Looking the cow in the eye: deletion in the NID1 gene is associated with recessive inherited cataract in Romagnola cattle

Cataract is a known condition leading to opacification of the eye lens causing partial or total blindness. Mutations are known to cause autosomal dominant or recessive inherited forms of cataracts in humans, mice, rats, guinea pigs and dogs. The use of large-sized animal models instead of those using mice for the study of this condition has been discussed due to the small size of rodent lenses. Four juvenile-onset cases of bilateral incomplete immature nuclear cataract were recently observed in Romagnola cattle. Pedigree analysis suggested a monogenic autosomal recessive inheritance. In addition to the cataract, one of the cases displayed abnormal head movements. Genome-wide association and homozygosity mapping and subsequent whole genome sequencing of a single case identified two perfectly associated sequence variants in a critical interval of 7.2 Mb on cattle chromosome 28: a missense point mutation located in an uncharacterized locus and an 855 bp deletion across the exon 19/intron 19 border of the bovine nidogen 1 (NID1) gene (c.3579_3604+829del). RT-PCR showed that NID1 is expressed in bovine lenses while the transcript of the second locus was absent. The NID1 deletion leads to the skipping of exon 19 during transcription and is therefore predicted to cause a frameshift and premature stop codon (p.1164fs27X). The truncated protein lacks a C-terminal domain essential for binding with matrix assembly complexes. Nidogen 1 deficient mice show neurological abnormalities and highly irregular crystal lens alterations. This study adds NID1 to the list of candidate genes for inherited cataract in humans and is the first report of a naturally occurring mutation leading to non-syndromic catarct in cattle provides a potential large animal model for human cataract.

Wattles in goats are associated with the FMN1/GREM1 region on chromosome 10.

The presence of congenital appendages (wattles) on the throat of goats is supposed to be under genetic control with a dominant mode of inheritance. Wattles contain a cartilaginous core covered with normal skin resembling early stages of extremities. To map the dominant caprine wattles (W) locus, we collected samples of 174 goats with wattles and 167 goats without wattles from nine different Swiss goat breeds. The samples were genotyped with the 53k goat SNP chip for a subsequent genome-wide association study. We obtained a single strong association signal on chromosome 10 in a region containing functional candidate genes for limb development and outgrowth. We sequenced the whole genomes of an informative family trio containing an offspring without wattles and its heterozygous parents with wattles. In the associated goat chromosome 10 region, a total of 1055 SNPs and short indels perfectly co-segregate with the W allele. None of the variants were perfectly associated with the phenotype after analyzing the genome sequences of eight additional goats. We speculate that the causative mutation is located in one of the numerous gaps in the current version of the goat reference sequence and/or represents a larger structural variant which influences the expression of the FMN1 and/or GREM1 genes. Also, we cannot rule out possible genetic or allelic heterogeneity. Our genetic findings support earlier assumptions that wattles are rudimentary developed extremities.

Antipredator defences of young are independently determined by genetic inheritance, maternal effects and own early experience in mouthbrooding cichlids.

1. Predation is a prime force of natural selection. Vulnerability to predation is typically highest early in life, hence effective antipredator defences should work already shortly after birth. Such early defences may be innate, transmitted through non-genetic parental effects or acquired by own early experience. 2. To understand potential joint effects of these sources of antipredator defences on pheno- typic expression, they should be manipulated within the same experiment. We investigated innate, parental and individual experience effects within a single experiment. Females of the African cichlid Simochromis pleurospilus were exposed to the offspring predator Ctenochromis horei or a benign species until spawning. Eggs and larvae were hand-reared, and larvae were then exposed to odour cues signalling the presence or absence of predators in a split-brood design. 3. Shortly after independence of maternal care, S. pleurospilus undergo a habitat shift from a deeper, adult habitat to a shallow juvenile habitat, a phase where young are thought to be par- ticularly exposed to predation risk. Thus, maternal effects induced by offspring predators pres- ent in the adult habitat should take effect mainly shortly after independence, whereas own experience and innate antipredator responses should shape behaviour and life history of S. pleurospilus during the later juvenile period. 4. We found that the manipulated environmental components independently affected different offspring traits. (i) Offspring of predator-exposed mothers grew faster during the first month of life and were thus larger at termination of maternal care, when the young migrate from the adult to the juvenile habitat. (ii) The offspring’s own experience shortly after hatching exerted lasting effects on predator avoidance behaviour. (iii) Finally, our results suggest that S. pleuro- spilus possess a genetically inherited ability to distinguish dangerous from benign species. 5. In S. pleurospilus, maternal effects were limited to a short but critical time window, when young undergo a niche shift. Instead, own environmental sampling of predation risk combined with an innate predisposition to correctly identify predators appears to prepare the young best for the environment, in which they grow up as juveniles.

