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In this study, the effects of breed composition and predictor dimensionality on the accuracy of direct genomic values (DGV) in a multiple breed (MB) cattle population were investigated. A total of 3559 bulls of three breeds were genotyped at 54 001 single nucleotide polymorphisms: 2093 Holstein (H), 749 Brown Swiss (B) and 717 Simmental (S). DGV were calculated using a principal component (PC) approach for either single (SB) or MB scenarios. Moreover, DGV were computed using all SNP genotypes simultaneously with SNPBLUP model as comparison. A total of seven data sets were used: three with a SB each, three with different pairs of breeds (HB, HS and BS), and one with all the three breeds together (HBS), respectively. Editing was performed separately for each scenario. Reference populations differed in breed composition, whereas the validation bulls were the same for all scenarios. The number of SNPs retained after data editing ranged from 36 521 to 41 360. PCs were extracted from actual genotypes. The total number of retained PCs ranged from 4029 to 7284 in Brown Swiss and HBS respectively, reducing the number of predictors by about 85% (from 82% to 89%). In all, three traits were considered: milk, fat and protein yield. Correlations between deregressed proofs and DGV were used to assess prediction accuracy in validation animals. In the SB scenarios, average DGV accuracy did not substantially change when either SNPBLUP or PC were used. Improvement of DGV accuracy were observed for some traits in Brown Swiss, only when MB reference populations and PC approach were used instead of SB-SNPBLUP (+10% HBS, +16%HB for milk yield and +3% HBS and +7% HB for protein yield, respectively). With the exclusion of the abovementioned cases, similar accuracies were observed using MB reference population, under the PC or SNPBLUP models. Random variation owing to sampling effect or size and composition of the reference population may explain the difficulty in finding a defined pattern in the results.

Current guidelines recommend that clinical surveillance for patients with moderate aortic stenosis (AS) and aortic valve replacement (AVR) may be considered if there is an indication for coronary revascularization. Recent observational studies, however, have shown that moderate AS is associated with an increased risk of cardiovascular events and mortality. Whether the increased risk of adverse events is caused by associated comorbidities, or to the underlying moderate AS itself, is incompletely understood. Similarly, which patients with moderate AS need close follow-up or could potentially benefit from early AVR is also unknown. In this review, the authors provide a comprehensive overview of the current published reports on moderate AS. They first provide an algorithm that helps to diagnose moderate AS correctly, especially when discordant grading is observed. Although the traditional focus of AS assessment has been on the valve, it is increasingly acknowledged that AS is not only a disease of the aortic valve but also of the ventricle. The authors therefore discuss how multimodality imaging can help to evaluate the left ventricular remodeling response and improve risk stratification in patients with moderate AS. Finally, they summarize current evidence on the management of moderate AS and highlight ongoing trials on AVR in moderate AS. [Display omitted] • Moderate AS is associated with a high risk of adverse cardiovascular events, including death. • DSE and cardiac CT can help to improve an accurate diagnosis of moderate AS. • Multimodality imaging can help to evaluate the left ventricular remodeling response caused by the underlying moderate AS. • Randomized controlled trials are ongoing to evaluate whether AVR can improve outcomes in patients with moderate AS. [ABSTRACT FROM AUTHOR]

DNA methylation of regulatory and growth-related genes contributes to fetal programming which is important for maintaining the correct development of three germ layers of the embryo that develope into different tissues and organs, and which persists into adult life. In this study, a preliminary epigenetic screen was performed to define genomic regions that are involved in fetal epigenome remodeling. Embryonic ectodermic tissues (origin of nervous tissue), mesenchymal tissues (origin of connective and muscular tissues), and foregut endoderm tissues (origin of epithelial tissue), from day 28 sheep fetuses were collected and the distribution of methylated CpGs was analyzed using whole-genome bisulfite sequencing. Patterns of methylation among the three tissues showed a high level of conservation of hypo-methylated CpG islands CGIs, and a consistent level of methylation in regulatory genetic elements. Analysis of tissue specific differentially methylated regions, revealed that 20% of the total CGIs differed between tissues. A proportion of the methylome was remodeled in gene bodies, 5′ UTRs and 3′ UTRs (7, 11, and 11%, respectively). Genes with overlapping differentially methylated regions in gene bodies and CGIs showed a significant enrichment for tissue morphogenesis and development pathways. The data presented here provides a “reference” for the epigenetic status of genes potentially involved in the maintenance and regulation of fetal developmental during early life, a period expected to be particularly prone to epigenetic alterations induced by environmental and nutritional stressors.

Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The hierarchical clustering of CNVRs indicated low differentiation and sharing of high-frequency CNVRs between European cattle populations. Various CNVRs identified in the present study overlapped with olfactory receptor genes and genes related to immune system. In addition, we also detected a CNV overlapping the Kit gene in English longhorn cattle which has previously been associated with color-sidedness. To conclude, we provide a comprehensive overview of CNV distribution in genome of European cattle. Our results indicate an important role of purifying selection and genomic drift in shaping CNV diversity that exists between different European cattle populations.

Bacterial toxin–antitoxin (TA) systems are genetic elements composed of a toxin gene and its cognate antitoxin, with the ability to regulate growth. TA systems have not previously been reported in marine Synechococcus or Prochlorococcus. Here we report the finding of seven TA system pairs (Type II) in the estuarine Synechococcus CB0101, and their responses of these TA genes to under different stress conditions, which include; nitrogen and phosphate starvation, phage infection, zinc toxicity, and photo-oxidation. Database searches discovered that eight other marine Synechococcus strains also contain at least one TA pair but none were found in Prochlorococcus. We demonstrate that the relB/relE TA pair was active and resulted in RNA degradation when CB0101 was under oxidative stress caused by either zinc toxicity or high light intensities, but the growth inhibition was released when the stress was removed. Having TA systems allows Synechococcus CB0101 to adapt to the low light and highly variable environments in the Chesapeake Bay. We propose that TA systems could be more important for picocyanobacteria living in the freshwater and estuarine environments compared to those living in the open ocean.

Non-Hodgkin’s lymphoma (NHL) is a lymphoproliferative disorder, from a subgroup of heterogeneous hematologic malignancies; the term “extranodal” refers to malignant involvement of tissues other than lymph nodes, tonsils, spleen, pharyngeal lymphatic ring, or thymus. Only 0.6% of all NHL are at mandible alone, and it may involve the inferior alveolar canal. We describe a case of bilateral enlargement of the mandibular canal without symptomatology, which was shown in a panoramic radiograph and cone beam computed tomography in a rehabilitation routine exam, as an early sign of primary extranodal NHL.

The availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here.The genomes of 73 buffaloes of 4 different breeds were sequenced and aligned against the bovine genome, which facilitated the identification of 22 million of sequence variants among the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome, inferred from the bovine genome sequence, 90,000 putative single nucleotide polymorphisms were selected to create an Axiom® Buffalo Genotyping Array 90K.This 90K "SNP-Chip" was tested in several river buffalo populations and found to have ∼70% high quality and polymorphic SNPs. Of the 90K SNPs about 24K were also found to be polymorphic in swamp buffalo. The SNP chip was used to investigate the structure of buffalo populations, and could distinguish buffalo from different farms. A Genome Wide Association Study identified genomic regions on 5 chromosomes putatively involved in milk production.The 90K buffalo SNP chip described here is suitable for the analysis of the genomes of river buffalo breeds, and could be used for genetic diversity studies and potentially as a starting point for genome-assisted selection programmes. This SNP Chip could also be used to analyse swamp buffalo, but many loci are not informative and creation of a revised SNP set specific for swamp buffalo would be advised.

This work is the final step of a research project that aims at evaluating the possibility of delaying the surge of a centrifugal compressor stage using a boundary-layer suction technique. It is based on Reynolds-Averaged Navier-Stokes numerical simulations. Boundary-layer suction is applied within the radial vaned diffuser. Previous work has shown the necessity to take into account the unsteady behavior of the flow when designing the active flow control technique. In this paper, a multislot strategy is designed according to the characteristics of the unsteady pressure field. Its implementation results in a significant increase of the stable operating range predicted by the unsteady RANS numerical model. A hub-corner separation still exists further downstream in the diffuser passage but does not compromise the stability of the compressor stage.

