Assessing protein stability of the dimeric DNA-binding domain of E2 human papillomavirus 18 with molecular dynamics

The objective of this study is to understand the structural flexibility and curvature of the E2 protein of human papillomavirus type 18 using molecular dynamics (6 ns). E2 is required for viral DNA replication and its disruption could be an anti-viral strategy. E2 is a dimer, with each monomer folding into a stable open-faced β-sandwich. We calculated the mobility of the E2 dimer and found that it was asymmetric. These different mobilities of E2 monomers suggest that drugs or vaccines could be targeted to the interface between the two monomers.

Spatial variability of aggregate stability in latosols under sugarcane

The spatial variability of soils under a same management system is differentiated, as expressed in the properties. The spatial variability of aggregate stability of a eutrophic Red Latosol (ERL) and a dystrophic Red Latosol (DRL) under sugarcane was characterized. Samples were collected in a regular 10 m grid, in the layers 0.0-0.2 and 0.2-0.4 m, with 100 points per area, and the following properties were determined: geometric mean diameter (GMD) of aggregates, mean weight diameter (MWD) of aggregates, percent of aggregates in the > 2.0 mm class and organic matter (OM) content. The eutrophic Red Latosol (ERL) had a higher aggregate stability thn the dystrophic Red Latosol (DRL), which may be attributed to the higher clay and OM content and the gibbsitic mineralogy of this soil class. The differentiated evolution of the studied Oxisols explains the wider range and lower variation coefficient and variability, for all properties studied in the eutrophic Red Latosol.

Aggregate stability as affected by short and long-term tillage systems and nutrient sources of a hapludox in southern Brazil

The ability of a soil to keep its structure under the erosive action of water is usually high in natural conditions and decreases under frequent and intensive cultivation. The effect of five tillage systems (NT = no-till; CP = chisel plowing and one secondary disking; CT = primary and two secondary distings; CTb = CT with crop residue burning; and CTr = CT with removal of crop residues from the field), combined with five nutrient sources (C = control, no nutrient application; MF = mineral fertilizers according to technical recommendations for each crop; PL = 5 Mg ha-1 y-1 fresh matter of poultry litter; CM = 60 m³ ha-1 y-1 slurry cattle manure; and SM = 40 m³ ha-1 y-1 slurry swine manure) on wet-aggregate stability was determined after nine years (four sampled soil layers) and on five sampling dates in the 10th year (two sampled soil layers) of the experiment. The size distribution of the air-dried aggregates was strongly affected by soil bulk density, and greater values of geometric mean diameter (GMD AD) found in some soil tillage or layer may be partly due to the higher compaction degree. After nine years, the GMD AD on the surface was greater in NT and CP compared to conventional tillage systems (CT, CTb and CTr), due to the higher organic matter content, as well as less soil mobilization. Aggregate stability in water, on the other hand, was affected by the low variation in previous gravimetric moisture of aggregates, which contributed to a high coefficient of variation of this attribute. The geometric mean diameter of water-stable aggregates (GMD WS) was highest in the 0.00-0.05 m layer in the NT system, in the layers 0.05-0.10 and 0.12-0.17 m in the CT, and values were intermediate in CP. The stability index (SI) in the surface layers was greater in treatments where crop residues were kept in the field (NT, CP and CT), which is associated with soil organic matter content. No differences were found in the layer 0.27-0.32 m. The effect of nutrient sources on GMD AD and GMD WS was small and did not affect SI.

Redox index of soil carbon stability

As an alternative to the relatively complex and expensive spectroscopic methods, the redox properties of humic acids, determined by potentiometric titrations, have been used to evaluate the stability of soil organic C. The objective of the present study was to establish a Redox Index of C Stability (RICS) and to correlate it with some properties of the humic acids extracted from different modal soils in Brazil (distinct weathering stages or management) to facilitate system comparison. The RICS was efficient for soil comparison and variations were comparable to those of the chemical and spectroscopic methods used for humic acid characterization. The values of soil pH, point of zero salt effect, sum of bases, exchangeable Ca content, weathering index, as well as the humic acid O/C ratio, quinone and semiquinone free radical contents, aromatic C and fluorescence intensity were closely related with the RICS. The RICS was higher in less weathered soils, with more active clays and higher fertility. The RICS values of soils under long-term sugarcane management were ranked in decreasing order: unburned, burned with vinasse, burned without vinasse.

