Molecular characerization of the interaction between the fungal pathogen Cladosporium fulvum and tomato

The fungus Cladosprium fulvum is a biotrophic leaf pathogen of tomato. The fungus develops in the intercellular space without forming specialized feeding structures and does not affect the leaf tissue. The outcome of the C. fulvum-tomato interaction can be described by the gene-for-gene model. Failure of infection is expressed by a hypersensitive response. Two fungal proteins, ECP1 and ECP2, have been isolated and their corresponding genes have been cloned. In a compatible interaction including many physiological races ECP1 and ECP2 are highly produced and a role in pathogenicity is suggestive. The ecp1 gene shows some homology with tumor necrosis factor receptors (TNFRs) while the ecp2 gene shows no homology with sequences known in data bases. However, disruption of one of the two genes showed no reduced pathogenicity of the fungus. Two race-specific elicitors, AVR4 and AVR9, have been isolated and their corresponding genes have been cloned. The avirulence genes Avr4 and Avr9 are only present in C. fulvum avirulent on Cf-4 and Cf-9 cultivars, respectively. The expression of these two genes is, like the expression of the ecp genes, highly induced when the fungus grows in planta. Disruption of the Avr9 gene in wild type avirulent races leads to virulence on tomato genotypes carrying the complementary resistance gene Cf-9. A single base-pair change in the avirulence gene Avr4 leads to virulence on tomato genotypes carrying the Cf-4 resistance gene. Isolation, characterization and possible function of ECP1, ECP2, AVR4, and AVR9 will be discussed.     

Organics captured from comet 81P/Wild 2 by the Stardust spacecraft

Organics found in comet 81P/Wild 2 samples show a heterogeneous and unequilibrated distribution in abundance and composition. Some organics are similar, but not identical, to those in interplanetary dust particles and carbonaceous meteorites. A class of aromatic-poor organic material is also present. The organics are rich in oxygen and nitrogen compared with meteoritic organics. Aromatic compounds are present, but the samples tend to be relatively poorer in aromatics than are meteorites and interplanetary dust particles. The presence of deuterium and nitrogen-15 excesses suggest that some organics have an interstellar/protostellar heritage. Although the variable extent of modification of these materials by impact capture is not yet fully constrained, a diverse suite of organic compounds is present and identifiable within the returned samples.     

Evaluation of 12-month interval methods for estimating animal-times at risk in a traditional African livestock farming system

Demographic parameters are useful for assessing productivity and dynamics of tropical livestock populations. Common parameters are the annual instantaneous hazard rates, which can be estimated by m/T (where m represents the number of the considered demographic events occurred during the year and T the cumulated animal-time at risk). Different approaches are encountered in the literature for computing T from on-farm survey data. One crude approach (“the 12-month interval approach”) only uses estimations of herds’ sizes at beginning and end of the year and aggregated counts of demographic events over the year. I evaluated the potential biases in using four 12-month interval methods (M1–M4) to estimate T. Biases were evaluated by comparing the 12-month estimates to gold-standard values of T. Data came from long-term herd monitoring on cattle and small ruminants in extensive agro-pastoral systems. Animal-times at risks were correctly estimated in average by methods M1, M2 and M4 (average relative biases <=6% in absolute values), except for adult-male small ruminants. For young animals, M2 and M4 showed equivalent biases. M2 is simple to implement and has the advantage of being applicable for any age-group, although M4 is only applicable for young animals. M3 was highly biased and I do not recommend it. Although accurate in average, 12-month interval methods showed highly variable biases. This variability results from interactions between the dates delimiting the 12-month interval and the distributions of the demographic events over time. This phenomenon is particularly important for the adult-male small ruminants. Based on the bias variability observed in the study, the user of 12-month interval methods has to remember that they only provide approximate results and that they cannot completely replace the gold-standard approaches.     

