Genetic and genomic analyses of latent variables related to the milk fatty acid profile, milk composition, and udder health in dairy cattle

The aim of this study was to perform genetic, genome-wide association (GWAS), and gene-set enrichment analyses with latent variables related to milk fatty acid profile (i.e., fatty acids factor scores; FAF), milk composition, and udder health in a cohort of 1,158 Italian Brown Swiss cows. The phenotypes under study were 12 FAF previously identified through factor analysis and classified as follows: de novo FA (F1), branched-chain FA-milk yield (F2), biohydrogenation (F3), long-chain fatty acids (F4), desaturation (F5), short-chain fatty acids (F6), milk protein and fat contents (F7), odd fatty acids (F8), conjugated linoleic acids (F9), linoleic acid (F10), udder health (F11) and vaccelenic acid (F12). (Co)variance components were estimated for factor scores using a Bayesian linear animal model via Gibbs sampling. The animals were genotyped with the Illumina BovineSNP50 BeadChip v.2 (Illumina Inc., San Diego, CA). A single marker regression model was fitted for GWAS analysis. The gene-set enrichment analysis was run on the GWAS results using the Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway databases to identify the ontologies and pathways associated with the FAF. Marginal posterior means of the heritabilities of the aforementioned FAF ranged from 0.048 for F12 to 0.310 for F5. Factors F1 and F6 had the highest number of relevant genetic correlations with the other traits. The genomic analysis detected a total of 39 significant SNP located on 17 Bos taurus autosomes. All latent variables produced signals except for F2 and F10. The traits with the highest number of significant associations were F11 (17) and F12 (7). Gene-set enrichment analyses identified significant pathways (false discovery rate 5%) for F3 and F7. In particular, systemic lupus erythematosus was enriched for F3, whereas the MAPK (mitogen-activated protein kinase) signaling pathway was overrepresented for F7. The results support the existence of important and exploitable genetic and genomic variation in these latent explanatory phenotypes. Information acquired might be exploited in selection programs and when designing further studies on the role of the putative candidate genes identified in the regulation of milk composition and udder health

Removal of benzene and toluene from a refinery waste air stream by water sorption and biotrickling filtration

ABSTRACT The paper presents the results of an analysis of a two-stage pilot plant for the removal of toluene and benzene from the exhaust air of an industrial wastewater treatment plant (WWTP). The two-stage air process combines a water scrubber and a biotrickling filter (BTF) in sequence, and treats air stripped from the liquid phase compartments of the WWTP. During the experimental period, the pilot plant treated an airflow of 600 Nm 3 h -1 . Average concentrations of the waste air stream entering the water scrubber were 10.61 mg Nm -3 benzene and 9.26 mg Nm -3 toluene. The water scrubber obtained medium-high removal efficiencies (averages 51% and 60%, for benzene and toluene, respectively). Subsequent passage through the BTF allowed a further reduction of average concentrations, which decreased to 2.10 mg Nm -3 benzene and to 0.84 mg Nm -3 toluene, thereby allowing overall average removal efficiencies (REs) of 80% and 91% for benzene and toluene, respectively. Results prove the benefits obtained from a combination of different removal technologies: water scrubbers to remove peak concentrations and soluble compounds, and BTFs to remove compounds with lower solubility, due to the biodegradation performed by microorganisms

Dual polarization of human alveolar macrophages progressively increases with smoking and COPD severity

BACKGROUND: It is known that tissue macrophages derive not only from blood monocytes but also from yolk sac or fetal liver, and the tissue of residence guides their function. When isolated, they lose tissue specific signatures, hence studies of human macrophages should be ideally done directly in the tissue. The aim of this study was to investigate directly in human lung tissue the polarization of alveolar macrophage (AM), classic (M1) or alternative (M2), in health and disease, using COPD as a model. METHODS: Surgical lungs from 53 subjects were studied: 36 smokers whose FEV(1) varied from normal to severe COPD, 11 non-smokers and 6 normal donors. iNOS and CD206 immunohistochemistry was used to quantify the percentage of AM polarized as M1 or M2 in lung sections. RESULTS AND DISCUSSION: The percentage of M1 and M2 increased progressively with smoking and COPD severity, from 26% to 84% for M1 and from 7% to 78% for M2. In donors 74% of AM were negative for M1 and 93% for M2. Confocal microscopy showed co-localization of M1 and M2 in the same AM in severe COPD. CONCLUSION: In normal lungs alveolar macrophages were mostly non-polarized. With smoking and COPD severity, M1 and M2 polarization increased significantly and so did the co-expression of M1 and M2 in the same alveolar macrophage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12931-017-0522-0) contains supplementary material, which is available to authorized users

Multiplicities of charged pions and unidentified charged hadrons from deep-inelastic scattering of muons off an isoscalar target

Multiplicities of charged pions and unidentified hadrons produced in deep-inelastic scattering were measured in bins of the Bjorken scaling variable $x$, the relative virtual-photon energy $y$ and the relative hadron energy $z$. Data were obtained by the COMPASS Collaboration using a 160 GeV muon beam and an isoscalar target ($^6$LiD). They cover the kinematic domain in the photon virtuality $Q^2$ > 1(GeV/c$)^2$, $0.004 < x < 0.4$, $0.2 < z < 0.85$ and $0.1 < y < 0.7$. In addition, a leading-order pQCD analysis was performed using the pion multiplicity results to extract quark fragmentation functions

Hybrid MPGD-based detectors of single photons for the upgrade of COMPASS RICH-1

A seven year-long R&D programme has been performed and the resulting detector architecture is a hybrid MPGD including two THick GEM (THGEM) multiplication stages followed a MICROMEGAS. The first THGEM board forms the photocathode support: its upper face is CsI coated. The properties of THGEM-based photocathodes have been studied in details. The two THGEM layers act as pre-amplification stages and, thanks to a staggered configuration, namely by the misalignment of the holes of the two THGEMs, the electron shower produced in the pre-amplification phase is distributed onto a larger surface portion of the following MICROMEGAS unit, where the final multiplication takes place: it is so possible to operate at gains as high as 105 and more even in radioactive environments. COMPASS RICH-1 is a large-size Cherenkov imaging counter with gaseous radiator for hadron identification up to 50 GeV/c. The construction of a set of large-size (unit size: 60 760 cm2) gaseous photon detectors based on the hybrid MPGD architecture for the upgrade of COMPASS RICH-1 is ongoing and the upgraded detector will be in operation in 2016. The R&D studies, the engineering aspects and the construction challenges are presented

Multiplicities of charged kaons from deep-inelastic muon scattering off an isoscalar target

Precise measurements of charged-kaon multiplicities in deep inelastic scattering were performed. The results are presented in three-dimensional bins of the Bjorken scaling variable x, the relative virtual-photon energy y, and the fraction z of the virtual-photon energy carried by the produced hadron. The data were obtained by the COMPASS Collaboration by scattering 160 GeV muons off an isoscalar 6LiD target. They cover the kinematic domain View the MathML source in the photon virtuality, 0.0045 GeV/c2 in the invariant mass of the hadronic system. The results from the sum of the z -integrated K+ and K 12 multiplicities at high x point to a value of the non-strange quark fragmentation function larger than obtained by the earlier DSS fit