Improved detection of Mycobacterium tuberculosis and M. bovis in African wildlife samples using cationic peptide decontamination and mycobacterial culture supplementation

In South Africa, mycobacterial culture is regarded as the gold standard for the detection of Mycobacterium tuberculosis complex (MTBC) infection in wildlife even though it is regarded as “imperfect.” We compared a novel decontamination and mycobacterial culture technique (TiKa) to the conventional mycobacterium growth indicator tube (MGIT) system using known amounts of bacilli and clinical samples from MTBC-infected African buffaloes (Syncerus caffer), white rhinoceros (Ceratotherium simum), and African elephants (Loxodonta africana). Use of the TiKa-KiC decontamination agent on samples spiked with 10,000 to 10 colony forming units (cfu) of M. bovis (SB0121) and M. tuberculosis (H37Rv) had no effect on isolate recovery in culture. In contrast, decontamination with MGIT MycoPrep resulted in no growth of M. bovis samples at concentrations < 1,000 cfu and M. tuberculosis samples < 100 cfu. Subsequently, we used the TiKa system with stored clinical samples (various lymphatic tissues) collected from wildlife and paucibacillary bronchoalveolar lavage fluid, trunk washes, and endotracheal tube washes from 3 species with known MTBC infections. Overall, MTBC recovery by culture was improved significantly (p < 0.01) by using TiKa compared to conventional MGIT, with 54 of 57 positive specimens versus 25 of 57 positive specimens, respectively. The TiKa mycobacterial growth system appears to significantly enhance the recovery of MTBC members from tissue and paucibacillary respiratory samples collected from African buffaloes, African elephants, and white rhinoceros. Moreover, the TiKa system may improve success of MTBC culture from various sample types previously deemed unculturable from other species.     

Modelling optimal timing and frequency of insecticide sprays for knockdown in preparation for other control measures

A modelling investigation was conducted into optimizing the number of sprays and inter-spray interval to reduce an insect population to a low level, for example, prior to pheromone trapping or the release of sterile males. The model population was age-structured and density-dependent. If spray mortality is 100% for each spray, then the ideal spraying schedule is easily determined from the durations of the various life stages. For spray mortality of less than 100%, a simulation was used to determine optimal spraying schedules. Relative length of the larval period, fertility rate and age to first oviposition were found to be the most important biotic parameters for this determination. Their importance is magnified as spray mortality decreases. The stage targeted by sprays and the percent mortality caused by each spray are also important in determining the required number of sprays. Using medfly (Ceratitis capitata Wiedmann) biotic parameters as an example when the spray targets adults, it appeared that neither the stage at which density-dependent mortality takes effect, nor the form of the adult survivorship curve are important in determining the optimal spray schedule.     

EXPLORING THE RECYCLING OF MANURE FROM URBAN LIVESTOCK FARMS: A CASE STUDY IN ETHIOPIA

• Livestock manure was the main organic waste in urban and peri-urban areas.• Manure production will increase by a factor of 3–10 between 2015–2050.• Only 13%–38% of excreted N by livestock will be recycled in croplands.• Intensification of urban livestock production greatly increased N surpluses.• Reducing population growth and increasing livestock productivity needed.Urban population growth is driving the expansion of urban and peri-urban agriculture (UPA) in developing countries. UPA is providing nutritious food to residents but the manures produced by UPA livestock farms and other wastes are not properly recycled. This paper explores the effects of four scenarios: (1) a reference scenario (business as usual), (2) increased urbanization, (3) UPA intensification, and (4) improved technology, on food-protein self-sufficiency, manure nitrogen (N) recycling and balances for four different zones in a small city (Jimma) in Ethiopia during the period 2015-2050. An N mass flow model with data from farm surveys, field experiments and literature was used. A field experiment was conducted and N use efficiency and N fertilizer replacement values differed among the five types of composts derived from urban livestock manures and kitchen wastes. The N use efficiency and N fertilizer replacement values were used in the N mass flow model.Livestock manures were the main organic wastes in urban areas, although only 20 to 40% of animal-sourced food consumed was produced in UPA, and only 14 to 19% of protein intake by residents was animal-based. Scenarios indicate that manure production in UPA will increase 3 to 10 times between 2015 and 2050, depending on urbanization and UPA intensification. Only 13 to 38% of manure N will be recycled in croplands. Farm-gate N balances of UPA livestock farms will increase to>1 t·ha⁻¹ in 2050. Doubling livestock productivity and feed protein conversion to animal-sourced food will roughly halve manure N production.Costs of waste recycling were high and indicate the need for government incentives. Results of these senarios are wake-up calls for all stakeholders and indicate alternative pathways.     

