Deciphering the role of the electrostatic interactions in the alpha-tropomyosin head-to-tail complex

Skeletal alpha-tropomyosin (Tm) is a dimeric coiled-coil protein that forms linear assemblies under low ionic strength conditions in vitro through head-to-tail interactions. A previously published NMR structure of the Tin head-to-tail complex revealed that it is formed by the insertion of the N-terminal coiled-coil of one molecule into a cleft formed by the separation of the helices at the C-terminus of a second molecule. To evaluate the contribution of charged residues to complex stability, we employed single and double-mutant Tm fragments in which specific charged residues were changed to alanine in head-to-tail binding assays, and the effects of the mutations were analyzed by thermodynamic double-mutant cycles and protein-protein docking. The results show that residues K5, K7, and D280 are essential to the stability of the complex. Though D2, K6, D275, and H276 are exposed to the solvent and do not participate in intermolecular contacts in the NMR structure, they may contribute to head-to-tail complex stability by modulating the stability of the helices at the Tm termini.

Isotopic view of vegetation and carbon and nitrogen cycles in a cerrado ecosystem, southeastern Brazil

Carbon and nitrogen biogeochemical cycles in savannas are strongly regulated by the seasonal distribution of precipitation and pulses of nutrients released during the wetting of the dry soil and are critical to the dynamics of microorganisms and vegetation. The objective of this study was to investigate the spatial and temporal variability of C and N isotope ratios as indicators of the cycling of these elements in a cerrado sensu stricto area, within a protected area in a State Park in the state of São Paulo, Brazil. The foliar δ13C and δ15N values varied from -33.6 to -24.4 ‰ and -2.5 to 4.5 ‰, respectively. The δ13C values showed a consistent relationship with canopy height, revealing the importance of structure of the canopy over the C isotopic signature of the vegetation. Carbon isotopic variations associated with the length of the dry season indicated the importance of recent fixed C to the integrated isotopic signature of the leaf organic C. The studied Cerrado species showed a depleted foliar δ15N, but a wide range of foliar Nitrogen with no difference among canopy heights. However, seasonal variability was observed, with foliar δ15N values being higher in the transition period between dry and rainy seasons. The variation of the foliar C and N isotope ratios presented here was consistent with highly diverse vegetation with high energy available but low availability of water and N.

Study of the antimicrobial peptide indolicidin and a mutant in micelle medium by molecular dynamics simulation

The antimicrobial peptide indolicidin (IND) and the mutant CP10A in hydrated micelles were studied using molecular dynamics simulations in order to observe whether the molecular dynamics and experimental data could be sufficiently correlated and a detailed description of the interaction of the antimicrobial peptides with a model of the membrane provided by a hydrated micelle system could be obtained. In agreement with the experiments, the simulations showed that the peptides are located near the surface of the micelles. Peptide insertions agree with available experimental data, showing deeper insertion of the mutant compared with the peptide IND. Major insertion into the hydrophobic core of the micelle by all tryptophan and mutated residues of CP10A in relation to IND was observed. The charged residues of the terminus regions of both peptides present similar behavior, indicating that the major differences in the interactions with the micelles of the peptides IND and CP10A occur in the case of the hydrophobic residues.

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.

Role of noise in population dynamics cycles

Noise is an intrinsic feature of population dynamics and plays a crucial role in oscillations called phase-forgetting quasicycles by converting damped into sustained oscillations. This function of noise becomes evident when considering Langevin equations whose deterministic part yields only damped oscillations. We formulate here a consistent and systematic approach to population dynamics, leading to a Fokker-Planck equation and the associate Langevin equations in accordance with this conceptual framework, founded on stochastic lattice-gas models that describe spatially structured predator-prey systems. Langevin equations in the population densities and predator-prey pair density are derived in two stages. First, a birth-and-death stochastic process in the space of prey and predator numbers and predator-prey pair number is obtained by a contraction method that reduces the degrees of freedom. Second, a van Kampen expansion in the inverse of system size is then performed to get the Fokker-Planck equation. We also study the time correlation function, the asymptotic behavior of which is used to characterize the transition from the cyclic coexistence of species to the ordinary coexistence.

On the resilience of long cycles in random graphs

In this paper we determine the local and global resilience of random graphs G(n,p) (p >> n(-1)) with respect to the property of containing a cycle of length at least (1 - alpha)n. Roughly speaking, given alpha > 0, we determine the smallest r(g) (G, alpha) with the property that almost surely every subgraph of G = G(n,p) having more than r(g) (G, alpha)vertical bar E(G)vertical bar edges contains a cycle of length at least (1 - alpha)n (global resilience). We also obtain, for alpha < 1/2, the smallest r(l) (G, alpha) such that any H subset of G having deg(H) (v) larger than r(l) (G, alpha) deg(G) (v) for all v is an element of V(G) contains a cycle of length at least (1 - alpha)n (local resilience). The results above are in fact proved in the more general setting of pseudorandom graphs.

