Rice Yellow Mottle Virus is Seed-borne but not Seed Transmitted in Rice Seeds

Seed transmission of two pathogroups of rice yellow mottle virus from Soudano-Sahelian areas of West Africa was studied in several rice genotypes. The virus was detected by enzyme-linked immunosorbent assay and the highly susceptible rice variety BG 90-2 was used for infectivity assays. In most of the rice genotypes studied (17 out of 21), rice yellow mottle virus was detected in all seed parts including glumella, endosperm and embryo at a rate ranging from 65 to 100%. Nevertheless, no seed-borne infection was found. Infectivity of the virus decreased throughout the process of seed formation suggesting inactivation of the virus as a result of seed maturation and desiccation. It was concluded that rice yellow mottle epidemics do not develop from seed-borne infections in rice seeds.     

Early mortality of lambs in African traditional livestock production systems

Early mortality of lambs is a major constraint on total productivity. In 6 different environments the early death rate varied from 12 to 30% of all lambs born. Cause of death differed among systems but only a proportion could definitely be ascribed to infectious disease: nutrition, management and other environmental factors also contribute to the mortality rate. Mortality can be reduced by isolating solutions due to any of these factors but best results (lowest death rates) would be obtained by an integrated package containing elements of all these aspects.     

In vitro anti Mycobacterium tuberculosis H37Rv activity of Lannea acida A. Rich from Burkina Faso

The cytotoxic and anti-Mycobacterium tuberculosis H37Rv activities of hydro-alcoholic extract of Lannea acida A. Rich (Anacardiaceae) were assessed. The cytoxicity evaluation was carried out on THP1 monocytoid cell line (after 24 h at 1; 5 and 10 microg mL(-1)) and showed only a slight modification of lactate dehydrogenase (LDH) release. The rate of monocytes in different stages of mitosis had been amended in absence and presence of extract as follows: Go/G1 58.83-59.83%; synthesis 21.95-18.64%; mitosis 16.67-15.77%; necrosis 2.65-5.64%. The percentage of inhibition of Mycobacterium tuberculosis proliferation was respectively 77.6 and 36.8% at 1.2 and 0.6 mg mL(-1) of extract. This is an interesting experimental study on antimicrobial and immune-stimulating properties of Lannea acida ethanol-water (70% v/v) extract which may contain potential antibacterial and immune-stimulating agents for clinical use.     

Inhibitory effects of fibrinogen on phagocytic killing of streptococcal isolates from humans, cattle and horses

The effects of fibrinogen on phagocytic killing of Streptococcus dysgalactiae from cattle and S. equi from horses were studied in comparison to that of S. pyogenes from humans. Phagocytic killing was determined by a fluorometric microassay using glass adherent polymorphonuclear neutrophils (PMN) from the respective host species, preopsonization with homologous sera led to a dose-dependent increase in phagocytic killing of all streptococcal cultures, preincubation of streptococci with fibrinogen significantly inhibited their phagocytic killing. Fibrinogen had no effect on phagocytic killing of non-fibrinogen binding S. agalactiae cultures. Further characterization studies with S. dysgalactiae and S. pyogenes revealed that a partial inhibition of phagocytic killing could also be achieved by preincubation with monomeric beta-chains of fibrinogen. Digestion of the fibrinogen binding sites on streptococci with proteases resulted in an almost complete loss of the inhibitory effects of fibrinogen on phagocytic killing. It could thus be concluded that by binding fibrinogen animal pathogenic streptococci could evade phagocytic killing in a similar manner as M protein carrying S. pyogenes isolates from human infections.     

Can earthworms be used as bio-indicators of land-use perturbations in semi-deciduous forest?

The potential of tropical earthworms as bio-indicators of forest degradation by human-induced activities was assessed at a landscape level in the Ivory Coast. The study site covered 400 ha and was characterized by a set of land-use types along a gradient of perturbation from semi-deciduous forest, through reforestation, fallow systems to cultivated annual crops. Samples were taken on a grid at each sampling point and earthworms were hand-sorted from a 25 × 25 × 30-cm soil monolith. Results showed a potential increase in relative populations (number: +53.1%, biomass: +94.8%) of species in the earthworm communities following forest conversion. Furthermore, the impact of land-use change was higher in relation to land-use intensification in terms of earthworm populations and diversity in intermediate-disturbed systems (Multispecies plantations, old fallows). Earthworm diversity was the most sensitive response to land-use change. The species Dichogaster saliens Beddard 1893, Hyperiodrilus africanus Beddard 1891, Millsonia omodeoi Sims 1986, Dichogaster baeri Sciacchitano 1952, Dichogaster ehrhardti Michaelsen 1898, Agastrodrilus sp., Stuhlmannia palustris Omodeo and Vaillaud 1967 and, to some extent, Millsonia sp. appeared to be most sensitive to land-use change. More field and laboratory investigations are needed to find out the most efficient species to be used in bio-monitoring programmes aimed at preventing ecosystem degradation due to anthropogenic activities in the forest areas of Ivory Coast.     

