In vitro whole-genome analysis identifies a susceptibility locus for HIV-1.

Advances in large-scale analysis of human genomic variability provide unprecedented opportunities to study the genetic basis of susceptibility to infectious agents. We report here the use of an in vitro system for the identification of a locus on HSA8q24.3 associated with cellular susceptibility to HIV-1. This locus was mapped through quantitative linkage analysis using cell lines from multigeneration families, validated in vitro, and followed up by two independent association studies in HIV-positive individuals. Single nucleotide polymorphism rs2572886, which is associated with cellular susceptibility to HIV-1 in lymphoblastoid B cells and in primary T cells, was also associated with accelerated disease progression in one of two cohorts of HIV-1-infected patients. Biological analysis suggests a role of the rs2572886 region in the regulation of the LY6 family of glycosyl-phosphatidyl-inositol (GPI)-anchored proteins. Genetic analysis of in vitro cellular phenotypes provides an attractive approach for the discovery of susceptibility loci to infectious agents.

Root growth of tomato seedlings intensified by humic substances from peat bogs

Peats are an important reserve of humified carbon in terrestrial ecosystems. The interest in the use of humic substances as plant growth promoters is continuously increasing. The objective of this study was to evaluate the bioactivity of alkaline soluble humic substances (HS), humic (HA) and fulvic acids (FA) isolated from peats with different decomposition stages of organic matter (sapric, fibric and hemic) in the Serra do Espinhaço Meridional, state of Minas Gerais. Dose-response curves were established for the number of lateral roots growing from the main plant axis of tomato seedlings. The bioactivity of HA was greatest (highest response in lateral roots at lowest concentration) while FA did not intensify root growth. Both HS and HA stimulated root hair formation. At low concentrations, HS and HA induced root hair formation near the root cap, a typical hormonal imbalance effect in plants. Transgenic tomato with reporter gene DR5::GUS allowed the observation that the auxin-related signalling pathway was involved in root growth promotion by HA.

Alpine and pre-Alpine magmatism in the root-zone of the western Central Alps

The highest grade of metamorphism and associated structural elements in orogenic belts may be inherited from earlier orogenic events. We illustrate this point using magmatic and metamorphic rocks from the southern steep belt of the Lepontine Gneiss Dome (Central Alps). The U-Pb zircon ages from an anatectic granite at Verampio and migmatites at Corcapolo and Lavertezzo yield 280-290 Ma, i.e., Hercynian ages. These ages indicate that the highest grade of metamorphism in several crystalline nappes of the Lepontine Gneiss Dome is pre-Alpine. Alpine metamorphism reached sufficiently high grade to reset the Rb-Sr and K-Ar systematics of mica and amphibole, but generally did not result in crustal melting, except in the steep belt to the north of the Insubric Line, where numerous 29 to 26 Ma old pegmatites and aplites had intruded syn- and post-kinematically into gneisses of the ductile Simplon Shear Zone. The emplacement age of these pegmatites gives a minimum estimate for the age of the Alpine metamorphic peak in the Monte Rosa nappe. The U-Pb titanite ages of 33 to 31 Ma from felsic porphyritic veins represent a minimum-age estimate for Alpine metamorphism in the Sesia Zone. A porphyric vein emplaced at 448 +/- 5 Ma (U-Pb monazite) demonstrates that there existed a consolidated Caledonian basement in the Sesia Zone.

Soil physical properties and sugarcane root growth in a red oxiso

Sugarcane, which involves the use of agricultural machinery in all crop stages, from soil preparation to harvest, is currently one of the most relevant crops for agribusiness in Brazil. The purpose of this study was to investigate soil physical properties and root growth in a eutroferric red Oxisol (Latossolo Vermelho eutroférrico) after different periods under sugarcane. The study was carried out in a cane plantation in Rolândia, Paraná State, where treatments consisted of a number of cuts (1, 3, 8, 10 and 16), harvested as green and burned sugarcane, at which soil bulk density, macro and microporosity, penetration resistance, as well as root length, density and area were determined. Results showed that sugarcane management practices lead to alterations in soil penetration resistance, bulk density and porosity, compared to native forest soil. These alterations in soil physical characteristics impede the full growth of the sugarcane root system beneath 10 cm, in all growing seasons analyzed.

