Equilibration of a two-level primitive equation model on the sphere

The equilibration of a two-level primitive equation model forced by relaxation towards a fixed axisymmetric temperature profile is studied as a function of the forcing equator-to-pole temperature difference. We find that the mean equilibrated temperature gradient rises quickly with the forcing. It is found also that the mean eddy momentum flux convergence induces a strong barotropic jet at mid-to-high latitudes. We suggest that, as found in previous work, the barotropic governor effect induced by the jet is responsible for the sensitivity of the equilibrated temperature gradient to the forcing

Equilibration of a two-level primitive equation model on the sphere

The equilibration of a two-level primitive equation model forced by relaxation towards a fixed axisymmetric temperature profile is studied as a function of the forcing equator-to-pole temperature difference. We find that the mean equilibrated temperature gradient rises quickly with the forcing. It is found also that the mean eddy momentum flux convergence induces a strong barotropic jet at mid-to-high latitudes. We suggest that, as found in previous work, the barotropic governor effect induced by the jet is responsible for the sensitivity of the equilibrated temperature gradient to the forcing

A combined genome-wide approach identifies a new potential candidate marker associated with the coat color sidedness in cattle

Coat color is one of the most important phenotypic features in livestock breeds. Cinisara is a local cattle breed generally of uniform black color which occasionally presents a particular phenotype, with animals typically display a white band along their spine, from the head to the tail, and on the ventral line (color sidedness). Therefore, this breed provides an ideal model to study the genetic components underlying phenotypic variation in coat color. A total of 63 animals, ten with sidedness phenotype and 53 with uniform black color were genotyped with Illumina Bovine 50 K. The comparison among genome-wide association study and FST analysis revealed a single nucleotide polymorphism (SNP), ARS-BFGL-NGS-55928, significantly associated with the trait. Only one gene (PLK2)was annotated near the associated SNP in a window of ±200 kb. The protein encoded by this gene is a member of the polo-like kinases, the same family of several known coat-color candidate genes. Based on the reported results, we draw the possible conclusion that the identified marker is potentially associated with the coat color sidedness in Cinisara. The local breeds with their genetic variability represent an important resource and model to study the genetic basis affecting peculiar traits. Future studies would be particularly relevant to refine these results and to better understand the genetic basis for this phenotype

Stochastic Resonance in Two Dimensional Landau Ginzburg Equation

We study the mechanism of stochastic resonance in a two dimensional Landau Ginzburg equation perturbed by a white noise. We shortly review how to renormalize the equation in order to avoid ultraviolet divergences. Next we show that the renormalization amplifies the effect of the small periodic perturbation in the system. We finally argue that stochastic resonance can be used to highlight the effect of renormalization in spatially extended system with a bistable equilibria

Swinging of red blood cells under shear flow

We reveal that under moderate shear stress (of the order of 0.1 Pa) red blood cells present an oscillation of their inclination (swinging) superimposed to the long-observed steady tanktreading (TT) motion. A model based on a fluid ellipsoid surrounded by a visco-elastic membrane initially unstrained (shape memory) predicts all observed features of the motion: an increase of both swinging amplitude and period (1/2 the TT period) upon decreasing the shear stress, a shear stress-triggered transition towards a narrow shear stress-range intermittent regime of successive swinging and tumbling, and a pure tumbling motion at lower shear stress-values.Comment: 4 pages 5 figures submitted to Physical Review Letter

Classification and imaging of ankle impingement syndromes.

Learning Objectives: To review the classification of ankle impingement syndromes. To describe and illustrate the spectrum of appearance of ankle impingement syndromes using conventional radiography (CR), multidetector computed tomography (MDCT), ultrasonography (US), magnetic resonance imaging (MRI), and MR arthrography (MRA). Background: Ankle impingement syndromes are a spectrum of diseases common in both athletic and general population and depend on many causes that can be distinguished by the type of tissue which determines the conflict (bone, fibrous, synovial). In general, classification of ankle impingement syndromes takes into account the anatomical site relative to the tibio-tarsal joint, and thus they may be classified as anterior, antero-medial, antero-lateral, posterior and postero-medial. Imaging findings: CR alone already suffices to demonstrate a bone impingement in most cases, while there is necessity to use MDCT where the site of impingement is in an anatomical site not clearly demonstrable by CR because of the presence of superimposed structures. US has the ability to recognize the presence of an anterior impingement and it may assess tendon disorders (stenosing tenosynovitis) which may be an associate sign of an impingement syndrome. MRI is the method of choice to assess synovial or fibrous impingement syndromes thanks to its excellent contrast resolution. MRA is used when there is capsular thickening that could not be detected by simple MRI. Conclusion: Diagnostic imaging has a very important role in the recognition of the cause of impingement and of the anatomical site where such a conflict takes place, thus allowing a correct therapeutic management