The Arctic climate system includes numerous highly interactive small-scale physical processes in the atmosphere, sea ice, and ocean. During and since the International Polar Year 2007–2009, significant advances have been made in understanding these processes. Here, these recent advances are reviewed, synthesized, and discussed. In atmospheric physics, the primary advances have been in cloud physics, radiative transfer, mesoscale cyclones, coastal, and fjordic processes as well as in boundary layer processes and surface fluxes. In sea ice and its snow cover, advances have been made in understanding of the surface albedo and its relationships with snow properties, the internal structure of sea ice, the heat and salt transfer in ice, the formation of superimposed ice and snow ice, and the small-scale dynamics of sea ice. For the ocean, significant advances have been related to exchange processes at the ice–ocean interface, diapycnal mixing, double-diffusive convection, tidal currents and diurnal resonance. Despite this recent progress, some of these small-scale physical processes are still not sufficiently understood: these include wave–turbulence interactions in the atmosphere and ocean, the exchange of heat and salt at the ice–ocean interface, and the mechanical weakening of sea ice. Many other processes are reasonably well understood as stand-alone processes but the challenge is to understand their interactions with and impacts and feedbacks on other processes. Uncertainty in the parameterization of small-scale processes continues to be among the greatest challenges facing climate modelling, particularly in high latitudes. Further improvements in parameterization require new year-round field campaigns on the Arctic sea ice, closely combined with satellite remote sensing studies and numerical model experiments.

Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle have shifted the haplogroup distributions considerably with a reduction of the number of haplogroups and/or an expansion of haplotypes that are rare or absent in the ancestral populations. The most extreme case is the almost exclusive colonization of Africa by the T1 haplogroup, which is rare in Southwest Asian cattle. In contrast, ancient samples invariably show continuity with present-day cattle from the same location. These findings indicate strong maternal founder effects followed by limited maternal gene flow when new territories are colonized. However, effects of adaptation to new environments may also play a role.

Over the last decade, several distinct research groups tested possible uses of membrane contactors for the wine industry, notably for the management of dissolved gases in wines, adjustment of the CO2 concentration while reducing the O2 concentration at the same time. Other experiments were done with partial alcohol reduction and addition of N2 to wines. The contactor's heart is its Liqui-Cel™ membrane where the two separate circuits meet. The membrane's hydrophobic characteristics allows a liquid to get in contact with a gas, without dispersing into it. The directions that these gases take through the membrane depend on their partial pressure differences within the two circuits. However, other factors need to be considered to determine exact exchange rates for each target gas. The present article describes the new membrane contactor prototype that was co-developed by the University of applied Sciences and Arts, Viticulture and Enology at Changins, Switzerland, and the School of Engineering and Architecture at Fribourg, Switzerland. The prototype was designed for small scale operations. Flow rates, temperatures and internal pressures can be instantly measured and graphically visualized. Also, O2 concentrations are measured inside the liquid. CO2 concentrations in the liquid can be measured with a device that is connected to the liquid circuit through a bypass after the membranes.

A fast and accurate measurement of soil carbon is needed in current scientific issues. Today there are many sensors suitable for these purposes, but choosing the appropriate sensor depends on the spatial scale at which the studies are conducted. There are few detailed studies that validate these types of measures allowing their immediate use. Here it is validated the quick use of a sensor in execution at Pantelleria, chosen for size, use and variability of the parameter measured, to give an operational tool for carbon stocks studies. The DRIFT sensor used here has been validated in the first 60 cm of the soil of the whole island, and it has shown predictivity higher than 90%.

