Pressure-jump-induced kinetics reveals a hydration dependent folding/unfolding mechanism of ribonuclease A

Pressure-jump (p-jump)-induced relaxation kinetics was used to explore the energy landscape of protein folding/unfolding of Y115W, a fluorescent variant of ribonuclease A. Pressure-jumps of 40MPa amplitude (5ms dead-time) were conducted both to higher (unfolding) and to lower (folding) pressure, in the range from 100 to 500MPa, between 30 and 50°C. Significant deviations from the expected symmetrical protein relaxation kinetics were observed. Whereas downward p-jumps resulted always in single exponential kinetics, the kinetics induced by upward p-jumps were biphasic in the low pressure range and monophasic at higher pressures. The relative amplitude of the slow phase decreased as a function of both pressure and temperature. At 50°C, only the fast phase remained. These results can be interpreted within the framework of a two-dimensional energy surface containing a pressure- and temperature-dependent barrier between two unfolded states differing in the isomeric state of the Asn-113–Pro-114 bond. Analysis of the activation volume of the fast kinetic phase revealed a temperature-dependent shift of the unfolding transition state to a larger volume. The observed compensation of this effect by glycerol offers an explanation for its protein stabilizing effect

A simple model for predicting soil temperature in snow-covered and seasonally frozen soil: model description and testing

Microbial processes in soil are moisture, nutrient and temperature dependent and, consequently, accurate calculation of soil temperature is important for modelling nitrogen processes. Microbial activity in soil occurs even at sub-zero temperatures so that, in northern latitudes, a method to calculate soil temperature under snow cover and in frozen soils is required. This paper describes a new and simple model to calculate daily values for soil temperature at various depths in both frozen and unfrozen soils. The model requires four parameters average soil thermal conductivity, specific beat capacity of soil, specific heat capacity due to freezing and thawing and an empirical snow parameter. Precipitation, air temperature and snow depth (measured or calculated) are needed as input variables. The proposed model was applied to five sites in different parts of Finland representing different climates and soil types. Observed soil temperatures at depths of 20 and 50 cm (September 1981-August 1990) were used for model calibration. The calibrated model was then tested using observed soil temperatures from September 1990 to August 2001. R-2-values of the calibration period varied between 0.87 and 0.96 at a depth of 20 cm and between 0.78 and 0.97 at 50 cm. R-2 -values of the testing period were between 0.87 and 0.94 at a depth of 20cm. and between 0.80 and 0.98 at 50cm. Thus, despite the simplifications made, the model was able to simulate soil temperature at these study sites. This simple model simulates soil temperature well in the uppermost soil layers where most of the nitrogen processes occur. The small number of parameters required means, that the model is suitable for addition to catchment scale models.

Influence of the solvent on the self-assembly of a modified amyloid beta peptide fragment. II. NMR and computer simulation investigation

The conformation of a model peptide AAKLVFF based on a fragment of the amyloid beta peptide A beta 16-20, KLVFF, is investigated in methanol and water via solution NMR experiments and Molecular dynamics computer simulations. In previous work, we have shown that AAKLVFF forms peptide nanotubes in methanol and twisted fibrils in water. Chemical shift measurements were used to investigate the solubility of the peptide as a function of concentration in methanol and water. This enabled the determination of critical aggregation concentrations, The Solubility was lower in water. In dilute solution, diffusion coefficients revealed the presence of intermediate aggregates in concentrated solution, coexisting with NMR-silent larger aggregates, presumed to be beta-sheets. In water, diffusion coefficients did not change appreciably with concentration, indicating the presence mainly of monomers, coexisting with larger aggregates in more concentrated solution. Concentration-dependent chemical shift measurements indicated a folded conformation for the monomers/intermediate aggregates in dilute methanol, with unfolding at higher concentration. In water, an antiparallel arrangement of strands was indicated by certain ROESY peak correlations. The temperature-dependent solubility of AAKLVFF in methanol was well described by a van't Hoff analysis, providing a solubilization enthalpy and entropy. This pointed to the importance of solvophobic interactions in the self-assembly process. Molecular dynamics Simulations constrained by NOE values from NMR suggested disordered reverse turn structures for the monomer, with an antiparallel twisted conformation for dimers. To model the beta-sheet structures formed at higher concentration, possible model arrangements of strands into beta-sheets with parallel and antiparallel configurations and different stacking sequences were used as the basis for MD simulations; two particular arrangements of antiparallel beta-sheets were found to be stable, one being linear and twisted and the other twisted in two directions. These structures Were used to simulate Circular dichroism spectra. The roles of aromatic stacking interactions and charge transfer effects were also examined. Simulated spectra were found to be similar to those observed experimentally.(in water or methanol) which show a maximum at 215 or 218 nm due to pi-pi* interactions, when allowance is made for a 15-18 nm red-shift that may be due to light scattering effects.

