Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy

To understand the molecular origins of diseases caused by ultraviolet and visible light, and also to develop photodynamic therapy, it is important to resolve the mechanism of photoinduced DNA damage. Damage to DNA bound to a photosensitizer molecule frequently proceeds by one-electron photo-oxidation of guanine, but the precise dynamics of this process are sensitive to the location and the orientation of the photosensitizer, which are very difficult to define in solution. To overcome this, ultrafast time-resolved infrared (TRIR) spectroscopy was performed on photoexcited ruthenium polypyridyl–DNA crystals, the atomic structure of which was determined by X-ray crystallography. By combining the X-ray and TRIR data we are able to define both the geometry of the reaction site and the rates of individual steps in a reversible photoinduced electron-transfer process. This allows us to propose an individual guanine as the reaction site and, intriguingly, reveals that the dynamics in the crystal state are quite similar to those observed in the solvent medium.

Robust comparison of climate models with observations using blended land air and ocean sea surface temperatures

The level of agreement between climate model simulations and observed surface temperature change is a topic of scientific and policy concern. While the Earth system continues to accumulate energy due to anthropogenic and other radiative forcings, estimates of recent surface temperature evolution fall at the lower end of climate model projections. Global mean temperatures from climate model simulations are typically calculated using surface air temperatures, while the corresponding observations are based on a blend of air and sea surface temperatures. This work quantifies a systematic bias in model-observation comparisons arising from differential warming rates between sea surface temperatures and surface air temperatures over oceans. A further bias arises from the treatment of temperatures in regions where the sea ice boundary has changed. Applying the methodology of the HadCRUT4 record to climate model temperature fields accounts for 38% of the discrepancy in trend between models and observations over the period 1975–2014.

Monitoring scan asymmetry of microwave humidity sounding channels using simultaneous all angle collocations (SAACs)

Simultaneous all angle collocations (SAACs) of microwave humidity sounders (AMSU-B and MHS) on-board polar orbiting satellites are used to estimate scan-dependent biases. This method has distinct advantages over previous methods, such as that the estimated scan-dependent biases are not influenced by diurnal differences between the edges of the scan and the biases can be estimated for both sides of the scan. We find the results are robust in the sense that biases estimated for one satellite pair can be reproduced by double differencing biases of these satellites with a third satellite. Channel 1 of these instruments shows the least bias for all satellites. Channel 2 has biases greater than 5 K, thus needs to be corrected. Channel 3 has biases of about 2 K and more and they are time varying for some of the satellites. Channel 4 has the largest bias which is about 15 K when the data are averaged for 5 years, but biases of individual months can be as large as 30 K. Channel 5 also has large and time varying biases for two of the AMSU-Bs. NOAA-15 (N15) channels are found to be affected the most, mainly due to radio frequency interference (RFI) from onboard data transmitters. Channel 4 of N15 shows the largest and time varying biases, so data of this channel should only be used with caution for climate applications. The two MHS instruments show the best agreement for all channels. Our estimates may be used to correct for scan-dependent biases of these instruments, or at least used as a guideline for excluding channels with large scan asymmetries from scientific analyses.

Tests of sunspot number sequences: 1. Using ionosonde data

More than 70 years ago it was recognised that ionospheric F2-layer critical frequencies [foF2] had a strong relationship to sunspot number. Using historic datasets from the Slough and Washington ionosondes, we evaluate the best statistical fits of foF2 to sunspot numbers (at each Universal Time [UT] separately) in order to search for drifts and abrupt changes in the fit residuals over Solar Cycles 17-21. This test is carried out for the original composite of the Wolf/Zürich/International sunspot number [R], the new “backbone” group sunspot number [RBB] and the proposed “corrected sunspot number” [RC]. Polynomial fits are made both with and without allowance for the white-light facular area, which has been reported as being associated with cycle-to-cycle changes in the sunspot number - foF2 relationship. Over the interval studied here, R, RBB, and RC largely differ in their allowance for the “Waldmeier discontinuity” around 1945 (the correction factor for which for R, RBB and RC is, respectively, zero, effectively over 20 %, and explicitly 11.6 %). It is shown that for Solar Cycles 18-21, all three sunspot data sequences perform well, but that the fit residuals are lowest and most uniform for RBB. We here use foF2 for those UTs for which R, RBB, and RC all give correlations exceeding 0.99 for intervals both before and after the Waldmeier discontinuity. The error introduced by the Waldmeier discontinuity causes R to underestimate the fitted values based on the foF2 data for 1932-1945 but RBB overestimates them by almost the same factor, implying that the correction for the Waldmeier discontinuity inherent in RBB is too large by a factor of two. Fit residuals are smallest and most uniform for RC and the ionospheric data support the optimum discontinuity multiplicative correction factor derived from the independent Royal Greenwich Observatory (RGO) sunspot group data for the same interval.

