Codon usage bias and A+T content variation in human papillomavirus genomes

We analyzed the codon usage bias of eight open reading frames (ORFs) across up to 79 human papillomavirus (HPV) genotypes from three distinct phylogenetic groups. All eight ORFs across HPV genotypes show a strong codon usage bias, amongst degenerately encoded amino acids, toward 18 codons mainly with T at the 3rd position. For all 18 degenerately encoded amino acids, codon preferences amongst human and animal PV ORFs are significantly different from those averaged across mammalian genes. Across the HPV types, the L2 ORFs show the highest codon usage bias (73.2 +/- 1.6% and the E4 ORFs the lowest (51.1 +/- 0.5%), reflecting as similar bias in codon 3rd position A + T content (L2: 76.1 +/- 4.2%; E4: 58.6 +/- 4.5%). The E4 ORF, uniquely amongst the HPV ORFs, is G + C rich, while the other ORFs are A + T rich. Codon usage bias correlates positively with A + T content at the codon 3rd position in the E2, E6, L1 and L2 ORFs, but negatively in the E4 ORFs. A general conservation of preferred codon usage across human and non-human PV genotypes whether they originate from a same supergroup or not, together with observed difference between the preferred codon usage for HPV ORFs and for genes of the cells they infect, suggests that specific codon usage bias and A + T content variation may somehow increase the replicational fitness of HPVs in mammalian epithelial cells, and have practical implications for gene therapy of HPV infection. (C) 2003 Elsevier B.V. All rights reserved.

Integrated control of nitrate recirculation and external carbon addition in a predenitrification system

The integrated control of nitrate recirculation and external carbon addition in a predenitrification biological wastewater treatment system is studied. The proposed control structure consists of four feedback control loops, which manipulate the nitrate recirculation and the carbon dosage flows in a highly coordinated manner such that the consumption of external carbon is minimised while the nitrate discharge limits (based on both grab and composite samples) are met. The control system requires the measurement of the nitrate concentrations at the end of both the anoxic and the aerobic zones. Distinct from ordinary control systems, which typically minimise the variation in the controlled variables, the proposed control system essentially maximises the diurnal variation of the effluent nitrate concentration and through this maximises the use of influent COD for denitrification, thus minimising the requirement for external carbon source. Simulation studies using a commonly accepted simulation benchmark show that the controlled system consistently achieves the designated effluent quality with minimum costs.

Nitrate ammonification and its relationship to the accumulation of ammonium in a Vertisol subsoil

High concentrations of ammonium ( up to 270 kg N/ha) have been observed in a Vertisol soil below 1 m depth near Warra in south-east Queensland. This study examined the possibility that increased water movement into the subsoil after the removal of native vegetation, and a subsequent increase in periods of waterlogging, could have triggered nitrate ammonification and be responsible for the production of ammonium. Two incubation experiments were conducted to test this hypothesis. The first involved the incubation of repacked cores that had been amended with 30 mg N/kg of 5 atom% N-15 nitrate under low oxygen conditions for a period of 360 days. Over this time period the N-15 enrichment of the exchangeable ammonium fraction was monitored in order to detect any reduction of nitrate to ammonium. The second experiment involved the incubation of soil amended with 30 mg N/ kg of 5 atom% N-15 nitrate under waterlogged and low oxygen conditions for 75 days. During this period the redox potential of the soil was monitored using a field test to determine if reducing conditions would develop in this soil over a period of waterlogging, combined with the monitoring of any nitrate reduction to ammonium. The results of these experiments indicated that a small amount of nitrate ammonification (< 0.1 mg N/ kg) could be observed in the Warra subsoil, but that unless the rate of reduction were to significantly increase with time, this could not account for the accumulation of ammonium observed in the field. The environmental conditions that would make either dissimilatory or abiotic nitrate ammonification favourable were not observed to develop. Consequently, it has been concluded that the observed nitrate ammonification occurred via an assimilatory pathway. Due to the low rate of microbial activity in this subsoil it is considered unlikely that this process was responsible for the subsoil ammonium accumulation at Warra.

