Toxoplasma gondii virulence prediction using hierarchical cluster analysis based on coding sequences (CDS) of sag1, gra7 and rop18

Toxoplasma gondii consists of three genotypes, namely genotype I, II and III. Based on its virulence, T. gondii can be divided into virulent and avirulent strains. This study intends to evaluate an alternative method for predicting T. gondii virulence using hierarchical cluster analysis based on complete coding sequences (CDS) of sag1, gra7 and rop18 genes. Dendrogram was constructed using UPGMA with a Kimura 80 nucleotide distance measurement. The results showed that the prediction errors of T. gondii virulence using sag1, gra7 and rop18 were 7.41%, 6.89% and 9.1%, respectively. Analysis based on CDS of gra7 and rop18 was able to differentiate avirulent strains into genotypes II and III, whereas sag1 failed to differentiate.     

Leaf physiological and anatomical characters contribute to drought tolerance of Nusa Tenggara Timur local rice cultivars

Journal of Crop Science and Biotechnology - Morpho-anatomical characters supporting the resilience of a plant under certain environmental conditions cannot be interpreted individually but...     

Variable responses of the depth of tree nitrogen uptake to pruning and competition

Trees in cropped fields may improve nitrogen (N) use efficiency by intercepting leached N, but crop yield will be reduced if the trees compete strongly with crops for N. Ideal trees for intercropping will take up N from deeper soil layers not accessed by the crop species. Spatiotemporal aspects of tree nitrogen capture niches were investigated within a hedgerow intercropping system by placing 15N at three depths and monitoring 15N uptake by trees pruned either 25 or 4 days before application of 15N. Trees with contrasting rooting patterns (Gliricidia sepium L. and Peltophorum dasyrrachis (Miq.) Kurz) were grown in mixed hedgerows and intercropped with maize (Zea mays L.). Neither species showed significant N uptake during the 5-14 days after pruning, even though some shoot regrowth occurred during this time. Mean topsoil (0-5 cm depth) root length density of G. sepium was 520% greater than that of P. dasyrrachis, whereas total root length (0-100 cm depth) of G. sepium was only 450% greater. On average, G. sepium recovered 15 times as much 15N as P. dasyrrachis, following application of 15N at 5 cm depth, but the two species recovered a similar amount following application at 80 cm depth, suggesting that P. dasyrrachis had better niche complementarity with shallow rooting crops. However, both species showed strong plasticity in vertical N uptake pattern in response to competition from establishing maize plants. The species differed in their response: N uptake activity by G. sepium shifted down the soil profile in response to increasing competition from a growing maize crop (uptake from 80 cm depth changed from 4 to 9% of uptake from 5 cm depth), whereas N uptake by P. dasyrrachis became relatively shallow (uptake from 80 cm depth changed from 305 to 25% of uptake from 5 cm depth). Niche avoidance and increased competitiveness within the topsoil represent alternative responses to competition. The response displayed may be related to soil fertility in the species' natural habitats.     

The inherent 'safety-net' of an Acrisol: measuring and modelling retarded leaching of mineral nitrogen

The inherent features of Acrisols with their increasing clay content with depth are conducive to reducing nutrient losses by nutrient adsorption on the matrix soil surfaces. Ammonium (NH₄⁺) and nitrate (NO₃^?) adsorption by a Plinthic Acrisol from Lampung, Indonesia was studied in column experiments. The peak of the H₂¹⁸O breakthrough occurred at 1 pore volume, whereas the median pore volumes for NH₄⁺ and NO₃^? ranged from 6.4 to 6.9 and 1.1 to 1.6, respectively. The adsorption coefficients (K_a in cm³ g^–1) measured were 1.81, 1.51, 1.64 and 1.47 for NH₄⁺ and 0.03, 0.09, 0.10 and 0.17 for NO₃^?, respectively, in the 0–0.2, 0.2–0.4, 0.4–0.6 and 0.6–0.8 m soil depth layers. The NH₄⁺ and NO₃^? adsorption coefficients derived from this study were put in to the Water, Nutrient and Light Capture in Agroforestry Systems (WaNuLCAS) model to evaluate their effect on leaching in the context of several cropping systems in the humid tropics. The resulting simulations indicate that the inherent ‘safety‐net’ (retardation mechanism) of a shallow (0.8–1 m) Plinthic Acrisol can reduce the leaching of mineral N by between 5 and 33% (or up to 2.1 g m^?2), mainly due to the NH₄⁺ retardation factor, and that the effectiveness in reducing N leaching increases with increasing depth. However, the inherent ‘safety‐net’ is useful only if deep‐rooted plants can recover the N subsequently.     

Diversity,Physicochemical, and Structural Properties of Indonesian Aromatic Rice Cultivars

Journal of Crop Science and Biotechnology - The most important component of rice qualities are its appearance, cooking quality, eating quality, and nutritional quality. Indonesian had been...     

Factors affecting soil loss at plot scale and sediment yield at catchment scale in a tropical volcanic agroforestry landscape

Tropical deforestation and land use change is often perceived as the major cause of soil loss by water erosion and of sediment load in rivers that has a negative impact on the functioning of hydropower storage reservoirs. The Sumberjaya area in Sumatra, Indonesia is representative for conflicts and evictions arising from this perception. The purpose of this study as part of a Negotiation Support System approach was to assess sediment yield both at plot and catchment scale and to relate it to a variety of possible clarifying factors i.e. land use, geology, soil and topography. Sediment yield at catchment scale per unit area, was found to be 3–10 times higher than soil loss measured in erosion plots. A stepwise regression showed that the dominant factors explaining sediment yield differences at catchment scale in this volcanic landscape were a particular lithology (Old Andesites) and slope angle followed by the silt fraction of the top soil. In lithologically sensitive areas soil loss at the plot scale under monoculture coffee gardens decreases over time from on average 7–11 Mg ha^? 1 yr^? 1 to 4–6 Mg ha^? 1 yr^? 1, mainly because of the development of surface litter layers as filters and top soil compaction in the areas without litter, but remains higher than under shade coffee systems or forest. The runoff coefficient under monoculture coffee remains on average significantly higher (10–15%) than under forest (4%) or under shade coffee systems (4–7%). In lithologically stable areas soil loss remained below 1.8 Mg ha^? 1 yr^? 1 and the runoff coefficient below 2.5% under all land use types, even bare soil plots or monoculture coffee gardens. Less than 20% of the catchment area produces almost 60% of the sediment yield. The reduction of negative off-site effects on e.g. the life time of a storage reservoir would benefit greatly from an improved assessment of the lithologies in volcanic landscapes and the consideration of potential sediment source and sink areas. In lithologically sensitive areas, a shift from sun to shade coffee systems may result in reducing surface runoff and soil loss, although water erosion at the plot scale is not the main contributor to sediment yield at the catchment scale. The quantification of land use effects on dominant erosive processes such as river bank and river bed erosion, landslides and the concentrated flow erosion on footpaths and roads can contribute to more targeted efforts and relevant incentives to reduce (or live with) sediment load of the rivers.