An original method to quantify the amplitude of inertial motion of oceanic and ice drifters, through the introduction of a non-dimensional parameter M defined from a spectral analysis, is presented. A strong seasonal dependence of the magnitude of sea ice inertial oscillations is revealed, in agreement with the corresponding annual cycles of sea ice extent, concentration, thickness, advection velocity, and deformation rates. The spatial pattern of the magnitude of the sea ice inertial oscillations over the Arctic Basin is also in agreement with the sea ice thickness and concentration patterns. This argues for a strong interaction between the magnitude of inertial motion on one hand, the dissipation of energy through mechanical processes, and the cohesiveness of the cover on the other hand. Finally, a significant multi-annual evolution towards greater magnitudes of inertial oscillations in recent years, in both summer and winter, is reported, thus concomitant with reduced sea ice thickness, concentration and spatial extent.

Two complementary methods, namely Multi-Trait Meta-Analysis and Versatile Gene-Based Test for Genome-wide Association Studies (VEGAS), were used to identify putative pleiotropic genes affecting carcass traits in Bos indicus (Nellore) cattle. The genotypic data comprised over 777,000 single-nucleotide polymorphism markers scored in 995 bulls, and the phenotypic data included deregressed breeding values (dEBV) for weight measurements at birth, weaning and yearling, as well visual scores taken at weaning and yearling for carcass finishing precocity, conformation and muscling. Both analyses pointed to the pleomorphic adenoma gene 1 (PLAG1) as a major pleiotropic gene. VEGAS analysis revealed 224 additional candidates. From these, 57 participated, together with PLAG1, in a network involved in the modulation of the function and expression of IGF1 (insulin like growth factor 1), IGF2 (insulin like growth factor 2), GH1 (growth hormone 1), IGF1R (insulin like growth factor 1 receptor) and GHR (growth hormone receptor), suggesting that those pleiotropic genes operate as satellite regulators of the growth pathway.

Functional agro biodiversity defines the exploitation of biodiversity to provide ecosystem services, support sustainable agricultural production and benefit the regional and global environment and the public at large (ELN-FAB, 2009; www.eln_fab.eu). Tracking of animal products back to the breed of origin based on their genetic make-up undoubtedly falls in this category. The aim of this paper was to identify and validate a set of single nucleotide polymorphisms (SNPs) in goat coat colour genes, most of which have not been investigated before, to trace five goat populations of the Italian Alps and their product. Several regions of 28 genes influencing coat colour pathways were amplified in eight animals (two per breed). Sequence comparison revealed 48 SNPs and three INDEL (INsertion DELetion). No breed-specific alleles were detected; however, several SNPs showed an uneven frequency distribution between breeds. In BIO, the genotype frequency distribution of a non-synonymous SNP suggested a possible role of TYRP1 in brown eumelanic goat coat colour. A total of 29 independent SNPs in 20 genes were selected and used to allocate 159 minimally related goat samples using STRUCTURE 2.2 and GeneClass 2 software. STRUCTURE 2.2 assigns 99% of individuals to the correct breed considering the prior information on putative breed of origin for each sample and 81% using only the genotypic data. The three algorithms available in GeneClass 2 performed with nearly equal efficiency, with 86% and 87% correct allocations. All the methods yielded an average probability of assignment >0.92 and a specificity index >0.86. Despite their coat colour variability, individuals belonging to ORO were fully assigned, showing that, in the absence of a breed-specific allele tied to coat colour, the best assignment resulted for the most genetically distinct breed. The lowest rate of correct assignment was observed in Verzaschese (73%), not ascertained in the breed panel used in the SNP discovery phase.

Livestock conservation practice is changing rapidly in light of policy, climate change and market demands. The last decade saw a step change in technological and analytical approaches to define, manage and conserve Farm Animal Genomic Resources (FAnGR). These changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and the methodologies needed to exploit new, multidimensional data. The ESF Genomic Resources program final conference addressed these problems attempting to contribute to the development of the research and policy agenda for the next decade. We broadly identified four areas related to methodological and analytical challenges, data management and conservation. The overall conclusion is that there is a need for the use of current state-of-the-art tools to characterise the state of genomic resources in non-commercial and local breeds. The livestock genomic sector, which has been relatively well-organised in applying such methodologies so far, needs to make a concerted effort in the coming decade to enable to the democratisation of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.

