Aims
A new multiplex qPCR, targeting Mycoplasma (M.) hyopneumoniae, M. hyorhinis and M. flocculare, was developed and the relationship between detection of those mycoplasma species and the extent of ...gross pneumonia‐like lesions in slaughtered pigs lungs were investigated.
Methods and Results
The multiplex qPCR method targets the p102, p37 and fruA genes and has detection limits of 14, 146 and 16 genome equivalents μl−1 for M. hyopneumoniae, M. hyorhinis and M. flocculare, respectively. In all, 671 lungs were collected and analysed, among them 666 were scored for macroscopic pneumonia and categorized according to the extent of the lesions (no or minor lesions, moderate lesions and extensive lesions). According to results of multiplex qPCR, 59·5% were positive for M. hyopneumoniae, 3·4% for M. hyorhinis and 34·7% for M. flocculare, with on average, 3·1 × 107, 9·7 × 106 and 5·7 × 106 genome equivalents of mycoplasma ml−1, respectively. More results showed that no or minor lesions were associated with multiplex qPCR‐negative results or qPCR‐positive results for M. flocculare. Moderate to extensive lesions were positively correlated with qPCR‐positive results for M. hyopneumoniae. Extensive lesions were associated with qPCR‐positive results for at least two mycoplasma species (M. hyopneumoniae and M. hyorhinis).
Conclusion
The findings also indicated that M. hyopneumoniae and M. hyorhinis significantly increased the odds for a lung to have macroscopic pneumonia. No relationship was found between the extent of lesions and the mycoplasma genome load.
Significance and Impact of the study
This new multiplex qPCR appears to be specific, sufficiently sensitive and repeatable. The validation of this method with field samples guarantees its use for field epidemiological investigations, particularly to gain more insight into the aetiology of the porcine respiratory disease complex.
ABSTRACT We present new astrometric measurements from our ongoing monitoring campaign of the HR 8799 directly imaged planetary system. These new data points were obtained with NIRC2 on the W.M. Keck ...II 10 m telescope between 2009 and 2014. In addition, we present updated astrometry from previously published observations in 2007 and 2008. All data were reduced using the SOSIE algorithm, which accounts for systematic biases present in previously published observations. This allows us to construct a self-consistent data set derived entirely from NIRC2 data alone. From this data set, we detect acceleration for two of the planets (HR 8799b and e) at >3 . We also assess possible orbital parameters for each of the four planets independently. We find no statistically significant difference in the allowed inclinations of the planets. Fitting the astrometry while forcing coplanarity also returns χ2 consistent to within 1 of the best fit values, suggesting that if inclination offsets of 20° are present, they are not detectable with current data. Our orbital fits also favor low eccentricities, consistent with predictions from dynamical modeling. We also find period distributions consistent to within 1 with a 1:2:4:8 resonance between all planets. This analysis demonstrates the importance of minimizing astrometric systematics when fitting for solutions to highly undersampled orbits.
A study was carried out in 125 farrow-to-finish pig herds to assess the relationships between pathogens involved in respiratory disorders and to relate these findings to clinical signs of respiratory ...diseases and pneumonia and pleuritis at slaughter. Clinical examination and sampling were carried out on four different batches in each herd (pigs aged 4, 10, 16 and 22 weeks). Mycoplasma hyopneumoniae, Actinobacillus pleuropneumoniae, swine influenza viruses (SIV), porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) were detected by serological or PCR tests. Pneumonia-like gross lesions and pleuritis were scored at the slaughterhouse. The results indicate that the percentage of pigs PCR-positive for PCV2 at 4, 10 and 16 weeks old was associated with the percentage of pigs PCR-positive for M. hyopneumoniae at these ages. On the other hand, the percentage of pigs with antibodies against PRRSV at 10, 16 and 22 weeks was positively correlated with the percentage of pigs seropositive for M. hyopneumoniae at 22 weeks, with the percentage of pigs with antibodies against SIV H1N1 and SIV H1N2 and the percentage of pigs sero-positive for A. pleuropneumoniae serotype 2. The findings also indicate that, within the five studied pathogens, M. hyopneumoniae, PRRSV and SIV H1N1 are the major pathogens involved in pneumonia-like gross lesions even though PCV2 may play a role. A. pleuropneumoniae serotype 2, in association with PRRSV, is significantly associated with extensive pleuritis. Respiratory diseases could be significantly reduced by implementing measures including appropriate management practices to control these pathogens.