Influence of Post and Resin Cement on Stress Distribution of Maxillary Central Incisors Restored with Direct Resin Composite

The current study evaluated the influence of two endodontic post systems and the elastic modulus and film thickness of resin cement on stress distribution in a maxillary central incisor (MCI) restored with direct resin composite using finite element analysis (FEA). A three-dimensional model of an MCI with a coronary fracture and supporting structures was performed. A static chewing pressure of 2.16 N/mm(2) was applied to two areas on the palatal surface of the composite restoration. Zirconia ceramic (ZC) and glass fiber (GF) posts were considered. The stress distribution was analyzed in the post, dentin and cement layer when ZC and GF posts were fixed to the root canals using resin cements of different elastic moduli (7.0 and 18.6 GPa) and different layer thicknesses (70 and 200 mu m). The different post materials presented a significant influence on stress distribution with lesser stress concentration when using the GF post. The higher elastic modulus cement created higher stress levels within itself. The cement thicknesses did not present significant changes.

ESTIMATING SENSORY SHELF LIFE OF CHOCOLATE AND CARROT CUPCAKES USING ACCEPTANCE TESTS

This study determined the sensory shelf life of a commercial brand of chocolate and carrot cupcakes, aiming at increasing the current 120 days of shelf life to 180. Appearance, texture, flavor and overall quality of cakes stored at six different storage times were evaluated by 102 consumers. The data were analyzed by analysis of variance and linear regression. For both flavors, the texture presented a greater loss in acceptance during the storage period, showing an acceptance mean close to indifference on the hedonic scale at 120 days. Nevertheless, appearance, flavor and overall quality stayed acceptable up to 150 days. The end of shelf life was estimated at about 161 days for chocolate cakes and 150 days for carrot cakes. This study showed that the current 120 days of shelf life can be extended to 150 days for carrot cake and to 160 days for chocolate cake. However, the 180 days of shelf life desired by the company were not achieved. PRACTICAL APPLICATIONS This research shows the adequacy of using sensory acceptance tests to determine the shelf life of two food products (chocolate and carrot cupcakes). This practical application is useful because the precise determination of the shelf life of a food product is of vital importance for its commercial success. The maximum storage time should always be evaluated in the development or reformulation of new products, changes in packing or storage conditions. Once the physical-chemical and microbiological stability of a product is guaranteed, sensorial changes that could affect consumer acceptance will determine the end of the shelf life of a food product. Thus, the use of sensitive and reliable methods to estimate the sensory shelf life of a product is very important. Findings show the importance of determining the shelf life of each product separately and to avoid using the shelf time estimated for a specific product on other, similar products.

Thermodynamic and statistical analysis of soybean oil extraction process using renewable solvent

The main goal of this work was to evaluate thermodynamic parameters of the soybean oil extraction process using ethanol as solvent. The experimental treatments were as follows: aqueous solvents with water contents varying from 0 to 13% (mass basis) and extraction temperature varying from 50 to 100 degrees C. The distribution coefficients of oil at equilibrium have been used to calculate enthalpy, entropy and free energy changes. The results indicate that oil extraction process with ethanol is feasible and spontaneous, mainly under higher temperature. Also, the influence of water level in the solvent and temperature were analysed using the response surface methodology (RSM). It can be noted that the extraction yield was highly affected by both independent variables. A joint analysis of thermodynamic and RSM indicates the optimal level of solvent hydration and temperature to perform the extraction process.

Importance of estimating matrix quality for modeling species distribution in complex tropical landscapes: a test with Atlantic forest small mammals

Information to guide decision making is especially urgent in human dominated landscapes in the tropics, where urban and agricultural frontiers are still expanding in an unplanned manner. Nevertheless, most studies that have investigated the influence of landscape structure on species distribution have not considered the heterogeneity of altered habitats of the matrix, which is usually high in human dominated landscapes. Using the distribution of small mammals in forest remnants and in the four main altered habitats in an Atlantic forest landscape, we investigated 1) how explanatory power of models describing species distribution in forest remnants varies between landscape structure variables that do or do not incorporate matrix quality and 2) the importance of spatial scale for analyzing the influence of landscape structure. We used standardized sampling in remnants and altered habitats to generate two indices of habitat quality, corresponding to the abundance and to the occurrence of small mammals. For each remnant, we calculated habitat quantity and connectivity in different spatial scales, considering or not the quality of surrounding habitats. The incorporation of matrix quality increased model explanatory power across all spatial scales for half the species that occurred in the matrix, but only when taking into account the distance between habitat patches (connectivity). These connectivity models were also less affected by spatial scale than habitat quantity models. The few consistent responses to the variation in spatial scales indicate that despite their small size, small mammals perceive landscape features at large spatial scales. Matrix quality index corresponding to species occurrence presented a better or similar performance compared to that of species abundance. Results indicate the importance of the matrix for the dynamics of fragmented landscapes and suggest that relatively simple indices can improve our understanding of species distribution, and could be applied in modeling, monitoring and managing complex tropical landscapes.

