Search for QTL affecting the shape of the egg laying curve of the Japanese quail

BACKGROUND: Egg production is of critical importance in birds not only for their reproduction but also for human consumption as the egg is a highly nutritive and balanced food. Consequently, laying in poultry has been improved through selection to increase the total number of eggs laid per hen. This number is the cumulative result of the oviposition, a cyclic and repeated process which leads to a pattern over time (the egg laying curve) which can be modelled and described individually. Unlike the total egg number which compounds all variations, the shape of the curve gives information on the different phases of egg laying, and its genetic analysis using molecular markers might contribute to understand better the underlying mechanisms. The purpose of this study was to perform the first QTL search for traits involved in shaping the egg laying curve, in an F(2 )experiment with 359 female Japanese quail. RESULTS: Eight QTL were found on five autosomes, and six of them could be directly associated with egg production traits, although none was significant at the genome-wide level. One of them (on CJA13) had an effect on the first part of the laying curve, before the production peak. Another one (on CJA06) was related to the central part of the curve when laying is maintained at a high level, and the four others (on CJA05, CJA10 and CJA14) acted on the last part of the curve where persistency is determinant. The QTL for the central part of the curve was mapped at the same position on CJA06 than a genome-wide significant QTL for total egg number detected previously in the same F(2). CONCLUSION: Despite its limited scope (number of microsatellites, size of the phenotypic data set), this work has shown that it was possible to use the individual egg laying data collected daily to find new QTL which affect the shape of the egg laying curve. Beyond the present results, this new approach could also be applied to longitudinal traits in other species, like growth and lactation in ruminants, for which good marker coverage of the genome and theoretical models with a biological significance are available

A parameter identification problem in stochastic homogenization

In porous media physics, calibrating model parameters through experiments is a challenge. This process is plagued with errors that come from modelling, measurement and computation of the macroscopic observables through random homogenization -- the forward problem -- as well as errors coming from the parameters fitting procedure -- the inverse problem. In this work, we address these issues by considering a least-square formulation to identify parameters of the microscopic model on the basis on macroscopic observables. In particular, we discuss the selection of the macroscopic observables which we need to know in order to uniquely determine these parameters. To gain a better intuition and explore the problem without a too high computational load, we mostly focus on the one-dimensional case. We show that the Newton algorithm can be efficiently used to robustly determine optimal parameters, even if some small statistical noise is present in the system

Effect of Saprotrophic Soil Fungi on Toxocara canis Eggs

The purpose of this work was to assess the ovicidal activity of Chrysosporium merdarium, Trichoderma harzianum, Fusarium oxysporum, F. moniliforme and F. sulphureum isolated from public areas in the city of La Plata, Argentina, on Toxocara canis eggs in vitro. Each species were cultured on water agar 2% with a suspension of immature-stage T. canis eggs. At 4, 7, 14, 21 and 28 days post-culture, they were observed by light and scanning electron microscopy. One hundred eggs were evaluated and scored according to Lỳsek’s ovicidal effect classification. These procedures were repeated three times which each fungal species. Chrysosporium merdarium and F. oxysporum showed very high ovicidal activity, F. sulphureum high ovicidal activity, F. moniliforme intermediate ovicidal activity and T. harzianum did not affect the viability of T. canis eggs. Taking into account the effects on human and animal health and the environment, the species with better prospects for studying its potential use as biological control was F. sulphureum

Campylobacter in the Pork Food Chain : a quantitative hazard analysis

Campylobacter are one of the most frequent causes of bacterial enteritis in industrialized countries and are widespread in food animals. Pigs are known to be largely contaminated in farms, but few data exist about the status of the pork food chain. The purpose of this study was to quantify the Campylobacter contamination of the French pork food chain: prevalence, contamination level, bactenal species in primary production (piglets and fattening pigs when slaughtered), and in first and second transformation process (from carcasses before chilling to deboned meat cuts)

Dual Requirement for Yeast hnRNP Nab2p in mRNA poly(A) Tail Length Control and Nuclear Export

Recent studies of mRNA export factors have provided additional evidence for a mechanistic link between mRNA 3′‐end formation and nuclear export. Here, we identify Nab2p as a nuclear poly(A)‐binding protein required for both poly(A) tail length control and nuclear export of mRNA. Loss of NAB2 expression leads to hyperadenylation and nuclear accumulation of poly(A)+ RNA but, in contrast to mRNA export mutants, these defects can be uncoupled in a nab2 mutant strain. Previous studies have implicated the cytoplasmic poly(A) tail‐binding protein Pab1p in poly(A) tail length control during polyadenylation. Although cells are viable in the absence of NAB2 expression when PAB1 is overexpressed, Pab1p fails to resolve the nab2Δ hyperadenylation defect even when Pab1p is tagged with a nuclear localization sequence and targeted to the nucleus. These results indicate that Nab2p is essential for poly(A) tail length control in vivo, and we demonstrate that Nab2p activates polyadenylation, while inhibiting hyperadenylation, in the absence of Pab1p in vitro. We propose that Nab2p provides an important link between the termination of mRNA polyadenylation and nuclear export

