Nitrogen uptake by ryegrass from organic wastes applied to a sandy loam soil

Sandy‐textured Mediterranean soils are invariably depleted in organic matter and supply only small amounts of N to crops. To compensate for these deficiencies, we tested the N supply from six organic wastes applied to a Cambic Arenosol in pots growing ryegrass. The results showed that the behaviour of the wastes in supplying N to a ryegrass crop grown in this soil can be predicted by observing their performance in laboratory aerobic incubations. The N made available during these incubations fitted well to a one‐pool kinetic model.     

Biometrical, biological, biochemical and molecular characteristics of Meloidogyne incognita isolates and related species

Meloidogyne incognita is one of the most polyphagous species of root-knot nematodes occurring in Brazil and worldwide. Eight M. incognita isolates were studied, representing two enzymatic phenotypes (esterase and malate desydrogenase: I1/N1, I2/N1) and four cryptic Meloidogyne sp.1 (S2/N1) isolates, representing one cytological type (3n?=?40–46). Three M. hispanica isolates (Hi3/N1, 2n?=?32–36) and two of an atypical Meloidogyne sp.2 (S2a/N3, 3n?=?40–44) were included in this study for comparison. All isolates were tested with three M. incognita-specific molecular markers. The primer pairs B06F/R, miF/R and incK14F/R amplified three species-specific fragments of 1,200?bp, 955?bp and 399?bp, respectively for M. incognita and Meloidogyne sp.1 isolates. No amplification occurred in the M. hispanica and Meloidogyne sp.2 isolates, except with primers miF/R (1,650?bp). The genetic variability of the Meloidogyne spp. isolates was evaluated, using RAPD and ISSR markers. The phylogenetic analyses revealed two strongly supported monophyletic clades: clade I, consisting of M. hispanica and the atypical Meloidogyne sp.2 isolates, and clade II, clustering together all M. incognita and the Meloidogyne sp.1 isolates. Considering the biometrical, cytological and molecular approaches, it was possible to conclude that the isolates with three enzymatic phenotypes (I1/N1, I2/N1 and S2/N1) presented the characteristics described for M. incognita. Some correlations were detected between the isozymatic phenotypes and the tree topology (S2a/N3, Hi3/N1, I1/N1, S2/N1), but no strict correlation could be observed for the phenotype I2/N1 and one isolate of S2/N1. Morphologically, the Msp.2 isolates differ from M. incognita and M. hispanica by the female stylet features presenting straight cone tip and round pear shaped knobs, posteriorly sloping. The results of this study suggested that the Msp.2 isolates with phenotypes S2aN3 belong to a new or an unidentified species closely related to M. hispanica.     

Molecular, physiological and pathological characterization of Corynespora leaf spot fungi from rubber plantations in Sri Lanka

The plant pathogenic fungus Corynespora cassiicola causes a severe leaf spot disease on more than 70 host plant species including Hevea brasiliensis . Genetic variability in 32 isolates of C. cassiicola collected from diverse hosts and locations in Sri Lanka and Australia was assessed using restriction fragment length polymorphism (RFLP) analysis of the internal transcribed spacer (ITS) region of ribosomal DNA and random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) analysis of total fungal DNA. Amplified ITS fragments from all 32 C. cassiicola isolates exhibited an identical size, and restriction analysis with seven different restriction endonucleases revealed identity in all of the detected DNA fragments. This finding of high genetic relatedness was further supported by the cloning and DNA sequencing of the ITS2 region from one Sri Lankan and one Australian isolate. However, RAPD-PCR profiles generated by 15 oligonucleotide decamer primers revealed significant polymorphism between groups of organisms. Genetic relationships among the isolates were determined by cluster analysis of the RAPD-PCR data and seven different RAPD groups were identified. Isolates showed strong correlations between the assigned RAPD group and the location and host plant genotype from which the isolate was collected. Correlations were also observed between the RAPD group, growth of the isolate and pathogenicity on different plant hosts.     