Nitrate retention under sugarcane in wet tropical Queensland deep soil profiles

Nitrate leaching below the crop root-zone in variable charge soils may be adsorbed at anion exchange sites, thereby temporarily reducing the risk of contamination of water bodies. The objectives of this study were (i) to investigate whether nitrate adsorption, accumulation, and retention in the Johnstone River Catchment of Far North Queensland wet tropics is widespread; (ii) to assess the capacity of soil in the Johnstone River Catchment to retain nitrate; and (iii) to deduce the consequences of nitrate adsorption/desorption on contamination of water bodies. Soil cores ranging from 8 to 12.5 m depth were taken from 28 sites across the catchment, representing 9 Ferrosol soil types under sugarcane (Saccharum officinarum-S) cultivation for at least 50 years and from rainforest. The cores were segmented at 0.5-m depth increments and subsamples were analysed for nitrate-N, cation and anion exchange capacities, pH, exchangeable cations (Ca, Mg, K, Na), soil organic C, electrical conductivity, sulfate-S, and chloride. Nitrate-N concentration under sugarcane ranged from 0 to 72.5 mg/kg, compared with 0 to 0.31 mg/kg under rainforest, both Pin Gin soils. The average N load in 1-12 m depth across 19 highly oxidic profiles of the Pin Gin soil series was 1550 kg/ha, compared with 185 kg/ha under 8 non-Pin Gin soils and 11 kg/ha in rainforest on a Pin Gin soil. Most of the nitrate retention was observed at depth of 2-12 m, particularly at 4-10 m, indicating that the accumulation was well below the crop root-zone. The average maximum potential nitrate retention capacity was 10.8 t/ha for the Pin Gin and 4.7 t/ha for the non-Pin Gin soil. Compared with the current N load, the soils still possess a large capacity to adsorb and retain nitrate in profiles. Retention of large quantities of the leached nitrate deep in most of the profiles has reduced the risk of contamination of water bodies. However, computations show that substantial quantities of the nitrate leached below the root-zone were not adsorbed and remain unaccounted for. This unaccounted nitrate might have entered both on- and off-site water bodies and/or have been denitrified.

Efeitos da depleção de nitrogênio sobre a biomassa e produção lipídica lipídica de três espécies de microalgas fitoplânticas

O uso de lipídios obtidos a partir da biomassa de microalgas tem sido descrito como uma alternativa promissora para a indústria petro-diesel e envolve etapas como o cultivo de microalgas, separação da biomassa e extração de lipídios. Para viabilizar a produção em larga escala, é necessário selecionar as espécies mais produtivas, diminuir os custos de produção e determinar as condições ideais de cultivo. Os gêneros Chlorella, Desmodesmus e Ankistrodesmus apresentam características favoráveis à produção comercial, tendo sido então selecionada uma espécie de cada no presente trabalho. O objetivo do estudo foi avaliar diferentes condições de cultivo de Ankistrodesmus fusiformis, Chlorella vulgaris e Desmodesmus spinosus visando o aumento da produtividade em biomassa e lipídios totais. As algas foram identificadas e cultivadas em laboratório, em condições controladas de temperatura a 26ºC (±1), aeração por borbulhamento à pressão ambiente e luminosidade fornecida por lâmpadas fluorescentes, com intensidade de 47,25 μmol de fótons m-2.s-1 (3500 lux), fotoperiodo de 12h e pH 7, sob duas concentrações estressantes de nitrato de sódio (0,10 g/L e 0,05g/L). Os cultivos duraram em média 16 dias, sendo as curvas de crescimento construídas com dados de espectrofotometria óptica coletados a cada 48h, e a biomassa obtida ao final do cultivo por centrifugação e liofilização de cada unidade experimental. Para extração dos lipídios totais, foi utilizada a mistura de clorofórmio: metanol (1:2), segundo a metodologia de Bligh & Dyer (1959). Os tratamentos de estresse em D.spinosus resultaram em maior acúmulo lipídico, com aumento de até 149,7%, porém com drástica diminuição do crescimento e biomassa. Em C. vulgaris, nos tratamentos de estresse, verificou-se apenas ligeiro aumento do peso seco e teor de lipídios, não havendo diferença significativa entre os tratamentos e o controle. Da mesma forma, A.fusiformis não mostrou respostas significativas ao estresse pela redução de nitrato de sódio do meio, havendo ligeira diminuição do conteúdo lipídico e aumento do crescimento e biomassa. Com respostas diferentes para cada espécie estudada, evidencia-se a necessidade do conhecimento da fisiologia e autoecologia da cepa a ser cultivada em escala comercial visando à produção de ácidos graxos para fins de biodiesel.

