The driver landscape of sporadic chordoma

Chordoma is a malignant, often incurable bone tumour showing notochordal differentiation. Here, we defined the somatic driver landscape of 104 cases of sporadic chordoma. We reveal somatic duplications of the notochordal transcription factor brachyury (T) in up to 27% of cases. These variants recapitulate the rearrangement architecture of the pathogenic germline duplications of T that underlie familial chordoma. In addition, we find potentially clinically actionable PI3K signalling mutations in 16% of cases. Intriguingly, one of the most frequently altered genes, mutated exclusively by inactivating mutation, was LYST (10%), which may represent a novel cancer gene in chordoma

High Throughput Screening for Small Molecule Therapy for Gaucher Disease Using Patient Tissue as the Source of Mutant Glucocerebrosidase

Gaucher disease (GD), the most common lysosomal storage disorder, results from the inherited deficiency of the lysosomal enzyme glucocerebrosidase (GCase). Previously, wildtype GCase was used for high throughput screening (HTS) of large collections of compounds to identify small molecule chaperones that could be developed as new therapies for GD. However, the compounds identified from HTS usually showed reduced potency later in confirmatory cell-based assays. An alternate strategy is to perform HTS on mutant enzyme to identify different lead compounds, including those enhancing mutant enzyme activities. We developed a new screening assay using enzyme extract prepared from the spleen of a patient with Gaucher disease with genotype N370S/N370S. In tissue extracts, GCase is in a more native physiological environment, and is present with the native activator saposin C and other potential cofactors. Using this assay, we screened a library of 250,000 compounds and identified novel modulators of mutant GCase including 14 new lead inhibitors and 30 lead activators. The activities of some of the primary hits were confirmed in subsequent cell-based assays using patient-derived fibroblasts. These results suggest that primary screening assays using enzyme extracted from tissues is an alternative approach to identify high quality, physiologically relevant lead compounds for drug development

Tracing Water Sources of Terrestrial Animal Populations with Stable Isotopes: Laboratory Tests with Crickets and Spiders

Fluxes of carbon, nitrogen, and water between ecosystem components and organisms have great impacts across levels of biological organization. Although much progress has been made in tracing carbon and nitrogen, difficulty remains in tracing water sources from the ecosystem to animals and among animals (the “water web”). Naturally occurring, non-radioactive isotopes of hydrogen and oxygen in water provide a potential method for tracing water sources. However, using this approach for terrestrial animals is complicated by a change in water isotopes within the body due to differences in activity of heavy and light isotopes during cuticular and transpiratory water losses. Here we present a technique to use stable water isotopes to estimate the mean mix of water sources in a population by sampling a group of sympatric animals over time. Strong correlations between H and O isotopes in the body water of animals collected over time provide linear patterns of enrichment that can be used to predict a mean mix of water sources useful in standard mixing models to determine relative source contribution. Multiple temperature and humidity treatment levels do not greatly alter these relationships, thus having little effect on our ability to estimate this population-level mix of water sources. We show evidence for the validity of using multiple samples of animal body water, collected across time, to estimate the isotopic mix of water sources in a population and more accurately trace water sources. The ability to use isotopes to document patterns of animal water use should be a great asset to biologists globally, especially those studying drylands, droughts, streamside areas, irrigated landscapes, and the effects of climate change

The Role of Motor Learning in Spatial Adaptation near a Tool

Some visual-tactile (bimodal) cells have visual receptive fields (vRFs) that overlap and extend moderately beyond the skin of the hand. Neurophysiological evidence suggests, however, that a vRF will grow to encompass a hand-held tool following active tool use but not after passive holding. Why does active tool use, and not passive holding, lead to spatial adaptation near a tool? We asked whether spatial adaptation could be the result of motor or visual experience with the tool, and we distinguished between these alternatives by isolating motor from visual experience with the tool. Participants learned to use a novel, weighted tool. The active training group received both motor and visual experience with the tool, the passive training group received visual experience with the tool, but no motor experience, and finally, a no-training control group received neither visual nor motor experience using the tool. After training, we used a cueing paradigm to measure how quickly participants detected targets, varying whether the tool was placed near or far from the target display. Only the active training group detected targets more quickly when the tool was placed near, rather than far, from the target display. This effect of tool location was not present for either the passive-training or control groups. These results suggest that motor learning influences how visual space around the tool is represented

Soil water content effects on net ecosystem CO2 exchange and actual evapotranspiration in a Mediterranean semiarid savanna of Central Chile