A novel Gateway®-compatible binary vector allows direct selection of recombinant clones in Agrobacterium tumefaciens

Background

In vivo detection of protein-bound genomic regions can be achieved by combining chromatin-immunoprecipitation with next-generation sequencing technology (ChIP-seq). The large amount of sequence data produced by this method needs to be analyzed in a statistically proper and computationally efficient manner. The generation of high copy numbers of DNA fragments as an artifact of the PCR step in ChIP-seq is an important source of bias of this methodology.

Results

We present here an R package for the statistical analysis of ChIP-seq experiments. Taking the average size of DNA fragments subjected to sequencing into account, the software calculates single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the ratio test or the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutations. Computational efficiency is achieved by implementing the most time-consuming functions in C++ and integrating these in the R package. An analysis of simulated and experimental ChIP-seq data is presented to demonstrate the robustness of our method against PCR-artefacts and its adequate control of the error rate.

Conclusions

The software ChIP-seq Analysis in R (CSAR) enables fast and accurate detection of protein-bound genomic regions through the analysis of ChIP-seq experiments. Compared to existing methods, we found that our package shows greater robustness against PCR-artefacts and better control of the error rate.     

Effect of nitrate/ammonium ratio on biomass production,nitrogen accumulation,and use efficiency in sorghums of different origin

Plant nitrogen (N) uptake, growth, and N use efficiency may be affected by N form (NO₃ ^‐or NH₄ ⁺) available to the root. The objectives of this study were to determine the effect of mixed N form on dry matter production and partitioning, N uptake, and biomass N use efficiency defined as total dry matter produced per unit plant N (NUE₁) in U.S. and tropical grain sorghums [Sorghum bicolor (L.) Moench]. The U.S. derived genotype CK 60 and three tropical genotypes, Malisor‐7, M 35–1, and S 34, were evaluated in a greenhouse trial using three nutrient solutions differing in their NO₃ ^‐/NH₄ ⁺ ratio (100/0, 75/25, 50/50). Shoot and root biomass, N accumulation, and NUE, were determined at 10‐leaf and boot stages. Averaged over all genotypes, shoot and root biomass decreased when NH₄ ⁺ concentration was increased in the solution. Shoot biomass was reduced by 11% for 75/25 and 26% for 50/50 ratios, as compared to 100/0 NO₃ ^‐/NH₄ ⁺. Similarly, root biomass reduction was about 34% and 45% for the same ratios, respectively. Increasing NH₄ ⁺ concentration also altered biomass partitioning between shoot and root as indicated by decreasing root/shoot ratio. Total plant N content and NUE₁ were also reduced by mixed N source. Marked genotypic variability was found for tolerance to higher rates of NH₄ ⁺. The tropical line M 35–1 was well adapted to either NO₃ ^‐ as a sole source, or to an N source containing high amounts of NH₄ ⁺. Such a characteristic may exist in some exotic lines and may be used to improve genotypes which do not do well in excessively wet soil conditions where N uptake can be reduced.     

Soil organic carbon dynamics and crop yield for different crop rotations in a degraded ferruginous tropical soil in a semi-arid region: a simulation approach

In recent years, simulation models have been used as a complementary tool for research and for quantifying soil carbon sequestration under widely varying conditions. This has improved the understanding and prediction of soil organic carbon (SOC) dynamics and crop yield responses to soil and climate conditions and crop management scenarios. The goal of the present study was to estimate the changes in SOC for different cropping systems in West Africa using a simulation model. A crop rotation experiment conducted in Farak?-Ba, Burkina Faso was used to evaluate the performance of the cropping system model (CSM) of the Decision Support System for Agrotechnology Transfer (DSSAT) for simulating yield of different crops. Eight crop rotations that included cotton, sorghum, peanut, maize and fallow, and three different management scenarios, one without N (control), one with chemical fertilizer (N) and one with manure applications, were studied. The CSM was able to simulate the yield trends of various crops, with inconsistencies for a few years. The simulated SOC increased slightly across the years for the sorghum-fallow rotation with manure application. However, SOC decreased for all other rotations except for the continuous fallow (native grassland), in which the SOC remained stable. The model simulated SOC for the continuous fallow system with a high degree of accuracy normalized root mean square error (RMSE)=0·001, while for the other crop rotations the simulated SOC values were generally within the standard deviation (s.d.) range of the observed data. The crop rotations that included a supplemental N-fertilizer or manure application showed an increase in the average simulated aboveground biomass for all crops. The incorporation of this biomass into the soil after harvest reduced the loss of SOC. In the present study, the observed SOC data were used for characterization of production systems with different SOC dynamics. Following careful evaluation of the CSM with observed soil organic matter (SOM) data similar to the study presented here, there are many opportunities for the application of the CSM for carbon sequestration and resource management in Sub-Saharan Africa.