Efficient but destructive: a test of the dental wash technique using secondary electron microscopy

The Boyadjian et al dental wash technique provides, in certain contexts, the only chance to analyze and quantify the use of plants by past populations and is therefore an important milestone for the reconstruction of paleodiet. With this paper we present recent investigations and results upon the influence of this method on teeth. A series of six teeth from a three thousand years old Brazilian shellmound (Jabuticabeira II) was examined before and after dental wash. The main focus was documenting the alteration of the surfaces and microstructures. The status of all teeth were documented using macrophotography, optical light microscopy, and atmospheric Secondary Electron Microscopy (aSEM) prior and after applying the dental wash technique. The comparison of pictures taken before and after dental wash showed the different degrees of variation and damage done to the teeth but, also, provided additional information about microstructures, which have not been visible before. Consequently we suggest that dental wash should only be carried out, if absolutely necessary, after dental pathology, dental morphology and microwear studies have been accomplished. (C) 2010 Elsevier Ltd. All rights reserved.

Cloning and characterization of a zebrafish homologue of human AQP1: a bifunctional water and gas channel

Chen LM, Zhao J, Musa-Aziz R, Pelletier MF, Drummond IA, Boron WF. Cloning and characterization of a zebrafish homologue of human AQP1: a bifunctional water and gas channel. Am J Physiol Regul Integr Comp Physiol 299: R1163-R1174, 2010. First published August 25, 2010; doi:10.1152/ajpregu.00319.2010.-The mammalian aquaporins AQP1, AQP4, and AQP5 have been shown to function not only as water channels but also as gas channels. Zebrafish have two genes encoding an AQP1 homologue, aqp1a and aqp1b. In the present study, we cloned the cDNA that encodes the zebrafish protein Aqp1a from the 72-h postfertilization (hpf) embryo of Danio rerio, as well as from the swim bladder of the adult. The deduced amino-acid sequence of aqp1a consists of 260 amino acids and is 59% identical to human AQP1. By analyzing the genomic DNA sequence, we identified four exons in the aqp1a gene. By in situ hybridization, aqp1a is expressed transiently in the developing vasculature and in erythrocytes from 16 to 48 h of development. Later, at 72 hpf, aqp1a is expressed in dermal ionocytes and in the swim bladder. Western blot analysis of adult tissues reveals that Aqp1a is most highly expressed in the eye and swim bladder. Xenopus oocytes expressing aqp1a have a channel-dependent (*) osmotic water permeability (P(f)*) that is indistinguishable from that of human AQP1. On the basis of the magnitude of the transient change in surface pH (Delta pHS) that were recorded as the oocytes were exposed to either CO(2) or NH(3), we conclude that zebrafish Aqp1a is permeable to both CO(2) and NH(3). The ratio (Delta pHS*)CO2/P(f)* is about half that of human AQP1, and the ratio (Delta pHS*)NH3/P(f)* is about one-quarter that of human AQP1. Thus, compared with human AQP1, zebrafish Aqp1a has about twice the selectivity for CO(2) over NH(3).

Study of the mechanism of action of anoplin, a helical antimicrobial decapeptide with ion channel-like activity, and the role of the amidated C-terminus

Anoplin, an antimicrobial, helical decapeptide from wasp venom, looses its biological activities by mere deamidation of its C-terminus. Secondary structure determination, by circular dichroism spectroscopy in amphipathic environments, and lytic activity in zwitterionic and anionic vesicles showed quite similar results for the amidated and the carboxylated forms of the peptide. The deamidation of the C-terminus introduced a negative charge at an all-positive charged peptide, causing a loss of amphipathicity, as indicated by molecular dynamics simulations in TFE/water mixtures and this subtle modification in a peptide`s primary structure disturbed the interaction with bilayers and biological membranes. Although being poorly lytic, the amidated form, but not the carboxylated, presented ion channel-like activity on anionic bilayers with a well-defined conductance step; at approximately the same concentration it showed antimicrobial activity. The pores remain open at trans-negative potentials, preferentially conducting cations, and this situation is equivalent to the interaction of the peptide with bacterial membranes that also maintain a high negative potential inside. Copyright (C) 2007 European Peptide Society and John Wiley & Sons, Ltd.

