Prefazione al volume CIBB2015 edito da springer

Free-living bacteria grown under aerobic conditions were used to investigate, by next-generation RNA sequencing analysis, the transcriptional profiles of Sinorhizobium meliloti wild-type 1021 and its derivative, RD64, overproducing the main auxin indole-3-acetic acid (IAA). Among the upregulated genes in RD64 cells, we detected the main nitrogen-fixation regulator fixJ, the two intermediate regulators fixK and nifA, and several other genes known to be FixJ targets. The gene coding for the sigma factor RpoH1 and other genes involved in stress response, regulated in a RpoH1-dependent manner in S. meliloti, were also induced in RD64 cells. Under microaerobic condition, quantitative real-time polymerase chain reaction analysis revealed that the genes fixJL and nifA were up-regulated in RD64 cells as compared with 1021 cells. This work provided evidence that the overexpression of IAA in S. meliloti free-living cells induced many of the transcriptional changes that normally occur in nitrogen-fixing root nodule.

questa presentazione rivisiteremo il concetto di interazione geneambiente alla luce delle conoscenze scientifiche emergenti e dell'utilizzo delle tecnologie ad alta risoluzione, quali i moderni sequenziatori. In particolare, illustreremo l'importanza della stima di tale interazione per la comprensione delle patologie complesse. Quindi, forniremo una panoramica dei metodi esistenti per l'analisi di dati di NGS con particolare enfasi riguardo l'individuazione di varianti genomiche ed l'analisi dell'epigenomica e della trascrittomica. Infine, discuteremo come i dati multiomici possono essere utilizzati per migliorare in nostro grado di comprensione delle patologie e fornire nuove prospettive di ricerca In this talk, first, we review the concept of gene-environmental interaction on the light of emerging results and the use of modern high-throughput technologies; we illustrate its impact on the understanding of complex human diseases. Then, we provide an overview of the methods available to process NGS data with particular emphasis to the detection of genomic variants, the analysis of epigenomic and transcriptional data produced by modern sequencers. Finally, we discuss how multiomic data can be used to improve our way of studying complex diseases and can provide novel research perspectives.

Mass spectrometry is a set of technologies with many applications in characterizing biological samples. Due to the huge quantity of data, often biased and contaminated by different source of errors, and the amount of results that is possible to extract, an easy-to-learn and complete workflow is essential. GeenaR is a robust web tool for pre-processing, analysing, visualizing and comparing a set of MALDI-ToF mass spectra. It combines PHP, Perl and R languages and allows different levels of control over the parameters, in order to adapt the work to the needs and expertise of the users.

Vesicles are involved in a vast variety of transport processes in living organisms. Additionally, they serve as a model for the dynamics of cell suspensions. Predicting the rheological properties of their suspensions is still an open question, as even the interaction of pairs is yet to be fully understood. Here we analyse the effect of a single vesicle, undergoing tank-treading motion, on its surrounding shear flow by studying the induced disturbance field delta(V) over right arrow, the difference between the velocity field in its presence and absence. The comparison between experiments and numerical simulations reveals an impressive agreement. Tracking ridges in the disturbance field magnitude landscape, we identify the principal directions along which the velocity difference field is analysed in the vesicle vicinity. The disturbance magnitude is found to be significant up to about 4 vesicle radii and can be described by a power law decay with the distance d from the vesicle parallel to delta(V) over right arrow parallel to proportional to d(-3/2). This is consistent with previous experimental results on the separation distance between two interacting vesicles under similar conditions, for which their dynamics is altered. This is an indication of vesicles long-range effect via the disturbance field and calls for the proper incorporation of long-range hydrodynamic interactions when attempting to derive rheological properties of vesicle suspensions. Copyright (C) EPLA, 2016

A deep understanding of the dynamics and rheology of suspensions of vesicles, cells, and capsules is relevant for different applications, ranging from soft glasses to blood flow [1]. I will present the study of suspensions of fluid vesicles by a combination of molecular dynamics and mesoscale hydrodynamics simulations (multi-particle collision dynamics) in two dimensions [2], pointing out the big potential of the numerical method to address problems in soft matter. The flow behavior is studied as a function of the shear rate, the volume fraction of vesicles, and the viscosity ratio between inside and outside fluids. Results are obtained for the interactions of two vesicles, the intrinsic viscosity of the suspension, and the cell-free layer near the walls [3-4]. [1] D. Barthes-Biesel, Annu. Rev. Fluid Mech. 48, 25 (2016) [2] R. Finken, A. Lamura, U. Seifert, and G. Gompper, Eur. Phys. J. E 25, 309 (2008) [3] A. Lamura and G. Gompper, EPL 102, 28004 (2013) [4] A. Lamura and G. Gompper, Procedia IUTAM 16, 3 (2015)

We investigate front propagation in systems with diffusive and subdiffusive behavior. The scaling behavior of moments of the diffusive problem, both in the standard and in the anomalous cases, is not enough to determine the features of the reactive front. In fact, the shape of the bulk of the probability distribution of the transport process, which determines the diffusive properties, is important just for preasymptotic behavior of front propagation, while the precise shape of the tails of the probability distribution determines asymptotic behavior of front propagation.

