A Program for Fractal and Multifractal Analysis of Two-Dimensional Binary Images. Computer Algorithms versus Mathematical Theory.

In this paper we present a tool to carry out the multifractal analysis of binary, two-dimensional images through the calculation of the Rényi D(q) dimensions and associated statistical regressions. The estimation of a (mono)fractal dimension corresponds to the special case where the moment order is q = 0.

Phytoextraction of heavy metals from mine soils using hyperaccumulator plants.

Phytoextraction is an environmental-friendly and cost-effective technology that uses metal hyperaccumulator plants to remove heavy metals from soils. The metals are absorbed by the roots, transported and accumulated in the aerial parts of the plants, which can be harvested and eliminated. The aim of this work was to study some hyperaccumulator species that could be useful to decontaminate mine soils and also to investigate the bioavailability and uptake of these metals by plants with the addition of organic amendments. Pot experiments were performed with soil samples collected from two mining areas in the north of Madrid, where there was an intense mining activity more than 50 years ago. Three species (Thlaspi arvense, Brassica juncea and Atriplex halimus) were grown under controlled conditions in pots filled with contaminated soils mixed with 0 Mg, 30 Mg and 60 Mg per hectare of two different organic amendments: a commercial compost made of pine bark, peat and wood fiber and other made of horse and sheep manure and wood fiber. Plants were harvested at the end of their crop cycle and were digested in order to measure metal concentration (Zn, Cu and Cd) in roots and shoots. Highest plant metal concentration was observed in pots treated with pine bark amendment and with pure soil due to an increase in metal bioavailability with decreasing pH. Also in those treatments the total plant biomass was lower, even some plants could not germinate. On the contrary, there was a lower metal concentration in plant tissues of pots with manure because its higher pH whereas plant growth was significantly larger so there was an incresing amount of metals removed from soil by plants. Comparing the three species results indicate a higher total metal uptake in A. halimus than B. juncea and T. arvense. In conclusion, results show that pH affects metal bioavailability and uptake by hyperaccumulator plants. Addition of organic amendments could be a successful technique for stabilization of metals in contaminated soils.

The family of DOF transcription factors in Brachypodium distachyon: phylogenetic comparison with rice and barley DOFs and expression profiling

ABSTRACT: Transcription factors (TFs) are proteins that have played a central role both in evolution and in domestication, and are major regulators of development in living organisms. Plant genome sequences reveal that approximately 7% of all genes encode putative TFs. The DOF (DNA binding with One Finger) TF family has been associated with vital processes exclusive to higher plants and to their close ancestors (algae, mosses and ferns). These are seed maturation and germination, light-mediated regulation, phytohormone and plant responses to biotic and abiotic stresses, etc. In Hordeum vulgare and Oryza sativa, 26 and 30 different Dof genes, respectively, have been annotated. Brachypodium distachyon has been the first Pooideae grass to be sequenced and, due to its genomic, morphological and physiological characteristics, has emerged as the model system for temperate cereals, such as wheat and barley. RESULTS: Through searches in the B. distachyon genome, 27 Dof genes have been identified and a phylogenetic comparison with the Oryza sativa and the Hordeum vulgare DOFs has been performed. To explore the evolutionary relationship among these DOF proteins, a combined phylogenetic tree has been constructed with the Brachypodium DOFs and those from rice and barley. This phylogenetic analysis has classified the DOF proteins into four Major Cluster of Orthologous Groups (MCOGs). Using RT-qPCR analysis the expression profiles of the annotated BdDof genes across four organs (leaves, roots, spikes and seeds) has been investigated. These results have led to a classification of the BdDof genes into two groups, according to their expression levels. The genes highly or preferentially expressed in seeds have been subjected to a more detailed expression analysis (maturation, dry stage and germination). CONCLUSIONS: Comparison of the expression profiles of the Brachypodium Dof genes with the published functions of closely related DOF sequences from the cereal species considered here, deduced from the phylogenetic analysis, indicates that although the expression profile has been conserved in many of the putative orthologs, in some cases duplication followed by subsequent divergence may have occurred (neo-functionalization).