Fish assemblages in the Southern California Current: relationships with climate, 1951–2008

We examined the dominant patterns of variability in the fish fauna of the southern California Current based on a principal component (PC) analysis of the California Cooperative Oceanic Fisheries Investigations ichthyoplankton data set, 1951–2008. Eighty‐six taxa were analyzed, including all ecologically dominant fish species, both exploited and unexploited. The first three PCs accounted for 20.5, 12.4 and 6.8% of the variance of the data, respectively (total: 39.7%). Each was dominated by taxa from particular adult or larval habitats. PC 1 predominantly represented the coherent response of 24 mesopelagic taxa from 10 families and was most highly correlated with long‐term trends in midwater oxygen levels. PC 2 was dominated by six of the seven most abundant ichthyoplankton taxa in the region, predominantly California Current endemics including key pelagic species (northern anchovy, Pacific sardine and Pacific hake), rockfishes (genus Sebastes) and two midwater taxa. It was correlated primarily with sea surface temperature and exhibited a significant declining trend. PC 3 was dominated by coastal and reef‐associated fishes with predominantly southerly affinities. It was positively correlated with sea surface temperature and sea level height, a proxy for diminished flow of the California Current. The taxa dominating PCs 2 and 3 mostly spatially co‐occur as ichthyoplankton. These results suggest that fish assemblages in the California Current are predominantly influenced by environmental forcing of their ocean habitats as adults or larvae, or both.     

A comparison of the population genetics of Lethrinus miniatus and Lutjanus sebae from the east and west coasts of Australia: Evidence for panmixia and isolation

Lethrinus miniatus and Lutjanus sebae are important commercial and recreational species of reef fish. Within Australian waters the former species is less widespread than the latter and has a discontinuous distribution, whilst the latter is continuously distributed in tropical Australian waters. The demographic attributes of these species (e.g. long life span, low rates of natural mortality) make them vulnerable to over-exploitation. Consequently, conservative harvest strategies including no-take zones for these species have been adopted by fisheries management agencies to control exploitation. Information on the genetic stock structure of these species is important for developing specific management strategies. However, little is known about genetic stock structures within and between east and west Australian populations of these species. The current study used the mitochondrial genome hypervariable region 1 (HVR1) of the control region to examine variation between two sites from both the east and west Australian coasts for each species. HVR1 for L. sebae did not differ genetically either within or between coasts (F_st < 0.018, p > 0.15) at the sites studied, suggesting a panmictic population structure. Similarly, L. miniatus did not differ significantly between sites sampled within coast. However, the west coast HVR1 for L. miniatus east and west coast populations, were discrete (F_st of at least 0.92, p < 0.0001). The degree of genetic sub-division between east and west coast populations indicates that they should be managed as discrete stocks. Further, when considering both species, the lower genetic (both haplotype and nucleotide) diversity in three of the four sites on the west coast of Australia, indicates that this region is genetically impoverished and neutrality tests suggest that selection is responsible. Consequently, west Australian populations will be less resilient to perturbations (e.g. fishing, climate change) than east Australian populations, which have higher genetic diversity.     

Heritability estimates and response to selection for growth of Nile tilapia (Oreochromis niloticus) in low-input earthen ponds

This study presents results of two generations of selection (G₁ and G₂) for growth of Nile tilapia. The selection environment consisted of earthen ponds which were fertilized daily with 50 kg dry matter (dm)/ha chicken manure. No supplementary feeds were provided. In total, 6429 fully pedigreed experimental fish were included in the analysis. Survival till harvest was highly variable ranging from 35% to 77% and was affected by initial weight, pond, and age effects. Body weight at harvest (BW) increased from a mean of 67.4 g in the grandparental (unselected) population (G₀) to 129.5 g in G₂ was affected by initial weight, pond, sex and age effects. Generations were discrete and therefore genetic parameters were estimated separately for each year. Heritability estimates for BW ranged from 0.38 to 0.60, and the heritability for survival ranged from 0.03 to 0.14. The estimated selection response was 23.4 g (34.7%) between G₀ and G₁ and 13.0 g (14.9%) between G₁ and G₂. These results demonstrate the feasibility of selection for growth of Nile tilapia in low-input environments.     

