Next Generation Semiconductor Based-Sequencing of a Nutrigenetics Target Gene (GPR120) and Association with Growth Rate in Italian Large White Pigs

The GPR120 gene (also known as FFAR4 or O3FAR1) encodes for a functional omega-3 fatty acid receptor/sensor that mediates potent insulin sensitizing effects by repressing macrophage-induced tissue inflammation. For its functional role, GPR120 could be considered a potential target gene in animal nutrigenetics. In this work we resequenced the porcine GPR120 gene by high throughput Ion Torrent semiconductor sequencing of amplified fragments obtained from 8 DNA pools derived, on the whole, from 153 pigs of different breeds/populations (two Italian Large White pools, Italian Duroc, Italian Landrace, Casertana, Pietrain, Meishan, and wild boars). Three single nucleotide polymorphisms (SNPs), two synonymous substitutions and one in the putative 3′-untranslated region (g.114765469C > T), were identified and their allele frequencies were estimated by sequencing reads count. The g.114765469C > T SNP was also genotyped by PCR-RFLP confirming estimated frequency in Italian Large White pools. Then, this SNP was analyzed in two Italian Large White cohorts using a selective genotyping approach based on extreme and divergent pigs for back fat thickness (BFT) estimated breeding value (EBV) and average daily gain (ADG) EBV. Significant differences of allele and genotype frequencies distribution was observed between the extreme ADG-EBV groups (P < 0.001) whereas this marker was not associated with BFT-EBV.     

Effects of the diatom-Emiliana huxleyi succession on photosynthesis, calcification and carbon metabolism by size-fractioned phytoplankton

Changes in the species composition, photosynthesis, calcification and size-fractionated carbon metabolism by natural phytoplankton assemblages were monitored in three mesocosms under different nutrient conditions during May 1993. In the 3 enclosures, the decline of the diatom-dominated assemblages was followed by the development of a bloom of the coccolithoporid Emiliania huxleyi. Highest growth of E. huxleyi was observed in the mesocosm with a high N : P ratio, suggesting this species is a good competitor at low phosphate concentrations. The transition from diatom- to E. huxleyi-dominated assemblages brought about a sharp reduction of the phytoplankton standing stock and carbon-specific photosynthetic rate. The relative contribution of the smaller size fraction to total photosynthesis increased as the succession progressed. Calcification rate and E. huxleyi cell-specified calcite production were highest during the early stages of development of the E. huxleyi bloom. Distinct changes in the patterns of ¹⁴C allocation into biomolecules were noticed during the diatom-E. huxleyi succession. The diatom-dominated assemblage showed high relative ¹⁴C incorporation into low molecular weight metabolites (LMWM), whereas proteins and, specially, lipids accounted for the largest proportion of carbon incorporation in the E. huxleyi bloom. The patterns of photoassimilated carbon metabolism proved to be strongly dependent on cellular size, as protein relative synthesis was significantly higher in the smaller than in the larger size fraction, irrespective of the nutrient regime and the successional stage. These results are discussed in relation to the ecological and physiological features of small phytoplankton.     

Polyclonal hypergammaglobulinemia and autoantibody production induced by vaccination in farmed Atlantic salmon

The introduction of oil-adjuvanted vaccines in salmon aquaculture made large-scale production feasible by reducing the impact of infections. Vaccines given intraperitoneally (ip) contain oil adjuvant such as mineral oil. However, in rodents, a single ip injection of adjuvant hydrocarbon oil induces lupus-like systemic autoimmune syndrome. We have recently reported that autoimmune disease in farmed salmon, characterized by production of various autoantibodies, immune complex glomerulonephritis, liver thrombosis, and spinal deformity, are previously unrecognized side effects of vaccination. In the present study, we examined whether vaccination-induced autoantibody production in farmed Atlantic salmon is a mere result of polyclonal B-cell activation. Sera were collected from 205 vaccinated and unvaccinated Atlantic salmon (experimental, 7 farms) and wild salmon. Total IgM levels and autoantibodies to salmon blood cell (SBC) extract in sera were measured by ELISA and the relationship between hypergammaglobulinemia and autoantibody production was analyzed. Comparison of endpoint titers vs levels/units using a single dilution of sera in detection of autoantibodies to SBC showed near perfect correlation, justifying the use of the latter for screening. Both total IgM and anti-SBC antibodies are increased in vaccinated salmon compared with unvaccinated controls, however, they do not always correlate well when compared between groups or between individuals, suggesting the involvement of antigen-specific mechanisms in the production of anti-SBC autoantibodies. The primary considerations of successful vaccine for aquaculture are cost-effectiveness and safety. Vaccination-induced autoimmunity in farmed Atlantic salmon may have consequences on future vaccine development and salmon farming strategy. Evaluation for polyclonal hypergamamglobulinemia and autoimmunity should be included as an important trait when vaccine efficacy and safety are evaluated in future.     

