Modeling Two-Oscillator Circadian Systems Entrained by Two Environmental Cycles

Several experimental studies have altered the phase relationship between photic and non-photic environmental, 24 h cycles (zeitgebers) in order to assess their role in the synchronization of circadian rhythms. To assist in the interpretation of the complex activity patterns that emerge from these ""conflicting zeitgeber'' protocols, we present computer simulations of coupled circadian oscillators forced by two independent zeitgebers. This circadian system configuration was first employed by Pittendrigh and Bruce (1959), to model their studies of the light and temperature entrainment of the eclosion oscillator in Drosophila. Whereas most of the recent experiments have restricted conflicting zeitgeber experiments to two experimental conditions, by comparing circadian oscillator phases under two distinct phase relationships between zeitgebers (usually 0 and 12 h), Pittendrigh and Bruce compared eclosion phase under 12 distinct phase relationships, spanning the 24 h interval. Our simulations using non-linear differential equations replicated complex non-linear phenomena, such as ""phase jumps'' and sudden switches in zeitgeber preferences, which had previously been difficult to interpret. Our simulations reveal that these phenomena generally arise when inter-oscillator coupling is high in relation to the zeitgeber strength. Manipulations in the structural symmetry of the model indicated that these results can be expected to apply to a wide range of system configurations. Finally, our studies recommend the use of the complete protocol employed by Pittendrigh and Bruce, because different system configurations can generate similar results when a ""conflicting zeitgeber experiment'' incorporates only two phase relationships between zeitgebers.

High performance magnetic separation of gold nanoparticles for catalytic oxidation of alcohols

We present the magnetic separation approach to facilitate the recovery of gold nanoparticle (AuNP) catalysts. The use of magnetically recoverable supports for the immobilization of AuNPs instead of traditional oxides, polymers or carbon based solids guarantees facile, clean, fast and efficient separation of the catalyst at the end of the reaction cycle. Magnetic separation can be considered an environmentally benign separation approach, since it minimizes the use of auxiliary substances and energy for achieving catalyst recovery. The catalyst preparation is based on the immobilization of Au(3+) on the surface of core-shell silica-coated magnetite nanoparticles, followed by metal reduction using two different methods. AuNPs were prepared by thermal reduction in air and by hydrogen reduction at mild temperature. Interestingly, the mean particle size of the supported AuNPs was similar (ca. 5.9 nm), but the polydispersity of the samples is quite different. The catalytic activity of both catalysts in the aerobic oxidation of alcohols was investigated and a distinct selectivity for benzyl alcohol oxidation was observed.

Protecting a quantum state from environmental noise by an incompatible finite-time measurement

We show that measurements of finite duration performed on an open two-state system can protect the initial state from a phase-noisy environment, provided the measured observable does not commute with the perturbing interaction. When the measured observable commutes with the environmental interaction, the finite-duration measurement accelerates the rate of decoherence induced by the phase noise. For the description of the measurement of an observable that is incompatible with the interaction between system and environment, we have found an approximate analytical expression, valid at zero temperature and weak coupling with the measuring device. We have tested the validity of the analytical predictions against an exact numerical approach, based on the superoperator-splitting method, that confirms the protection of the initial state of the system. When the coupling between the system and the measuring apparatus increases beyond the range of validity of the analytical approximation, the initial state is still protected by the finite-time measurement, according with the exact numerical calculations.

Optical fiber laser induced fluorescence spectroscopy as a citrus canker diagnostic

Citrus canker is a serious disease caused by Xanthomonas citri subsp. citri bacteria, which infects citrus plants (Citrus spp.) leading to large economic losses in citrus production worldwide. In this work, laser induced fluorescence spectroscopy (LIF) was investigated as a diagnostic technique for citrus canker disease in citrus trees at an orchard using a portable optical fiber based spectrometer. For comparison we have applied LIF to leaves contaminated with citrus canker, citrus scab, citrus variegates chlorosis, and Huanglongbing (HLB, Greening). In order to reduce the noise in the data, we collected spectra from ten leaves with visual symptoms of diseases and from five healthy leaves per plant. This procedure is carried out in order to minimize the environmental effect on the spectrum (water and nutrient supply) of each plant. Our results show that this method presents a high sensitivity (similar to 90%), however it does present a low specificity (similar to 70%) for citrus canker diagnostic. We believe that such poor performance is due to the fact that the optical fiber collects light from only a small part of the leaf. Such results may be improved using the fluorescence imaging technique on the whole leaf. (C) 2010 Optical Society of America