Distribution of latent bovine herpesvirus 2 DNA in tissues of experimentally infected sheep

The biology of latent infection by bovine herpesvirus 2 (BoHV-2), the agent of mammillitis in cows, remains largely unknown. We herein report attempts to reactivate the latent infection and investigated the sites of BoHV-2 latency in experimentally infected sheep. Ewes inoculated with BoHV-2 in the udder’s skin shed virus for up to five days, developed mammillitis and seroconverted. However, attempts to reactivate latent infection by dexamethasone administration at day 40 pi failed. Nevertheless, viral DNA - and not infectious virus - was detected by PCR in several nerve ganglia and/or regional lymph nodes (LNs) of all animals at day 40 post-reactivation. Likewise, lambs previously inoculated with BoHV-2 in the nose harbored latent viral DNA in trigeminal ganglia, tonsils and regional LNs. These results demonstrate that BoHV-2 establishes latent infection in nerve ganglia and in regional lymphoid tissues, yet virus reactivation is not easily achieved by standard protocols used.     

Is single-step genomic REML with the algorithm for proven and young more computationally efficient when less generations of data are present?

Efficient computing techniques allow the estimation of variance components for virtually any traditional dataset. When genomic information is available, variance components can be estimated using genomic REML (GREML). If only a portion of the animals have genotypes, single-step GREML (ssGREML) is the method of choice. The genomic relationship matrix (G) used in both cases is dense, limiting computations depending on the number of genotyped animals. The algorithm for proven and young (APY) can be used to create a sparse inverse of G (GAPY~-1) with close to linear memory and computing requirements. In ssGREML, the inverse of the realized relationship matrix (H⁻¹) also includes the inverse of the pedigree relationship matrix, which can be dense with a long pedigree, but sparser with short. The main purpose of this study was to investigate whether costs of ssGREML can be reduced using APY with truncated pedigree and phenotypes. We also investigated the impact of truncation on variance components estimation when different numbers of core animals are used in APY. Simulations included 150K animals from 10 generations, with selection. Phenotypes (h² = 0.3) were available for all animals in generations 1–9. A total of 30K animals in generations 8 and 9, and 15K validation animals in generation 10 were genotyped for 52,890 SNP. Average information REML and ssGREML with G⁻¹ and GAPY~-1 using 1K, 5K, 9K, and 14K core animals were compared. Variance components are impacted when the core group in APY represents the number of eigenvalues explaining a small fraction of the total variation in G. The most time-consuming operation was the inversion of G, with more than 50% of the total time. Next, numerical factorization consumed nearly 30% of the total computing time. On average, a 7% decrease in the computing time for ordering was observed by removing each generation of data. APY can be successfully applied to create the inverse of the genomic relationship matrix used in ssGREML for estimating variance components. To ensure reliable variance component estimation, it is important to use a core size that corresponds to the number of largest eigenvalues explaining around 98% of total variation in G. When APY is used, pedigrees can be truncated to increase the sparsity of H and slightly reduce computing time for ordering and symbolic factorization, with no impact on the estimates.     

Leucocyte profile and growth rates as indicators of crowding stress in pejerrey fingerlings (Odontesthes bonariensis)

Crowding is one of the most common stressors found in intensive aquaculture, compromising growth rates and immune function. Plasmatic cortisol is a classic stress biomarker for fish, but its quantification is expensive and demands blood volumes that small individuals do not provide, constraining the usage of this technique to assess stress in fingerlings. The leucocyte profile is an alternative methodology to quantify stress with reduced costs and volumes of blood. Stress conditions promote neutrophilia and lymphocytopenia as response to elevated glucocorticoids levels. Considering the difficulties to assess stress imposed by intensive fish farming using measurement of glucocorticoid hormones, this study aimed to evaluate the stress‐induced changes in leucocyte profiles and growth rates imposed by crowding in fingerlings of Odontesthes bonariensis, a promising South‐American candidate for freshwater aquaculture. To meet these objectives, fingerlings (initial weight 0.05 ± 0.06 g and length 1.68 ± 0.13 cm) were reared for 45 days under three rearing densities (1, 5 and 10 fingerlings L^?1). At the end of this period, fish were anaesthetized and euthanized to obtain the leucocyte profile, neutrophil:lymphocyte ratio (N:L) and growth rate. Increasing density promoted: significant reduction in growth (final length, weight and specific growth rate); neutrophilia and lymphocytopenia; and increased N:L ratio. Concluding, the tested rearing densities imposed distinct levels of stress characterized by different N:L ratio, demonstrating that the leucocyte profile is a reliable alternative to measure stress levels in O. bonariensis fingerlings and probably in other fish species.