ALBERT

Description: Author(s): P. Monaghan, A. Accardi, M. E. Christy, C. E. Keppel, W. Melnitchouk, and L. Zhu We present an extraction of the lowest three moments of the proton longitudinal structure function F L from world data between Q 2 =0.75 and 45  (GeV/ c ) 2 . The availability of new F L data at low Bjorken x from HERA and at large x from Jefferson Lab allows the first determination of these moments over a ... [Phys. Rev. Lett. 110, 152002] Published Tue Apr 09, 2013

Description: Amyotrophic lateral sclerosis (ALS) is an uncommon neurodegenerative disease caused by degeneration of upper and lower motor neurons. Several genes, including SOD1, TDP-43, FUS, Ubiquilin 2, C9orf72 and Profilin 1, have been linked with the sporadic and familiar forms of ALS. FUS is a DNA/RNA-binding protein (RBP) that forms cytoplasmic inclusions in ALS and frontotemporal lobular degeneration (FTLD) patients' brains and spinal cords. However, it is unknown whether the RNA-binding ability of FUS is required for causing ALS pathogenesis. Here, we exploited a Drosophila model of ALS and neuronal cell lines to elucidate the role of the RNA-binding ability of FUS in regulating FUS-mediated toxicity, cytoplasmic mislocalization and incorporation into stress granules (SGs). To determine the role of the RNA-binding ability of FUS in ALS, we mutated FUS RNA-binding sites (F305L, F341L, F359L, F368L) and generated RNA-binding-incompetent FUS mutants with and without ALS-causing mutations (R518K or R521C). We found that mutating the aforementioned four phenylalanine (F) amino acids to leucines (L) (4F-L) eliminates FUS RNA binding. We observed that these RNA-binding mutations block neurodegenerative phenotypes seen in the fly brains, eyes and motor neurons compared with the expression of RNA-binding-competent FUS carrying ALS-causing mutations. Interestingly, RNA-binding-deficient FUS strongly localized to the nucleus of Drosophila motor neurons and mammalian neuronal cells, whereas FUS carrying ALS-linked mutations was distributed to the nucleus and cytoplasm. Importantly, we determined that incorporation of mutant FUS into the SG compartment is dependent on the RNA-binding ability of FUS. In summary, we demonstrate that the RNA-binding ability of FUS is essential for the neurodegenerative phenotype in vivo of mutant FUS (either through direct contact with RNA or through interactions with other RBPs).

Description: Whole-community DNA barcoding reveals a spatio-temporal continuum of biodiversity at species and genetic levels Nature Communications 4, 1892 (2013). doi:10.1038/ncomms2881 Authors: Andrés Baselga, Tomochika Fujisawa, Alexandra Crampton-Platt, Johannes Bergsten, Peter G. Foster, Michael T. Monaghan & Alfried P. Vogler

Description: Foehn winds are a prominent feature of McMurdo Dry Valleys (MDVs) climate, and are responsible for periods of strong winds and warming. The foehn mechanism determined from a case study presented in earlier work is shown here to be robust for a set of MDVs summer foehn events over the 1994–2009 period using output from the Polar Weather Research and Forecasting Model (Polar WRF). Gap flow south of the MDVs is evidenced by the positive relationship between the pressure gradient and near-surface wind speed along the gap. Subsequently, mountain waves are generated and result in adiabatic warming and the downward transport of warm air into the MDVs, and differences in mountain wave characteristics depend on the ambient wind direction and the degree of flow nonlinearity. Pressure-driven channelling then brings warm foehn air down-valley. While a large range of synoptic-scale circulation patterns can drive foehn events, the warmest foehn events are typically associated with blocking highs over the Australian sector of the Southern Ocean, leading to warm air advection over continental Antarctica. The episodic nature of foehn events, and the tenuous connections between such events and interannual modes of climate variability, suggests that intraseasonal variability may be more important for determining their frequency and magnitude. The extraordinarily warm austral summer of 2001/2002 across Antarctica shows that advection of warm maritime air into the continental interior and strong flow aloft result in warm foehn conditions and significant melt for the MDVs.

Description: Background: The scarcity of certain nucleic acid species and the small size of target sequences such as miRNA, impose a significant barrier to subcellular visualization and present a major challenge to cell biologists. Here, we offer a generic and highly sensitive visualization approach (oligo fluorescent in situ hybridization, O-FISH) that can be used to detect such nucleic acids using a single-oligonucleotide probe of 19--26 nucleotides in length. Results: We used O-FISH to visualize miR146a in human and avian cells. Furthermore, we reveal the sensitivity of O-FISH detection by using a HIV-1 model system to show that as little as 1--2 copies of nucleic acids can be detected in a single cell. We were able to discern newly synthesized viral cDNA and, moreover, observed that certain HIV RNA sequences are only transiently available for O-FISH detection. Conclusions: Taken together, these results suggest that the O-FISH method can potentially be used for in situ probing of, as few as, 1--2 copies of nucleic acid and, additionally, to visualize small RNA such as miRNA. We further propose that the O-FISH method could be extended to understand viral function by probing newly transcribed viral intermediates; and discern the localisation of nucleic acids of interest. Additionally, interrogating the conformation and structure of a particular nucleic acid in situ might also be possible, based on the accessibility of a target sequence.