Implementation of two high through-put techniques in a novel application: detecting point mutations in large EMS mutated plant populations

Background  

The establishment of mutant populations together with the strategies for targeted mutation detection has been applied successfully to a large number of organisms including many species in the plant kingdom. Considerable efforts have been invested into research on tomato as a model for berry-fruit plants. With the progress of the tomato sequencing project, reverse genetics becomes an obvious and achievable goal.     

A European irrigation map for spatially distributed agricultural modelling

We present a pan-European irrigation map based on regional European statistics, a European land use map and a global irrigation map. The map provides spatial information on the distribution of irrigated areas per crop type which allows determining irrigated areas at the level of spatial modelling units. The map is a requirement for a European scale assessment of the impacts of irrigated agriculture on water resources based on spatially distributed modelling of crop growth and water balance. The irrigation map was compiled in a two step procedure. First, irrigated areas were distributed to potentially irrigated crops at a regional level (European statistical regions NUTS3), combining Farm Structure Survey (FSS) data on irrigated area, crop-specific irrigated area for crops whenever available, and total crop area. Second, crop-specific irrigated area was distributed within each statistical region based on the crop distribution given in our land use map. A global map of irrigated areas with a 5′ resolution was used to further constrain the distribution within each NUTS3 based on the density of irrigated areas. The constrained distribution of irrigated areas as taken from statistics to a high resolution dataset enables us to estimate irrigated areas for various spatial entities, including administrative, natural and artificial units, providing a reasonable input scenario for large-scale distributed modelling applications. The dataset bridges a gap between global datasets and detailed regional data on the distribution of irrigated areas and provides information for various assessments and modelling applications.     

Analysis of return flows in a tank cascade system in Sri Lanka

In Sri Lanka, irrigation reservoirs (tanks) are usually connected sequentially and form cascades along the landscape. A study was carried out in the Anuradhapura District in the dry zone of Sri Lanka to understand the role of return flows in such tank cascade systems. The water balance of a tank cascade system was estimated using hydrological data collected over a one-year period. The system was extended about 25 km along a river composed of three small reservoirs having the command area of 31, 55, and 55 ha, respectively. In this system, about 46% of seepage water from tanks entered the paddy fields of the command area. The crop consumed part of the water and the rest returned to the downstream tank through the drainage canals. Percolation loss in the command areas was low (3.6 mm/day) since a considerable portion of the percolation returned to the downstream tank. These results showed that return flows, which are generally disregarded in the water budget, contributed considerably to the water supply of the tank cascade system.     

Grain number and grain weight in wheat lines contrasting for stem water soluble carbohydrate concentration

In wheat, the ability to store and remobilise large amounts of stem water soluble carbohydrates (WSC) to grain constitutes a desirable trait to incorporate into germplasm targeted to regions with frequent terminal drought. The main aim of this paper was to examine the relationships between WSC storage, grain number and grain weight across several environments. A small set of recombinant inbred lines (2–4) contrasting in stem WSC were grown in six field trials where water availability, sowing date and/or N level were manipulated, with line yields ranging from 400 to 850 g m⁻² across experiments. Biomass, N and WSC concentration (WSCc, mg g⁻¹ dry weight) and amount (WSCa, g m⁻²) were monitored. A resource-oriented area-based model [Fischer, R.A., 1984. Growth and yield of wheat. In: Smith, W.H., Bante, S.J. (Eds.), Potential Productivity of Field Crops Under Different Environments. International Rice Research Institute, Los Baños, pp. 129–154] and intrinsic rates of organ growth were used to investigate the consequences on grain number of potential competition between spike and stem around flowering.