Biotransformations of Substituted Phenylethanols and Acetophenones by Environmental Bacteria

Whole cells of hydrocarbon-degrading bacteria, isolated from polluted sediments in the Santos Estuary (Baixada Santista, Sao Paulo, Brazil), were able to catalyse oxidoreduction reactions with various substituted phenylethanols and acetophenones as substrates. A number of substituted phenylethanols were formed with high (>99 %) enantiomeric excess. The results of microbial oxidation of phenylethanols 2, 3, 5-7 by Acinetobacter sp. 6.4T and the reduction of acetophenones 1a-6a by Serratia marcescens 5.4T showed that the bacteria used as biocatalysts in this study present significant potential for exploitation in biotechnological processes. The reduction of prochiral acetophenones by Serratia marcescens 3.5T yielded optically active alcohols with 90-99 % enantiomeric excess, and Acinetobacter sp. 6.4T is a potential biocatalyst for the oxidation of alcohols.

Environmental stresses inhibit splicing in the aquatic fungus Blastocladiella emersonii

Background: Exposure of cells to environmental stress conditions can lead to the interruption of several intracellular processes, in particular those performed by macromolecular complexes such as the spliceosome. Results: During nucleotide sequencing of cDNA libraries constructed using RNA isolated from B. emersonii cells submitted to heat shock and cadmium stress, a large number of ESTs with retained introns was observed. Among the 6,350 ESTs obtained through sequencing of stress cDNA libraries, 181 ESTs presented putative introns (2.9%), while sequencing of cDNA libraries from unstressed B. emersonii cells revealed only 0.2% of ESTs containing introns. These data indicate an enrichment of ESTs with introns in B. emersonii stress cDNA libraries. Among the 85 genes corresponding to the ESTs that retained introns, 19 showed more than one intron and three showed three introns, with intron length ranging from 55 to 333 nucleotides. Canonical splicing junctions were observed in most of these introns, junction sequences being very similar to those found in introns from genes previously characterized in B. emersonii, suggesting that inhibition of splicing during stress is apparently a random process. Confirming our observations, analyses of gpx3 and hsp70 mRNAs by Northern blot and S1 protection assays revealed a strong inhibition of intron splicing in cells submitted to cadmium stress. Conclusion: In conclusion, data indicate that environmental stresses, particularly cadmium treatment, inhibit intron processing in B. emersonii, revealing a new adaptive response to cellular exposure to this heavy metal.

High performance gold nanorods and silver nanocubes in surface-enhanced Raman spectroscopy of pesticides

The behavior of Au nanorods and Ag nanocubes as analytical sensors was evaluated for three different classes of herbicides. The use of such anisotropic nanoparticles in surface-enhanced Raman scattering (SERS) experiments allows the one to obtain the spectrum of crystal violet dye in the single molecule regime, as well as the pesticides dichlorophenoxyacetic acid (2,4-D), trichlorfon and ametryn. Such metallic substrates show high SERS performance at low analyte concentrations making them adequate for use as analytical sensors. Density functional theory (DFT) calculations of the geometries and vibrational wavenumbers of the adsorbates in the presence of silver or gold atoms were used to elucidate the nature of adsorbate-nanostructure bonding in each case and support the enhancement patterns observed in each SERS spectrum.

