Assessment of commercial and recreational fishing effects on trophic interactions in the Cap Roux area (north‐western Mediterranean)

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Efficacy of a modified polymerase chain reaction assay for detection of Ehrlichia canis infection.

Detection of Ehrlichia canis in acutely infected and convalescent dogs is important for effective treatment and control. However, accurate detection has been difficult to achieve, in part because dogs that have been treated therapeutically often remain seropositive for extended periods. A new method, polymerase chain reaction (PCR) assay using biotinylated E. canis-specific primers (PCR-BP), was developed for detection of E. canis. Four dogs experimentally infected with E. canis by intravenous inoculation of whole blood from carrier dogs and 2 naturally infected convalescent carriers were used to compare the specificity and sensitivity of the new method with that of microscopy/blood smear evaluation, serologic test, and conventional PCR assay using E. canis-specific primers. In experimentally infected animals, infection was detected as early as 7 days post-exposure using PCR-BP. Although the 2 naturally infected dogs were positive by serologic test and PCR-BP, both were negative by conventional PCR. Results suggest that the new method is a sensitive assay for detection of E. canis infection. In addition, results were obtained more rapidly than with other PCR-based assays.     

Validation of a feeding strategy to deliver bacterially expressed dsRNA to marine amoeba from the genus Neoparamoeba

RNA interference (RNAi) mediated by double stranded RNA (dsRNA) has emerged as one of the most promising techniques to study gene function of non‐model protozoan parasites. We have previously demonstrated that bacterially expressed dsRNA delivered by immersion elicited successful knockdown in Neoparamoeba pemaquidensis, the non‐infective species closely related to the causative agent of salmonid amoebic gill disease (AGD). However, considering that amoebae naturally feeds on microorganisms, direct ingestion of bacteria designed to express dsRNA could allow rapid and low‐cost analysis of gene function on a large‐scale. Therefore, the main objective of this study was to investigate whether ingestion of bacteria‐expressing dsRNAs would also induce suppression of N. pemaquidensis β‐actin and EF1α. Despite effective bacterial uptake, no significant variation in EF1α relative copy number was triggered by dsRNA ingestion. β‐actin, on the other hand, presented similar silencing efficiency to what was observed in our previous soaking study. However, the observed RNAi response was delayed by at least 72 h. The present work provides evidence that delivery of bacterially expressed dsRNA through feeding can be successfully achieved in N. pemaquidensis, albeit not as efficiently as by soaking. Therefore, further investigation is required to develop more efficient and specific RNAi delivery systems in Neoparamoeba species. To our knowledge, this is the first time that RNAi‐mediated knockdown through ingestion was attempted to manipulate gene function of a marine amoeba.     

Changes of protein profile in fresh-cut lotus tuber before and after browning

Browning is a critical problem, which often limits the shelf life and marketability in fresh-cut lotus tuber. Proteome level changes in response to the browning metabolism were investigated using two-dimensional electrophoresis (2-DE) and MALDI-TOF-TOF. A total of 34 functional protein spots were identified by comparing 2-DE protein patterns of fresh-cut lotus tuber before and after browning. These 34 identified proteins could be classified into 7 functional groups based on the NCBI database, that is, material and energy metabolism (35%), stress response (20%), respiration metabolism (12%), cell structure (12%), signal transduction (6%), gene expression regulation (6%), and unclassified proteins (9%). The group with the greatest difference in protein expression was related to material metabolism and regulation, reactive oxygen species metabolism, and respiratory control. The distinct proteins included universal stress protein (USP), superoxide dismutase (SOD), peroxidase (POD), ferritin, and ATPase.     

The REFLEX project: Comparing different algorithms and implementations for the inversion of a terrestrial ecosystem model against eddy covariance data

We describe a model-data fusion (MDF) inter-comparison project (REFLEX), which compared various algorithms for estimating carbon (C) model parameters consistent with both measured carbon fluxes and states and a simple C model. Participants were provided with the model and with both synthetic net ecosystem exchange (NEE) of CO₂ and leaf area index (LAI) data, generated from the model with added noise, and observed NEE and LAI data from two eddy covariance sites. Participants endeavoured to estimate model parameters and states consistent with the model for all cases over the two years for which data were provided, and generate predictions for one additional year without observations. Nine participants contributed results using Metropolis algorithms, Kalman filters and a genetic algorithm. For the synthetic data case, parameter estimates compared well with the true values. The results of the analyses indicated that parameters linked directly to gross primary production (GPP) and ecosystem respiration, such as those related to foliage allocation and turnover, or temperature sensitivity of heterotrophic respiration, were best constrained and characterised. Poorly estimated parameters were those related to the allocation to and turnover of fine root/wood pools. Estimates of confidence intervals varied among algorithms, but several algorithms successfully located the true values of annual fluxes from synthetic experiments within relatively narrow 90% confidence intervals, achieving >80% success rate and mean NEE confidence intervals <110 gC m⁻² year⁻¹ for the synthetic case. Annual C flux estimates generated by participants generally agreed with gap-filling approaches using half-hourly data. The estimation of ecosystem respiration and GPP through MDF agreed well with outputs from partitioning studies using half-hourly data. Confidence limits on annual NEE increased by an average of 88% in the prediction year compared to the previous year, when data were available. Confidence intervals on annual NEE increased by 30% when observed data were used instead of synthetic data, reflecting and quantifying the addition of model error. Finally, our analyses indicated that incorporating additional constraints, using data on C pools (wood, soil and fine roots) would help to reduce uncertainties for model parameters poorly served by eddy covariance data.     