Validation of microsatellite markers for cytotype discrimination in the model grass Brachypodium distachyon

Brachypodium distachyon (2n = 2x = 10) is a small annual grass species where the existence of three different cytotypes (10, 20 and 30 chromosomes) has long been regarded as a case of autopolyploid series, with x = 5. However, it has been demonstrated that the cytotypes assumed to be polyploids represent two separate Brachypodium species recently named as B. stacei (2n = 2x = 20) and B. hybridum (2n = 4x = 30). The aim of this study was to find a PCR-based alternative approach that could replace standard cytotyping methods (i. e., chromosome counting and flow cytometry) to characterize each of the three Brachypodium species. We have analyzed with four microsatellite (SSR) markers eighty-three Brachypodium distachyon-type lines from varied locations in Spain, including the Balearic and Canary Islands. Within this set of lines, 64, 4 and 15 had 10, 20 and 30 chromosomes, respectively. The surveyed markers produced cytotype-specific SSR profiles. So, a single amplification product was generated in the diploid samples, with non-overlapping allelic ranges between the 2n = 10 and 2n = 20 cytotypes, whereas two bands, one in the size range of each of the diploid cytotypes, were amplified in the 2n = 30 lines. Furthermore, the remarkable size difference obtained with the SSR ALB165 allowed the identification of the Brachypodium species by simple agarose gel electrophoresis.

A PCR-based method for discriminating between high molecular weight glutenin subunits Bx7 and Bx7* in Triticum aestivum L

The correct assignment of high molecular weight glutenin subunit variants is a key task in wheat breeding. However, the traditional analysis by protein electrophoresis is sometimes difficult and not very precise. This work describes a novel DNA marker for the accurate discrimination between the Glu-B1 locus subunits Bx7 and Bx7*. The analysis of one hundred and forty two bread wheat cultivars from different countries has highlighted a great number of misclassifications in the literature that could lead to wrong conclusions in studies of the relationship between glutenin composition and wheat quality.

Diversity and Genetic structure of the Spanish collection of durum wheat (Triticum turgidum L) landraces

The objectives of this study were to assess diversity and genetic structure of a collection of Spanish durum wheat (Triticum turgidum L) landraces, using SSRs, DArTs and gliadin-markers, and to correlate the distribution of diversity with geographic and climatic features, as well as agro-morphological traits. A high level of diversity was detected in the genotypes analyzed, which were separated into nine populations with a moderate to great genetic divergence among them. The three subspecies taxa, dicoccon, turgidum and durum, present in the collection, largely determined the clustering of the populations. Genotype variation was lower in dicoccon (one major population) and turgidum (two major populations) than in durum (five major populations). Genetic differentiation by the agro-ecological zone of origin was greater in dicoccon and turgidum than in durum. DArT markers revealed two geographic substructures, east-west for dicoccon and northeast-southwest for turgidum. The ssp. durum had a more complex structure, consisting of seven populations with high intra-population variation. DArT markers allowed the detection of subgroups within some populations, with agro-morphological and gliadin differences, and distinct agro-ecological zones of origin. Two different phylogenetic groups were detected; revealing that some durum populations were more related to ssp. turgidum from northern Spain, while others seem to be more related to durum wheats from North Africa

Community Structurein Soil Porous System.

Soil is well recognized as a highly complex system. The interaction and coupled physical, chemical, and biological processes and phenomena occurring in the soil environment at different spatial and temporal scales are the main reasons for such complexity. There is a need for appropriate methodologies to characterize soil porous systems with an interdisciplinary character. Four different real soil samples, presenting different textures, have been modeled as heterogeneous complex networks, applying a model known as the heterogeneous preferential attachment. An analytical study of the degree distributions in the soil model shows a multiscaling behavior in the connectivity degrees, leaving an empirically testable signature of heterogeneity in the topology of soil pore networks. We also show that the power-law scaling in the degree distribution is a robust trait of the soil model. Last, the detection of spatial pore communities, as densely connected groups with only sparser connections between them, has been studied for the first time in these soil networks. Our results show that the presence of these communities depends on the parameter values used to construct the network. These findings could contribute to understanding the mechanisms of the diffusion phenomena in soils, such as gas and water diffusion, development and dynamics of microorganisms, among others.

Spatial variability patterns of some Vertisol properties at a field scale using standardized data