Validation of dot blot hybridization and denaturing high performance liquid chromatography as reliable methods for TP53 codon 72 genotyping in molecular epidemiologic studies

Background: Mutations in TP53 are common events during carcinogenesis. In addition to gene mutations, several reports have focused on TP53 polymorphisms as risk factors for malignant disease. Many studies have highlighted that the status of the TP53 codon 72 polymorphism could influence cancer susceptibility. However, the results have been inconsistent and various methodological features can contribute to departures from Hardy-Weinberg equilibrium, a condition that may influence the disease risk estimates. The most widely accepted method of detecting genotyping error is to confirm genotypes by sequencing and/or via a separate method. Results: We developed two new genotyping methods for TP53 codon 72 polymorphism detection: Denaturing High Performance Liquid Chromatography (DHPLC) and Dot Blot hybridization. These methods were compared with Restriction Fragment Length Polymorphism (RFLP) using two different restriction enzymes. We observed high agreement among all methodologies assayed. Dot-blot hybridization and DHPLC results were more highly concordant with each other than when either of these methods was compared with RFLP. Conclusions: Although variations may occur, our results indicate that DHPLC and Dot Blot hybridization can be used as reliable screening methods for TP53 codon 72 polymorphism detection, especially in molecular epidemiologic studies, where high throughput methodologies are required.

Environmental and grazing influence on spatial variability of intertidal biofilm on subtropical rocky shores

Epilithic biofilm on rocky shores is regulated by physico-chemical and biological factors and is important as a source of food for benthic organisms. The influences of environmental and grazing pressure on spatial variability of biomass of biofilm were evaluated on shores on the north coast of Sao Paulo State (SE Brazil). A general trend of greater abundance of microalgae was observed lower on the shore, but neither of the environmental factors evaluated (wave exposure and shore level) showed consistent effects, and differences were found among specific shores or times (September 2007 and March 2008). The abundance of slow-moving grazers (limpets and littorinids) showed a negative correlation with chlorophyll a concentration on shores. However, experimental exclusion of these grazers failed to show consistent results at small spatial scales. Observations of divergent abundances of the isopod Ligia exotica and biomass of biofilm on isolated boulders on shores led to a short exclusion experiment, where the grazing pressure by L. exotica significantly decreased microalgal biomass. The result suggests that grazing activities of this fast-moving consumer probably mask the influence of slow-moving grazers at small spatial scales, while both have an additive effect at larger scales that masks environmental influences. This is the first evaluation of the impact of the fast-moving herbivore L. exotica on microalgal biomass on rocky shores and opens an interesting discussion about the role of these organisms in subtropical coastal environments.

Simulation of Soil Carbon Dynamics under Sugarcane with the CENTURY Model

Currently there is a trend for the expansion of the area cropped with sugarcane (Saccharum officinarum L.), driven by an increase in the world demand for biofuels, due to economical, environmental, and geopolitical issues. Although sugarcane is traditionally harvested by burning dried leaves and tops, the unburned, mechanized harvest has been progressively adopted. The use of process based models is useful in understanding the effects of plant litter in soil C dynamics. The objective of this work was to use the CENTURY model in evaluating the effect of sugarcane residue management in the temporal dynamics of soil C. The approach taken in this work was to parameterize the CENTURY model for the sugarcane crop, to simulate the temporal dynamics of soil C, validating the model through field experiment data, and finally to make predictions in the long term regarding soil C. The main focus of this work was the comparison of soil C stocks between the burned and unburned litter management systems, but the effect of mineral fertilizer and organic residue applications were also evaluated. The simulations were performed with data from experiments with different durations, from 1 to 60 yr, in Goiana and Timbauba, Pernambuco, and Pradopolis, Sao Paulo, all in Brazil; and Mount Edgecombe, Kwazulu-Natal, South Africa. It was possible to simulate the temporal dynamics of soil C (R(2) = 0.89). The predictions made with the model revealed that there is, in the long term, a trend for higher soil C stocks with the unburned management. This increase is conditioned by factors such as climate, soil texture, time of adoption of the unburned system, and N fertilizer management.