We employed mtDNA and nuclear SNPs to investigate the genetic diversity of sheep breeds of three countries of the Mediterranean basin: Albania, Greece, and Italy. In total, 154 unique mtDNA haplotypes were detected by means of D-loop sequence analysis. The major nucleotide diversity was observed in Albania. We identified haplogroups, A, B, and C in Albanian and Greek samples, while Italian individuals clustered in groups A and B. In general, the data show a pattern reflecting old migrations that occurred in postneolithic and historical times. PCA analysis on SNP data differentiated breeds with good correspondence to geographical locations. This could reflect geographical isolation, selection operated by local sheep farmers, and different flock management and breed admixture that occurred in the last centuries.

The introduction of livestock species in Europe has been followed by various genetic events, which created a complex spatial pattern of genetic differentiation. Spatial principal component (sPCA) analysis and spatial metric multidimensional scaling (sMDS) incorporate geography in multivariate analysis. This method was applied to three microsatellite data sets for 45 goat breeds, 46 sheep breeds, and 101 cattle breeds from Europe, Southwest Asia, and India. The first two sPCA coordinates for goat and cattle, and the first sPCA coordinate of sheep, correspond to the coordinates of ordinary PCA analysis. However, higher sPCA coordinates suggest, for all three species, additional spatial structuring. The goat is the most geographically structured species, followed by cattle. For all three species, the main genetic cline is from southeast to northwest, but other geographic patterns depend on the species. We propose sPCA and sMDS to be useful tools for describing the correlation of genetic variation with geography.

El Magdaleniense del abrigo Duruthy en el Sorde-L'Abbaye, publicado en 1978 por ARAMBOURO y colaboradoes ofrece una larga secuencia (Magdaleniense III hasta VI, medio sin arpones y superior con arpones. En dicha secuencia, el Magdaleniense de la capa c3' era atribuido a un Magdaleniense V, integrado al Magdaleniense superior. Se propone, después de un nuevo análisis, realizado con el material más numeroso recogido en las excavaciones realizadas hasta 1986, otra interprtación. La industria está relacionada con el Magdaleniense medio de los niveles inferiores c4 y c5, y resulta más en concordancia con los datos de la estratigrafía, de la vegetación y de la fauna cazada.

Abstract The genetic diversity of the casein locus in cattle was studied on the basis of haplotype analysis. Consideration of recently described genetic variants of the casein genes which to date have not been the subject of diversity studies, allowed the identification of new haplotypes. Genotyping of 30 cattle breeds from four continents revealed a geographically associated distribution of haplotypes, mainly defined by frequencies of alleles at CSN1S1 and CSN3. The genetic diversity within taurine breeds in Europe was found to decrease significantly from the south to the north and from the east to the west. Such geographic patterns of cattle genetic variation at the casein locus may be a result of the domestication process of modern cattle as well as geographically differentiated natural or artificial selection. The comparison of African Bos taurus and Bos indicus breeds allowed the identification of several Bos indicus specific haplotypes (CSN1S1*C-CSN2*A2-CSN3*AI/CSN3*H) that are not found in pure taurine breeds. The occurrence of such haplotypes in southern European breeds also suggests that an introgression of indicine genes into taurine breeds could have contributed to the distribution of the genetic variation observed.

Genomic maps of ordered markers and expressed sequences are basic tools for the identification and positional cloning of QTLs and genes involved in economic traits in farm animals. The analysis of donor/hamster Radiation Hybrid (RH) panels represent a powerful method to map genes ESTs and markers. RH maps are generally characterised and anchored to linkage maps using SSR markers employing a quite large experimental effort. In addition, the number of available SSRs may in some case be insufficient to assemble complete RH maps, particularly in high-resolution panels. We have adapted the high-throughput AFLP® technology (Vos et al., 1995) to the typing of RH cell lines, and have used it to increase the number of anchor points in the bovine RH map.