Some determinants of the spatio-temporal fire cycle in a mediterranean landscape (Corsica,France)

Based on recent needs to accurately understand fire regimes and post-fire vegetation resilience at a supra-level for carbon cycle studies, this article focusses on the coupled history of fire and vegetation pattern for 40 years on a fire-prone area in central Corsica (France). This area has been submitted since the beginning of the 20^th century to land abandonment and the remaining land management has been largely controlled by frequent fires. Our objectives were to rebuild vegetation and fire maps in order to determine the factors which have driven the spatial and temporal distribution of fires on the area, what were the feed backs on the vegetation dynamics, and the long-term consequences of this inter-relationship. The results show a stable but high frequency of small fires, coupled with forest expansion over the study period. The results particularly illustrate the spatial distribution of fires according to topography and vegetation, leading to a strong contrast between areas never burnt and areas which have been burnt up to 7 times. Fires, when occuring, affect on average 9 to 12% of the S, SE and SW facing slopes (compared to only 2 to 5% for the N facing slopes), spread recurrently over ridge tops, affect all the vegetation types but reburn preferentially shrublands and grasslands. As these fire-proning parameters have also been shown to decrease the regeneration capacity of forests, this study highlights the needs in spatial studies (both in terms of fire spread and vegetation dynamic) to accurately apprehend vegetation dynamic and functionning in fire-prone areas.This revised version was published online in May 2005 with corrections to the Cover Date.     

Tissue distribution of Red Spotted Grouper Nervous Necrosis Virus (RGNNV) genome in experimentally infected juvenile European seabass (Dicentrarchus labrax)

The distribution of viral genome in the tissues of juvenile European seabass (Dicentrarchus labrax) during the course of a Red Spotted Grouper Nervous Necrosis Virus (RGNNV) infection has not yet been described. The present study addresses this and indicates which target organs may be involved in viral replication. This information should enable more accurate detection of virus in asymptomatic carriers, and in turn help to control the spread of the disease. The aim of this study was to examine the pattern of expression of viral genomic segments RNA1 and RNA2, using two absolute real-time PCRs (RT-qPCR), over the course of a RGNNV infection after administering the virus by intramuscular injection. In situ hybridization was also used to locate the RNA2 viral segment in different organs throughout the infection. The experimental challenge provoked an acute form of viral nervous necrosis (VNN), with a resulting cumulative mortality of 37%. The RT-qPCRs designed allowed the detection of both genomic segments in all the organs tested (nervous and non-nervous tissues) at all sampling times examined. The highest viral RNA copy number was found in eyes, although viral replication appeared to begin in the brain. Viral replication was also recorded in pooled internal organs and in caudal fin. However, the increase in the viral RNA copy number in these organs did not result in an increased viral titre, which may indicate that a productive infection does not take place in non-nervous tissues, possibly due to a failure in a viral post-replication step.     

Rough vaccines in animal brucellosis: structural and genetic basis and present status

Brucellosis control and eradication requires serological tests and vaccines. Effective classical vaccines (S19 in cattle and Rev 1 in small ruminants), however, induce antibodies to the O-polysaccharide of the lipopolysaccharide which may be difficult to distinguish from those resulting from infection and may thus complicate diagnosis. Rough attenuated mutants lack the O-polysaccharide and would solve this problem if eliciting protective immunity; the empirically obtained rough mutants 45/20 and RB51 have been used as vaccines. Strain 45/20 is reportedly unstable and it is not presently used. RB51 is increasingly used instead of S19 in some countries but it is rifampicin resistant and its effectiveness is controversial. Some controlled experiments have found good or absolute protection in adult cattle vaccinated orally (full dose) or subcutaneously (reduced dose) and in one field experiment, RB51 was reported to afford absolute protection to calves and to perform better than S19. Controlled experiments in calves, however, have shown reduced doses of RB51 to be ineffective, full doses only partially effective, and RB51 less effective than S19 against severe challenges. Moreover, other observations suggest that RB51 is ineffective when prevalence is high. RB51 is not useful in sheep and evidence in goats is preliminary and contradictory. Rough mutants obtained by molecular biology methods on the knowledge of the genetics and structure of Brucella lipopolysaccharide may offer alternatives. The B. abortus manBcore (rfbK) mutant seems promising in cattle, and analyses in mice suggest that mutations affecting only the O-polysaccharide result in better vaccines than those affecting both core and O-polysaccharide. Possible uses of rough vaccines also include boosting immunity by revaccination but solid evidence on its effectiveness, safety and practicality is not available.     