Genome-wide scan for Runs of Homozygosity in Valle del Belice sheep

The current availability of very large numbers of single nucleotide polymorphisms (SNPs) throughout the genome makes these markers particularly suitable for the detection of genomic regions where a reduction in heterozygosity occurred and offers new opportunities to improve the accuracy of inbreeding (F) estimates. Runs of homozygosity (ROH) are contiguous lengths of homozygous segments of the genome where the two haplotypes inherited from the parents are identical. Here, we investigated the occurrence and the distribution of ROH in medium-density SNP genotypes (~ 50 000) in order to characterize autozygosity in 512 individuals of Valle del Belice sheep and identify the regions of the genome with high ROH frequencies. A total of 11 629 ROH were identified. All individuals displayed at least one ROH > 1 Mb. The mean value of FROH>1Mb was 0.084\ub10.061. ROH that were shorter than 10 Mb predominated. The highest coverage of chromosome (OAR) by ROH was observed on OAR24, whereas the lowest one was observed on OAR1. A typical pattern was observed for the number of ROH per OAR with higher values in the first three chromosomes. There was a considerable difference among animals for the number of ROH segments and the length of the genome covered by ROH. The genomic regions most commonly associated with ROH were identified by selecting the top 1% of the SNPs most commonly observed in ROH within breed. A total of 239 SNPs were considered as candidate SNPs and we identified 107 potential candidate genes that may be under directional selection. Six genomic regions located on six chromosomes (OAR2, OAR3, OAR4, OAR10, OAR11 and OAR23), corresponding to ROH island, presented hotspot of autozygosity. According to KEGG database, a majority of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. The ROH islands spanned several candidate genes which influence traits that are associated with adaptability and with the regulation of immune responses (NPAS2, PDCL3, SERPINF1 and SERPINF2) and we did not identified candidate genes with important influence on milk production traits in sheep. The Valle del Belice breed is subjected to limited breeding selection programs for milk production traits, but shows excellent adaptability to the local environments. Therefore, these results suggest at least a partial role of natural selection in shaping the genome of Valle del Belice sheep breed

Genome wide Copy Number Variation (CNV) detection in Cinisara cattle breed

Copy Number Variations (CNVs) are classes of polymorphic genomic regions including deletions, duplications and insertions of DNA fragments from at least 0.5 kb up to several Mb. CNV represents an important source of genetic variability that provides genomics structural information complementary to the single nucleotide polymorphism (SNP) data. Some CNVs have been shown to be important in both normal phenotypic variability and disease susceptibility in livestock. Several approaches to identify CNVs including FISH, aCGH, SNP array or NGS, were proposed and among these SNP genotyping is relatively low cost, high-throughput and high coverage method. The aim of this study was to identify the CNVs in 71 animals of Cinisara breed using Illumina BovineSNP50 BeadChip v2. PennCNV software, which incorporates Log R ratio and B allele frequency at each SNP marker, was used to identify CNVs. Seven animals showed not shared CNVs, as well as autosomes 19, 21, 22. Chromosome 25 presented no CNVs at all. A final number of 322 CNVs were detected. The average number of CNVs was 4.5 per individual, with an average length and median size of 143.04 kb and 122.14 kb, respectively. All CNVs were grouped in CNV regions (CNVRs) and a total of 107 CNVRs, ranged from 50 to ~500 kb, were detected, which covered 4.90 Mb of polymorphic sequence and corresponded to 0.18% of the total genome length. In particular, we found 81 CNVRs with only gain (duplication), 22 with only loss (deletion), and four CNVRs with both. Furthermore, 8 CNVRs with >1%, 77 with >2.5%, and 22 with >5% frequency, were found. CNVRs having the highest frequency were located on Chr3:120501439-120647330 and Chr23:34673581-35007295, whereas the greatest number of genes was mapped in only one CNVR located on Chr 17:74123863-74393620. A total of 241 genes were included in the identified CNVRs. According to KEGG and DAVID database, most of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes, such as immune response, adaptability, and olfactory receptors pathway. Further studies, using different algorithms and validating the CNVs discovered, will be conducted to corroborate these preliminary results on the CNVRs detected. These results will be used for the investigation of genomic changes and features of interest in the Cinisara breed, such as for association with functional or production traits and for biodiversity studies

Distribution of functional variants within Runs of Homozygosity in four Italian cattle breeds

Several methods have been used to identify genomic regions subjected to selective sweeps. An alternative method can make use of runs of homozygosity (ROH), defined as stretches of homozygous regions in a genome. The aim of the present study was to detect selective sweeps using ROH in four cattle breeds. Individuals of Cinisara (71), Modicana (72),Reggiana (168) and Italian Holstein (96) were genotyped with the Illumina Bovine50SNP v2 BeadChip. To identify genomic regions that were most commonly associated with ROH within each breed, the percentage of occurrences of a single nucleotide polymorphism (SNP) in ROH was calculated across animals. The genomic regions most commonly associated with ROH were identified by selecting the top 1% of the SNPs most commonly observed in ROH in each breed. This approach resulted in the identification of 11 genomic regions in the Cinisara and Italian Holstein, and 8 in Modicana and Reggiana showing increased frequency of ROH. Generally, ROH patterns differed between breeds. There were two commons genomic regions between breed pairs, and in particular one in BTA6 between Modicana and Reggiana and one in BTA10 between Cinisara and Italian Holstein. A highly homozygous region (> 45% of individuals with ROH) was found only in Modicana breed in BTA6 (6:37,019,972- 39,069,719) within a QTL affecting milk fat and protein concentration. In these genomic regions we identified from 126 to 347 genes for each breed. According to Panther and KEGG database, a majority of the genes was involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. Several of these genes were also comprised in a list of genes related to phenotypes for which cattle breeds have been subjected to strong positive selection. For most genes associated with ROH islands, a biological link to traits such as milk yield and composition, reproduction, immune response, coat colour, genetic disorders and resistance/susceptibility to infectious and diseases, which are known to be under selection, can be hypothesized. These results showed that selective sweeps detected with ROH approach are shared among breeds and that scanning the genome for ROH might be an alternative or complementary strategy to detect selective sweep related with important economically traits