Stress-induced changes in the Schizosaccharomyces pombe proteome using two-dimensional difference gel electrophoresis, mass spectrometry and a novel integrated robotics platform

Robotic and manual methods have been used to obtain identification of significantly changing proteins regulated when Schizosaccharomyces pombe is exposed to oxidative stress. Differently treated S. pombe cells were lysed, labelled with CyDye (TM) and analysed by two-dimensional difference gel. electrophoresis. Gel images analysed off-line, using the DeCyder (TM) image analysis software [GE Healthcare, Amersham, UK] allowed selection of significantly regulated proteins. Proteins displaying differential expression were excised robotically for manual digestion and identified by matrix-assisted laser desorption/ionisation - mass spectrometry (MALDI-MS). Additionally the same set of proteins displaying differential expression were automatically cut and digested using a prototype robotic platform. Automated MALDI-MS, peak label assignment and database searching were utilised to identify as many proteins as possible. The results achieved by the robotic system were compared to manual methods. The identification of all significantly altered proteins provides an annotated peroxide stress-related proteome that can be used as a base resource against which other stress-induced proteomic changes can be compared.

Towards dynamical system models of language-related brain potentials

Event-related brain potentials (ERP) are important neural correlates of cognitive processes. In the domain of language processing, the N400 and P600 reflect lexical-semantic integration and syntactic processing problems, respectively. We suggest an interpretation of these markers in terms of dynamical system theory and present two nonlinear dynamical models for syntactic computations where different processing strategies correspond to functionally different regions in the system's phase space.

A numerical scheme for two-dimensional, open channel flows with non-rectangular geometries

An algorithm based on flux difference splitting is presented for the solution of two-dimensional, open channel flows. A transformation maps a non-rectangular, physical domain into a rectangular one. The governing equations are then the shallow water equations, including terms of slope and friction, in a generalized coordinate system. A regular mesh on a rectangular computational domain can then be employed. The resulting scheme has good jump capturing properties and the advantage of using boundary/body-fitted meshes. The scheme is applied to a problem of flow in a river whose geometry induces a region of supercritical flow.

Extensivity of two-dimensional turbulence

This study is concerned with how the attractor dimension of the two-dimensional Navier–Stokes equations depends on characteristic length scales, including the system integral length scale, the forcing length scale, and the dissipation length scale. Upper bounds on the attractor dimension derived by Constantin, Foias and Temam are analysed. It is shown that the optimal attractor-dimension estimate grows linearly with the domain area (suggestive of extensive chaos), for a sufficiently large domain, if the kinematic viscosity and the amplitude and length scale of the forcing are held fixed. For sufficiently small domain area, a slightly “super-extensive” estimate becomes optimal. In the extensive regime, the attractor-dimension estimate is given by the ratio of the domain area to the square of the dissipation length scale defined, on physical grounds, in terms of the average rate of shear. This dissipation length scale (which is not necessarily the scale at which the energy or enstrophy dissipation takes place) can be identified with the dimension correlation length scale, the square of which is interpreted, according to the concept of extensive chaos, as the area of a subsystem with one degree of freedom. Furthermore, these length scales can be identified with a “minimum length scale” of the flow, which is rigorously deduced from the concept of determining nodes.

Wave-breaking characteristics of Northern Hemisphere winter blocking: a two-dimensional approach

This paper generalises and applies recently developed blocking diagnostics in a two- dimensional latitude-longitude context, which takes into consideration both mid- and high-latitude blocking. These diagnostics identify characteristics of the associated wave-breaking as seen in the potential temperature (θ) on the dynamical tropopause, in particular the cyclonic or anticyclonic Direction of wave-Breaking (DB index), and the Relative Intensity (RI index) of the air masses that contribute to blocking formation. The methodology is extended to a 2-D domain and a cluster technique is deployed to classify mid- and high-latitude blocking according to the wave-breaking characteristics. Mid-latitude blocking is observed over Europe and Asia, where the meridional gradient of θ is generally weak, whereas high-latitude blocking is mainly present over the oceans, to the north of the jet-stream, where the meridional gradient of θ is much stronger. They occur respectively on the equatorward and poleward flank of the jet- stream, where the horizontal shear ∂u/∂y is positive in the first case and negative in the second case. A regional analysis is also conducted. It is found that cold-anticyclonic and cyclonic blocking divert the storm-track respectively to the south and to the north over the East Atlantic and western Europe. Furthermore, warm-cyclonic blocking over the Pacific and cold-anticyclonic blocking over Europe are identified as the most persistent types and are associated with large amplitude anomalies in temperature and precipitation. Finally, the high-latitude, cyclonic events seem to correlate well with low- frequency modes of variability over the Pacific and Atlantic Ocean.

Bubbling transition to spatial mode excitation in an extended dynamical system

We investigated the transition to spatio-temporal chaos in spatially extended nonlinear dynamical systems possessing an invariant subspace with a low-dimensional attractor. When the latter is chaotic and the subspace is transversely stable we have a spatially homogeneous state only. The onset of spatio-temporal chaos, i.e. the excitation of spatially inhomogeneous modes, occur through the loss of transversal stability of some unstable periodic orbit embedded in the chaotic attractor lying in the invariant subspace. This is a bubbling transition, since there is a switching between spatially homogeneous and nonhomogeneous states with statistical properties of on-off intermittency. Hence the onset of spatio-temporal chaos depends critically both on the existence of a chaotic attractor in the invariant subspace and its being transversely stable or unstable. (C) 2008 Elsevier B.V. All rights reserved.