New genes of Xanthomonas citri subsp citri involved in pathogenesis and adaptation revealed by a transposon-based mutant library

Background: Citrus canker is a disease caused by the phytopathogens Xanthomonas citri subsp. citri, Xanthomonas fuscans subsp. aurantifolli and Xanthomonas alfalfae subsp. citrumelonis. The first of the three species, which causes citrus bacterial canker type A, is the most widely spread and severe, attacking all citrus species. In Brazil, this species is the most important, being found in practically all areas where citrus canker has been detected. Like most phytobacterioses, there is no efficient way to control citrus canker. Considering the importance of the disease worldwide, investigation is needed to accurately detect which genes are related to the pathogen-host adaptation process and which are associated with pathogenesis. Results: Through transposon insertion mutagenesis, 10,000 mutants of Xanthomonas citri subsp. citri strain 306 (Xcc) were obtained, and 3,300 were inoculated in Rangpur lime (Citrus limonia) leaves. Their ability to cause citrus canker was analyzed every 3 days until 21 days after inoculation; a set of 44 mutants showed altered virulence, with 8 presenting a complete loss of causing citrus canker symptoms. Sequencing of the insertion site in all 44 mutants revealed that 35 different ORFs were hit, since some ORFs were hit in more than one mutant, with mutants for the same ORF presenting the same phenotype. An analysis of these ORFs showed that some encoded genes were previously known as related to pathogenicity in phytobacteria and, more interestingly, revealed new genes never implicated with Xanthomonas pathogenicity before, including hypothetical ORFs. Among the 8 mutants with no canker symptoms are the hrpB4 and hrpX genes, two genes that belong to type III secretion system (TTSS), two hypothetical ORFS and, surprisingly, the htrA gene, a gene reported as involved with the virulence process in animal-pathogenic bacteria but not described as involved in phytobacteria virulence. Nucleic acid hybridization using labeled cDNA probes showed that some of the mutated genes are differentially expressed when the bacterium is grown in citrus leaves. Finally, comparative genomic analysis revealed that 5 mutated ORFs are in new putative pathogenicity islands. Conclusion: The identification of these new genes related with Xcc infection and virulence is a great step towards the understanding of plant-pathogen interactions and could allow the development of strategies to control citrus canker.

Cryptic species, life cycles, and the phylogeny of Clytia (Cnidaria: Hydrozoa: Campanulariidae)

Medusae and polyps of Clytia are abundantly found in coastal marine environments and one species in the genus-Clytia hemisphaerica (Linnaeus, 1767)-has become an important experimental model. Yet, only 10 species in the genus have had their life cycle investigated. Most species of Clytia are also poorly described, and detailed life cycle and morphological studies are needed for accurate species-level identifications. Here, we investigated the life cycle of Clytia elsaeoswaldae Stechow, 1914, a species described for the tropical western Atlantic and subsequently considered conspecific to the nearly-cosmopolitan species Clytia gracilis (Sars, 1850) and Clytia hemisphaerica, originally described for the temperate North Atlantic. Based on observations of mature medusae and multiple colonies from southeastern Brazil and the U. S. Virgin Islands (type locality), our results show that C. elsaeoswaldae is morphologically distinct from C. gracilis and C. hemisphaerica. The morphological results are corroborated by a multigene phylogenetic analysis of the genus Clytia, which shows that C. gracilis-like species form a polyphyletic group of several species. These results suggest that the nearly-cosmopolitan distribution attributed to some species of Clytia may be due to the non-recognition of morphologically similar species with more restricted ranges.

Fermentation kinetics for xylitol production by a Pichia stipitis D-Xylulokinase mutant previously grown in spent sulfite liquor