The development of high-efficiency porous catalyst membranes critically depends on our understanding of where the majority of the chemical conversions occur within the porous structure. This requires mapping of chemical reactions and mass transport inside the complex nanoscale architecture of porous catalyst membranes which is a multiscale problem in both the temporal and spatial domains. To address this problem, we developed a multiscale mass transport computational framework based on the lattice Boltzmann method that allows us to account for catalytic reactions at the gas-solid interface by introducing a new boundary condition. In good agreement with experiments, the simulations reveal that most catalytic reactions occur near the gas-flow facing side of the catalyst membrane if chemical reactions are fast compared to mass transport within the porous catalyst membrane.

We study a nonlinear boundary value problem involving a nonlocal (integral) operator in the coefficients of the unknown function. Provided sufficient conditions for the existence and uniqueness of the solution, for its approximation, we propose a numerical method consisting of a classical discretization of the problem and an algorithm to solve the resulting nonlocal and nonlinear algebraic system by means of some iterative procedures. The second order of convergence is assured by different sufficient conditions, which can be alternatively used in dependence on the given data. The theoretical results are confirmed by several numerical tests. (C) 2015 Elsevier B.V. All rights reserved.

For the effective operation of sonar systems mounted inside the bulb of fast ships, it is important to reduce all the possible noise and vibration sources that radiate noise and interfere with sonar sensor response. In particular, pressure fluctuations induced by turbulent boundary layers on the sonar dome surface represent the major source of self-noise for on-board sensors. Reliable calculations of structural vibrations and noise radiated inside the dome require valid statistical descriptions of wall pressure fluctuations beneath the turbulent boundary layer. Previous research about wall pressure fluctuations deals with equilibrium turbulent boundary layers on flat plates in zero pressure gradient flow, for which scaling laws for power spectral densities and empirical models for the cross spectral densities are well established. On the contrary, turbulent boundary layers on bulbous bow exhibit the combined effects of three-dimensionality, streamline and spanwise curvatures and pressure gradients. In order to collect information about realistic configurations, wall pressure fluctuations were measured in an experimental campaign performed in a towing tank; data were collected at two different locations along a large scale model of a ship bulb and their spectral characteristics were investigated in terms of auto and cross spectral densities. Mean flow parameters of the boundary layer, required in the analysis, were obtained by a finite volume code that solves the Reynolds Averaged Navier Stokes Equations. The applicability of classical scaling laws for pressure spectra on zero pressure gradient flat plate was investigated, together with the spatial characterization of the wall pressure fluctuations in the space-frequency domain; parameters of some semi-empirical models available in the scientific literature were tuned to fit the measured pressure field.

Abstract

Systems and synthetic biology for health

Immunosenescence is thought to result from cellular aging and to reflect exposure to environmental stressors and antigens, including cytomegalovirus (CMV). However, not all of the features of immunosenescence are consistent with this view, and this has led to the emergence of the sister theory of "inflammaging". The recently discovered diffuse tissue distribution of resident memory T cells (TRM) which don't recirculate, calls these theories into question. These cells account for most T cells residing in barrier epithelia which sit in and travel through the extracellular matrix (ECM). With almost all studies to date carried out on peripheral blood, the age-related changes of the ECM and their consequences for T cell mobility, which is crucial for the function of these cells, have been largely ignored. We propose an update of the theoretical framework of immunosenescence, based on a novel hypothesis: the increasing stiffness and cross-linking of the senescent ECM lead to a progressive immunodeficiency due to an age-related decrease in T cell mobility and eventually the death of these cells. A key element of this mechanism is the mechanical stress to which the cell cytoplasm and nucleus are subjected during passage through the ECM. This hypothesis is based on an "evo-devo" perspective bringing together some major characteristics of aging, to create a single interpretive framework for immunosenescence.

In this paper we consider drug binding in the arterialwall following delivery by a drug-eluting stent. Whilst it is now generally accepted that a non-linear saturable reversible binding model is required to properly describe the binding process, the precise form of the binding model varies between authors. Our particular interest in this manuscript is in assessing to what extent modelling specific and non-specific binding in the arterial wall as separate phases is important. We study this issue by extending a recently developed coupled model of drug release and arterial tissue distribution, and comparing simulated profiles of drug concentration and drug mass in each phase within the arterial tissue.

