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PURPOSE. To describe the phenotypic spectrum of retinal disease caused by the c.2991+1655A>G mutation in CEP290 and to compare disease severity between homozygous and compound heterozygous patients. METHODS. Medical records were reviewed for best-corrected visual acuity (BCVA), age of onset, fundoscopy descriptions. Foveal outer nuclear layer (ONL) and ellipsoid zone (EZ) presence was assessed using spectral-domain optical coherence tomography (SD-OCT). Differences between compound heterozygous and homozygous patients were analyzed based on visual performance and visual development. RESULTS. A total of 66 patients were included. The majority of patients had either light perception or no light perception. In the remaining group of 14 patients, median BCVA was 20/195 Snellen (0.99 LogMAR; range 0.12–1.90) for the right eye, and 20/148 Snellen (0.87 LogMAR; range 0.22–1.90) for the left. Homozygous patients tended to be more likely to develop light perception compared to more severely affected compound heterozygous patients (P = 0.080) and are more likely to improve from no light perception to light perception (P = 0.022) before the age of 6 years. OCT data were available in 12 patients, 11 of whom had retained foveal ONL and EZ integrity up to 48 years (median 23 years) of age. CONCLUSIONS. Homozygous patients seem less severely affected compared to their compound-heterozygous peers. Improvement of visual function may occur in the early years of life, suggesting a time window for therapeutic intervention up to the approximate age of 17 years. This period may be extended by an intact foveal ONL and EZ on OCT.

Inelastic neutron scattering has been used to study the magnetoelastic excitations in the multiferroic manganite hexagonal YMnO3. An avoided crossing is found between magnon and phonon modes close to the Brillouin zone boundary in the (a,b) plane. Neutron polarization analysis reveals that this mode has mixed magnon-phonon character. An external magnetic field along the c axis is observed to cause a linear field-induced splitting of one of the spin-wave branches. A theoretical description is performed, using a Heisenberg model of localized spins, acoustic phonon modes, and a magnetoelastic coupling via the single-ion magnetostriction. The model quantitatively reproduces the dispersion and intensities of all modes in the full Brillouin zone, describes the observed magnon-phonon hybridized modes, and quantifies the magnetoelastic coupling. The combined information, including the field-induced magnon splitting, allows us to exclude several of the earlier proposed models and point to the correct magnetic ground state symmetry, and provides an effective dynamic model relevant for the multiferroic hexagonal manganites.

The use of environmental DNA (eDNA) has become an applicable noninvasive tool with which to obtain information about biodiversity. A subdiscipline of eDNA is iDNA (invertebrate-derived DNA), where genetic material ingested by invertebrates is used to characterize the biodiversity of the species that served as hosts. While promising, these techniques are still in their infancy, as they have only been explored on limited numbers of samples from only a single or a few different locations. In this study, we investigate the suitability of iDNA extracted from more than 3,000 haematophagous terrestrial leeches as a tool for detecting a wide range of terrestrial vertebrates across five different geographical regions on three different continents. These regions cover almost the full geographical range of haematophagous terrestrial leeches, thus representing all parts of the world where this method might apply. We identify host taxa through metabarcoding coupled with high-throughput sequencing on Illumina and IonTorrent sequencing platforms to decrease economic costs and workload and thereby make the approach attractive for practitioners in conservation management. We identified hosts in four different taxonomic vertebrate classes: mammals, birds, reptiles and amphibians, belonging to at least 42 different taxonomic families. We find that vertebrate blood ingested by haematophagous terrestrial leeches throughout their distribution is a viable source of DNA with which to examine a wide range of vertebrates. Thus, this study provides encouraging support for the potential of haematophagous terrestrial leeches as a tool for detecting and monitoring terrestrial vertebrate biodiversity.

Inelastic neutron scattering has been used to study the magnetoelastic excitations in the multiferroic manganite hexagonal YMnO3. An avoided crossing is found between magnon and phonon modes close to the Brillouin zone boundary in the (a,b) plane. Neutron polarization analysis reveals that this mode has mixed magnon-phonon character. An external magnetic field along the c axis is observed to cause a linear field-induced splitting of one of the spin-wave branches. A theoretical description is performed, using a Heisenberg model of localized spins, acoustic phonon modes, and a magnetoelastic coupling via the single-ion magnetostriction. The model quantitatively reproduces the dispersion and intensities of all modes in the full Brillouin zone, describes the observed magnon-phonon hybridized modes, and quantifies the magnetoelastic coupling. The combined information, including the field-induced magnon splitting, allows us to exclude several of the earlier proposed models and point to the correct magnetic ground state symmetry, and provides an effective dynamic model relevant for the multiferroic hexagonal manganites.

Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary adaptation. Specifically, we assembled its high-quality reference genome (scaffold N50?=?26.9?Mb, contig N50?=?36.6?kb) and gut metagenome, and compared them against those of insectivorous, frugivorous and carnivorous bats. Our analyses showed a particular common vampire bat genomic landscape regarding integrated viral elements, a dietary and phylogenetic influence on gut microbiome taxonomic and functional profiles, and that both genetic elements harbour key traits related to the nutritional (for example, vitamin and lipid shortage) and non-nutritional (for example, nitrogen waste and osmotic homeostasis) challenges of sanguivory. These findings highlight the value of a holistic study of both the host and its microbiota when attempting to decipher adaptations underlying radical dietary lifestyles.

Sixty-two strains of Pasteurellaceae-like bacteria were isolated from the tracheas of 87 clinically healthy psittacine birds in two Danish zoos. The isolates were identified by a combination of rpoB and 16S rRNA gene sequencing and by matrix-assisted laser desorption–ionization time of flight. Twenty-eight strains belonged to the genus Volucribacter or were related to this genus and to the unnamed taxon 34 of Bisgaard, and 28 strains were related to the unnamed taxon 44 of Bisgaard. Four strains were identified as Pasteurella multocida, two isolates were classified with the related taxon 45 of Bisgaard, and a single isolate was classified as Pasteurella sp. The investigation documented an unrecognized reservoir of rarely reported and unclassified or unnamed species of Pasteurellaceae-like bacteria in psittacine birds. The results were in accordance with a recent report on isolation of Pasteurellaceae from diseased psittacine birds, and the investigation documented that the same taxa of Pasteurellaceae-like bacteria can be isolated from apparently healthy birds as well as from diseased birds.

We report on the study of fast-neutron background for the BIFROST spectrometer at ESS. We investigate the effect of background radiation induced by the interaction of fast neutrons from the source with the material of the neutron guide and devise a reasonable fast, thermal/cold neutron shielding solution for the current guide geometry using McStas and MCNPX. We investigate the effectiveness of the steel shielding around the guide by running simulations with three different steel thicknesses. The same approach is used to study the efficiencies of the steel wall a flat cylinder pierced by the guide in the middle and the polyethylene layer. The final model presented here has a 3 cm thick steel shielding around the guide, 30 cm of polyethylene around the shielding, two 5 mm thick B4C layers and a steel wall at position Z = 38 m, being 1 m thick and 10 m in radius. The final model finally proves that it is sufficient to bring the background level below the cosmic neutron rate, which defines an order of magnitude of the lowest obtainable background in the instruments.

Item does not contain fulltext, Leber congenital amaurosis (LCA) represents the most severe form of inherited retinal dystrophies with an onset during the first year of life. Currently, 21 genes are known to be associated with LCA and recurrent mutations have been observed in AIPL1, CEP290, CRB1 and GUCY2D. In addition, sequence analysis of LRAT and RPE65 may be important in view of treatments that are emerging for patients carrying variants in these genes. Screening of the aforementioned variants and genes was performed in 64 Danish LCA probands. Upon the identification of heterozygous variants, Sanger sequencing was performed of the relevant genes to identify the second allele. In combination with prior arrayed primer extension analysis, this led to the identification of two variants in 42 of 86 cases (49%). Remarkably, biallelic RPE65 variants were identified in 16% of the cases, and one novel variant, p.(D110G), was found in seven RPE65 alleles. We also collected all previously published RPE65 variants, identified in 914 alleles of 539 patients with LCA or early-onset retinitis pigmentosa, and deposited them in the RPE65 Leiden Open Variation Database (LOVD). The in silico pathogenicity assessment of the missense and noncanonical splice site variants, as well as an analysis of their frequency in ~60 000 control individuals, rendered 864 of the alleles to affect function or probably affect function. This comprehensive database can now be used to select patients eligible for gene augmentation or retinoid supplementation therapies.

