Overproduction, purification and preliminary X-ray diffraction analysis of YncE, an iron-regulated Sec-dependent periplasmic protein from Escherichia coli

The yncE gene of Escherichia coli encodes a predicted periplasmic protein of unknown function. The gene is de-repressed under iron restriction through the action of the global iron regulator Fur. This suggests a role in iron acquisition, which is supported by the presence of the adjacent yncD gene encoding a potential TonB-dependent outer-membrane transporter. Here, the preliminary crystallographic structure of YncE is reported, revealing that it consists of a seven-bladed beta-propeller which resembles the corresponding domain of the `surface-layer protein' of Methanosarcina mazei. A full structure determination is under way in order to provide insight into the function of this protein.

The exclusive use of integer-order spots for LEED-IV structure analysis of adsorption systems: p(2×2)-O on Ni{111}

Two different ways of performing low-energy electron diffraction (LEED) structure determinations for the p(2 x 2) structure of oxygen on Ni {111} are compared: a conventional LEED-IV structure analysis using integer and fractional-order IV-curves collected at normal incidence and an analysis using only integer-order IV-curves collected at three different angles of incidence. A clear discrimination between different adsorption sites can be achieved by the latter approach as well as the first and the best fit structures of both analyses are within each other's error bars (all less than 0.1 angstrom). The conventional analysis is more sensitive to the adsorbate coordinates and lateral parameters of the substrate atoms whereas the integer-order-based analysis is more sensitive to the vertical coordinates of substrate atoms. Adsorbate-related contributions to the intensities of integer-order diffraction spots are independent of the state of long-range order in the adsorbate layer. These results show, therefore, that for lattice-gas disordered adsorbate layers, for which only integer-order spots are observed, similar accuracy and reliability can be achieved as for ordered adsorbate layers, provided the data set is large enough.

Global retrieval of ATSR cloud parameters and evaluation (GRAPE): dataset assessment

The Along-Track Scanning Radiometers (ATSRs) provide a long time-series of measurements suitable for the retrieval of cloud properties. This work evaluates the freely-available Global Retrieval of ATSR Cloud Parameters and Evaluation (GRAPE) dataset (version 3) created from the ATSR-2 (1995�2003) and Advanced ATSR (AATSR; 2002 onwards) records. Users are recommended to consider only retrievals flagged as high-quality, where there is a good consistency between the measurements and the retrieved state (corresponding to about 60% of converged retrievals over sea, and more than 80% over land). Cloud properties are found to be generally free of any significant spurious trends relating to satellite zenith angle. Estimates of the random error on retrieved cloud properties are suggested to be generally appropriate for optically-thick clouds, and up to a factor of two too small for optically-thin cases. The correspondence between ATSR-2 and AATSR cloud properties is high, but a relative calibration difference between the sensors of order 5�10% at 660 nm and 870 nm limits the potential of the current version of the dataset for trend analysis. As ATSR-2 is thought to have the better absolute calibration, the discussion focusses on this portion of the record. Cloud-top heights from GRAPE compare well to ground-based data at four sites, particularly for shallow clouds. Clouds forming in boundary-layer inversions are typically around 1 km too high in GRAPE due to poorly-resolved inversions in the modelled temperature profiles used. Global cloud fields are compared to satellite products derived from the Moderate Resolution Imaging Spectroradiometer (MODIS), Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) measurements, and a climatology of liquid water content derived from satellite microwave radiometers. In all cases the main reasons for differences are linked to differing sensitivity to, and treatment of, multi-layer cloud systems. The correlation coefficient between GRAPE and the two MODIS products considered is generally high (greater than 0.7 for most cloud properties), except for liquid and ice cloud effective radius, which also show biases between the datasets. For liquid clouds, part of the difference is linked to choice of wavelengths used in the retrieval. Total cloud cover is slightly lower in GRAPE (0.64) than the CALIOP dataset (0.66). GRAPE underestimates liquid cloud water path relative to microwave radiometers by up to 100 g m�2 near the Equator and overestimates by around 50 g m�2 in the storm tracks. Finally, potential future improvements to the algorithm are outlined.

Genetic parameters for body weight, carcass chemical composition and yield in a broiler-layer cross developed for QTL mapping

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

Short-term temporal changes of soil carbon losses after tillage described by a first-order decay model

Tillage stimulates soil carbon (C) losses by increasing aeration, changing temperature and moisture conditions, and thus favoring microbial decomposition. In addition, soil aggregate disruption by tillage exposes once protected organic matter to decomposition. We propose a model to explain carbon dioxide (CO2) emission after tillage as a function of the no-till emission plus a correction due to the tillage disturbance. The model assumes that C in the readily decomposable organic matter follows a first-order reaction kinetics equation as: dC(sail)(t)/dt = -kC(soil)(t) and that soil C-CO2 emission is proportional to the C decay rate in soil, where C-soil(t) is the available labile soil C (g m(-2)) at any time (t). Emissions are modeled in terms soil C available to decomposition in the tilled and non-tilled plots, and a relationship is derived between no-till (F-NT) and tilled (F-Gamma) fluxes, which is: F-T = a1F(NT)e(-a2t), where t is time after tillage. Predicted and observed fluxes showed good agreement based on determination coefficient (R-2), index of agreement and model efficiency, with R-2 as high as 0.97. The two parameters included in the model are related to the difference between the decay constant (k factor) of tilled and no-till plots (a(2)) and also to the amount of labile carbon added to the readily decomposable soil organic matter due to tillage (a,). These two parameters were estimated in the model ranging from 1.27 and 2.60 (a(1)) and - 1.52 x 10(-2) and 2.2 x 10(-2) day(-1) (a(2)). The advantage is that temporal variability of tillage-induced emissions can be described by only one analytical function that includes the no-till emission plus an exponential term modulated by tillage and environmentally dependent parameters. (C) 2008 Elsevier B.V. All rights reserved.