Spent sulfite pulping liquor (SSL) contains lignin, which is present as lignosulfonate, and hemicelluloses that are present as hydrolyzed carbohydrates. To reduce the biological oxygen demand of SSL associated with dissolved sugars, we studied the capacity of Pichia stipitis FPL-YS30 (xyl3 Delta) to convert these sugars into useful products. FPL-YS30 produces a negligible amount of ethanol while converting xylose into xylitol. This work describes the xylose fermentation kinetics of yeast strain P.stipitis FPL-YS30. Yeast was grown in rich medium supplemented with different carbon sources: glucose, xylose, or ammonia-base SSL. The SSL and glucose-acclimatized cells showed similar maximum specific growth rates (0.146 h(-1)). The highest xylose consumption at the beginning of the fermentation process occurred using cells precultivated in xylose, which showed relatively high specific activity of glucose-6-phosphate dehydrogenase (EC 1.1.1.49). However, the maximum specific rates of xylose consumption (0.19 g(xylose)/g(cel) h) and xylitol production (0.059 g(xylitol)/g(cel) h) were obtained with cells acclimatized in glucose, in which the ratio between xylose reductase (EC 1.1.1.21) and xylitol dehydrogenase (EC 1.1.1.9) was kept at higher level (0.82). In this case, xylitol production (31.6 g/l) was 19 and 8% higher than in SSL and xylose-acclimatized cells, respectively. Maximum glycerol (6.26 g/l) and arabitol (0.206 g/l) production were obtained using SSL and xylose-acclimatized cells, respectively. The medium composition used for the yeast precultivation directly reflected their xylose fermentation performance. The SSL could be used as a carbon source for cell production. However, the inoculum condition to obtain a high cell concentration in SSL needs to be optimized.

Electrochemical impedance spectroscopy investigation of the electrochemical behaviour of copper coated with artificial patina layers and submitted to wet and dry cycles

Due to rain events historical monuments exposed to the atmosphere are frequently submitted to wet and dry cycles. During drying periods wetness is maintained in some confined regions and the corrosion product layer, generally denominated patinas, builds up and gets thicker. The aim of this study is to use electrochemical impedance spectroscopy (EIS) to investigate the electrochemical behaviour of pure copper coated with two artificial patina layers and submitted either to continuous or to intermittent immersion tests, this latter aiming to simulate wet and dry cycles. The experiments were performed in 0.1 mol dm(-3) NaCl solution and in artificial rainwater containing the most significant pollutants of the city of Sao Paulo. The results of the continuous immersion tests in the NaCl solution have shown that the coated samples behave like a porous electrode with finite pore length. On the other hand, in the intermittent tests a porous electrode response with semi-infinite pore length can be developed. The results were interpreted based on the model of de Levie and a critical comparison with previous interpretations reported in the literature for similar systems is presented. (C) 2011 Elsevier Ltd. All rights reserved.

Supercritical steam cycles and biomass integrated gasification combined cycles for sugarcane mills

Back in 1970s and 1980s, cogeneration plants in sugarcane mills were primarily designed to consume all bagasse, and produce steam and electricity to the process. The plants used medium pressure steam boilers (21 bar and 300 degrees C) and backpressure steam turbines. Some plants needed also an additional fuel, as the boilers were very inefficient. In those times, sugarcane bagasse did not have an economic value, and it was considered a problem by most mills. During the 1990s and the beginning of the 2000s, sugarcane industry faced an open market perspective, thus, there was a great necessity to reduce costs in the production processes. In addition, the economic value of by-products (bagasse, molasses, etc.) increased, and there was a possibility of selling electricity to the grid. This new scenario led to a search for more advanced cogeneration systems, based mainly on higher steam parameters (40-80 bar and 400-500 degrees C). In the future, some authors suggest that biomass integrated gasification combined cycles are the best alternative to cogeneration plants in sugarcane mills. These systems might attain 35-40% efficiency for the power conversion. However, supercritical steam cycles might also attain these efficiency values, what makes them an alternative to gasification-based systems. This paper presents a comparative thermoeconomic study of these systems for sugarcane mills. The configurations studied are based on real systems that could be adapted to biomass use. Different steam consumptions in the process are considered, in order to better integrate these configurations in the mill. (C) 2009 Elsevier Ltd. All rights reserved.

Obtaining and selection of hexokinases-less strains of Saccharomyces cerevisiae for production of ethanol and fructose from sucrose

Saccharomyces cerevisiae hexokinase-less strains were produced to study the production of ethanol and fructose from sucrose. These strains do not have the hexokinases A and B. Twenty-three double-mutant strains were produced, and then, three were selected for presenting a smaller growth in yeast extract-peptone-fructose. In fermentations with a medium containing sucrose (180.3 g L-1) and with cell recycles, simulating industrial conditions, the capacity of these mutant yeasts in inverting sucrose and fermenting only glucose was well characterized. Besides that, we could also see their great tolerance to the stresses of fermentative recycles, where fructose production (until 90 g L-1) and ethanol production (until 42.3 g L-1) occurred in cycles of 12 h, in which hexokinase-less yeasts performed high growth (51.2% of wet biomass) and viability rates (77% of viable cells) after nine consecutive cycles.