The dominant role of semi-arid ecosystems in the trend and variability of the land CO2 sink

The growth rate of atmospheric carbondioxide(CO2) concentrations since industrialization is characterized by large interannual variability, mostly resulting from variability in CO 2 uptake by terrestrial ecosystems (typically termed carbon sink). However, the contributions of regional ecosystems to that variability are not well known. Using an ensemble of ecosystem and land-surface models and an empirical observation-based product of global gross primary production, we show that the mean sink, trend, and interannual variability in CO2 uptake by terrestrial ecosystems are dominated by distinct biogeographic regions. Whereas the mean sink is dominated by highly productive lands (mainly tropical forests), the trend and interannual variability of the sink are dominated by semi-arid ecosystems whose carbon balance is strongly associated with circulation-driven variations in both precipitation and temperature.

Genetic analysis of white facial and leg markings in the Swiss Franches-Montagnes Horse Breed

White markings and spotting patterns in animal species are thought to be a result of the domestication process. They often serve for the identification of individuals but sometimes are accompanied by complex pathological syndromes. In the Swiss Franches-Montagnes horse population, white markings increased vastly in size and occurrence during the past 30 years, although the breeding goal demands a horse with as little depigmented areas as possible. In order to improve selection and avoid more excessive depigmentation on the population level, we estimated population parameters and breeding values for white head and anterior and posterior leg markings. Heritabilities and genetic correlations for the traits were high (h(2) > 0.5). A strong positive correlation was found between the chestnut allele at the melanocortin-1-receptor gene locus and the extent of white markings. Segregation analysis revealed that our data fit best to a model including a polygenic effect and a biallelic locus with a dominant-recessive mode of inheritance. The recessive allele was found to be the white trait-increasing allele. Multilocus linkage disequilibrium analysis allowed the mapping of the putative major locus to a chromosomal region on ECA3q harboring the KIT gene.

Minor inheritance inhibits the calibration of the 10Be production rate from the AD 1717 Val Ferret rock avalanche, European Alps

To calibrate the in situ 10Be production rate, we collected surface samples from nine large granitic boulders within the deposits of a rock avalanche that occurred in AD 1717 in the upper Ferret Valley, Mont Blanc Massif, Italy. The 10Be concentrations were extremely low and successfully measured within 10% analytical uncertainty or less. The concentrations vary from 4829 ± 448 to 5917 ± 476 at g−1. Using the historical age exposure time, we calculated the local and sea level-high latitude (i.e. ≥60°) cosmogenic 10Be spallogenic production rates. Depending on the scaling schemes, these vary between 4.60 ± 0.38 and 5.26 ± 0.43 at g−1 a−1. Although they correlate well with global values, our production rates are clearly higher than those from more recent calibration sites. We conclude that our 10Be production rate is a mean and an upper bound for production rates in the Massif region over the past 300 years. This rate is probably influenced by inheritance and will yield inaccurate (e.g. too young) exposure ages when applied to surface-exposure studies in the area. Other independently dated rock-avalanche deposits in the region that are approximately 103 years old could be considered as possible calibration sites.