Demographic dynamics and off-take of cattle herds in southern Mali

The herds of 95 families were monitored for 1 year in eight villages in the cotton-growing region of southern Mali. In 2006–2007, reproduction performances were average, with 0.54 calvings/year per cow, and mortality was low. Herd numerical productivity is not very high, less than 0.13/year, because of the high proportion of males kept for animal draught. Depending on the herd size, the behaviour of the families differs, in terms of off-take and in-take of animals. Families that only have one or two draught animals seek to increase their animal draught capacity, with a negative net off-take (−0.13/year). Families with two to three cows have a very low net off-take (0.02/year), with culling of adult animals compensated by purchase. They therefore capitalised this year, with an annual herd growth of 8%. Families with a very large herd (20 to 50 cows) take off more of their stock, with a net off-take of 0.08/year (very few animal purchases) and make a stock growth of 5%. And finally, families with an average-sized herd (6 to 19 cows) take off the whole of the year’s production, with a net off-take of 0.11/year and a nil stock growth rate. The use of a demographic model made it possible to measure the sensitivity of the productivity rate to the different demographic parameters.     

Use of Akaike information criteria for model selection and inference. An application to assess prevention of gastrointestinal parasitism and respiratory mortality of Guinean goats in Kolda,Senegal

A field experiment was carried out in Kolda (southern Senegal) from July 1986 to July 1988. Its goals were to: (1) describe the patterns of mortality of female Guinean goats by age, season and year; (2) assess preventive measures against respiratory diseases and gastrointestinal parasitism in reducing mortality; and (3) estimate the overall impact of these measures on survival to 1 year of age. Preventive measures for respiratory disease included vaccination against peste des petits ruminants (PPR) and pneumonic pasteurellosis (Pasteurella multocida types A and D). Control of gastrointestinal parasites was by deworming does with morantel (7.5 mg kg⁻¹, three times during the rainy season). The effects of vaccines and deworming were tested in a randomised factorial field experiment with villages being the experimental units. A total of 19 villages, 113 goat herds and 1458 goats were included in the study.

Generalised linear models of survival for five cohorts of goats (defined by five different birth seasons) used a binomial assumption for the response distribution and a complementary log–log link. Explanatory variables included age, season, year, vaccination, deworming and their interactions. A complex a priori model was built on the basis of previous epidemiological knowledge; a purposively selected set of simpler models was compared to this full model by the Akaike information criterion (AIC) and derived statistics. Inference on 1-year survival and treatment effects accounted for model-selection uncertainty. It was carried out with a bootstrap procedure and used information from the whole set of selected models.

Large variations in mortality by year and season were observed but no regular seasonal pattern was apparent. Mortality probabilities of kids in dewormed groups decreased quickly after birth, but remained elevated up to 9 months of age in the non-dewormed groups. Deworming lowered the risk of mortality. Vaccination alone was not protective (except during an observed outbreak of PPR).     

Within-herd spread of contagious bovine pleuropneumonia in Ethiopian highlands

Contagious bovine pleuropneumonia (CBPP) is a major threat for cattle health and production in Africa. This disease is caused by the small-colony type of Mycoplasma mycoides subspecies mycoides (MmmSC). Transmission occurs from direct and repeated contacts between sick and healthy animals. Veterinary services recently reported a resurgence of CBPP in the province of West Wellega, in the Ethiopian highlands. A research program was set up to estimate the epidemiological parameters of the within-herd infection spread. A follow-up survey was implemented in 71 sampled herds of the Boji district (West Wellega province). Fifteen herds were classified as newly infected and used in a serological- and clinical-incidence study. The overall 16-month cumulative sero-incidence risk was 34%. Clinical cases were recorded for 39% of the seropositive cattle; case-fatality risk was 13%. There was no evidence of benefit on infection spread of CBPP-control measures used locally by farmers (isolation or antibiotic treatments of sick animals). This might be related to a lack of power in the statistical analyses or to a quality problem for the medications used (and more generally, for health-care delivery in the Boji district).     

Tuberculosis and brucellosis prevalence survey on dairy cattle in Mbarara milk basin (Uganda)

We determined the prevalence of tuberculosis and brucellosis reactors in the dairy herds in the Mbarara district of Uganda in 2002. This is one of the most important dairy-production areas of the country and includes both pastoral and agro-pastoral zones. A total of 340 (of 11,995) randomly selected herds were tested for tuberculosis, using the intradermal tuberculosis-skin test and 315 (of 10,562) herds tested for brucellosis using the serum Rose Bengal test.