SPAD-502 readings in response to photon fluence in leaves with different chlorophyll content

The chlorophyll meter (SPAD-502) is widely used to estimate chlorophyll content, but non-uniform chloroplast distribution can affect its accuracy. This study aimed to assess the effect of photon fluence (F, irradiance x time of illumination) in leaves with different chlorophyll content and determine the effect of chlorophyll a/b on SPAD values of four tropical tree species (Croton draconoides Müll. Arg., Hevea guianensis Aubl., Hymenaea courbaril L. and Matisia cordata H.B.K.). There were also determined calibration equations for the chlorophyll meter and assessed the effect of F on SPAD values between 07:00 h and 17:00 h. Calibration equations were obtained after determining leaf chlorophyll content in the laboratory. Increases in F with time caused a reduction in SPAD values in species with a high chlorophyll content, with reductions of 20% in M. cordata and 10% in H. guianensis. Leaves of C. draconoides and H. courbaril had lower chlorophyll content and showed no changes in SPAD values with increase in F. The chlorophyll a/b ratio increased with SPAD values and the SPAD/chlorophyll relationship was best described by an exponential equation. It seems that F may affect SPAD values in leaves with high chlorophyll content, probably due to non-uniform chloroplast distribution at high irradiance. This indicates that SPAD values tend to be more accurate if recorded early in morning when irradiance is low.

Correlation between grain nutritional content and pasting properties of pre-gelatinized red rice flour

As with any variety of rice, red rice characteristics are subject to varietal differences, growing conditions, types of processing, and nutritional and rheological properties. This study determined the nutritional characteristics (centesimal composition and minerals) and paste viscosity properties of raw grains of four red rice genotypes (Tradicional MNAPB0405, MNACE0501 and MNACH0501) and the paste viscosity properties of pre-gelatinized flours obtained at different cooking times (20, 30 and 40 min). The main nutritional properties were correlated with the pasting properties of the pre-gelatinized flours. The samples showed differences in nutritional properties and paste viscosity. MNAPB0405 and MNACE0501 showed higher levels of fiber and fat and provided higher caloric energy than Tradicional and MNACH0501, which, in turn, showed higher levels of amylose. MNACH0501 showed higher peak viscosity (2402 cP), higher breakdown viscosity (696 cP) and a greater tendency to retrogradation (1510 cP), while Tradicional, MNAPB0405 and MNACE0501 had pasting profiles with peak viscosities varying between 855 and 1093 cP, breaking viscosity below 85 cP and retrogradation tendency between 376 and 1206 cP. The factors genotype and cooking time influenced the rheological behavior of pre-gelatinized flours, decreasing their pasting properties. The protein and amylose levels are correlated with the pasting properties and can be used as indicators of these properties in different genotypes of red rice, whether raw or processed into pre-gelatinized flours.