Inferring Cetacean Population Densities from the Absolute Dynamic Topography of the Ocean in a Hierarchical Bayesian Framework

We inferred the population densities of blue whales (Balaenoptera musculus) and short-beaked common dolphins (Delphinus delphis) in the Northeast Pacific Ocean as functions of the water-column’s physical structure by implementing hierarchical models in a Bayesian framework. This approach allowed us to propagate the uncertainty of the field observations into the inference of species-habitat relationships and to generate spatially explicit population density predictions with reduced effects of sampling heterogeneity. Our hypothesis was that the large-scale spatial distributions of these two cetacean species respond primarily to ecological processes resulting from shoaling and outcropping of the pycnocline in regions of wind-forced upwelling and eddy-like circulation. Physically, these processes affect the thermodynamic balance of the water column, decreasing its volume and thus the height of the absolute dynamic topography (ADT). Biologically, they lead to elevated primary productivity and persistent aggregation of low-trophic-level prey. Unlike other remotely sensed variables, ADT provides information about the structure of the entire water column and it is also routinely measured at high spatial-temporal resolution by satellite altimeters with uniform global coverage. Our models provide spatially explicit population density predictions for both species, even in areas where the pycnocline shoals but does not outcrop (e.g. the Costa Rica Dome and the North Equatorial Countercurrent thermocline ridge). Interannual variations in distribution during El Niño anomalies suggest that the population density of both species decreases dramatically in the Equatorial Cold Tongue and the Costa Rica Dome, and that their distributions retract to particular areas that remain productive, such as the more oceanic waters in the central California Current System, the northern Gulf of California, the North Equatorial Countercurrent thermocline ridge, and the more southern portion of the Humboldt Current System. We posit that such reductions in available foraging habitats during climatic disturbances could incur high energetic costs on these populations, ultimately affecting individual fitness and survival.     

LUMOS - A Sensitive and Reliable Optode System for Measuring Dissolved Oxygen in the Nanomolar Range

Most commercially available optical oxygen sensors target the measuring range of 300 to 2 μmol L^-1. However these are not suitable for investigating the nanomolar range which is relevant for many important environmental situations. We therefore developed a miniaturized phase fluorimeter based measurement system called the LUMOS (Luminescence Measuring Oxygen Sensor). It consists of a readout device and specialized “sensing chemistry” that relies on commercially available components. The sensor material is based on palladium(II)-5,10,15,20-tetrakis-(2,3,4,5,6-pentafluorphenyl)-porphyrin embedded in a Hyflon AD 60 polymer matrix and has a K_SV of 6.25 x 10^-3 ppmv^-1. The applicable measurement range is from 1000 nM down to a detection limit of 0.5 nM. A second sensor material based on the platinum(II) analogue of the porphyrin is spectrally compatible with the readout device and has a measurement range of 20 μM down to 10 nM. The LUMOS device is a dedicated system optimized for a high signal to noise ratio, but in principle any phase flourimeter can be adapted to act as a readout device for the highly sensitive and robust sensing chemistry. Vise versa, the LUMOS fluorimeter can be used for read out of less sensitive optical oxygen sensors based on the same or similar indicator dyes, for example for monitoring oxygen at physiological conditions. The presented sensor system exhibits lower noise, higher resolution and higher sensitivity than the electrochemical STOX sensor previously used to measure nanomolar oxygen concentrations. Oxygen contamination in common sample containers has been investigated and microbial or enzymatic oxygen consumption at nanomolar concentrations is presented.     