Kinetic parameters of soil β-glucosidase response to environmental temperature and moisture regimes

Soil β-glucosidase participates in the final step of cellulose biodegradation. It is significant in the soil C cycle and is used as an indicator of the biological fertility of soil. However, the response of its kinetic parameters to environmental temperature and moisture regimes is not well understood. This study tested the β-glucosidase response in the main agricultural soils (black soil, albic soil, brown soil, and cinnamon soil) of Northeast China. Incubation tests were conducted to measure the kinetic parameters Km, Vmax or Vmax/Km of soil β-glucosidase at environmental temperatures of 10, 20 and 30 ºC and at 10, 20 and 30 % soil moisture content. The insensitive response of the kinetic parameters to temperature changes indicates that soil β-glucosidase was present primarily in immobilized form. The significant response of the kinetic parameters of soil β-glucosidase to soil moisture rather than to environmental temperatures suggests that the catalytic ability of soil β-glucosidase was sensitive to changing soil moisture regimes.

Kinetic parameters of silicon uptake by rice cultivars

Silicon is considered an important chemical element for rice, because it can improve tolerance to biotic and abiotic stress. However, in many situations no positive effect of silicon was observed, probably due to genetic factors. The objective of this research was to monitor Si uptake kinetics and identify responses of rice cultivars in terms of Si uptake capacity and use. The experiment was carried out in a greenhouse of the São Paulo State University (UNESP), Brazil. The experiment was arranged in a completely randomized, factorial design with three replications. that consisted of two rice cultivars and two Si levels. Kinetic parameters (Vmax, Km, and Cmin), root morphology variables, dry matter yield, Si accumulation and levels in shoots and roots, uptake efficiency, utilization efficiency, and root/shoot ratio were evaluated. Higher Si concentrations in the nutrient solution did not increase rice dry matter. The development of the low-affinity silicon uptake system of the rice cultivar 'Caiapó' was better than of 'Maravilha'.

Aggregate stability by the "high energy moisture characteristic" method in an oxisol under differentiated management

Studies testing the High Energy Moisture Characteristic (HEMC) technique in tropical soils are still incipient. By this method, the effects of different management systems can be evaluated. This study investigated the aggregation state of an Oxisol under coffee with Brachiaria between crop rows and surface-applied gypsum rates using HEMC. Soil in an experimental area in the Upper São Francisco region, Minas Gerais, was studied at depths of 0.05 and 0.20 m in coffee rows. The treatments consisted of 0, 7, and 28 Mg ha-1 of agricultural gypsum rates distributed on the soil surface of the coffee rows, between which Brachiaria was grown and periodically cut, and compared with a treatment without Brachiaria between coffee rows and no gypsum application. To determine the aggregation state using the HEMC method, soil aggregates were placed in a Büchner funnel (500 mL) and wetted using a peristaltic pump with a volumetric syringe. The wetting was applied increasingly at two pre-set speeds: slow (2 mm h-1) and fast (100 mm h-1). Once saturated, the aggregates were exposed to a gradually increasing tension by the displacement of a water column (varying from 0 to 30 cm) to obtain the moisture retention curve [M = f (Ψ) ], underlying the calculation of the stability parameters: modal suction, volume of drainable pores (VDP), stability index (slow and fast), VDP ratio, and stability ratio. The HEMC method conferred sensitivity in quantifying the aggregate stability parameters, and independent of whether gypsum was used, the soil managed with Brachiaria between the coffee rows, with regular cuts discharged in the crop row direction, exhibited a decreased susceptibility to disaggregation.