We present a method for applying a class of velocity-dependent forces within a multicomponent lattice Boltzmann equation simulation that is designed to recover continuum regime incompressible hydrodynamics. This method is applied to the problem, in two dimensions, of constraining to uniformity the tangential velocity of a vesicle membrane implemented within a recent multicomponent lattice Boltzmann simulation method, which avoids the use of Lagrangian boundary tracers. The constraint of uniform tangential velocity is carried by an additional contribution to an immersed boundary force, which we derive here from physical arguments. The result of this enhanced immersed boundary force is to apply a physically appropriate boundary condition at the interface between separated lattice fluids, defined as that region over which the phase-field varies most rapidly. Data from this enhanced vesicle boundary method are in agreement with other data obtained using related methods [e.g., T. Kruger, S. Frijters, F. Gunther, B. Kaoui, and J. Harting, Eur. Phys. J. 222, 177 (2013)] and underscore the importance of a correct vesicle membrane condition.

Nowadays, several models of unidimensional fluid jets exploit discrete element methods. In some cases, as for models aiming at describing the electrospinning nanofabrication process of polymer fibers, discrete element methods suffer a non-constant resolution of the jet representation. We develop a dynamic mesh- refinement method for the numerical study of the electro-hydrodynamic behavior of charged jets using discrete element methods. To this purpose, we import ideas and techniques from the string method originally developed in the framework of free-energy landscape simulations. The mesh-refined discrete element method is demonstrated for the case of electrospinning applications.

Classical as well as quantum features of the late-time evolution of cosmological models with fluids obeying a Shan-Chen-like equation of state are studied. The latter is of the type p=weff(?)? and has been used in previous works to describe, e.g., a possible scenario for the growth of the dark-energy content of the present Universe. At the classical level, the fluid dynamics in a spatially flat Friedmann-Robertson-Walker background implies the existence of two possible equilibrium solutions depending on the model parameters associated with (asymptotic) finite pressure and energy density. We show that no future cosmological singularity is developed during the evolution for this specific model. The corresponding quantum effects in the late-time behavior of the system are also investigated within the framework of quantum geometrodynamics, i.e., by solving the (minisuperspace) Wheeler-DeWitt equation in the Born-Oppenheimer approximation, constructing wave packets and analyzing their behavior.

We analytically compute, through the six-and-a-half post-Newtonian order, the second-order-in-eccentricity piece of the Detweiler-Barack-Sago gauge-invariant redshift function for a small mass in eccentric orbit around a Schwarzschild black hole. Using the first law of mechanics for eccentric orbits [A. Le Tiec, First law of mechanics for compact binaries on eccentric orbits, Phys. Rev. D 92, 084021 (2015).] we transcribe our result into a correspondingly accurate knowledge of the second radial potential of the effective-one-body formalism [A. Buonanno and T. Damour, Effective one-body approach to general relativistic two-body dynamics, Phys. Rev. D 59, 084006 (1999).]. We compare our newly acquired analytical information to several different numerical self-force data and find good agreement, within estimated error bars. We also obtain, for the first time, independent analytical checks of the recently derived, comparable-mass fourth-post-Newtonian order dynamics [T. Damour, P. Jaranowski, and G. Schaefer, Nonlocal-in-time action for the fourth post-Newtonian conservative dynamics of two-body systems, Phys. Rev. D 89, 064058 (2014).].

We raise the analytical knowledge of the eccentricity expansion of the Detweiler-Barack-Sago redshift invariant in a Schwarzschild spacetime up to the 9.5th post-Newtonian order (included) for the e(2) and e(4) contributions, and up to the 4th post-Newtonian order for the higher eccentricity contributions through e(20). We convert this information into an analytical knowledge of the effective-one-body radial potentials (d) over bar (u), p(u) and q(u) through the 9.5th post-Newtonian order. We find that our analytical results are compatible with current corresponding numerical self-force data.

Popular models of fast radio bursts (FRBs) involve the gravitational collapse of neutron star progenitors to black holes. It has been proposed that the shedding of the strong neutron star magnetic field (B) during the collapse is the power source for the radio emission. Previously, these models have utilized the simplicity of the Schwarzschild metric which has the restriction that the magnetic flux is magnetic 'hair' that must be shed before final collapse. But neutron stars have angular momentum and charge and a fully relativistic Kerr-Newman solution exists in which B has its source inside of the event horizon. In this Letter, we consider the magnetic flux to be shed as a consequence of the electric discharge of a metastable collapsed state of a Kerr-Newman black hole. It has also been argued that the shedding model will not operate due to pair creation. By considering the pulsar death line, we find that for a neutron star with B = 10(11)-10(13) G and a long rotation period, >1s this is not a concern. We also discuss the observational evidence supporting the plausibility of magnetic flux shedding models of FRBs that are spawned from rapidly rotating progenitors.