New enantiornithine bird (Aves, Ornithothoraces) from the Late Cretaceous of NW Argentina

A new enantiornithine bird, Intiornis inexpectatus gen. et sp. nov, is described here. It is based on a partial hind limb found in beds of the Upper Cretaceous Las Curtiembres Formation (Campanian), North-West Argentina. The new taxon is referred to the family Avisauridae on the basis of its cranially convex third metatarsal. Several features suggest close relationships between Intiornis and the avisaurid Soroavisaurus, from the Lecho Formation (Maastrichtian; North-West Argentina). Intiornis was the size of a sparrow, thus representing the smallest Enantiornithes known from South America. The new species shows adaptations for a perching mode of life. Moreover, the hypothesis suggesting that the flying pterosaur reptiles decrease in taxonomic diversity due to competitive interaction with birds is discussed. The new species shows adaptations for a perching mode of life. Moreover, the hypothesis suggesting that the flying pterosaur reptiles decrease in taxonomic diversity due to competitive interaction with birds is discussed.     

Upper Cretaceous woods from the Olmos Formation (late Campanian-early Maastrichtian), Coahuila, Mexico

? Premise of the study: The Olmos Formation was part of a system of deltas that existed in the southern portion of the Western Interior of North America during the Campanian-Maastrichtian. The paleofloristic composition from the northern portions of the Epicontinental Sea is relatively well known, but less intensive exploration in the south has precluded more detailed floristic comparison across the entire latitudinal span of the Sea. The Olmos Formation flora, with more than 100 different leaf morphotypes so far recognized and several wood types, has the most diverse Cretaceous fossil plant assemblage in Mexico and represents a valuable opportunity for comparative studies. ? Methods: The fossil woods here described were collected in the Coahuila State, Mexico. The samples were studied using standard thin section technique and identified by comparison with fossil and extant material. ? Key results: We described four new genera (Olmosoxylon, cf. Lauraceae; Coahuiloxylon, ?Anacardiaceae, ?Burseraceae; Muzquizoxylon, Cornaceae; and Wheeleroxylon, Malvaceae s.l.) and three xylotypes of angiosperms. ? Conclusions: Some of the genera present in the Olmos Formation such as Javelinoxylon and Metcalfeoxylon have been described from geologic units in the USA (San Juan Basin, New Mexico and Big Bend National Park, Texas), suggesting similarity in the taxonomic composition of the floras that inhabited southern portions of the western margin of the Campanian-Maastrichtian Epicontinental Sea. Other species, however, have only been reported for the Olmos Formation, indicating some degree of local floristic differentiation among the assemblages that inhabited the southern portion of the Western Interior.     

PI3Kγ Protects from Myocardial Ischemia and Reperfusion Injury through a Kinase-Independent Pathway

Background

PI3Kγ functions in the immune compartment to promote inflammation in response to G-protein-coupled receptor (GPCR) agonists and PI3Kγ also acts within the heart itself both as a negative regulator of cardiac contractility and as a pro-survival factor. Thus, PI3Kγ has the potential to both promote and limit M I/R injury.

Methodology/Principal Findings

Complete PI3Kγ^−/− mutant mice, catalytically inactive PI3Kγ^KD/KD (KD) knock-in mice, and control wild type (WT) mice were subjected to in vivo myocardial ischemia and reperfusion (M I/R) injury. Additionally, bone-marrow chimeric mice were constructed to elucidate the contribution of the inflammatory response to cardiac damage. PI3Kγ^−/− mice exhibited a significantly increased infarction size following reperfusion. Mechanistically, PI3Kγ is required for activation of the Reperfusion Injury Salvage Kinase (RISK) pathway (AKT/ERK1/2) and regulates phospholamban phosphorylation in the acute injury response. Using bone marrow chimeras, the cardioprotective role of PI3Kγ was mapped to non-haematopoietic cells. Importantly, this massive increase in M I/R injury in PI3Kγ^−/− mice was rescued in PI3Kγ kinase-dead (PI3Kγ^KD/KD) knock-in mice. However, PI3Kγ^KD/KD mice exhibited a cardiac injury similar to wild type animals, suggesting that specific blockade of PI3Kγ catalytic activity has no beneficial effects.

Conclusions/Significance

Our data show that PI3Kγ is cardioprotective during M I/R injury independent of its catalytic kinase activity and that loss of PI3Kγ function in the hematopoietic compartment does not affect disease outcome. Thus, clinical development of specific PI3Kγ blockers should proceed with caution.