Characterization of the soil fertility and root system of restinga forests

The Restinga vegetation consists of a mosaic of plant communities, which are defined by the characteristics of the substrates, resulting from the type and age of the depositional processes. This mosaic complex of vegetation types comprises restinga forest in advanced (high restinga) and medium regeneration stages (low restinga), each with particular differentiating vegetation characteristics. The climate along the coast is tropical (Köppen). Of all ecosystems of the Atlantic Forest, Restinga is the most fragile and susceptible to anthropic disturbances. Plants respond to soil characteristics with physiological and morphological modifications, resulting in changes in the architecture (spatial configuration) of the root system. The purpose of this study was to characterize the soil fertility of high and low restinga forests, by chemical and physical parameters, and its relation to the root system distribution in the soil profile. Four locations were studied: (1) Ilha Anchieta State Park, Ubatuba; (2) two Ecological Stations of Jureia-Itatins and of Chauás, in the municipality of Iguape; (3) Vila de Pedrinhas in the municipality of Ilha Comprida; and (4) Ilha do Cardoso State Park, Cananeia. The soil fertility (chemical and physical properties) was analyzed in the layers 0-5, 0-10, 0-20, 20-40 and 40-60 cm. In addition, the distribution of the root system in the soil profile was evaluated, using digital images and the Spring program. It was concluded that the root system of all vegetation types studied is restricted to the surface layers, 0-10 and 10-20 cm, but occupies mainly the 0-10 cm layer (70 %); that soil fertility is low in all environments studied, with base saturation values below 16 %, since most exchange sites are occupied by aluminum; and that restinga vegetation is edaphic.

Aluminum in corn plants: influence on growth and morpho-anatomy of root and leaf

Aluminum (Al) toxicity is one of the most limiting factors for productivity. This research was carried out to assess the influence of Al nutrient solution on plant height, dry weight and morphoanatomical alterations in corn (Zea mays L.) roots and leaves. The experiment was conducted in a greenhouse with five treatments consisting of Al doses (0, 25, 75, 150, and 300 µmol L-1) and six replications. The solutions were constantly aerated, and the pH was initially adjusted to 4.3. The shoot dry matter, root dry matter and plant height decreased significantly with increasing Al concentrations. Compared to the control plants, it was observed that the root growth of corn plants in Al solutions was inhibited, there were fewer lateral roots and the development of the root system reduced. The leaf anatomy of plants grown in solutions containing 75 and 300 µmol L-1 Al differed in few aspects from the control plants. The leaf sheaths of the plants exposed to Al had a uniseriate epidermis coated with a thin cuticle layer, and the cells of both the epidermis and the cortex were less developed. In the vascular bundle, the metaxylem and protoxylem had no secondary walls, and the diameter of both was much smaller than of the control plants.

Estimation of soil moisture in the root-zone from remote sensing data

Field-based soil moisture measurements are cumbersome. Thus, remote sensing techniques are needed because allows field and landscape-scale mapping of soil moisture depth-averaged through the root zone of existing vegetation. The objective of the study was to evaluate the accuracy of an empirical relationship to calculate soil moisture from remote sensing data of irrigated soils of the Apodi Plateau, in the Brazilian semiarid region. The empirical relationship had previously been tested for irrigated soils in Mexico, Egypt, and Pakistan, with promising results. In this study, the relationship was evaluated from experimental data collected from a cotton field. The experiment was carried out in an area of 5 ha with irrigated cotton. The energy balance and evaporative fraction (Λ) were measured by the Bowen ratio method. Soil moisture (θ) data were collected using a PR2 - Profile Probe (Delta-T Devices Ltd). The empirical relationship was tested using experimentally collected Λ and θ values and was applied using the Λ values obtained from the Surface Energy Balance Algorithm for Land (SEBAL) and three TM - Landsat 5 images. There was a close correlation between measured and estimated θ values (p<0.05, R² = 0.84) and there were no significant differences according to the Student t-test (p<0.01). The statistical analyses showed that the empirical relationship can be applied to estimate the root-zone soil moisture of irrigated soils, i.e. when the evaporative fraction is greater than 0.45.