Decontamination on pork carcasses: qualification of thermic treatment by thermal imaging

Singeing improves the visual quality of rind in pig slaughterhouses. In addition, the thermic inactivation allows the bacterial contamination of carcass surfaces to be reduced. However, the thermal image of pig carcasses shows temperature differences along the carcasses. The objective of this study was to develop a method to analyze a thermal image. After defining an imaging protocol adapted to pig slaughterhouses, image analysis was carried out with the free software: ImageJ©. Three methods were developed in order to preserve the spatial arrangement and time information for each measurement: (1) Method by line profile, (2) Method by mouse over, (3) Method by mouse over and line profile. Moreover, the method had to be simple and accurate. After a statistical comparison (mean, variance, distribution) between the three methods on 20 carcasses, the method by line profile was validated to analyze the characteristics of heat treatment in four pig slaughterhouses during process. This validated method of image acquisition and analysis was a tool used to measure the temperature variability on carcasses. The reference temperature was the temperature of carcasses after 90 minutes of continuous process. This method confirmed temperature differences on carcass surfaces (the top part of the carcass is warmer than the bottom part within a range of 2-7°C) and within a production day; the lowest temperatures were observed when the process started or re-started (after breaks), on average 4°C. These temperature variations along the working day were observed in every slaughterhouse studied. Bacterial contamination was evaluated on carcasses prior and following singeing for two heating settings. Results were similar to the literature (reduction of 3 Log10 CFU/cm² of the Aerobic colony counts). With this pragmatic method, companies could have access to a measurement tool not only for characterizing, checking, optimizing and qualifying the efficiency of singeing, but also for investigating all thermic treatments on meat in slaughterhouses

Investigation of the potential effects of transportation and lairage on the contamination of pig carcasses with Yersinia enterocolitica

Pathogenic Yersinia enterocolitica is frequently isolated from pig tonsils, but can also be found in the feces and lymph nodes of infected animals; which represent potential sources for the surface carcass contamination during slaughter. The aim of the study was to investigate the respective effects of the transportation and lairage steps on the overall contamination of the carcass, taking also into account the contamination of their environment. Each Trial was conducted in two abattoirs, whose environmental contamination was assessed. In each abattoir, 6 trucks and 6 lairage pens were sampled in duplicate at the end of the day, for 5 consecutive days, in spring and autumn. Four groups of 8 pigs from the Anses Specific Pathogen-Free herd (SPF) were mixed with conventional pigs for different contact times during transportation (1h) or lairage (2, 4 or 8h) prior to slaughter, and one group had no contact with other pigs. Each group of SPF pigs was sampled at the end of the slaughter line for the presence of pathogenic Y. enterocolitica for internal (tonsils, caecal content, mesenteric lymph nodes) and external (carcass surface) contamination. Samples were placed in ITC broth for enrichment at 25°C for 48h. Broth was streaked on CIN plates. After 24H at 30°C, typical colonies were streaked on YeCM plates. Biochemical tests were done to confirm Y. enterocolitica and to identify the biotype. The environmental contamination of trucks and lairage was very low. Y. enterocolitica was only detected in 11/240 lairage swabs. All internal and external samples from SPF pigs mixed with conventional pigs during transportation or lairage were negative after slaughter. Four tonsils of the SPF pigs slaughtered directly on the slaughter line after 4 hours of activity, with no prior contact with conventional pigs, and one of the corresponding surface carcasses, were found positive in one abattoir. In our experimental conditions with SPF pigs, we were not able to demonstrate contamination by contact with conventional pigs during transportation and lairage steps, whose environmental contamination appeared to be scarce. Limited cross contaminations were observed during the slaughter process, which emphasizes the importance of good hygiene procedures to limit carcass contamination by pathogenic Y. enterocolitica

Impact of the slaughter process on the pork carcasses contamination by Yersinia entrocolitica

The aim of the study was to evaluate the impact of the tongue handling practice on the contamination of the pork carcasses: the tongue removed with the pluck set (3 slaughterhouses) vs the intact tongue inside the head (3 slaughterhouses). A total of 1920 pigs from 120 different farms were sampled both on their tonsils and carcass surfaces over a one year period. The individual prevalence of Y. enterocolitica on tonsils and carcasses was unexpectedly low and estimated respectively to be 5.7% [4.7-6.9] and 0.6% [0.3-1.0] from the pooled samples. The presence of Y. enterocolitica on the carcasses was statistically linked to its presence on tonsils. It was nearly five times higher on pigs with positive tonsils, than on pigs with negative tonsils. Despite the experimental design, we were not able to confirm that the removal of the tongue on the slaughter line had a significant impact on the carcass contamination with Yersinia enterocolitica. These results confirm that cross contaminations occur during the slaughtering process and that good hygiene practices are necessary to limit the transfer of Y. enterocolitca from the tonsils, or the feces, to the carcasses

The hRPC62 subunit of human RNA polymerase III displays helicase activity.