Phenotypic stability and genetic gains in six-year girth growth of Hevea clones

Rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Müell. Arg.] budgrafts of seven clones were evaluated on five contrasting sites in the plateau region of the São Paulo State, Brazil. The objective of this work was to study the phenotypic stability for girth growth. The experimental design was a randomized block design with three replications and seven treatments. Analysis of variance of girth at six-year plant growth indicated a highly significant clone x site interaction. Only linear sites and clone x site components of clone x year interaction were significant, indicating that the performance of clones over sites for this trait could be predicted. The clones GT 1 and PB 235 showed the greatest stability in relation to girth growth, with foreseen responses to change, introduced in the sites. The clones PB 235 and IAN 873 showed significative difference in relation to regression coefficient, representing clones with specific adaptability on favorable and unfavorable sites respectively. The clone GT 1 became the most promissory one in the study of stability and adaptability even showing low girth growth. Expected genetic gains from planting sites, along with estimates of clonal variance and repeatability of clonal means are generally greatest or close to the greatest when selection is done at the same site.

Stability of soybean yield through different sowing periods

Soybean yield is highly affected by sowing period and there are significant productivity losses when sowings are done outward a relatively restricted period in many regions of Brazil. Breeding cultivars less sensitive to photoperiod and to temperature variations is desirable for adaptation to wider sowing period and wider latitude range and also make irrigated soybean cultivation possible during the fall-winter seasons in frost free regions. The possibility of selecting high yielding and stable lines for yield during various sowing periods was studied by analyzing the behavior of 100 non-selected advanced lines (F9 and F10), from each one of all possible biparental crosses involving the genotypes BR85-29009, OCEPAR 8, FT-2, and BR-13. Experiments were set up in a completely randomized design with single-plant hill plots and received supplementary irrigation. Sowing was on Sept 27, Oct 20, Nov 17, and Dec 17 in 1993/94 and Sept 20, Oct 20, Nov 17, and Dec 14 in 1994/95 at Londrina, PR, Brazil. Procedures of regression analysis and minimum variance among planting date means were efficient for selecting stable lines during the four sowing seasons. It was possible to select stable and high yielding genotypes through the four sowing periods in all the crosses. No specific cross was clearly better to produce a greater number of stable genotypes.

Agronomic performance, chromosomal stability and resistance to velvetbean caterpillar of transgenic soybean expressing cry1Ac gene

The objective of this work was to analyze the agronomic performance and chromosomal stability of transgenic homozygous progenies of soybean [Glycine max (L.) Merrill.], and to confirm the resistance of these plants against Anticarsia gemmatalis. Eleven progenies expressing cry1Ac, hpt and gusA genes were evaluated for agronomic characteristics in relation to the nontransformed parent IAS 5 cultivar. Cytogenetical analysis was carried out on transgenic and nontransgenic plants. Two out of the 11 transgenic progenies were also evaluated, in vitro and in vivo, for resistance to A. gemmatalis. Two negative controls were used in resistance bioassays: a transgenic homozygous line, containing only the gusA reporter gene, and nontransgenic 'IAS 5' plants. The presence of cry1Ac transgene affected neither the development nor the yield of plants. Cytogenetical analysis showed that transgenic plants presented normal karyotype. In detached-leaf bioassay, cry1Ac plants exhibited complete efficacy against A. gemmatalis, whereas negative controls were significantly damaged. Whole-plant feeding assay confirmed a very high protection of cry1Ac against velvetbean caterpillar, while nontransgenic 'IAS 5' plants and homozygous gusA line exhibited 56.5 and 71.5% defoliation, respectively. The presence of cry1Ac transgene doesn't affect the majority of agronomic traits (including yield) of soybean and grants high protection against A. gemmatalis.

Seed priming and sulfur effects on soybean cell membrane stability and yield in saline soil

The objective of this work was to determine the effects of seed priming and sulfur application on cell membrane characteristics, seedling emergence, chlorophyll content and grain yield of soybean (Glycine max) in saline soil. A complete-block design in 4x3 factorial arrangement with three replicates was used to test four types of seed priming (water, auxin, gibberellin and non-priming) and three levels of sulfate availability (0, 70 and 140 kg ha-1 K2SO4). The soil had a silty loam texture with an electrical conductivity of 3.61 ds m-1, a pH of 8.2 and a saturation percentage of about 46%. Seed priming had significant effects on mean emergence rate (MER), emergence percentage, relative water content (RWC) of leaves, relative chlorophyll content, time of maturity, shoot length and grain yield. The highest values for these variables were observed in the priming treatments, except for the time of maturity. Sulfur application had significant effects on MER, shoot length, RWC, membrane injury index and grain yield. Priming treatments provide greater emergence rates and grain yields and interact sinergicaly with sulfur rates.