Effects of yeast and yeast cell wall polysaccharides supplementation on beef cattle growth performance,rumen microbial populations and lipopolysaccharides production

This experiment was conducted to investigate the effects of live yeast and yeast cell wall polysaccharides on growth performance, rumen function and plasma lipopolysaccharides(LPS) content and immunity parameters of beef cattle. Forty Qinchuan cattle were randomly assigned to one of four treatments with 10 replicates in each treatment. The dietary treatments were: control diet(CTR), CTR supplemented with 1 g live yeast(2×1010 live cell g–1 per cattle per day(YST1), CTR supplemented with 2 g live yeast per cattle per day(YST2) and CTR supplemented with 20 g of yeast cell wall polysaccharides(30.0%≤β-glucan≤35.0%, and 28.0%≤mannanoligosaccharide≤32.0%) per cattle per day(YCW). The average daily gain was higher(P=0.023) and feed conversion ratio was lower(P=0.042) for the YST2 than the CTR. The digestibility of neutral detergent fiber(P=0.039) and acid detergent fiber(P=0.016) were higher in yeast supplemented groups. The acetic acid:propionic acid of the YST2 was lower compared with the CTR(P=0.033). Plasma LPS(P=0.032), acute phase protein haptoglobin(P=0.033), plasma amyloid A(P=0.015) and histamine(P=0.038) were lower in the YST2 compared with the CTR. The copies of fibrolytic microbial populations such as Fibrobacter succinogenes S85, Ruminococcus albus 7 and Ruminococcus flavefaciens FD-1 of the YST2 were higher(P0.001), while the copies of typical lactate producing bacteria Streptococcus bovis JB1 was lower(P0.001) compared with the CTR. Little differences were observed between the CTR, YST1 and YCW in growth performance, ruminal fermentation characteristics, microbial populations, immunity indices and total tract nutrient digestibility. It is concluded that the YST2 could promote fibrolytic microbial populations, decrease starch-utilizing bacteria, reduce LPS production in the rumen and LPS absorption into plasma and decrease inflammatory parameters, which can lead to an improvement in growth performance in beef cattle.     

Molecular characterization of MHC class II region in guinea fowl

1. The MHC class II gene was amplified, cloned and sequenced in guinea fowl. 2. The NumeMHC II sequence of 754 nucleotides included complete exon 1 (91 nt), exon 2 (270 nt), exon 3 (282 nt) and exon 4 (110 nt). 3. The size of β(1) and β(2), domains were 89 and 93 amino acids, respectively in guinea fowl. 4. High amino acid variability (38·2%) was observed within guinea fowl in β(1) domain, while in β(2) domain, amino acid variability (6·3%) was low. 5. Among poultry species, the percent amino acid identity between guinea fowl and chicken, quail, pheasant and duck was 38·8, 42·2, 44·4 and 58·8 in β(1) domain; and 13·8, 17·0, 13·8 and 27·6 in β(2) domain, respectively. 6. Sequence alignment with mammalian and avian MHC showed that many of the conserved features of MHC class II glycoprotein was conserved in guinea fowl. 7. Within-species genetic distances (Poisson correction) based on cumulative amino acid variability in β(1) domain and β(2) domains was 0·141 in guinea fowl. 8. Guinea fowl showed low and similar genetic distances with all the poultry species (0·255-0·268) except duck (0·456). 9. Guinea fowl made separate branch within the major cluster having chicken, quail and pheasant, showing equal distance from these poultry species, whereas duck MHC II clustered separately.     

Differential Selection on Rhynchosporium secalis During Parasitic and Saprophytic Phases in the Barley Scald Disease Cycle

ABSTRACT Competition among eight Rhynchosporium secalis isolates was assessed during parasitic and saprophytic phases of the disease cycle in field experiments conducted at two locations and over two growing seasons. The eight isolates were inoculated onto six barley populations exhibiting varying degrees of resistance. Microsatellite analysis of 2,866 isolates recovered from the field experiments showed significant, and sometimes opposite, changes in the frequencies of R. secalis genotypes during the growing season (parasitic phase) and between growing seasons (saprophytic phase). Isolates that showed the most complex virulence in greenhouse seedling assays had the lowest fitness in the field experiment. Significant differences in isolate fitness were found on different host populations and in different environments. Selection coefficients were large, indicating that evolution can occur rapidly in field populations. Although inoculated isolates had the lowest overall fitness on the moderately resistant landrace cv. Arabi Aswad, some isolates were more virulent and consistently increased in frequency on this landrace, suggesting a risk of directional selection and possible erosion of the resistance following its widespread deployment in monoculture. These results provide the first direct evidence that R. secalis pathogen genotypes differ in their saprophytic ability and parasitic fitness under field conditions.