In Eukaryotes, tRNAs, 5S RNA and U6 RNA are transcribed by RNA polymerase (Pol) III. Human Pol III is composed of 17 subunits. Three specific Pol III subunits form a stable ternary subcomplex (RPC62-RPC39-RPC32α/β) being involved in pre-initiation complex formation. No paralogues for subunits of this subcomplex subunits have been found in Pols I or II, but hRPC62 was shown to be structurally related to the general Pol II transcription factor hTFIIEα. Here we show that these structural homologies extend to functional similarities. hRPC62 as well as hTFIIEα possess intrinsic ATP-dependent 3'-5' DNA unwinding activity. The ATPase activities of both proteins are stimulated by single-stranded DNA. Moreover, the eWH domain of hTFIIEα can replace the first eWH (eWH1) domain of hRPC62 in ATPase and DNA unwinding assays. Our results identify intrinsic enzymatic activities in hRPC62 and hTFIIEα

Direct radiative effect of the Russian wildfires and its impact on air temperature and atmospheric dynamics during August 2010

International audienceIn this study, we investigate the shortwave aerosol direct radiative forcing (ADRF) and its feedback on air temperature and atmospheric dynamics during a major fire event that occurred in Russia during August 2010. The methodology is based on an offline coupling between the CHIMERE chemistry-transport and the Weather Research and Forecasting (WRF) models. First, simulations for the period 5–12 August 2010 have been evaluated by using AERONET (AErosol RObotic NETwork) and satellite measurements of the POLarization and Directionality of the Earth's Reflectance (POLDER) and the Cloud-Aerosol LIdar with Orthogonal Polarization (CALIOP) sensors. During this period, elevated POLDER aerosol optical thickness (AOT) is found over a large part of eastern Europe, with values above 2 (at 550 nm) in the aerosol plume. According to CALIOP observations, particles remain confined to the first five kilometres of the atmospheric layer. Comparisons with satellite measurements show the ability of CHIMERE to reproduce the regional and vertical distribution of aerosols during their transport from the source region. Over Moscow, AERONET measurements indicate an important increase of AOT (340 nm) from 0.7 on 5 August to 2–4 between 6 and 10 August when the aerosol plume was advected over the city. Particles are mainly observed in the fine size mode (radius in the range 0.2–0.4 μm) and are characterized by elevated single-scattering albedo (SSA) (0.95–0.96 between 440 and 1020 nm). Comparisons of simulations with AERONET measurements show that aerosol physical–optical properties (size distribution, AOT, SSA) have been well simulated over Moscow in terms of intensity and/or spectral dependence. Secondly, modelled aerosol optical properties have been used as input in the radiative transfer code of WRF to evaluate their direct radiative impact. Simulations indicate a significant reduction of solar radiation at the ground (up to 80–150 W m−2 in diurnal averages over a large part of eastern Europe due to the presence of the aerosol plume. This ADRF causes an important reduction of the near-surface air temperature between 0.2 and 2.6° on a regional scale. Moscow has been affected by the aerosol plume, especially between 6 and 10 August. During this period, aerosol causes a significant reduction of surface shortwave radiation (up to 70–84 W m−2 in diurnal averages) with a moderate part (20–30%) due to solar absorption within the aerosol layer. The resulting feedbacks lead to a cooling of the air up to 1.6° at the surface and 0.1° at an altitude of 1500–2000 m (in diurnal averages), that contribute to stabilize the atmospheric boundary layer (ABL). Indeed, a reduction of the ABL height of 13 to 65% has been simulated during daytime in presence of aerosols. This decrease is the result of a lower air entrainment as the vertical wind speed in the ABL is shown to be reduced by 5 to 80% (at midday) when the feedback of the ADRF is taken into account. However, the ADRF is shown to have a lower impact on the horizontal wind speed, suggesting that the dilution of particles would be mainly affected by the weakening of the ABL development and associated vertical entrainment. Indeed, CHIMERE simulations driven by the WRF meteorological fields including this ADRF feedback result in a large increase in the modelled near-surface PM10 concentrations (up to 99%). This is due to their lower vertical dilution in the ABL, which tend to reduce model biases with the ground PM10 values observed over Moscow during this specific period