Stability of Citrus tristeza virus protective isolates in field conditions

The objective of this work was to monitor the maintenance of Citrus tristeza virus (CTV) protective isolates stability in selected clones of 'Pêra' sweet orange (Citrus sinensis), preimmunized or naturally infected by the virus, after successive clonal propagations. The work was carried out in field conditions in the north of Paraná State, Brazil. Coat protein gene (CPG) analysis of 33 isolates collected from 16 clones of 'Pêra' sweet orange was performed using single strand conformational polymorphism (SSCP). Initially, the isolates were characterized by symptoms of stem pitting observed in clones. Then viral genome was extracted and used as template for the amplification of CPG by reverse transcription polimerase chain reaction (RTPCR). RTPCR products electrophoretic profiles were analyzed using the Jaccard coefficient and the UPGMA method. The majority of the clones had weak to moderate stem pitting symptoms and its CTV isolates showed alterations in the SSCP profiles. However, the stability of the protective complex has been maintained, except for isolates from two analised clones. Low genetic variability was observed within the isolates during the studied years.

Aggregate stability in soils cultivated with eucalyptus

The objective of this work was to evaluate the aggregate stability of tropical soils under eucalyptus plantation and native vegetation, and assess the relationships between aggregate stability and some soil chemical and physical properties. Argisols, Cambisol, Latosols and Plinthosol within three eucalyptus-cultivated regions, in the states of Espírito Santo, Rio Grande do Sul and Minas Gerais, Brazil, were studied. For each region, soils under native vegetation were compared to those under minimum tillage with eucalyptus cultivation. The aggregate stability was measured using the high-energy moisture characteristic (HEMC) technique, i.e., the moisture release curve at very low suctions. This method compares the resistance of aggregates to slaking on a relative scale from zero to one. Thus, the aggregate stability from different soils and management practices can be directly compared. The aggregate stability ratio was greater than 50% for all soils, which shows that the aggregate stability index is high, both in eucalyptus and native vegetation areas. This suggests that soil management adopted for eucalyptus cultivation does not substantially modify this property. In these soils, the aggregate stability ratio does not show a good relationship with clay or soil organic matter contents. However, soil organic matter shows a positive relationship with clay content and cation exchange capacity.

Different methods to assess yield temporal stability in rubber

The objective of this work was to assess, during six years, the temporal stability of natural rubber yield of 25 superior Hevea brasiliensis genotypes, using the Wricke, Eberhart & Russell, Lin & Binns, additive main effect and multiplicative interaction (AMMI) analysis, and harmonic mean of the relative performance of the genetic values (HMRPGV) methods. The IAC 40 and IAC 300 genotypes were identified as stable and high yielding by the Eberhart & Russell, Lin & Binns, HMRPGV, and AMMI Biplot methods. The ranking of the other more stable genotypes identified by these analyses was altered. The observed results in the AMMI Biplot agreed with those observed in the Wricke method for identifying stable, but lower yielding genotypes. The simultaneous use of different methods allows a more accurate indication of stable genotypes. Stability analyses based on different principles show agreement in indicating stable genotypes.

Stability and adaptability of runner peanut genotypes based on nonlinear regression and AMMI analysis

The objective of this work was to estimate the stability and adaptability of pod and seed yield in runner peanut genotypes based on the nonlinear regression and AMMI analysis. Yield data from 11 trials, distributed in six environments and three harvests, carried out in the Northeast region of Brazil during the rainy season were used. Significant effects of genotypes (G), environments (E), and GE interactions were detected in the analysis, indicating different behaviors among genotypes in favorable and unfavorable environmental conditions. The genotypes BRS Pérola Branca and LViPE‑06 are more stable and adapted to the semiarid environment, whereas LGoPE‑06 is a promising material for pod production, despite being highly dependent on favorable environments.