BACKGROUND: Numerous studies describe the occurrence of post-traumatic stress disorder following disasters, but less is known about the risk of major depression.AIMS: To review the risk of depressive disorder in people surviving disasters and in soldiers returning from military deployment.METHOD: A systematic literature search combined with reference screening identified 23 controlled epidemiological studies. We used random effects models to compute pooled odds ratios (ORs).RESULTS: The average OR was significantly elevated following all types of exposures: natural disaster OR = 2.28 (95% CI 1.30-3.98), technological disaster OR = 1.44 (95% CI 1.21-1.70), terrorist acts OR = 1.80 (95% CI 1.38-2.34) and military combat OR = 1.60 (95% CI 1.09-2.35). In a subset of ten high-quality studies OR was 1.41 (95% CI 1.06-1.87).CONCLUSIONS: Disasters and combat experience substantially increase the risk of depression. Whether psychological trauma per se or bereavement is on the causal path is unresolved.

The Chelonid herpesvirus 5 (ChHV5) has been consistently associated with fibropapillomatosis (FP), a transmissible neoplastic disease of marine turtles. Whether ChHV5 plays a causal role remains debated, partly because while FP tumours have been clearly documented to contain high concentrations of ChHV5 DNA, recent PCRbased studies have demonstrated that large proportions of asymptomatic marine turtles are also carriers of ChHV5. We used a real-time PCR assay to quantify the levels of ChHV5 Glycoprotein B (gB) DNA in both tumour and non-tumour skin tissues, from clinically affected and healthy turtles drawn from distant ocean basins across four species. In agreement with previous studies, higher ratios of viral to host DNA were consistently observed in tumour versus non-tumour tissues in turtles with FP. Unexpectedly however, the levels of ChHV5 gB DNA in clinically healthy turtles were significantly higher than in non-tumour tissues from FP positive turtles. Thus, a large proportion of clinically healthy sea turtle populations worldwide across species carry ChHV5 gB DNA presumably through persistent latent infections. ChHV5 appears to be ubiquitous regardless of the animals' clinical conditions. Hence, these results support the theory that ChHV5 is a near ubiquitous virus with latency characteristics requiring co-factors, possibly environmental or immune related, to induce FP.

The histologic features of abnormal spectacles in 60 snakes from the 5 families of Boidae, Colubridae, Elapidae, Pythonidae, and Viperidae are described in a retrospective study conducted on specimens submitted to a private diagnostic service during a period of 15 years. Fifty-two snakes had inflammatory reactions in the spectacle. The stroma and outer epithelium of the spectacle were the layers most often involved in inflammatory disease. Lesions of the outer epithelium included edema, hyperkeratosis, and granulocyte infiltration occasionally with bacterial colonies and fungal elements. The stroma had infectious agents and inflammatory reactions in vessels and between the collagen fibrils. The inner epithelium had varying degrees of hyperplasia and hypertrophy, but no infectious agents were seen. Infectious agents in these cases included mites, bacterial disease, fungal disease, or a combination of bacterial and fungal disease. Special stains identified the bacteria most commonly involved to be Gram-positive cocci. Thirteen snakes had dysecdysis of the spectacle. Of these, 5 displayed a concurrent inflammatory reaction of the spectacle, while the remaining 8 snakes had extra keratin layers on a spectacle with an otherwise normal appearance. These keratin layers were attached to serocellular crusts located on the inner surface of the periocular scales. The cause for dyskeratotic lesions of the spectacle was not always apparent, and concurrent acariasis, other forms of dermatitis, trauma, suboptimal husbandry, and visceral disease were considered possible contributing factors. It was notable that only 4% of the submitted cases were found to have spectaculitis and/or spectacular dysecdysis.

© 2015 Macmillan Publishers Limited. Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

© 2015 The Authors. Recent studies have reported multiple cases of molecular adaptation in cetaceans related to their aquatic abilities. However, none of these has included the hippopotamus, precluding an understanding of whether molecular adaptations in cetaceans occurred before or after they split from their semi-aquatic sister taxa. Here, we obtained new transcriptomes from the hippopotamus and humpback whale, and analysed these together with available data from eight other cetaceans. We identified more than 11?000 orthologous genes and compiled a genome-wide dataset of 6845 coding DNA sequences among 23 mammals, to our knowledge the largest phylogenomic dataset to date for cetaceans. We found positive selection in nine genes on the branch leading to the common ancestor of hippopotamus and whales, and 461 genes in cetaceans compared to 64 in hippopotamus. Functional annotation revealed adaptations in diverse processes, including lipid metabolism, hypoxia, muscle and brain function. By combining these findings with data on protein–protein interactions, we found evidence suggesting clustering among gene products relating to nervous and muscular systems in cetaceans. We found little support for shared ancestral adaptations in the two taxa; most molecular adaptations in extant cetaceans occurred after their split with hippopotamids.