Accurate analysis of noble gas concentrations in small water samples and its application to fluid inclusions in stalagmites

The concentrations of dissolved noble gases in water are widely used as a climate proxy to determine noble gas temperatures (NGTs); i.e., the temperature of the water when gas exchange last occurred. In this paper we make a step forward to apply this principle to fluid inclusions in stalagmites in order to reconstruct the cave temperature prevailing at the time when the inclusion was formed. We present an analytical protocol that allows us accurately to determine noble gas concentrations and isotope ratios in stalagmites, and which includes a precise manometrical determination of the mass of water liberated from fluid inclusions. Most important for NGT determination is to reduce the amount of noble gases liberated from air inclusions, as they mask the temperature-dependent noble gas signal from the water inclusions. We demonstrate that offline pre-crushing in air to subsequently extract noble gases and water from the samples by heating is appropriate to separate gases released from air and water inclusions. Although a large fraction of recent samples analysed by this technique yields NGTs close to present-day cave temperatures, the interpretation of measured noble gas concentrations in terms of NGTs is not yet feasible using the available least squares fitting models. This is because the noble gas concentrations in stalagmites are not only composed of the two components air and air saturated water (ASW), which these models are able to account for. The observed enrichments in heavy noble gases are interpreted as being due to adsorption during sample preparation in air, whereas the excess in He and Ne is interpreted as an additional noble gas component that is bound in voids in the crystallographic structure of the calcite crystals. As a consequence of our study's findings, NGTs will have to be determined in the future using the concentrations of Ar, Kr and Xe only. This needs to be achieved by further optimizing the sample preparation to minimize atmospheric contamination and to further reduce the amount of noble gases released from air inclusions.

The impact of two coupled cirrus microphysics-radiation parameterizations on the temperature and specific humidity biases in the tropical tropopause layer in a climate model

The impact of two different coupled cirrus microphysics-radiation parameterizations on the zonally averaged temperature and humidity biases in the tropical tropopause layer (TTL) of a Met Office climate model configuration is assessed. One parameterization is based on a linear coupling between a model prognostic variable, the ice mass mixing ratio, qi, and the integral optical properties. The second is based on the integral optical properties being parameterized as functions of qi and temperature, Tc, where the mass coefficients (i.e. scattering and extinction) are parameterized as nonlinear functions of the ratio between qi and Tc. The cirrus microphysics parameterization is based on a moment estimation parameterization of the particle size distribution (PSD), which relates the mass moment (i.e. second moment if mass is proportional to size raised to the power of 2 ) of the PSD to all other PSD moments through the magnitude of the second moment and Tc. This same microphysics PSD parameterization is applied to calculate the integral optical properties used in both radiation parameterizations and, thus, ensures PSD and mass consistency between the cirrus microphysics and radiation schemes. In this paper, the temperature-non-dependent and temperature-dependent parameterizations are shown to increase and decrease the zonally averaged temperature biases in the TTL by about 1 K, respectively. The temperature-dependent radiation parameterization is further demonstrated to have a positive impact on the specific humidity biases in the TTL, as well as decreasing the shortwave and longwave biases in the cloudy radiative effect. The temperature-dependent radiation parameterization is shown to be more consistent with TTL and global radiation observations.

Independent fusions and recent origins of sex chromosomes in the evolution and diversification of glass knife fishes (Eigenmannia)

The genus Eigenmannia comprises several species groups that display a surprising variety of diploid chromosome numbers and sex-determining systems. In this study, hypotheses regarding phylogenetic relationships and karyotype evolution were investigated using a combination of molecular and cytogenetic methods. Phylogenetic relationships were analyzed for 11 cytotypes based on sequences from five mitochondrial DNA regions. Parsimony-based character mapping of sex chromosomes confirms previous suggestions of multiple origins of sex chromosomes. Molecular cytogenetic analyses involved chromosome painting using probes derived from whole sex chromosomes from two taxa that were hybridized to metaphases of their respective sister cytotypes. These analyses showed that a multiple XY system evolved recently (<7 mya) by fusion. Furthermore, one of the chromosomes that fused to form the neo-Y chromosome is fused independently to another chromosome in the sister cytotype. This may constitute an efficient post-mating barrier and might imply a direct function of sex chromosomes in the speciation processes in Eigenmannia. The other chromosomal sex-determination system investigated is shown to have differentiated by an accumulation of heterochromatin on the X chromosome. This has occurred in the past 0.6 my, and is the most recent chromosomal sex-determining system described to date. These results show that the evolution of sex-determining systems can proceed very rapidly. Heredity (2011) 106, 391-400; doi:10.1038/hdy.2010.82; published online 23 June 2010