In this paper, we review the impact of small sample statistics on detection thresholds and corresponding confidence levels (CLs) in high-contrast imaging at small angles. When looking close to the ...star, the number of resolution elements decreases rapidly toward small angles. This reduction of the number of degrees of freedom dramatically affects CLs and false alarm probabilities. Naively using the same ideal hypothesis and methods as for larger separations, which are well understood and commonly assume Gaussian noise, can yield up to one order of magnitude error in contrast estimations at fixed CL. The statistical penalty exponentially increases toward very small inner working angles. Even at 5-10 resolution elements from the star, false alarm probabilities can be significantly higher than expected. Here we present a rigorous statistical analysis that ensures robustness of the CL, but also imposes a substantial limitation on corresponding achievable detection limits (thus contrast) at small angles. This unavoidable fundamental statistical effect has a significant impact on current coronagraphic and future high-contrast imagers. Finally, the paper concludes with practical recommendations to account for small number statistics when computing the sensitivity to companions at small angles and when exploiting the results of direct imaging planet surveys.
The International Deep Planet Survey Galicher, R; Marois, C; Macintosh, B ...
Astronomy and astrophysics (Berlin),
10/2016, Volume:
594
Journal Article
Peer reviewed
Open access
Context. Radial velocity and transit methods are effective for the study of short orbital period exoplanets but they hardly probe objects at large separations for which direct imaging can be used. ...Aims. We carried out the international deep planet survey of 292 young nearby stars to search for giant exoplanets and determine their frequency. Methods. We developed a pipeline for a uniform processing of all the data that we have recorded with NIRC2/Keck II, NIRI/Gemini North, NICI/Gemini South, and NACO/VLT for 14 yr. The pipeline first applies cosmetic corrections and then reduces the speckle intensity to enhance the contrast in the images. Results. The main result of the international deep planet survey is the discovery of the HR8799 exoplanets. We also detected 59 visual multiple systems including 16 new binary stars and 2 new triple stellar systems, as well as 2279 point-like sources. We used Monte Carlo simulations and the Bayesian theorem to determine that (ProQuest: Formulae and/or non-USASCII text omitted) of stars harbor at least one giant planet between 0.5 and 14M sub(J) and between 20 and 300AU. This result is obtained assuming uniform distributions of planet masses and semi-major axes. If we consider power law distributions as measured for close-in planets instead, the derived frequency is (ProQuest: Formulae and/or non-USASCII text omitted), recalling the strong impact of assumptions on Monte Carlo output distributions. We also find no evidence that the derived frequency depends on the mass of the hosting star, whereas it does for close-in planets. Conclusions. The international deep planet survey provides a database of confirmed background sources that may be useful for other exoplanet direct imaging surveys. It also puts new constraints on the number of stars with at least one giant planet reducing by a factor of two the frequencies derived by almost all previous works.
With a combination of adaptive optics imaging and a multi-epoch common proper motion search, we have conducted a large volume-limited (D ≤ 75 pc) multiplicity survey of A-type stars, sensitive to ...companions beyond 30 au. The sample for the Volume-limited A-STar (VAST) survey consists of 435 A-type stars: 363 stars were observed with adaptive optics, 228 stars were searched for wide common proper motion companions and 156 stars were measured with both techniques. The projected separation coverage of the VAST survey extends from 30 to 45 000 au. A total of 137 stellar companions were resolved, including 64 new detections from the VAST survey, and the companion star fraction, projected separation distribution and mass ratio distribution were measured. The separation distribution forms a log-normal distribution similar to the solar-type binary distribution, but with a peak shifted to a significantly wider value of
au. Integrating the fit to the distribution over the 30 to 10 000 au observed range, the companion star fraction for A-type stars is estimated as 33.8 ± 2.6 per cent. The mass ratio distribution of closer (<125 au) binaries is distinct from that of wider systems, with a flat distribution for close systems and a distribution that tends towards smaller mass ratios for wider binaries. Combining this result with previous spectroscopic surveys of A-type stars gives an estimate of the total companion star fraction of 68.9 ± 7.0 per cent. The most complete assessment of higher order multiples was estimated from the 156 star subset of the VAST sample with both adaptive optics and common proper motion measurements, combined with a thorough literature search for companions, yielding a lower limit on the frequency of single, binary, triple, quadruple and quintuple A-type star systems of
,
,
,
and
per cent, respectively.