Carbon Nanofiber Type and Content Dependence of the Physical Properties of Carbon Nanofiber Reinforced Polypropylene Composites

The variation of the physical properties of four differ- ent carbon nanofibers (CNFs), based-polymer nano- composites incorporated in the same polypropylene (PP) matrix by twin-screw extrusion process was investigated. Nanocomposites fabricated with CNFs with highly graphitic outer layer revealed electrical isolation-to-conducting behaviors as function of CNF’s content. Nanocomposites fabricated with CNFs with an outer layer consisting on a disordered pyro- litically stripped layer, in contrast, revealed better mechanical performance and enhanced thermal sta- bility. Further, CNF’s incorporation into the polymer increased the thermal stability and the degree of crystallinity of the polymer, independently on the filler content and type. In addition, dispersion of the CNFs’ clusters in PP was analyzed by transmitted light opti- cal microscopy, and grayscale analysis (GSA). The results showed a correlation between the filler concentration and the variance, a parameter which measures quantitatively the dispersion, for all composites. This method indicated a value of 1.4 vol% above which large clusters of CNFs cannot be dispersed effectively and as a consequence only slight changes in mechanical performance are observed. Finally, this study establishes that for tailoring the physical properties of CNF based-polymer nanocomposites, both adequate CNFs structure and content have to be chosen.

Effect of filler content on morphology and physical-chemical characteristics of poly(vinylidene fluoride)/NaY-zeolite filled membranes

Poly(vinylidene fluoride) electrospun membranes have been prepared with different NaY zeolite contents up to 32%wt. Inclusion of zeolites induces an increase of average fiber size from ~200 nm in the pure polymer up to ~500 nm in the composite with 16%wt zeolite content. For higher filler contents, a wider distribution of fibers occurs leading to a broader size distributions between the previous fiber size values. Hydrophobicity of the membranes increases from ~115º water contact angle to ~128º with the addition of the filler and is independent on filler content, indicating a wrapping of the zeolite by the polymer. The water contact angle further increases with fiber alignment up to ~137º. Electrospun membranes are formed with ~80 % of the polymer crystalline phase in the electroactive  phase, independently on the electrospinning processing conditions or filler content. Viability of MC3T3-E1 cells on the composite membranes after 72 h of cell culture indicates the suitability of the membranes for tissue engineering applications.

Nitrate leaching through climatologic water balance in a fertigated coffee plantation

Nitrate losses from soil profiles by leaching should preferentially be monitored during high rainfall events and during irrigation when fertilizer nitrogen applications are elevated. Using a climatologic water balance, based on the models of Thornthwaite and Penman Monteith for potential evapotranspiration, drainage soil water fluxes below the root zone were estimated in a fertigated coffee crop. Soil solution extraction at the depth of 1 m allowed the calculation of nitrate leaching. The average nitrate concentration in soil solution for plots that received nitrogen by fertigation at a rate of 400 kg ha-1, was 5.42 mg L-1, surpassing the limit of the Brazilian legislation of 10.0 mg L-1, only during one month. For plots receiving 800 kg ha-1 of nitrogen, the average was 25.01 mg L-1, 2.5 times higher than the above-mentioned limit. This information indicates that nitrogen rates higher than 400 kg ha-1 are potentially polluting the ground water. Yearly nitrate amounts of leaching were 24.2 and 153.0 kg ha-1 for the nitrogen rates of 400 and 800 kg ha-1, respectively. The six times higher loss indicates a cost/benefit problem for coffee fertigations above 400 kg ha-1.

Leaf area and epicuticular wax content of Sida spp

Morpho-physiological characteristics and chemical composition are directly related to superior competitive ability of crops. This study intended to make a comparative analysis of dry matter production, leaf area and amount of epicuticular wax of three species of Sida spp: S. urens L., S. rhombifolia L. and S. spinosa L. Plants were collected at three growth stages: V1: stage described as up to 10 fully expanded leaves; V2: between 11 leaves and flowering; and R: after flowering. At stages V2 and R, the highest number of leaves was recorded for S. rhombifolia, followed by S. spinosa at V2 and S. urens at R. These results were relatively proportional to leaf area for all species. S. spinosa at the vegetative stage produced the highest values of specific leaf area (SLA), with no significant differences between species at the stage R. The amount of wax per unit of leaf area between species at the same developmental stage was significantly different only at the reproductive stage, where S. spinosa produced 23.18 and 6.23 fold more wax than S. urens and S. rhombifolia respectively. Between the growth stages of each species, there was decrease in the amount of wax with plant age and increase in leaf area (AFE), number of leaves and dry matter. The leaves of the Sida species exhibit different characteristics and this information can be used to optimize the use of herbicides in the control of these weeds.