Description: Background: The pigeon crop is specially adapted to produce milk that is fed to newly hatched young. The process of pigeon milk production begins when the germinal cell layer of the crop rapidly proliferates in response to prolactin, which results in a mass of epithelial cells that are sloughed from the crop and regurgitated to the young. We proposed that the evolution of pigeon milk built upon the ability of avian keratinocytes to accumulate intracellular neutral lipids during the cornification of the epidermis. However, this cornification process in the pigeon crop has not been characterised. Results: We identified the epidermal differentiation complex in the draft pigeon genome scaffold and found that, like the chicken, it contained beta-keratin genes. These beta-keratin genes can be classified, based on sequence similarity, into several clusters including feather, scale and claw keratins. The cornified cells of the pigeon crop express several cornification-associated genes including cornulin, S100-A9 and A16-like, transglutaminase 6-like and the pigeon 'lactating' crop-specific annexin cp35. Beta-keratins play an important role in 'lactating' crop, with several claw and scale keratins up-regulated. Additionally, transglutaminase 5 and differential splice variants of transglutaminase 4 are up-regulated along with S100-A10. Conclusions: This study of global gene expression in the crop has expanded our knowledge of pigeon milk production, in particular, the mechanism of cornification and lipid production. It is a highly specialised process that utilises the normal keratinocyte cellular processes to produce a targeted nutrient solution for the young at a very high turnover.

Description: Background: Body shape is one of the most variable traits of organisms and responds to a broad array of local selective forces. In freshwater fish, divergent body shapes within single species have been repeatedly observed along the littoral-pelagic axes of lakes, where the structural complexity of near shore habitats provides a more diverse set of resources compared to the open-water zones. It remains poorly understood whether similar resource-driven polymorphism occurs among lakes that vary in structural complexity and predation pressure, and whether this variation is heritable. Here, we analyzed body shape in four populations of omnivorous roach (Rutilus rutilus) inhabiting shallow lakes. We tested the relationship between body shape, gradients of resources, predation pressure, and, in a subset of two lakes, diet composition. We used genome scans of 331 polymorphic AFLP markers to test whether there was a heritable component to the observed morphological diversification. Results: Body shape differed among lakes and was significantly correlated to differences in predation pressure. Roach from the lake with highest predation pressure were most divergent from the average body shape of all populations, characterized by a more streamlined body and caudally inserted dorsal fins; features that facilitate predator escape. Surprisingly, diet composition was not associated with morphology. AFLP analysis revealed weak genetic differentiation among lakes and no isolation by distance (IBD). Outlier analysis detected three loci under positive selection with differing frequencies in the four populations. General linear models did not support an association of lake-specific genotypes with morphological variation. Conclusion: Body shape was divergent among lakes, suggesting that processes previously reported from within single lakes may also be operating at the scale of whole lakes. We found no evidence for body shape being heritable, although sample size was small in these natural populations. Rather than habitat structure and diet, we conclude that predation had a stronger effect on the prevalence of local morphotypes. A variable morphotype facilitating the efficient uptake of a variety of spatially and temporarily scattered resources seems to be favored in these small aquatic systems.

Description: In this paper we present a framework that allows for the automatic identification of sporting activities using commonly available smartphones. We extract discriminative informational features from smartphone accelerometers using the Discrete Wavelet Transform (DWT). Despite the poor quality of their accelerometers, smartphones were used as capture devices due to their prevalence in today’s society. Successful classification on this basis potentially makes the technology accessible to both elite and non-elite athletes. Extracted features are used to train different categories of classifiers. No one classifier family has a reportable direct advantage in activity classification problems to date; thus we examine classifiers from each of the most widely used classifier families. We investigate three classification approaches; a commonly used SVM-based approach, an optimized classification model and a fusion of classifiers. We also investigate the effect of changing several of the DWT input parameters, including mother wavelets, window lengths and DWT decomposition levels. During the course of this work we created a challenging sports activity analysis dataset, comprised of soccer and field-hockey activities. The average maximum F-measure accuracy of 87% was achieved using a fusion of classifiers, which was 6% better than a single classifier model and 23% better than a standard SVM approach.