In-situ, satellite measurement and model evidence on the dominant regional contribution to fine particulate matter levels in the Paris Megacity

A detailed characterization of air quality in the megacity of Paris (France) during two 1-month intensive campaigns and from additional 1-year observations revealed that about 70% of the urban background fine particulate matter (PM) is transported on average into the megacity from upwind regions. This dominant influence of regional sources was confirmed by in situ measurements during short intensive and longer-term campaigns, aerosol optical depth (AOD) measurements from ENVISAT, and modeling results from PMCAMx and CHIMERE chemistry transport models. While advection of sulfate is well documented for other megacities, there was surprisingly high contribution from long-range transport for both nitrate and organic aerosol. The origin of organic PM was investigated by comprehensive analysis of aerosol mass spectrometer (AMS), radiocarbon and tracer measurements during two intensive campaigns. Primary fossil fuel combustion emissions constituted less than 20%in winter and 40%in summer of carbonaceous fine PM, unexpectedly small for a megacity. Cooking activities and, during winter, residential wood burning are the major primary organic PM sources. This analysis suggests that the major part of secondary organic aerosol is of modern origin, i.e., from biogenic precursors and from wood burning. Black carbon concentrations are on the lower end of values encountered in megacities worldwide, but still represent an issue for air quality. These comparatively low air pollution levels are due to a combination of low emissions per inhabitant, flat terrain, and a meteorology that is in general not conducive to local pollution build-up. This revised picture of a megacity only being partially responsible for its own average and peak PM levels has important implications for air pollution regulation policies.

Pinus nigra (European black pine) as the dominant species of the last glacial pinewoods in south-western to central Iberia: a morphological study of modern and fossil pollen

Aim Our aim was to discriminate different species of Pinus via pollen analysis in order to assess the responses of particular pine species to orbital and millennial-scale climate changes, particularly during the last glacial period. Location Modern pollen grains were collected from current pine populations along transects from the Pyrenees to southern Iberia and the Balearic Islands. Fossil pine pollen was recovered from the south-western Iberian margin core MD95-2042. Methods We measured a set of morphological traits of modern pollen from the Iberian pine species Pinus nigra, P. sylvestris, P. halepensis, P. pinea and P. pinaster and of fossil pine pollen from selected samples of the last glacial period and the early to mid-Holocene. Classification and regression tree (CART) analysis was used to establish a model from the modern dataset that discriminates pollen from the different pine species and allows identification of fossil pine pollen at the species level. Results The CART model was effective in separating pollen of P. nigra and P. sylvestris from that of the Mediterranean pine group (P. halepensis, P. pinea and P. pinaster). The pollen of Pinus nigra diverged from that of P. sylvestris by having a more flattened corpus. Predictions using this model suggested that fossil pine pollen is mainly from P. nigra in all the samples analysed. Pinus sylvestris was more abundant in samples from Greenland stadials than Heinrich stadials, whereas Mediterranean pines increased in samples from Greenland interstadials and during the early to mid-Holocene. Main conclusions Morphological parameters can be successfully used to increase the taxonomic resolution of fossil pine pollen at the species level for the highland pines (P. nigra and P. sylvestris) and at the group of species level for the Mediterranean pines. Our study indicates that P. nigra was the dominant component of the last glacial south-western/central Iberian pinewoods, although the species composition of these woodlands varied in response to abrupt climate changes.

Schizophrenic Psychoses with Motor-Dominant Symptoms: Considerations for a System-Specific Approach

In order to reduce heterogeneity in schizophrenia, a system-specific approach consisting of the domains "language", "affect" and "motor behavior" has been proposed. We examined this system-specific approach for its applicability to clinical practice in the motor behavior domain, using the methodological approach of case studies, and discuss here the differences to the positive/negative concept. We analyzed eight cases with stable motor-dominant symptoms, and also quantitatively assessed motor behavior by using the Bern Psychopathology Scale (BPS), a standardized psychopathological assessment instrument, as well as actigraphic data. Characterization of cases using the positive/negative approach was not helpful. We found an overlap of the motor behavior domain with the other two domains. This complicates the application of the system-specific approach in the sense of a typology. Furthermore, we found both relapsing courses with full remission and chronic courses with deterioration within the motor-dominant subtype. Nevertheless, the system-specific approach has heuristic utility for the future.