In-depth search focused on furans, lactones, volatile phenols, and acetals as potential age markers of Madeira wines by comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry combined with solid phase microextraction

The establishment of potential age markers of Madeira wine is of paramount significance as it may contribute to detect frauds and to ensure the authenticity of wine. Considering the chemical groups of furans, lactones, volatile phenols, and acetals, 103 volatile compounds were tentatively identified; among these, 71 have been reported for the first time in Madeira wines. The chemical groups that could be used as potential age markers were predominantly acetals, namely, diethoxymethane, 1,1-diethoxyethane, 1,1-diethoxy-2-methyl-propane, 1-(1-ethoxyethoxy)-pentane, trans-dioxane and 2-propyl-1,3-dioxolane, and from the other chemical groups, 5-methylfurfural and cis-oak-lactone, independently of the variety and the type of wine. GC × GC-ToFMS system offers a more useful approach to identify these compounds compared to previous studies using GC−qMS, due to the orthogonal systems, that reduce coelution, increase peak capacity and mass selectivity, contributing to the establishment of new potential Madeira wine age markers. Remarkable results were also obtained in terms of compound identification based on the organized structure of the peaks of structurally related compounds in the GC × GC peak apex plots. This information represents a valuable approach for future studies, as the ordered-structure principle can considerably help the establishment of the composition of samples. This new approach provides data that can be extended to determine age markers of other types of wines.

Two-dimensional position-dependent massive particles in the presence of magnetic fields

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Non-Zeeman splitting for a spin-resolved STM with a Kondo adatom in a spin-polarized two-dimensional electron gas

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Comparison of Single-Standing or Connected Implants on Stress Distribution in Bone of Mandibular Overdentures: A Two-Dimensional Finite Element Analysis

This study aimed to compare the influence of single-standing or connected implants on stress distribution in bone of mandibular overdentures by means of two-dimensional finite element analysis. Two finite element models were designed using software (ANSYS) for 2 situations: bar-clip (BC) group-model of an edentulous mandible supporting an overdenture over 2 connected implants with BC system, and o'ring (OR) group-model of an edentulous mandible supporting an overdenture over 2 single-standing implants with OR abutments. Axial loads (100 N) were applied on either central (L1) or lateral (L2) regions of the models. Stress distribution was concentrated mostly in the cortical bone surrounding the implants. When comparing the groups, BC (L1, 52.0 MPa and L2, 74.2 MPa) showed lower first principal stress values on supporting tissue than OR (L1, 78.4 MPa and L2, 76.7 MPa). Connected implants with BC attachment were more favorable on stress distribution over peri-implant-supporting tissue for both loading conditions.

Implant Platform Switching: Biomechanical Approach Using Two-Dimensional Finite Element Analysis

In implant therapy, a peri-implant bone resorption has been noticed mainly in the first year after prosthesis insertion. This bone remodeling can sometimes jeopardize the outcome of the treatment, especially in areas in which short implants are used and also in aesthetic cases. To avoid this occurrence, the use of platform switching (PS) has been used. This study aimed to evaluate the biomechanical concept of PS with relation to stress distribution using two-dimensional finite element analysis. A regular matching diameter connection of abutment-implant (regular platform group [RPG]) and a PS connection (PS group [PSG]) were simulated by 2 two-dimensional finite element models that reproduced a 2-piece implant system with peri-implant bone tissue. A regular implant (prosthetic platform of 4.1 mm) and a wide implant (prosthetic platform of 5.0 mm) were used to represent the RPG and PSG, respectively, in which a regular prosthetic component of 4.1 mm was connected to represent the crown. A load of 100 N was applied on the models using ANSYS software. The RPG spreads the stress over a wider area in the peri-implant bone tissue (159 MPa) and the implant (1610 MPa), whereas the PSG seems to diminish the stress distribution on bone tissue (34 MPa) and implant (649 MPa). Within the limitation of the study, the PS presented better biomechanical behavior in relation to stress distribution on the implant but especially in the bone tissue (80% less). However, in the crown and retention screw, an increase in stress concentration was observed.

Mixing-demixing transition and collapse of a vortex state in a quasi-two-dimensional boson-fermion mixture

We investigate the mixing-demixing transition and the collapse in a quasi-two-dimensional degenerate boson-fermion mixture (DBFM) with a bosonic vortex. We solve numerically a quantum-hydrodynamic model based on a new density functional which accurately takes into account the dimensional crossover. It is demonstrated that with the increase of interspecies repulsion, a mixed state of DBFM could turn into a demixed state. The system collapses for interspecies attraction above a critical value which depends on the vortex quantum number. For interspecies attraction just below this critical limit there is almost complete mixing of boson and fermion components. Such mixed and demixed states of a DBFM could be experimentally realized by varying an external magnetic field near a boson-fermion Feshbach resonance, which will result in a continuous variation of interspecies interaction.

Two-dimensional background field gravity: A Hamilton-Jacobi analysis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Suppressing Fermi acceleration in a two-dimensional non-integrable time-dependent oval-shaped billiard with inelastic collisions

Some dynamical properties of a classical particle confined inside a closed region with an oval-shaped boundary are studied. We have considered both the static and time-dependent boundaries. For the static case, the condition that destroys the invariant spanning curves in the phase space was obtained. For the time-dependent perturbation, two situations were considered: (i) non-dissipative and (ii) dissipative. For the non-dissipative case, our results show that Fermi acceleration is observed. When dissipation, via inelastic collisions, is introduced Fermi acceleration is suppressed. The behaviour of the average velocity for both the dissipative as well as the non-dissipative dynamics is described using the scaling approach. (C) 2009 Elsevier B.V. All rights reserved.

THE EFFECT of WEAK DISSIPATION IN TWO-DIMENSIONAL MAPPING

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)