Spatial variability of Vertisol properties is relevant for identifying those zones with physical degradation. In this sense, one has to face the problem of identifying the origin and distribution of spatial variability patterns. The objectives of the present work were (i) to quantify the spatial structure of different physical properties collected from a Vertisol, (ii) to search for potential correlations between different spatial patterns and (iii) to identify relevant components through multivariate spatial analysis. The study was conducted on a Vertisol (Typic Hapludert) dedicated to sugarcane (Saccharum officinarum L.) production during the last sixty years. We used six soil properties collected from a squared grid (225 points) (penetrometer resistance (PR), total porosity, fragmentation dimension (Df), vertical electrical conductivity (ECv), horizontal electrical conductivity (ECh) and soil water content (WC)). All the original data sets were z-transformed before geostatistical analysis. Three different types of semivariogram models were necessary for fitting individual experimental semivariograms. This suggests the different natures of spatial variability patterns. Soil water content rendered the largest nugget effect (C0 = 0.933) while soil total porosity showed the largest range of spatial correlation (A = 43.92 m). The bivariate geostatistical analysis also rendered significant cross-semivariance between different paired soil properties. However, four different semivariogram models were required in that case. This indicates an underlying co-regionalization between different soil properties, which is of interest for delineating management zones within sugarcane fields. Cross-semivariograms showed larger correlation ranges than individual, univariate, semivariograms (A ≥ 29 m). All the findings were supported by multivariate spatial analysis, which showed the influence of soil tillage operations, harvesting machinery and irrigation water distribution on the status of the investigated area.

Nitrogen uptake dynamics, yield and quality as influenced by nitrogen fertilization in "Piel de sapo" melon.

The need to reduce nitrogen (N) fertilizer pollution strengthens the importance of improving the utilization efficiency of applied N to crops. This requires knowledge of crop N uptake characteristics and how fertilization management affects it. A three-year field experiment was conducted from May to September in central Spain to investigate the influence of different N rates, which ranged from 11 to 393 kg ha-1, applied through drip irrigation, on the dynamics of N uptake, nitrogen use efficiency (NUE), fruit yield and quality of a ?Piel de sapo? melon crop (Cucumis melo L. cv. Sancho). Both N concentration and N content increased in different plant parts with the N rate. Leaves had the highest N concentration, which declined by 40-50% from 34-41 days after transplanting (DAT), while the highest N uptake rate was observed from 30-35 to 70-80 DAT, coinciding with fruit development. In each year, NUE declined with increasing N rate. With N fertilizer applications close to the optimum N rate of 90-100 kg ha-1, the fruits removed approximately 60 kg N ha-1, and the amount of N in the crop residue was about 80 kg N ha-1; this serves to replenish the organic nutrient pool in the soil and may be used by subsequent crops following mineralization.

Fractal scaling of apparent soil moisture estimated from vertical planesof Vertisol pit images

Image analysis could be a useful tool for investigating the spatial patterns of apparent soil moisture at multiple resolutions. The objectives of the present work were (i) to define apparent soil moisture patterns from vertical planes of Vertisol pit images and (ii) to describe the scaling of apparent soil moisture distribution using fractal parameters. Twelve soil pits (0.70 m long × 0.60 m width × 0.30 m depth) were excavated on a bare Mazic Pellic Vertisol. Six of them were excavated in April/2011 and six pits were established in May/2011 after 3 days of a moderate rainfall event. Digital photographs were taken from each Vertisol pit using a Kodak? digital camera. The mean image size was 1600 × 945 pixels with one physical pixel ?373 ?m of the photographed soil pit. Each soil image was analyzed using two fractal scaling exponents, box counting (capacity) dimension (DBC) and interface fractal dimension (Di), and three prefractal scaling coefficients, the total number of boxes intercepting the foreground pattern at a unit scale (A), fractal lacunarity at the unit scale (?1) and Shannon entropy at the unit scale (S1). All the scaling parameters identified significant differences between both sets of spatial patterns. Fractal lacunarity was the best discriminator between apparent soil moisture patterns. Soil image interpretation with fractal exponents and prefractal coefficients can be incorporated within a site-specific agriculture toolbox. While fractal exponents convey information on space filling characteristics of the pattern, prefractal coefficients represent the investigated soil property as seen through a higher resolution microscope. In spite of some computational and practical limitations, image analysis of apparent soil moisture patterns could be used in connection with traditional soil moisture sampling, which always renders punctual estimates.

Nitrogen Fertirrigation: an Integrated Agronomic and Environmental Study

Proper management of the N applied to crops is necessary in order to increase yield, improve water use efficiency (WUE) and reduce the pollutions risks with the least economic, environmental and health costs. A field study with melon crops was conducted during 2005, 2006 and 2007 in central Spain, using 11 different amounts of N. Some environmental indexes have been proposed, to provide an essential tool for determining the groundwater pollution risks associated with common agricultural practices. These indexes are related to variation in the nitrate concentration of drinking water (Impact Index (II)) and groundwater (Environmental Impact Index (EII)). Also, the Management Efficiency (ME) was calculated, which is related to the amount of fruit produced per gram of N leached (Nl). To determine the optimum dose of N, it was also necessary to know the N mineralisation (NM). Our results show that 160 kg ha?1 of available N (Nav) produced the maximum fruit yield (FY), enhanced WUE and gave an NM of 85 kg ha?1, while the impact indexes did not exceed the fixed maximum allowable limits and ME was adequate. The proposed indexes proved to be an effective tool for determining the risk of nitrate contamination and confirmed that the optimum dose of N corresponded to the maximum FY with minimal loss of Nl.