Effect of biostimulant application on production and flavonoid content of marigold (Calendula officinalis L.)

The production of medicinal plants as raw material for industry must associate quality with biomass formation and, with this purpose, the application of plant growth regulators has been studied in these crops. The objective of this study was to evaluate the effect of a biostimulant on growth, inflorescence production and flavonoid content in marigold. The experiment was conducted in a greenhouse and the treatments consisted of increasing doses of the biostimulant (0, 3, 6, 9, 12 and 15 mL L-1) applied by foliar spraying in ten consecutive applications. The experiment was arranged in a completely randomized design, with six treatments and ten repetitions. The number of leaves and flowerheads and dry matter of roots increased linearly with increasing doses of the growth promoter, with 20%, 36.97% and 97.28% increases, respectively, compared with the control. The total dry mass and shoot dry mass showed maximum values at the highest dose tested of 15 mL L-1 (with increases of 40.09% and 46.30%, respectively). Plant height and flavonoid content reached the highest values at a dose of 6 mL L-1. The biostimulant promoted the development of marigold and positively influenced the synthesis of the secondary compound of medicinal interest. Among the tested doses, the application of rates between 6 and 9 mL L-1 of the biostimulant is recommended for more efficient large-scale production of marigold.

Juvenile tree growth correlates with photosynthesis and leaf phosphorus content in central Amazonia

Light and soil water availability may limit carbon uptake of trees in tropical rainforests. The objective of this work was to determine how photosynthetic traits of juvenile trees respond to variations in rainfall seasonality, leaf nutrient content, and opening of the forest canopy. The correlation between leaf nutrient content and annual growth rate of saplings was also assessed. In a terra firme rainforest of the central Amazon, leaf nutrient content and gas exchange parameters were measured in five sapling tree species in the dry and rainy season of 2008. Sapling growth was measured in 2008 and 2009. Rainfall seasonality led to variations in soil water content, but it did not affect leaf gas exchange parameters. Subtle changes in the canopy opening affected CO2 saturated photosynthesis (A pot, p = 0.04). Although A pot was affected by leaf nutrient content (as follows: P > Mg > Ca > N > K), the relative growth rate of saplings correlated solely with leaf P content (r = 0.52, p = 0.003). At present, reduction in soil water content during the dry season does not seem to be strong enough to cause any effect on photosynthesis of saplings in central Amazonia. This study shows that leaf P content is positively correlated with sapling growth in the central Amazon. Therefore, the positive effect of atmospheric CO2 fertilization on long-term tree growth will depend on the ability of trees to absorb additional amount of P

Productivity of irrigated beans due to sources of stabilized nitrogen fertilizer and controlled release

ABSTRACT New nitrogen fertilizers are available in the market actually, however, does not have results on the efficiency of the Cerrado conditions. With that objective of this study was to evaluate the effect of urea including stabilized and controlled release urea on yield of irrigated common beans (Phaseolus vulgaris L) in no-tillage system. The experiment was conducted in the winter crop, at Embrapa Arroz e Feijão, in Santo Antônio de Goiás, State of Goiás, Brazil. The experimental design was randomized blocks, with five replicates. Treatments consisted of five N sources (urea, urea + NBPT, urea + polymer, ammonium sulphate, and ammonium nitrate) and a control (without N) being applied 20 kg ha-1 of N at sowing and 80 kg ha-1 onf N in topdressing. We evaluated the chlorophyll content in leaves of common beans, the leaf N content and dry mass weight (MSPA) in the flowering of common beans, the number of pods per plant, number of grains per pod, mass of 100 grains, grain yield and final stand of the common beans. The sources of nitrogen fertilizer did not influence, leaf N content, the mass of MSPA and the relative chlorophyll index of common beans. The use of polymerized urea and urea with urease inhibitor, did not produce increases in the number of grains per pod, number of pods per plant, mass of 100 grains and common beans yield compared to traditional sources of N, urea, ammonium sulfate and ammonium nitrate.