the two plates of a capacitor. A circuit including the nonlinearity of the ferroelectric has been designed, while the parameters have been found by performing numerical integration with respect to different values of them. The circuit has been realized on a discrete components board. Experimental results, showing that for a suitable range of parameters a chaotic attractor emerges, are reported.     

Stacking interactions in the acridine dyes: spectrophotometric data and crystal structure of acridine orange hydroiodide and acridine orange hydrochloride monohydrate

The crystal structure of acridine orange hydroiodide and that of acridine orange hydrochloride monohydrate have been solved by X-ray diffraction analysis. The absorption spectra of both derivatives in the solid state have also been reported and compared with those of the acridinium ion in solution. The stacking interactions of the acridine orange molecule in both derivatives is discussed in the light of the visible absorption spectra in the solid state and in solution.     

Separation of human fibrinopeptides by capillary zone electrophoresis

We describe a method for the simultaneous determination of the five fibrinopeptide forms derived from the thrombin-promoted activation of human fibrinogen by capillary zone electrophoresis (CZE). The fibrinopeptide mixture was first desalted by a solid-phase extraction (SPE) step. The analysis was performed in reversed polarity in a highly cross-linked polyethylene glycol (PEG)-coated capillary with UV-light absorption detection at 200 nm. Several parameters including buffer concentration and pH, presence of an organic modifier, temperature, and applied voltage, have been tested. The best separations were obtained within 20 min, utilizing a 20 mM sodium phosphate buffer without organic modifier, in the narrow 6.1-6.2 pH range, at 25 degrees C, with an applied voltage of 20 kV. Quantitative analysis is made possible by the use of sheep fibrinopeptide A as an internal standard to correct for both extraction and injection errors.     

Controlling unpredictability in the randomly driven Hénon–Heiles system

Noisy scattering dynamics in the randomly driven Hénon–Heiles system is investigated in the range of initial energies where the motion is unbounded. In this paper we study, with the help of the exit basins and the escape time distributions, how an external perturbation, be it dissipation or periodic forcing with a random phase, can enhance or mitigate the unpredictability of a system that exhibit chaotic scattering. In fact, if basin boundaries have the Wada property, predictability becomes very complicated, since the basin boundaries start to intermingle, what means that there are points of different basins close to each other. The main responsible of this unpredictability is the external forcing with random phase, while the dissipation can recompose the basin boundaries and turn the system more predictable. Therefore, we do the necessary simulations to find out the values of dissipation and external forcing for which the exit basins present the Wada property. Through these numerical simulations, we show that the presence of the Wada basins have a specific relation with the damping, the forcing amplitude and the energy value. Our approach consists on investigating the dynamics of the system in order to gain knowledge able to control the unpredictability due to the Wada basins.