Density-dependent dynamics of a dominant rain forest tree change with juvenile stage and time of masting

Although negative density dependence (NDD) can facilitate tree species coexistence in forests, the underlying mechanisms can differ, and rarely are the dynamics of seedlings and saplings studied together. Herein we present and discuss a novel mechanism based on our investigation of NDD predictions for the large, grove-forming ectomycorrhizal mast fruiting tree, Microberlinia bisulcata (Caesalpiniaceae), in an 82.5-ha plot at Korup, Cameroon. We tested whether juvenile density, size, growth and survival decreases with increasing conspecific adult basal area for 3245 ‘new’ seedlings and 540 ‘old’ seedlings (< 75-cm tall) during an approximately 4-year study period (2008–2012) and for 234 ‘saplings’ (≥ 75-cm tall) during an approximately 6-year study period (2008–2014). We found that the respective densities of new seedlings, old seedlings and saplings were positively, not and negatively related to increasing BA. Maximum leaf numbers and heights of old seedlings were negatively correlated with increasing basal areas, as were sapling heights and stem diameters. Whereas survivorship of new seedlings decreased by more than one-half with increasing basal area over its range in 2010–2012, that of old seedlings decreased by almost two-thirds, but only in 2008–2010, and was generally unrelated to conspecific seedling density. In 2010–2012 relative growth rates in new seedlings’ heights decreased with increasing basal area, as well as with increasing seedling density, together with increasing leaf numbers, whereas old seedlings’ growth was unrelated to either conspecific density or basal area. Saplings of below-average height had reduced survivorship with increasing basal area (probability decreasing from approx. 0.4 to 0.05 over the basal area range tested), but only sapling growth in terms of leaf numbers decreased with increasing basal area. These static and dynamic results indicate that NDD is operating within this system, possibly stabilizing the M. bisulcata population. However, these NDD patterns are unlikely to be caused by symmetric competition or by consumers. Instead, an alternative mechanism for conspecific adult–juvenile negative feedback is proposed, one which involves the interaction between tree phenology and ectomycorrhizal linkages.

Canopy gaps promote selective stem-cutting by small mammals of two dominant tree species in an African lowland forest: the importance of seedling chemistry

Small mammals can impede tree regeneration by injuring seedlings and saplings in several ways. One fatal way is by severing their stems, but apparently this type of predation is not well-studied in tropical rain forest. Here, we report on the incidence of 'stem-cutting' to new, wild seedlings of two locally dominant, canopy tree species monitored in 40 paired forest understorey and gap-habitat areas in Korup, Cameroon following a 2007 masting event. In gap areas, which are required for the upward growth and sapling recruitment of both species, 137 seedlings of the long-lived, light-demanding, fast-growing large tropical tree (Microberlinia bisulcata) were highly susceptible to stem-cutting (83% of deaths) - it killed 39% of all seedlings over a c. 2-y period. In stark contrast, seedlings of the more shade-tolerant, slower-growing tree species (Tetraberlinia bifoliolata) were hardly attacked (4.3%). In the understorey, however, stem-cutting was virtually absent. Across the gap areas, the incidence of stem-cutting of M. bisulcata seedlings showed significant spatial variation that could not be explained significantly by either canopy openness or Janzen-Connell type effects (proximity and basal area of conspecific adult trees). To examine physical and chemical traits that might explain the species difference to being cut, bark and wood tissues were collected from a separate sample of seedlings in gaps (i.e. not monitored for stem-cutting). These analyses suggested that, compared with T. bifoliolata, the lower stem density, higher Mg and K and fatty acid concentrations in bark, and fewer phenolic and terpene compounds in M. bisulcata seedlings made them more palatable and attractive to small-mammal predators, likely rodents. We conclude that selective stem-cutting is a potent countervailing force to the current local canopy dominance of the grove-forming M. bisulcata by limiting the recruitment and abundance of its saplings. Given the ubiquity of gaps and ground-dwelling rodents in pantropical forests, it would be surprising if this form of lethal browsing was restricted to Korup.