Somewhere between illusion of control and powerlessness : trying to situate the pathological gambler's locus of control

It has been suggested that pathological gamblers develop illusory perceptions of control regarding the outcome of the games and should express higher Internal and Chance locus of control. A sample of 48 outpatients diagnosed with pathological gambling disorder who participated in this ex post facto study, completed the Internality, Powerful Others, and Chance scale, the South Oaks Gambling Screen questionnaire, and the Beck Depression Inventory. Results for the locus of control measure were compared with a reference group. Pathological gamblers scored higher than the reference group on the Chance locus of control, which increased with the severity of cases. Moreover, Internal locus of control did show a curvilinear relationship with the severity of cases. Pathological gamblers have specific locus of control scores that vary in function of the severity, in a linear fashion or a non-linear fashion according to the scale. This effect might be caused by competition between "illusion of control" and the tendency to attribute adverse consequence of gambling to external causes.

Surface characterization techniques for determining the root-mean-square roughness and power spectral densities of optical components

Surface topography and light scattering were measured on 15 samples ranging from those having smooth surfaces to others with ground surfaces. The measurement techniques included an atomic force microscope, mechanical and optical profilers, confocal laser scanning microscope, angle-resolved scattering, and total scattering. The samples included polished and ground fused silica, silicon carbide, sapphire, electroplated gold, and diamond-turned brass. The measurement instruments and techniques had different surface spatial wavelength band limits, so the measured roughnesses were not directly comparable. Two-dimensional power spectral density (PSD) functions were calculated from the digitized measurement data, and we obtained rms roughnesses by integrating areas under the PSD curves between fixed upper and lower band limits. In this way, roughnesses measured with different instruments and techniques could be directly compared. Although smaller differences between measurement techniques remained in the calculated roughnesses, these could be explained mostly by surface topographical features such as isolated particles that affected the instruments in different ways.

Soybean root growth and crop yield in reponse to liming at the beginning of a no-tillage system

Analyzing the soil near crop roots may reveal limitations to growth and yield even in a no-tillage system. The purpose of the present study was to relate the chemical and physical properties of soil under a no-tillage system to soybean root growth and plant yield after five years of use of different types of limestone and forms of application. A clayey Oxisol received application of dolomitic and calcitic limestones and their 1:1 combination in two forms: surface application, maintained on the soil surface; and incorporated, applied on the surface and incorporated mechanically. Soil physical properties (resistance to mechanical penetration, soil bulk density and soil aggregation), soil chemical properties (pH, exchangeable cations, H+Al, and cation exchange capacity) and plant parameters (root growth system, soybean grain yield, and oat dry matter production) were evaluated five years after setting up the experiment. Incorporation of lime neutralized exchangeable Al up to a depth of 20 cm without affecting the soil physical properties. The soybean root system reached depths of 40 cm or more with incorporated limestone, increasing grain yield an average of 31 % in relation to surface application, which limited the effect of lime up to a depth of 5 cm and root growth up to 20 cm. It was concluded that incorporation of limestone at the beginning of a no-tillage system ensures a favorable environment for root growth and soybean yield, while this intervention does not show long-term effects on soil physical properties under no-tillage. This suggests that there is resilience in the physical properties evaluated.

Variability of root traits in common bean genotypes at different levels of phosphorus supply and ontogenetic stages

Selection of common bean (Phaseolus vulgaris L.) cultivars with enhanced root growth would be a strategy for increasing P uptake and grain yield in tropical soils, but the strong plasticity of root traits may compromise their inclusion in breeding programs. The aim of this study was to evaluate the magnitude of the genotypic variability of root traits in common bean plants at two ontogenetic stages and two soil P levels. Twenty-four common bean genotypes, comprising the four growth habits that exist in the species and two wild genotypes, were grown in 4 kg pots at two levels of applied P (20 and 80 mg kg-1) and harvested at the stages of pod setting and early pod filling. Root area and root length were measured by digital image analysis. Significant genotype × P level and genotype × harvest interactions in analysis of variance indicate that the genotypic variation of root traits depended on soil nutrient availability and the stage at which evaluation was made. Genotypes differed for taproot mass, basal and lateral root mass, root area and root length at both P levels and growth stages; differences in specific root area and length were small. Genotypes with growth habits II (upright indeterminate) and III (prostrate indeterminate) showed better adaptation to limited P supply than genotypes of groups I (determinate) and IV (indeterminate climbing). Between the two harvests, genotypes of groups II and III increased the mass of basal and lateral roots by 40 and 50 %, respectively, whereas genotypes of groups I and IV by only 7 and 19 %. Values of the genotypic coefficient of determination, which estimates the proportion of phenotypic variance resulting from genetic effects, were higher at early pod filling than at pod setting. Correlations between shoot mass and root mass, which could indicate indirect selection of root systems via aboveground biomass, were higher at early pod filling than at pod setting. The results indicate that selection for root traits in common bean genotypes should preferentially be performed at the early pod-filling stage.