Infrared chiral anomaly at finite temperature

We study the Schwinger model at finite temperature and show that a temperature dependent chiral anomaly may arise from the long distance behavior of the electric field. At high temperature this anomaly depends linearly on the temperature T and is present not only in the two point function, but also in all even point amplitudes. (C) 2011 Elsevier B.V. All rights reserved.

Deactivation and regeneration of oxygen reduction reactivity on double perovskite Ba2Bi0.1Sc0.2Co1.7O6−x cathode for intermediate-temperature solid oxide fuel cells

in situ high-temperature X-ray diffraction and thermal gravimetric- differential thermal analysis on room-temperature powder, as well as X-ray diffraction, Raman spectroscopy, and transmission electron microscopy on quenched powder, were applied to study crystal structure and phase transformations in Ba₂Bi_0.1Sc_0.2Co _1.7O_6-x (BBSC). Heating BBSC in air to over 800 °C produces a pure cubic phase with space group Fm3m (no. 225), and cooling down below 800 °C leads to a mixture of three noncubic phases including an unknown phase between 200 and 650 °C, a 2H hexagonal BaCoO3 with space group P63/mmc (no. 194) between 600 and 800 °C, and an intermediate phase at 800 °C. These three phases exist concurrently with the major cubic phase. The weight gain and loss between 300 and 900 °C suggest the occurrence of cobalt reduction, oxidation, and disproportion reactions with dominant reduction reaction at above 600 °C. The thermal expansion of BBSC was also examined by dilatometry. BBSC has a highly temperature-dependent thermal expansion coefficient which relates well with its structure evolution. Furthermore, the oxygen reduction reaction (ORR) of BBSC was probed by symmetrical cell and three-electrode configurations. The presence of hexagonal phase at 700 °C rarely affects the ORR performance of BBSC as evidenced by a slight increase of its area-specific resistance (ASR) value following 48 h of testing in this three-electrode configuration. This observation is in contrast to the commonly held point of view that noncubic phase deteriorates performance of perovskite compounds (especially in oxygen transport applications). Moreover, cathodic polarization treatment, for example, current discharge from BBSC (tested in three-electrode configuration), can be utilized to recover the original ORR performance. The cubic structure seems to be retained on the cathodic polarization - the normal cathode operating mode in fuel cells. Stable 72-h performance of BBSC in cathodic polarization mode further confirms that despite the presence of phase impurities, BBSC still demonstrates good performance between 500 and 700 °C, the desired intermediate operating temperature in solid oxide fuel cells.

Aspectos da biologia e morfologia da broca do pedúnculo floral do coqueiro, Homalinotus coriaceus (Gyllenhal) (Coleoptera: Curculionidae)

A broca do pedúnculo floral do coqueiro, Homalinotus coriaceus (Gyllenhal), é uma praga limitante à produção de coco no Brasil, provocando a queda das flores e dos frutos imaturos. Sua biologia é pouco conhecida o que tem dificultado a seu manejo adequado no campo. Dessa forma, foi realizado o estudo da biologia desse inseto no Laboratório de Entomologia da Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) Tabuleiros Costeiros - CPATC, em Aracaju, SE, à temperatura de 25 ± 2°C, umidade relativa de 70% e fotofase de 12h. Para alimentação e oviposição dos adultos coletados no campo foram utilizados toletes de cana-de-açúcar como substrato, nos quais as fêmeas colocaram ovos individualizados, cujo período de incubação variou de seis a 14 dias. As larvas foram criadas no mesocarpo de coco, desenvolvendo-se em 144 dias em média, passando por cinco a sete ínstares. O período pupal médio foi de 31 dias. A longevidade do adulto variou de 303 a 695 dias para fêmeas e de 246 a 635 dias para machos, sendo o ciclo de ovo a adulto de 181,9 dias para fêmeas e 188,5 para machos. Foram observadas diferenças morfológicas nas pupas e nos adultos, que podem ser utilizadas para separação dos sexos. Ao contrário dos machos, as fêmeas apresentam, na fase de pupa, duas estruturas arredondadas e elevadas situadas na face ventral e final do abdome e, na fase adulta, o penúltimo tergito abdominal projeta-se sobre o último.