pATOM36 mediates mitochondrial protein import and mitochondrial DNA inheritance

The multisubunit ATOM complex mediates import of essentially all proteins across the outer mitochondrial membrane in T. brucei. Moreover, an additional protein termed pATOM36, which is loosely associated with the ATOM complex, has been implicated in the import of only a subset of mitochondrial matrix proteins. Here we have investigated more precisely which role pATOM36 plays in mitochondrial protein import. RNAi mediated ablation of pATOM36 specifically depletes a subset of ATOM complex subunits and as a consequence results in the collapse of the ATOM complex as shown by Blue native PAGE. In addition, a SILAC-based global proteomic analysis of uninduced and induced pATOM36 RNAi cells together with in vitro import experiments suggest that pATOM36 might be a novel protein insertase acting on a subset of alpha-helically anchored mitochondrial outer membrane proteins. Identification of pATOM36 interaction partners by co-immunoprecipitation together with immunofluorescence analysis furthermore shows that unexpectedly a fraction of the protein is associated with the tripartite attachment complex (TAC). This complex is essential for proper inheritance of the mtDNA; also called kinetoplast or kDNA; as it forms a physical connection between the kDNA and the basal body of the single flagellum throughout the cell cycle. Thus, the presence of pATOM36 in the TAC provides an exciting link between mitochondrial protein import and kDNA inheritance.

Patterns of landscape form in the upper Rhône basin, Central Swiss Alps, predominantly show lithologic controls despite multiple glaciations and variations in rock uplift rates

The development of topography depends mainly on the interplay between uplift and erosion. These processes are controlled by various factors including climate, glaciers, lithology, seismic activity and short-term variables, such as anthropogenic impact. Many studies in orogens all over the world have shown how these controlling variables may affect the landscape's topography. In particular, it has been hypothesized that lithology exerts a dominant control on erosion rates and landscape morphology. However, clear demonstrations of this influence are rare and difficult to disentangle from the overprint of other signals such as climate or tectonics. In this study we focus on the upper Rhône Basin situated in the Central Swiss Alps in order to explore the relation between topography, possible controlling variables and lithology in particular. The Rhône Basin has been affected by spatially variable uplift, high orographically driven rainfalls and multiple glaciations. Furthermore, lithology and erodibility vary substantially within the basin. Thanks to high-resolution geological, climatic and topographic data, the Rhône Basin is a suitable laboratory to explore these complexities. Elevation, relief, slope and hypsometric data as well as river profile information from digital elevation models are used to characterize the landscape's topography of around 50 tributary basins. Additionally, uplift over different timescales, glacial inheritance, precipitation patterns and erodibility of the underlying bedrock are quantified for each basin. Results show that the chosen topographic and controlling variables vary remarkably between different tributary basins. We investigate the link between observed topographic differences and the possible controlling variables through statistical analyses. Variations of elevation, slope and relief seem to be linked to differences in long-term uplift rate, whereas elevation distributions (hypsometry) and river profile shapes may be related to glacial imprint. This confirms that the landscape of the Rhône Basin has been highly preconditioned by (past) uplift and glaciation. Linear discriminant analyses (LDAs), however, suggest a stronger link between observed topographic variations and differences in erodibility. We therefore conclude that despite evident glacial and tectonic conditioning, a lithologic control is still preserved and measurable in the landscape of the Rhône tributary basins.

Traditional linkage analysis in admixed families

Currently there is no general method to study the impact of population admixture within families on the assumptions of random mating and consequently, Hardy-Weinberg equilibrium (HWE) and linkage equilibrium (LE) and on the inference obtained from traditional linkage analysis. ^ First, through simulation, the effect of admixture of two populations on the log of the odds (LOD) score was assessed, using Prostate Cancer as the typical disease model. Comparisons between simulated mixed and homogeneous families were performed. LOD scores under both models of admixture (within families and within a data set of homogeneous families) were closest to the homogeneous family scores of the population having the highest mixing proportion. Random sampling of families or ascertainment of families with disease affection status did not affect this observation, nor did the mode of inheritance (dominant/recessive) or sample size. ^ Second, after establishing the effect of admixture on the LOD score and inference for linkage, the presence of induced disequilibria by population admixture within families was studied and an adjustment procedure was developed. The adjustment did not force all disequilibria to disappear but because the families were adjusted for the population admixture, those replicates where the disequilibria exist are no longer affected by the disequilibria in terms of maximization for linkage. Furthermore, the adjustment was able to exclude uninformative families or families that had such a high departure from HWE and/or LE that their LOD scores were not reliable. ^ Together these observations imply that the presence of families of mixed population ancestry impacts linkage analysis in terms of the LOD score and the estimate of the recombination fraction. ^