The herd prevalence for tuberculosis reactors was 74.1% (95% confidence intervals 69, 78), the individual-animal prevalence was of 6.0% (5.6, 6.5) and within-herd range was 1–50% (up to 100% if suspicious reactors were included).

The herd prevalence for brucellosis was 55.6% (50, 61.2) individual-animal prevalence 15.8% (14.8, 16.7) and within-herd range 1–90%.

The reactor prevalence increased with the age of the animals for both tuberculosis and brucellosis.

Tuberculosis reactor prevalences were higher in animals from the agro-pastoral zone. However, the individual-animal and herd prevalences of brucellosis seroprevalences were higher in the pastoral zone.     

Evaluation of soybean genotypes for resistance against the rust-causing fungus Phakopsora pachyrhizi in East Africa

Soybean rust, caused by the biotrophic fungus Phakopsora pachyrhizi, is the most important foliar disease of soybean (Glycine max) worldwide. Deployment of resistant soybean cultivars is the best option for managing this disease. Genes conferring resistance to P. pachyrhizi have been identified, but pathotypes of the rust fungus overcoming these resistance genes have also been found. To identify novel resistance genes, soybean genotypes from both local and international sources were screened at multiple locations in Tanzania and Uganda in 2016 and 2017. The results from this screening revealed that infection types, disease severities, and sporulation levels varied among the genotypes and locations. The majority of the genotypes had tan-coloured (TAN) lesions and developed moderate sporulation, implying susceptibility, while only seven of the 71 lines had reddish-brown (RB) lesions and showed low disease severities in all of the screening environments. We identified seven genotypes that were the most resistant to rust in the most locations over the two years. These genotypes will be useful for further studies and, ultimately, for rust management, as they show broad resistance to various pathotypes of the rust fungus.     

Dynamics of microcrack propagation in hardwood during heat treatment investigated by synchrotron-based X-ray tomographic microscopy

The process of crack propagation in wood during pyrolysis is strongly linked to heterogeneities in its hierarchical porous structure. Fundamental understanding of this process is necessary for the analysis of the behavior of wood structural elements during fire exposure. Synchrotron-based X-ray tomographic microscopy combined with a recently developed laser-based furnace at the TOMCAT beamline of the Swiss Light Source provides a unique opportunity to study the heat-induced propagation of microcracks in hardwood in situ with high spatial and temporal resolutions. In this study, attention was focused on the 3D microstructure of beech and the interconnectivity between morphology and cracking patterns. It is shown that thermal cracks initiate mainly along the ray cells in hardwood and in the junction of seasonal growth layers. There is a clear indication of increased total porosity of the wood due to charring.     

Long-term phosphorus fertilisation increased the diversity of the total bacterial community and the phoD phosphorus mineraliser group in pasture soils

Fertilisers, especially nitrogen (N) and phosphorus (P) supplies, are frequently used in agricultural soil management to attain high crop yields. However, the intensive application of these chemical inputs can decrease the quality of agricultural soils and increase the probability of environmental pollution. In this study, the impact of P fertilisation on the diversity of the soil bacterial community was assessed. For this, a culture-independent approach targeting 16 rRNA and phoD genes was used on DNA extracted from pasture soils subjected to three different P fertilisation regimes for a long-term (42 years). As alkaline phosphomonoesterase (ALP) is necessary for mineralisation of organic P, an inverse relationship between the level of potential ALP activity and soil available P was expected. Indeed, a lower ALP activity was observed in soil subjected to higher chemical P fertiliser input. Analysis of the prevalence of three divergent families of ALP (PhoA, PhoD and PhoX) in metagenomic datasets revealed that PhoD is the most frequent ALP in soil samples and was selected as the most representative ALP possessed by the soil bacterial communities. Diversity of the phoD phosphorus mineraliser group, as well as the total bacterial community, was both increased in response to long-term P fertilisation. Specifically, phosphorus fertilisation decreased the relative abundance of certain taxa, including Acidobacteria and Pseudomonas fluorescens. In conclusion, this study shows that P fertilisation affects the microbial diversity of soil ecosystems, which might potentially modulate the soil biogeochemical cycle.