Comparison of univariate and multivariate calibration for the determination of micronutrients in pellets of plant materials by laser induced breakdown spectrometry

The application of laser induced breakdown spectrometry (LIBS) aiming the direct analysis of plant materials is a great challenge that still needs efforts for its development and validation. In this way, a series of experimental approaches has been carried out in order to show that LIBS can be used as an alternative method to wet acid digestions based methods for analysis of agricultural and environmental samples. The large amount of information provided by LIBS spectra for these complex samples increases the difficulties for selecting the most appropriated wavelengths for each analyte. Some applications have suggested that improvements in both accuracy and precision can be achieved by the application of multivariate calibration in LIBS data when compared to the univariate regression developed with line emission intensities. In the present work, the performance of univariate and multivariate calibration, based on partial least squares regression (PLSR), was compared for analysis of pellets of plant materials made from an appropriate mixture of cryogenically ground samples with cellulose as the binding agent. The development of a specific PLSR model for each analyte and the selection of spectral regions containing only lines of the analyte of interest were the best conditions for the analysis. In this particular application, these models showed a similar performance. but PLSR seemed to be more robust due to a lower occurrence of outliers in comparison to the univariate method. Data suggests that efforts dealing with sample presentation and fitness of standards for LIBS analysis must be done in order to fulfill the boundary conditions for matrix independent development and validation. (C) 2009 Elsevier B.V. All rights reserved.

Improving sample representativeness in environmental studies: a major component for the uncertainty budget

For environmental quality assessment, INAA has been applied for determining chemical elements in small (200 mg) and large (200 g) samples of leaves from 200 trees. By applying the Ingamells` constant, the expected percent standard deviation was estimated in 0.9-2.2% for 200 mg samples. Otherwise, for composite samples (200 g), expected standard deviation varied from 0.5 to 10% in spite of analytical uncertainties ranging from 2 to 30%. Results thereby suggested the expression of the degree of representativeness as a source of uncertainty, contributing for increasing of the reliability of environmental studies mainly in the case of composite samples.

Compton suppression instrumental neutron activation analysis performance in determining trace- and minor-element contents in foodstuff

In 2003-2004, several food items were purchased from large commercial outlets in Coimbra, Portugal. Such items included meats (chicken, pork, beef), eggs, rice, beans and vegetables (tomato, carrot, potato, cabbage, broccoli, lettuce). Elemental analysis was carried out through INAA at the Technological and Nuclear Institute (ITN, Portugal), the Nuclear Energy Centre for Agriculture (CENA, Brazil), and the Nuclear Engineering Teaching Lab of the University of Texas at Austin (NETL, USA). At the latter two, INAA was also associated to Compton suppression. It can be concluded that by applying Compton suppression (1) the detection limits for arsenic, copper and potassium improved; (2) the counting-statistics error for molybdenum diminished; and (3) the long-lived zinc had its 1115-keV photopeak better defined. In general, the improvement sought by introducing Compton suppression in foodstuff analysis was not significant. Lettuce, cabbage and chicken (liver, stomach, heart) are the richest diets in terms of human nutrients.

Total and inorganic mercury determination in fish tissue by flow injection cold vapour atomic fluorescence spectrometry

A simple and reliable method for Hg determination in fish samples has been developed. Lyophilised fish tissue samples were extracted in a 25% (w/v) tetramethylammonium hydroxide (TMAH) solution; the extracts were then analysed by FI-CVAFS. This method can be used to determine total and inorganic Hg, using the same FI manifold. For total Hg determination, a 0.1% (w/v) KMnO(4) solution was added to the FI manifold at the sample zone, followed by the addition of a 0.5% (w/v) SnCl(2) solution, whereas inorganic Hg was determined by adding a 0.1% (w/v) L-cysteine solution followed by a 1.0% (w/v) SnCl(2) solution to the FI system. The organic fraction was determined as the difference between total and inorganic Hg. Sample preparation, reagent consumption and parameters that can influence the FI-CVAFS performance were also evaluated. The limit of detection for this method is 3.7 ng g(-1) for total Hg and 4.3 ng g(-1) for inorganic Hg. The relative standard deviation for a 1.0 mu gL(-1) CH(3)Hg standard solution (n = 20) was 1.1%, and 1.3% for a 1.0 mu gL(-1) Hg(2+) standard solution (n = 20). Accuracy was assessed by the analysis of Certified Reference Material (dogfish: DORM-2, NRCC). Recoveries of 99.1% for total Hg and 93.9% inorganic Hg were obtained. Mercury losses were not observed when sample solutions were re-analysed after a seven day period of storage at 4 degrees C.