Electroluminescence and electric current response spectroscopy applied to the characterization of polymer light-emitting electrochemical cells

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

C programs for solving the time-dependent Gross-Pitaevskii equation in a fully anisotropic trap

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

Statements on chaos control designs, including a fractional order dynamical system, applied to a MEMS comb-drive actuator

In this work, we deal with a micro electromechanical system (MEMS), represented by a micro-accelerometer. Through numerical simulations, it was found that for certain parameters, the system has a chaotic behavior. The chaotic behaviors in a fractional order are also studied numerically, by historical time and phase portraits, and the results are validated by the existence of positive maximal Lyapunov exponent. Three control strategies are used for controlling the trajectory of the system: State Dependent Riccati Equation (SDRE) Control, Optimal Linear Feedback Control, and Fuzzy Sliding Mode Control. The controls proved effective in controlling the trajectory of the system studied and robust in the presence of parametric errors.

First-order decay models to describe soil C-CO2 Loss after rotary tillage

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

4f-4f intensities of the Tm3+ ions in fluoroindate glasses: the influence of third-order effects through odd intensity parameters

In this work an analysis of the phenomenological Omega(lambda) intensity parameters for the Tm3+ ion in fluoroindate glass is made using the standard Judd-Ofelt theory, and a modified oscillator strength taking into account odd-order contributions is utilized. Different sets of phenomenological intensity parameters Omega(lambda) (lambda=1,2,3,4,5,6) are discussed. The set of better quality is used to analyze the influence of third-order effects through odd intensity parameters in the new approximation. Fluoroindate glasses of compositions (40-x)InF3-20ZnF(2)-20SrF(2)-16BaF(2)-2GdF(3)-2NaF-xTmF(3) with x=1, 2 and 3 mol% were prepared, and the absorption spectra at room temperature in the spectral range from 300 to 2500 nm were obtained. The experimental oscillator strengths determined from the area under the absorption band are compared to the calculated ones. (C) 1998 Elsevier B.V. S.A.

Judd-Ofelt analysis of Pr3+ ions in fluoroindate glasses: Influence of odd third order intensity parameters

In this work an analysis of the Judd-Ofelt phenomenological Ωλ intensity parameters for the Pr3+ ion in fluoroindate glass is made. Different Pr3+ concentrations, namely 1, 2, 3 and 4 mol% are used. The experimental oscillator strengths have been determined from the absorption spectra. A consistent set of parameters is obtained only with the inclusion of odd rank third order intensity parameters and if the band at 21 470 cm-1 is assigned to the 3H4 → 3P1 transition and the 1I6 component is incorporated in the 3H4 → 3P2 transition at 22 700 cm-1.

Fitting the frequency-dependent parameters in the Bergeron line model

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

Homology in a context dependent predatory behavior in spiders (Araneae)

Stereotyped behaviors have been routinely used as characters for phylogeny inference, but the same cannot be said of the plastic aspects of performance, which routinely are taken as a result of ecological processes. In this paper we examine the evolution of one of these plastic behavioral phenotypes, thus fostering a bridge between ecological and evolutionary processes. Foraging behavior in spiders is context dependent in many aspects, since it varies with prey type and size, spider nutritional and developmental state, previous experience and, in webweavers, is dependent on the structure of the web. Reeling is a predatory tactic typical of cobweb weavers (Theridiidae), in which the spider moves the prey toward her by pulling the capture thread (gumfoot) to which it is adhered. Predatory reeling is dependent on the gumfoot for its expression, and has not been previously reported in orbweavers. In order to investigate the evolution of this web dependent behavior, we built artificial, pseudogumfoot lines in orbwebs and registered parameters of the predatory tactics in this modified web. Aspects of the predatory tactics of 240 individuals (12 species in 4 families) were measured, and the resulting data were optimized on the phylogeny of Orbiculariae. All species perform predatory reeling with the pseudogumfoot lines. Thus, predatory reeling is homologous for the whole Orbiculariae group. In nature, holes made by insects in ecribellate orbs produce pseudogumfoot lines (similar to out experimentally modified webs), and thus reeling occurred naturally in ecribellates. Nevertheless, outside lab conditions, predatory reeling does not occur among cribellate orbweavers, so that this behavior could not have been selected for in the cribellate ancester of orbweavers. Cribellate spiders are flexible enough as to present novel and adaptive predatory responses (reeling) even when exposed for the first time to conditions outside their usual environment. Thus, the evolution of reeling suggests and alternative mechanism for the production of evolutionary novelties; that is, the exploration of unusual ecological conditions and of the regular effects these abnormal conditions have on phenotype expression.

Electroluminescence and electric current response spectroscopy applied to the characterization of polymer light-emitting electrochemical cells

Frequency-dependent electroluminescence and electric current response spectroscopy were applied to polymeric light-emitting electrochemical cells in order to obtain information about the operation mechanism regimes of such devices. Three clearly distinct frequency regimes could be identified: a dielectric regime at high frequencies; an ionic transport regime, characterized by ionic drift and electronic diffusion; and an electrolytic regime, characterized by electronic injection from the electrodes and electrochemical doping of the conjugated polymer. From the analysis of the results, it was possible to evaluate parameters like the diffusion speed of electronic charge carriers in the active layer and the voltage drop necessary for operation. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4752438]