Impact of nitrogen uptake on field water balance in fertirrigated melon.

Agronomic management in Ciudad Real, a province in central Spain, is characteristic of semi-arid cropped areas whose water supplies have high nitrate (NO3?) content due to environmental degradation. This situation is aggravated by the existence of a restrictive subsurface layer of ?caliche? or hardpan at a depth of 0.60 m. Under these circumstances, fertirrigation rates, including nitrogen (N) fertilizer schedules, must be carefully calibrated to optimize melon yields while minimizing the N pollution and water supply. Such optimization was sought by fertilizing with different doses of N and irrigating at 100% of the ETc (crop evapotranspiration), adjusted for this crop and area. The N content in the four fertilizer doses used was: 0, 55, 82 and 109 kg N ha?1. Due to the NO3? content in the irrigation water, however, the actual N content was 30 kg ha?1 higher in all four treatments repeated in two different years. The results showed correlation between melon plant N uptake and drainage (Dr), which in turn affects the amount of N leached, as well as correlation between Dr and LAI (leaf area index) for each treatment. A fertilizer factor (?) was estimated through two methods, from difference in Dr and in LAI ratio with respect to the maximum N dose, to correct ETc based on N doses. The difference was found in the adjusted evapotranspiration in both years using the corresponding ? achieved 42?49 mm at vegetative period, depending on the method, and it was not significant at senescent period. Finally, a growth curve between N uptake and plant dry weight (DW) for each treatment was defined to confirm that the observed higher plant vigour, showing higher LAI and reduced Dr, was due mainly to higher N doses.

Influence of energy concentration and feed form of the diet on growth performance and digestive traits of brown egg-laying pullets from 1 to 120 days of age

Full paper reserch

The use of wind pumps for greenhouse microirrigation: a case study for tomato in Cuba.

Crop irrigation is a major consumer of energy. Only a few countries are self-sufficient in conventional non-renewable energy sources. Fortunately, there are renewable ones, such as wind, which has experienced recent developments in the area of power generation. Wind pumps can play a vital role in irrigation projects in remote farms. A methodology based on daily estimation balance between water needs and water availability was used to evaluate the feasibility of the most economic windmill irrigation system. For this purpose, several factors were included: three-hourly wind velocity (W3 h, m/s), flow supplied by the wind pump as a function of the elevation height (H, m) and daily greenhouse evapotranspiration as a function of crop planting date. Monthly volumes of water required for irrigation (Dr, m3/ha) and in the water tank (Vd, m3), as well as the monthly irrigable area (Ar, ha), were estimated by cumulative deficit water budgeting taking in account these factors. An example is given illustrating the use of this methodology on tomato crop (Lycopersicon esculentum Mill.) under greenhouse at Ciego de Ávila, Cuba. In this case two different W3 h series (average and low wind year), three different H values and five tomato crop planting dates were considered. The results show that the optimum period of wind-pump driven irrigation is with crop plating in November, recommending a 5 m3 volume tank for cultivated areas around 0.2 ha when using wind pumps operating at 15 m of height elevation.

Shadow Analysis of Soil Surface Roughness Compared to the Chain Set Method and Direct Measurement of Micro-relief.

Erosion potential and the effects of tillage can be evaluated from quantitative descriptions of soil surface roughness. The present study therefore aimed to fill the need for a reliable, low-cost and convenient method to measure that parameter. Based on the interpretation of micro-topographic shadows, this new procedure is primarily designed for use in the field after tillage. The principle underlying shadow analysis is the direct relationship between soil surface roughness and the shadows cast by soil structures under fixed sunlight conditions. The results obtained with this method were compared to the statistical indexes used to interpret field readings recorded by a pin meter. The tests were conducted on 4-m2 sandy loam and sandy clay loam plots divided into 1-m2 subplots tilled with three different tools: chisel, tiller and roller. The highly significant correlation between the statistical indexes and shadow analysis results obtained in the laboratory as well as in the field for all the soil?tool combinations proved that both variability (CV) and dispersion (SD) are accommodated by the new method. This procedure simplifies the interpretation of soil surface roughness and shortens the time involved in field operations by a factor ranging from 12 to 20.