Emerging issues in genomic selection

Genomic selection (GS) is now practiced successfully across many species. However, many questions remain, such as long-term effects, estimations of genomic parameters, robustness of genome-wide association study (GWAS) with small and large datasets, and stability of genomic predictions. This study summarizes presentations from the authors at the 2020 American Society of Animal Science (ASAS) symposium. The focus of many studies until now is on linkage disequilibrium between two loci. Ignoring higher-level equilibrium may lead to phantom dominance and epistasis. The Bulmer effect leads to a reduction of the additive variance; however, the selection for increased recombination rate can release anew genetic variance. With genomic information, estimates of genetic parameters may be biased by genomic preselection, but costs of estimation can increase drastically due to the dense form of the genomic information. To make the computation of estimates feasible, genotypes could be retained only for the most important animals, and methods of estimation should use algorithms that can recognize dense blocks in sparse matrices. GWASs using small genomic datasets frequently find many marker-trait associations, whereas studies using much bigger datasets find only a few. Most of the current tools use very simple models for GWAS, possibly causing artifacts. These models are adequate for large datasets where pseudo-phenotypes such as deregressed proofs indirectly account for important effects for traits of interest. Artifacts arising in GWAS with small datasets can be minimized by using data from all animals (whether genotyped or not), realistic models, and methods that account for population structure. Recent developments permit the computation of P-values from genomic best linear unbiased prediction (GBLUP), where models can be arbitrarily complex but restricted to genotyped animals only, and single-step GBLUP that also uses phenotypes from ungenotyped animals. Stability was an important part of nongenomic evaluations, where genetic predictions were stable in the absence of new data even with low prediction accuracies. Unfortunately, genomic evaluations for such animals change because all animals with genotypes are connected. A top-ranked animal can easily drop in the next evaluation, causing a crisis of confidence in genomic evaluations. While correlations between consecutive genomic evaluations are high, outliers can have differences as high as 1 SD. A solution to fluctuating genomic evaluations is to base selection decisions on groups of animals. Although many issues in GS have been solved, many new issues that require additional research continue to surface.     

Gastrointestinal parasitism reduces the plasma availability of doramectin in lambs

A study was undertaken to investigate the effect of parasitism on plasma availability and pharmacokinetic behaviour of doramectin (DRM) in lambs. Fourteen parasitised grey face Suffolk lambs (26.9 ± 1.5 kg bodyweight) were selected for the study. Seven pairs of lambs were allocated to two groups to obtain an approximately even weight distribution. Group I (non-parasitised) was pre-treated with three repeated administrations of 5 mg/kg fenbendazole to maintain a parasite free condition. In group II (parasitised), the lambs did not receive any anthelmintic treatment. After the 85-day pre-treatment period, both groups of animals were treated with DRM by subcutaneous (SC) injection in the shoulder area at 200 μg/kg. Throughout the experimental period, both groups were maintained together under similar feeding and management conditions. Blood samples were collected by jugular venepuncture at different set times between 0.5 h and 60 days post-treatment. After plasma extraction and derivatisation, samples were analysed by high performance liquid chromatography (HPLC) with fluorescence detection. A computerised kinetic analysis was performed and the data were compared using the Student’s paired t test.The parent molecule was detected in plasma between 30 min and either day 20 (parasitised) or day 35 (non-parasitised) post-DRM treatment. The AUC values of the parasitised group (143.0 ± 18 ng d/mL) were significantly lower (P < 0.05) than those observed in the parasitically naïve animals (229.6 ± 21.7 ng d/mL). The mean residence time (MRT) in the parasitised group (3.4 ± 0.3 days) was significantly shorter (P < 0.05) than in the healthy group (6.6 ± 0.6 days). Study results have shown that parasitic disease, through alteration in the body condition, can produce significant changes in the plasma disposition of DRM when administered SC to parasitised lambs.     