We present neutron-scattering studies of the interplanar magnetic correlations in the high-temperature superconductor La1.88Sr0.12CuO4 (Tc=27 K). The correlations are studied both in a magnetic field applied perpendicular to the CuO2 planes, and in zero field under different cooling conditions. We find that the effect of the magnetic field is to increase the magnetic scattering signal at all values of the out-of-plane wave vector L, indicating an overall increase of the magnetic moments. In addition, weak correlations between the copper oxide planes develop in the presence of a magnetic field. This effect is not taken into account in previous reports on the field effect of magnetic scattering, since usually only L≈0 is probed. Interestingly, the results of quench-cooling the sample are similar to those obtained by applying a magnetic field. Finally, a small variation of the incommensurate peak position as a function of L provides evidence that the incommensurate signal is twinned with the magnetic scattering from the dominant and subdominant structural twin displaying peaks at even and odd values of L, respectively, in our crystal.

Contains fulltext : 136408.pdf (publisher's version ) (Open Access), PURPOSE: The gene encoding nicotinamide nucleotide adenylyltransferase 1 (NMNAT1) was recently found to be mutated in a subset of patients with Leber congenital amaurosis (LCA) with macular atrophy. The aim of this study was to determine the occurrence and frequency of NMNAT1 mutations and associated phenotypes in different types of inherited retinal dystrophies. METHODS: DNA samples of 161 patients with LCA without genetic diagnosis were analyzed for variants in NMNAT1 using Sanger sequencing. Variants in exon 5 of NMNAT1, which harbors the majority of the previously identified mutations, were screened in 532 additional patients with retinal dystrophies. This cohort encompassed 108 persons with isolated or autosomal recessive cone-rod dystrophy (CRD), 271 with isolated or autosomal recessive retinitis pigmentosa (RP), and 49 with autosomal dominant RP, as well as 104 persons with LCA in whom the causative mutation was previously identified. RESULTS: Compound heterozygous alterations were found in six patients with LCA and in one person with early-onset RP. All except one carried the common p.E257K variant on one allele. Macular atrophy was absent in one patient, who carried this variant in combination with a truncating mutation on the other allele. The p.E257K alteration was also found in a heterozygous state in five individuals with LCA and one with RP while no mutation was detected on the other allele. Two individuals with LCA carried other NMNAT1 variants in a heterozygous state, whereas no NMNAT1 variants in exon 5 were identified in individuals with CRD. The p.E257K variant was found to be enriched in a heterozygous state in individuals with LCA (0.94%) compared to Caucasian controls (0.18%), although the difference was statistically insignificant (p=0.12). CONCLUSIONS: Although macular atrophy can occur in LCA and CRD, no NMNAT1 mutations were found in the latter cohort. NMNAT1 variants were also not found in a large group of patients with sporadic or autosom

Vegetative growth control is crucial for high fruit yield in pear orchards. The use of chemical growth retardants has been prohibited in Danish and European pear production due to increasing concerns about environment and chemical residues on fruits. Root pruning has been proven as a good alternative to control the vegetative growth of fruit trees substituting the use of chemical growth regulators. A field experiment was conducted in 2011 to investigate the effects of root pruning and different irrigation regimes on shoot growth, tree water status, leaf photosynthesis and fruit size and color in a pear orchard. The results showed that root pruning is very effective in controlling the vegetative growth of pear trees. In root pruned pear trees full irrigation and deficit irrigation did not stimulate additional shoot growth. Root pruning decreased the tree water status and stomatal conductance. However, leaf photosynthesis was not affected resulting in improved intrinsic water use efficiency. Root pruning resulted in lower fruit weight, size and less green color. Full irrigation and deficit irrigation tended to improve fruit weight and size in root pruned pear trees, and thus maybe used as an efficient tool to alleviate the negative effects of root pruning on fruit yield and quality.