Public-domain software for root image analysis

In the search for high efficiency in root studies, computational systems have been developed to analyze digital images. ImageJ and Safira are public-domain systems that may be used for image analysis of washed roots. However, differences in root properties measured using ImageJ and Safira are supposed. This study compared values of root length and surface area obtained with public-domain systems with values obtained by a reference method. Root samples were collected in a banana plantation in an area of a shallower Typic Carbonatic Haplic Cambisol (CXk), and an area of a deeper Typic Haplic Ta Eutrophic Cambisol (CXve), at six depths in five replications. Root images were digitized and the systems ImageJ and Safira used to determine root length and surface area. The line-intersect method modified by Tennant was used as reference; values of root length and surface area measured with the different systems were analyzed by Pearson's correlation coefficient and compared by the confidence interval and t-test. Both systems ImageJ and Safira had positive correlation coefficients with the reference method for root length and surface area data in CXk and CXve. The correlation coefficient ranged from 0.54 to 0.80, with lowest value observed for ImageJ in the measurement of surface area of roots sampled in CXve. The IC (95 %) revealed that root length measurements with Safira did not differ from that with the reference method in CXk (-77.3 to 244.0 mm). Regarding surface area measurements, Safira did not differ from the reference method for samples collected in CXk (-530.6 to 565.8 mm²) as well as in CXve (-4231 to 612.1 mm²). However, measurements with ImageJ were different from those obtained by the reference method, underestimating length and surface area in samples collected in CXk and CXve. Both ImageJ and Safira allow an identification of increases or decreases in root length and surface area. However, Safira results for root length and surface area are closer to the results obtained with the reference method.

The Vi element. A transposon-like repeated DNA sequence interspersed in the vitellogenin locus of Xenopus laevis.

A repeated DNA element in Xenopus laevis is described that is present in about 7500 copies dispersed throughout the genome. It was first identified in the 5' flanking region of one vitellogenin gene and was therefore named the Vi element. Seven copies are present within the vitellogenin gene region, three of them within introns of the genes A1, A2 and B2, and the other four copies in the gene flanking regions. Four of these copies have been sequenced. The Vi element is bounded by a well-conserved 13 base-pair inverted repeat; in addition, it is flanked by a three base-pair direct repeat that appears to be site-specific. The length of these four copies varies from 112 to 469 base-pairs; however, sequence homology between the different copies is very high. Their structural characteristics suggest that length heterogeneity may have arisen by either unequal recombinations, deletions or tandem duplications. Altogether, the characteristics and properties of the Vi element indicate that it might represent a mobile genetic element. One of the four copies sequenced is inserted close (position -535) to the transcription initiation site of the vitellogenin gene B2 in a region otherwise showing considerable homology with the closely related gene B1. Nevertheless, the presence of the Vi element does not seem to influence significantly the estrogen-controlled expression of gene B2. In addition, three alleles of this gene created by length polymorphism in intron 3 and in the Vi element inserted near the transcription initiation site are described.

Male-pattern baldness susceptibility locus at 20p11.

We conducted a genome-wide association study for androgenic alopecia in 1,125 men and identified a newly associated locus at chromosome 20p11.22, confirmed in three independent cohorts (n = 1,650; OR = 1.60, P = 1.1 x 10(-14) for rs1160312). The one man in seven who harbors risk alleles at both 20p11.22 and AR (encoding the androgen receptor) has a sevenfold-increased odds of androgenic alopecia (OR = 7.12, P = 3.7 x 10(-15)).