Demography,population dynamics and sustainability of the Patagonian sheep flocks

Sheep production is the main agricultural activity in Patagonia. Since the middle of the 20th century, sheep numbers have declined steadly. We used historical records of stock numbers in four ranches to analyze the importance of regional factors so as to explain the decline of the Patagonian sheep flocks. We found that the stocks of all the four ranches declined with a similar trend but fluctuated independently, thus reflecting a complex interaction between regional and local factors. Aboveground net primary production (ANPP) and vegetation physiognomy explained most of the differences in the flocks declining rates. We estimated demographic parameters for two ranches differing in their average annual growth rates. From these demographic parameters, we constructed deterministic and stochastic matrix models to establish the relative contribution of demographic processes to the observed decline. Matrix models projected a faster decline than that observed in the ranch used to calibrate the model. This suggests that the recorded demographic parameters could drive most stocks to extinction in less than 100 years. We concluded that the observed dynamics would be generated by demographic processes, but extinction is delayed or avoided by a continuous intake of animals. Ewe survival was the most important parameter in controlling the growth rate of the flocks. The environmental stochastic model showed that the growth of the stocks was highly sensitive to increases in the frequency of good years (those that produce a positive growth) and in the transition from normal years to bad years. All these evidences point out the existence of biological constraints to sheep production in Patagonia: ANPP and vegetation structure would control flock population dynamics throughout its effects on key demographic parameters, ewe survival and marking rate (a recruitment measure). Our model results suggest that the decline in sheep numbers, and hence the sustainability of the activity, is driven, to a large extent, by the demographic characteristics of the flocks.     

Brown shrimp (Farfantepenaeus aztecus) density distribution in the Northern Gulf of Mexico: an approach using boosted regression trees

The estuarine‐dependent brown shrimp, Farfantepenaeus aztecus, is a significant commercial fishery and important species in the Gulf of Mexico (GOM) ecosystem as well as being a key component in energy transfer between benthic and pelagic food web systems. Because of the economical and ecological importance of brown shrimp, we developed a spatial population model to identify places of high shrimp density under a set of spatial, environmental and temporal variables in the Northern Gulf of Mexico (NGOM). We used fisheries‐independent data collected by the Southeast Area Monitoring and Assessment Program (SEAMAP) from 1992 to 2007 (summer and fall seasons). The relationship between the predictor variables and shrimp density was modeled using Boosted Regression Trees (BRT). Within the environmental variables included in the model, bottom type and depth of the water column were the most important predictors of shrimp density in the NGOM. Spatial predictions performed using the trained BRT model for summer and fall seasons showed a spatial segregation of shrimp density. During the summer, higher densities were predicted near the Texas and Louisiana coast and during the fall, higher densities were predicted further offshore. The model performed well and allowed successful prediction of brown shrimp hot spots in the NGOM. Model results allow fisheries managers to evaluate the potential impact from fisheries on the resource and to develop future fisheries management strategies, understand the biology of brown shrimp as well as assess the potential impacts of oil spills or climate change.     

Biochemical,Physical, Chemical,and Microbiological Assessment of Blue Shrimp (Litopenaeus stylirostris) Stored in Ice

Postmortem changes in blue shrimp (Litopenaeus stylirostris) muscle were studied on the basis of biochemical, chemical, physical, and microbiological changes during an 18 day storage period at 0°C. Adenosine 5′-triphosphate (ATP) content, breakdown products, K-value, pH, trimethylamine nitrogen (TMA-N), total volatile basic nitrogen (TVB-N), water holding capacity (WHC), color, and texture (shear force) changes were examined. Also, total mesophilic and psychrophilic bacterial counts were measured. K-value increased linearly (r² = 0.98) from an initial value of 1.37 ± 0.59 to 59.42 ± 6.05% at Day 18. Spoilage indicators TVB-N and TMA-N increased from 29.56 ± 1.33 and 0.69 ± 0.25 to 39.04 and 2.04 ± 0.59 mg of N/100 g at Day 18, respectively; meanwhile, the total viable counts of mesophilic and psychrophilic bacteria increased from 3.48 ± 0.44 and 2.61 ± 0.29 log CFU/g to 6.27 ± 0.21 and 7.14 ± 0.39 log CFU/g, respectively, which indicated spoilage at the end of the storage period. The pH, texture, WHC, and color were affected (p < 0.05) during the storage period. Overall, results indicate that blue shrimp muscle quality was maintained for 12 days of storage in ice.