Sex chromosome evolution in fish: the formation of the neo-Y chromosome in Eigenmannia (Gymnotiformes)

Chromosomes of a species of Eigenmannia presenting a X1X1X2X2:X1X2Y sex chromosome system, resulting from a Y-autosome Robertsonian translocation, were analyzed using the C-banding technique, chromomycin A(3) (CMA(3)) and mithramycin (MM) staining and in situ digestion by the restriction endonuclease AluI. A comparison of the metacentric Y chromosome of males with the corresponding acrocentrics in females indicated that a C-band-positive, CMA(3)/MM-fluorescent and AluI digestion-resistant region had been lost during the process of translocation, resulting in a diminution of heterochromatin in the males. It is hypothesized that the presence of a smaller amount of G+C-rich heterochromatin in the sex chromosomes of the heteromorphic sex when compared with the homomorphic sex may be associated with the sex determination mechanism in this species and may be a more widely occurring phenomenon in fish with differentiated sex chromosomes than was initially thought.

Mesonic correlation functions at finite temperature in the NJL model

We employ the NJL model to calculate mesonic correlation functions at finite temperature and compare results with recent lattice QCD simulations. We employ an implicit regularization scheme to deal with the divergent amplitudes to obtain ambiguity-free, scale-invariant and symmetry-preserving physical amplitudes. Making the coupling constants of the model temperature dependent, we show that at low momenta our results agree qualitatively with lattice simulations.

Hadronic current correlation functions at finite temperature in the NJL model

Recently there have been suggestions that for a proper description of hadronic matter and hadronic correlation functions within the NJL model at finite density/temperature the parameters of the model should be taken density/temperature dependent. Here we show that qualitatively similar results can be obtained using a cutoff-independent regularization of the NJL model. In this regularization scheme one can express the divergent parts at finite density/temperature of the amplitudes in terms of their counterparts in vacuum.

Photoluminescence temperature dependence of doped parabolic quantum wells

Parabolic quantum wells (PQWs) have been studied by temperature dependent photoluminescence (PL). Two kind of samples have been studied. Concerning the undoped sample, the dominant luminescences were the bulk GaAs and the fundamental transition of the PQW. The evolution on temperature of the energy position of both PL emissions follows the well known Varshing formula. For the doped samples strong radiative recombination of the electron gas with photogenerated holes was observed. At low temperature strong Fermi level enhancement occurs in the luminescence as a result of the multi-electron-hole scattering, which is smear out increasing the temperature.

Influence of temperature upon paralyzing and myotoxic effects of bothropstoxin-I on mouse neuromuscular preparations

Bothropstoxin-I (BthTX-I), from B. jararacussu venom, is a phospholipase A(2) (PLA(2)) homologue devoid of enzymatic activity. Besides inducing severe myonecrosis, BthTX-I promotes paralysis of both directly and indirectly evoked contractions in isolated neuromuscular preparations. We applied an experimental paradigm in order to characterize the steps involved in the toxic effects of BthTX-I on mouse neuromuscular junction. Myotoxicity was assessed by microscopic analysis of extensor digitorum longus muscles; paralyzing activity was evaluated through the recording of isolated contractions indirectly evoked in phrenic-diaphragm preparations. After 90 min at 35 degreesC, BthTX-I induced complete and irreversible paralysis, and damaged 30.3 +/- 2.7% of muscle fibers. In contrast, no effect was observed when tissues were incubated with BthTX-I at 10degreesC for 60 min and subsequently washed with toxin-free solution and maintained at 35 degreesC. These results indicate that the binding of BthTX-I to the cellular tissue surface is very weak at low temperature and that an additional factor is necessary. However, when tissues were submitted to BthTX-I (10degreesC for 60 min), and the temperature was elevated to 35 degreesC, omitting the washing step, it was observed muscle paralysis and damage in 39.04 +/- 4.2% of muscle fibers. These results indicate that a temperature-dependent step is necessary for BthTX-I to promote both its myotoxic and paralyzing activities. (C) 2004 Elsevier B.V.. All rights reserved.

Temperature dependence on the electrical properties of Ba(Ti0.90Zr0.10)O-3:2V ceramics

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