Synthesis and structure of cage-like mesoporous silica using different precursors

In this work the synthesis of cubic, FDU-1 type, ordered mesoporous silica (OMS) was developed from two types of silicon source, tetraethyl orthosilicate (TEOS) and a less expensive compound, sodium silicate (Na(2)Si(3)O(7)), in the presence of a new triblock copolymer template Vorasurf 504 (EO(38)BO(46)EO(38)). For both silicon precursors the synthesis temperature was evaluated. For TEOS the effect of polymer dissolution in methanol and the acid solution (HCl and HBr) on the material structure was analyzed. For Na(2)Si(3)O(7) the influence of the polymer mass and the hydrothermal treatment time were the explored experimental parameters. The samples were examined by Small Angle X-ray Scattering (SAXS) and Nitrogen Sorption. For both precursors the decrease on the synthesis temperature from ambient, -25 degrees C, to -15 degrees C improved the ordered porous structure. For TEOS, the SAXS results showed that there is an optimum amount of hydrophobic methanol that contributed to dissolve the polymer but did not provoke structural disorder. The less electronegative Br-ions, when compared to Cl-, induced a more ordered porous structure, higher surface areas and larger lattice parameters. For Na(2)Si(3)O(7) the increase on the hydrothermal treatment time as well as the use of an optimized amount of polymer promoted a better ordered porous structure. (C) 2011 Elsevier B.V. All rights reserved.

Study of metals transfer from environment using teeth as biomonitor

We investigated chronic incorporation of metals in individuals from poor families, living in a small, restrict and allegedly contaminated area in Sao Paulo city, the surroundings of the Guarapiranga dam, responsible for water supply to 25% of the city population. A total of 59 teeth from individuals 7 to 60 years old were collected. The average concentrations of Pb, Cd, Fe, Zn, Mn, Ni and Cr were determined with an Atomic Absorption Spectrophotometer. The concentrations of all metals as function of the individuals` age exhibited a remarkable similarity: peaks between 7 and 10 years and sharply decreasing at higher ages, which could be attributed to alimentary habits and persistence to metals exposure all along the individuals` life span. From all the measured metals, lead and cadmium were a matter of much more concern since their measured values are close to the upper limits of the world wide averages. (C) 2009 Elsevier Ltd. All rights reserved.

Enzymatic hydrolysis of pretreated sugar cane bagasse using Penicillium funiculosum and Trichoderma harzianum cellulases

In this study, we investigated the enzymatic hydrolysis of pretreated sugarcane bagasse using eight different enzymatic blends obtained from concentrated crude enzyme extracts produced by Penicillium funiculosum and Trichoderma harzianum as well as from the extracts in combination with a commercial enzymatic cocktail. The influence of different levels of biomass delignification, degree of crystallinity of lignicellulose, composition of enzymatic activities and BSA on enzymatic hydrolysis yields (HYs) was evaluated. Our X-ray diffraction studies showed that crystallinity of lignocellulose is not a key determinant of its recalcitrance toward enzymatic hydrolysis. In fact, under the experimental conditions of our study, an increase in crystallinity of lignocellulosic samples resulted in increased glucose release by enzymatic hydrolysis. Furthermore, under the same conditions, the addition of BSA had no significant effect on enzymatic hydrolysis. The most efficient enzyme blends were obtained by mixing a commercial enzymatic cocktail with P. funiculosum or T. harzianum cellulase preparations (HYs above 97%) followed by the concentrated extract of P. funiculosum alone (HY= 88.5%). Increased hydrolytic efficiencies appeared to correlate with having an adequate level of both beta-glucosidase and xylanase activities in the blends. (C) 2011 Elsevier Ltd. All rights reserved.

Optimization of the ultrasound-assisted synthesis of allyl 1-naphthyl ether using response surface methodology

Allyl 1-naphthyl ethers are useful compounds for different purposes, but reported methods to synthesize them require long reaction times. In this work, we have obtained allyl 1-naphthyl ether in good yield using ultrasonic-assisted methodology in a 1-h reaction. A central composite design was used to obtain a statistical model and a response surface (p < 0.05; R(2) = 0.970; R(adj)(2) = 0.949; R(pred)(2) = 0.818) that can predict the optimal conditions to maximize the yield, validated experimentally. (C) 2010 Elsevier B.V. All rights reserved.