Biogeochemical cycles of nutrients in tropical Eucalyptus plantations Main features shown by intensive monitoring in Congo and Brazil

The sustainability of fast-growing tropical Eucalyptus plantations is of concern in a context of rising fertilizer costs, since large amounts of nutrients are removed with biomass every 6-7 years from highly weathered soils. A better understanding of the dynamics of tree requirements is required to match fertilization regimes to the availability of each nutrient in the soil. The nutrition of Eucalyptus plantations has been intensively investigated and many studies have focused on specific fluxes in the biogeochemical cycles of nutrients. However, studies dealing with complete cycles are scarce for the Tropics. The objective of this paper was to compare these cycles for Eucalyptus plantations in Congo and Brazil, with contrasting climates, soil properties, and management practices. The main features were similar in the two situations. Most nutrient fluxes were driven by crown establishment the two first years after planting and total biomass production thereafter. These forests were characterized by huge nutrient requirements: 155, 10, 52, 55 and 23 kg ha(-1) of N, P, K, Ca and Mg the first year after planting at the Brazilian study site, respectively. High growth rates the first months after planting were essential to take advantage of the large amounts of nutrients released into the soil solutions by organic matter mineralization after harvesting. This study highlighted the predominant role of biological and biochemical cycles over the geochemical cycle of nutrients in tropical Eucalyptus plantations and indicated the prime importance of carefully managing organic matter in these soils. Limited nutrient losses through deep drainage after clear-cutting in the sandy soils of the two study sites showed the remarkable efficiency of Eucalyptus trees in keeping limited nutrient pools within the ecosystem, even after major disturbances. Nutrient input-output budgets suggested that Eucalyptus plantations take advantage of soil fertility inherited from previous land uses and that long-term sustainability will require an increase in the inputs of certain nutrients. (C) 2009 Elsevier B.V. All rights reserved.

Biochemical responses of the ethylene-insensitive Never ripe tomato mutant subjected to cadmium and sodium stresses

In order to further address the known interaction between ethylene and components of the oxidative system, we have used the ethylene-insensitive Never ripe (Nr) tomato (Solanum lycopersicum L) mutant, which blocks ethylene responses. The mutant was compared to the control Micro-Tom (MT) cultivar subjected to two stressful situations: 100 mM NaCl and 0.5 mM CdCl(2). Leaf chlorophyll, lipid peroxidation and antioxidant enzyme activities in roots, leaves and fruits, and Na and Cd accumulation in tissues were determined. Although we verified a similar growth pattern and Na and Cd accumulation for MT and Nr, the mutant exhibited reduced leaf chlorophyll degradation following stress. In roots and leaves, the patterns of catalase (CAT), glutathione reductase (GR), ascorbate peroxidase (APX), guaiacol peroxidase (GPOX), superoxide dismutase (SOD) enzyme activity as well as malondialdehyde (MDA) and hydrogen peroxide (H(2)O(2)) production under the stressful conditions tested were very similar between MT and Nr mutant. However, Nr fruits showed increased H(2)O(2) production, reduced and enhanced APX activity in NaCl and CdCl(2), respectively, and enhanced GPOX in NaCl. Moreover, through non-denaturing PAGE, a similar reduction of SOD I band intensity in both, control MT and Nr mutant, treated with NaCl was observed. In leaves and fruits, a similar SOD activity pattern was observed for all periods, genotypes and treatments. Overall the results indicate that the ethylene signaling associated with NR receptor can modulate the biochemical pathways of oxidative stress in a tissue dependent manner, and that this signaling may be different following Na and Cd exposure. (C) 2011 Elsevier B.V. All rights reserved.

Enhanced transpiration rate in the high pigment 1 tomato mutant and its physiological significance

Tomato high pigment (hp) mutants represent an interesting horticultural resource due to their enhanced accumulation of carotenoids, flavonoids and vitamin C. Since hp mutants are known for their exaggerated light responses, the molecules accumulated are likely to be antioxidants, recruited to deal with light and others stresses. Further phenotypes displayed by hp mutations are reduced growth and an apparent disturbance in water loss. Here, we examined the impact of the hp1 mutation and its near isogenic line cv Micro-Tom (MT) on stomatal conductance (gs), transpiration (E), CO(2) assimilation (A) and water use efficiency (WUE). Detached hp1 leaves lost water more rapidly than control leaves, but this behaviour was reversed by exogenous abscisic acid (ABA), indicating the ability of hp1 to respond to this hormone. Although attached hp1 leaves had enhanced gs, E and A compared to control leaves, genotypic differences were lost when water was withheld. Both instantaneous leaf-level WUE and long-term whole plant WUE did not differ between hp1 and MT. Our results indicate a link between exaggerated light response and water loss in hp1, which has important implications for the use of this mutant in both basic and horticultural research.