Direct-imaging searches for planets reveal wide orbit planets amenable to spectroscopy, and their atmospheres represent an important comparison to the irradiated atmospheres of Hot Jupiters. Using AO ...integral field spectroscopy of 2M1207 b, the shape of the continuum emission over the J, H, and K bands from the atmosphere of this young, planetary mass companion is measured in order to compare with atmospheric and evolutionary models, and objects of similar temperature in young clusters and the field. The 2M1207 b spectrum has the highest spectral resolution (R ~ 300–1500) and largest wavelength coverage, including the first J-band spectrum, for this benchmark object. The high signal-to-noise of the data allow a clear identification of signatures of low surface gravity, and comparison with a grid of AMES-Dusty models reveals a best-fit effective temperature of T eff= 1600 K with a preferred surface gravity of log g = 4.5. The J-band flux is depressed relative to nearly all L-type objects, and the detailed shape of the absorption features across the H-band exhibit differences from the model predictions. The possible origins of 2M1207 b and its low luminosity are examined with the new data and analysis which suggest that extinction from a disk with large grains is a viable scenario and is preferred over scatttering off an optically thick disk. The 2M1207 b spectrum presents an important comparison for the types of features which may be present in upcoming spectra of the atmospheres of planets imaged in orbit around stellar primaries.
The aim of the study was to quantify Pasteurella multocida in experimentally infected pigs using a new qPCR assay based on the sodA gene and validated with 35 P. multocida strains, including strains ...isolated from pigs with pneumonia, clinically healthy pigs (nasal cavities), and human infections. The specificity of the test was verified with a collection of 60 strains of bacterial species other than P. multocida. The estimated detection threshold was 10 genome equivalents per microliter. The amplification efficiency and value of the correlation coefficients were 95.5% (±3.5%) and 0.995 (±0.005), respectively. Analysis of P. multocida suspensions in Buffered Peptone Water Broth and of samples prepared from lungs experimentally spiked with P. multocida revealed detection thresholds of 1.4CFU/μl and 8.4CFU/μl, respectively. In live pigs, experimentally-infected, approximately 105, 107 and 108genomeequivalents/ml of P. multocida DNA was detected on Day 8 post-infection in the nasal cavities, tonsils and trachea samples, respectively. In dead pigs, approximatively 107genomeequivalents/ml of P. multocida DNA was detected in the lung tissue with pneumonia. The qPCR assay's diagnostic specificity and sensitivity were 100% and 96%, respectively. This new qPCR assay should be a very useful tool for controlling enzootic pneumonia and studying the dynamics of infections in pig herds.
•A new qPCR assay was developed to quantify Pasteurella multocida in pigs.•Validation of the qPCR assay's specificity and sensitivity•Detection of all P. multocida strains analyzed (isolated from pigs or humans)•Quantification of P. multocida in specimens from experimentally infected pigs•A useful tool for controlling pig infections
•Biosecurity measures reduce PRRSV probability of introduction.•Practices favoring contacts between animals from different batches increase PRRSV infection.•Factors dealing with the control of indoor ...climate are related to PRRSV infection characteristics.
Factors associated with porcine reproductive and respiratory syndrome virus (PRRSV) infection were investigated in 109 herds. Serums from four batches of pigs (4, 10, 16 and 22 weeks, 15 pigs/batch) were tested by ELISA for PRRSV antibodies. Infection by Mycoplasma hyopneumoniae (Mhp), Actinobacillus pleuropneumoniae, H1N1 and H1N2 swine influenza A viruses (swIAV) and PCV2 were detected by specific serological or PCR tests. Data related to herd characteristics, biosecurity, management housing and climatic conditions were collected during a herd visit. Factors associated with the herd’s PRRSV seropositive status were identified by logistic regression. Large herd size, the lack of disinsectisation in the gestation facilities, on-farm semen collection, a short time-period for gilt quarantine and a low temperature setpoint for the ventilation controller in the fattening room significantly increased the odds of a herd being seropositive for PRRSV. Infection by Mhp and H1N2 swIAV were associated with a PRRSV seropositive status. A Cox proportional hazards model was used to identify the factors associated with the age-time to seroconversion in infected herds. Joint housing for the gilts and sows when lactating, a large nursery pen, a small number of pens per fattening room and lack of all-in all-out management in the fattening section significantly reduced the age-time to seroconversion. A small range of temperatures controlling ventilation rate in the nursery room was also associated with time to PRRSV seroconversion. Infection by Mhp and a high PCV2 infection pressure were associated with a shorter time to seroconversion. Biosecurity measures minimising the risk of introducing PRRSV into the herd, management practices reducing contacts between animals from different batches and within batches and favourable climatic conditions should be implemented to better control PRRSV infection.
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