Molecular detection of sugarcane striate virus and sugarcane white streak virus and their prevalence in the Miami World Collection of sugarcane and related grasses

Viruses in the genus Mastrevirus (family Geminiviridae), including those infecting sugarcane, have natural geographical ranges almost exclusively restricted to Africa and the Indian Ocean islands off the African coast. Only sugarcane white streak virus (SWSV) in Barbados and sugarcane striate virus (SStrV) in Florida and Guadeloupe are known to infect a few sugarcane varieties in the Western Hemisphere. In this study, PCR assays were developed to detect these two viruses in sugarcane. Five hundred and seventy-one DNA samples from Saccharum species and interspecific hybrids from the Miami World Collection of sugarcane and related grasses were tested for the presence of SStrV and SWSV by PCR. No variety was found infected by SWSV but SStrV was detected in 19 varieties. PCR data were confirmed by sequencing amplified fragments (248 bp). These fragments shared 93%–100% nucleotide identity with SStrV sequences from the GenBank database. SStrV isolates were distributed in six phylogenetic groups, including the four strains of the virus. Most varieties infected by SStrV originated from Asia, thus confirming a previous hypothesis stating that this virus originated from this continent. Absence of SStrV in commercial sugarcane in Florida also suggested that this virus has not been spread in this location, while infected plants have been present for several decades.     

Do cover crops change the lability of phosphorus in a clayey subtropical soil under different phosphate fertilizers?

Plants have developed different mechanisms to absorb and solubilize phosphorus (P) in the soil, especially in environments with low P availability. This study evaluated the effects of different winter cover crops on soil P availability in a clayey subtropical (Hapludox) soil receiving soluble P fertilizer and a rock phosphate applied to the summer crop, under no‐tillage. The experiment was carried out over 3 yrs (2009–2011) with five different cover crop species: common vetch, fodder radish, ryegrass, black oat, white clover and fallow as control. The soil was sampled after the third year of cover crop cultivation and analysed for inorganic and organic P forms according to the well‐established Hedley fractionation procedure. Phosphate fertilizers promoted accumulation of both labile and nonlabile P pools in soil in the near surface layer, especially under rock phosphate. Fertilizer applications were not able to change P fractions in deeper layers, emphasizing that the Brazilian clayey soils are a sink of P from fertilizer and its mobility is almost nil. Although the cover crops recycled a great amount of P in tissue, in a short‐term evaluation (3 yrs) they only changed the content of moderately labile P in soil, indicating that long‐term studies are needed for more conclusive results.     

Rapid sequence modification in the highly polymorphic region (HPR) of the hemagglutinin gene of the infectious salmon anaemia virus (ISAV) suggests intra-segmental template switching recombination

The ISAV has a genome composed of eight segments of (–)ssRNA, segment 6 codes for the hemagglutinin–esterase protein, and has the most variable region of the genome, the highly polymorphic region (HPR), which is unique among orthomyxoviruses. The HPR has been associated with virulence, infectivity and pathogenicity. The full length of the HPR is called HPR0 and the strain with this HPR is avirulent, in contrast to strains with deleted HPR that are virulent to varying degrees. The molecular mechanism that gives rise to the different HPRs remains unclear. Here, we studied in vitro the evolution of reassortant recombinant ISAV (rISAV) in Atlantic salmon head kidney (ASK) cells. To this end, we rescued and cultivated a set of rISAV with different segment 6-HPR genotypes using a reverse genetics system and then sequencing HPR regions of the viruses. Our results show rapid multiple recombination events in ISAV, with sequence insertions and deletions in the HPR, indicating a dynamic process. Inserted sequences can be found in four segments of the ISAV genome (segments 1, 5, 6, and 8). The results suggest intra-segmental heterologous recombination, probably by class I and class II template switching, similar to the proposed segment 5 recombination mechanism.     

Is it possible to differentiate between environmental and fishery effects on abundance‐biomass variation? A case study of blackspot seabream (Pagellus bogaraveo) in the Strait of Gibraltar

We assessed the potential for simulation and modelling of the blackspot seabream (Pagellus bogaraveo) population in the Strait of Gibraltar to discriminate the environmental effects of fishery impacts. A discrete biomass–abundance dynamic model was implemented to obtain a simulated monthly time series of blackspot seabream biomass. On this simulated time series, autoregressive integrated moving average (ARIMA) models were fitted. The best ARIMA fit provided a significant correlation of 0.76 and persistence index higher than 0.85. The proportion of variance non‐explained by the ARIMA models was correlated with a time series of sea surface temperature (SST) and North Atlantic Oscillation (NAO). The analysis of global, annual and winter correlation between the proportion of variance not explained by the ARIMA models and environmental variables showed that significant associations were not detected over the full time series. Our analysis therefore suggests that overexploitation is the main factor responsible for the commercial depletion of blackspot seabream in the Strait of Gibraltar.     

Investigation of biofilm production and icaA and icaD genes in Staphylococcus aureus isolated from heifers and cows with mastitis

Biofilm formation and antimicrobial resistance of Staphylococcus aureus are important virulence factors in cases of mastitis in dairy cows. However, few studies have investigated mastitis strains isolated from heifers. Within this context, the objective of the present study was to investigate biofilm formation on Congo red agar, the presence of the icaA and icaD genes by polymerase chain reaction (PCR), and the percentage of in vitro antimicrobial resistance of 110 S. aureus isolates from mammary gland secretions of heifers and cows with mastitis. PCR detected the icaA and icaD genes in 98% and 100% of isolates, respectively. However, only 55.5% of all isolates produced a biofilm on Congo red agar. Antimicrobial susceptibility testing revealed that 47.0% of isolates from heifers and 70.4% of isolates from cows were resistant to at least one of the antimicrobial agents tested. Resistance to penicillin and/or ampicillin was the most frequent (44.5%). These results indicate the need to implement prophylactic and control measures of mastitis for heifers. Heifers and cows can carry resistant strains with the capacity of biofilm production, a fact representing a threat to public health and animal well‐being and generating losses to dairy farmers.     

An overview of animal science research 1945–2011 through science mapping analysis

The conceptual structure of the field of Animal Science (AS) research is examined by means of a longitudinal science mapping analysis. The whole of the AS research field is analysed, revealing its conceptual evolution. To this end, an automatic approach to detecting and visualizing hidden themes or topics and their evolution across a consecutive span of years was applied to AS publications of the JCR category ‘Agriculture, Dairy & Animal Science’ during the period 1945–2011. This automatic approach was based on a coword analysis and combines performance analysis and science mapping. To observe the conceptual evolution of AS, six consecutive periods were defined: 1945–1969, 1970–1979, 1980–1989, 1990–1999, 2000–2005 and 2006–2011. Research in AS was identified as having focused on ten main thematic areas: ANIMAL‐FEEDING, SMALL‐RUMINANTS, ANIMAL‐REPRODUCTION, DAIRY‐PRODUCTION, MEAT‐QUALITY, SWINE‐PRODUCTION, GENETICS‐AND‐ANIMAL‐BREEDING, POULTRY, ANIMAL‐WELFARE and GROWTH‐FACTORS‐AND‐FATTY‐ACIDS. The results show how genomic studies gain in weight and integrate with other thematic areas. The whole of AS research has become oriented towards an overall framework in which animal welfare, sustainable management and human health play a major role. All this would affect the future structure and management of livestock farming.