Biosphere-atmosphere water and carbon fluxes depend on ecosystem structure, and their magnitudes and seasonal behavior are driven by environmental and biological factors. We studied the seasonal behavior of net ecosystem CO2 exchange (NEE), Gross Primary Productivity (GPP), Ecosystem Respiration (RE), and actual evapotranspiration (ETa) obtained by eddy covariance measurements during two years in a Mediterranean Acacia savanna ecosystem (Acacia caven) in Central Chile. The annual carbon balance was −53 g C m−2 in 2011 and −111 g C m−2 in 2012, showing that the ecosystem acts as a net sink of CO2, notwithstanding water limitations on photosynthesis observed in this particularly dry period. Total annual ETa was of 128 mm in 2011 and 139 mm in 2012. Both NEE and ETa exhibited strong seasonality with peak values recorded in the winter season (July to September), as a result of ecosystem phenology, soil water content and rainfall occurrence. Consequently, the maximum carbon assimilation rate occurred in wintertime. Results show that soil water content is a major driver of GPP and RE, defining their seasonal patterns and the annual carbon assimilation capacity of the ecosystem, and also modulating the effect that solar radiation and air temperature have on NEE components at shorter time scales.This work was funded by FONDECYT projects 1120713 and 1170429, a grant from the Inter-American Institute for Global Change Research (IAI) [grant number CRN3056], which is supported by the US National Science Foundation [grant number GEO-1128040], and the Spanish Ministry of Economy and Competitiveness project GEI Spain (CGL2014-52838-C2-1-R), including ERDF founds. F. Bravo-Martínez is grateful to CONICYT for the grants “Formación de Capital Humano Avanzado-2009′′, “Beca de Apoyo al término de la tesis doctoral-2012′′, and CORFO INNOVA Grant N° 09CN14-5704. We thank to Enrique Pérez Sanchez-Cañete and Borja Ruíz- Reverter for technical support. We also thank “CODELCO–División Andina” for use of the site. C. Montes acknowledges the NASA Postdoctoral Program and to Universities Space Research Association

Nephrin Regulates Lamellipodia Formation by Assembling a Protein Complex That Includes Ship2, Filamin and Lamellipodin

Actin dynamics has emerged at the forefront of podocyte biology. Slit diaphragm junctional adhesion protein Nephrin is necessary for development of the podocyte morphology and transduces phosphorylation-dependent signals that regulate cytoskeletal dynamics. The present study extends our understanding of Nephrin function by showing in cultured podocytes that Nephrin activation induced actin dynamics is necessary for lamellipodia formation. Upon activation Nephrin recruits and regulates a protein complex that includes Ship2 (SH2 domain containing 5′ inositol phosphatase), Filamin and Lamellipodin, proteins important in regulation of actin and focal adhesion dynamics, as well as lamellipodia formation. Using the previously described CD16-Nephrin clustering system, Nephrin ligation or activation resulted in phosphorylation of the actin crosslinking protein Filamin in a p21 activated kinase dependent manner. Nephrin activation in cell culture results in formation of lamellipodia, a process that requires specialized actin dynamics at the leading edge of the cell along with focal adhesion turnover. In the CD16-Nephrin clustering model, Nephrin ligation resulted in abnormal morphology of actin tails in human podocytes when Ship2, Filamin or Lamellipodin were individually knocked down. We also observed decreased lamellipodia formation and cell migration in these knock down cells. These data provide evidence that Nephrin not only initiates actin polymerization but also assembles a protein complex that is necessary to regulate the architecture of the generated actin filament network and focal adhesion dynamics

Undifferentiated Sarcomas Develop through Distinct Evolutionary Pathways

Undifferentiated sarcomas (USARCs) of adults are diverse, rare, and aggressive soft tissue cancers. Recent sequencing efforts have confirmed that USARCs exhibit one of the highest burdens of structural aberrations across human cancer. Here, we sought to unravel the molecular basis of the structural complexity in USARCs by integrating DNA sequencing, ploidy analysis, gene expression, and methylation profiling. We identified whole genome duplication as a prevalent and pernicious force in USARC tumorigenesis. Using mathematical deconvolution strategies to unravel the complex copy-number profiles and mutational timing models we infer distinct evolutionary pathways of these rare cancers. In addition, 15% of tumors exhibited raised mutational burdens that correlated with gene expression signatures of immune infiltration, and good prognosis. Steele et al. determine the molecular landscape of undifferentiated sarcomas. They identify tumors with high mutation burdens, which are enriched for activation of immune pathways and have good prognoses, and deduce four tumorigenic routes, all of which begin with driver mutations before whole genome duplication

Co-rumination buffers the link between social anxiety and depressive symptoms in early adolescence

Objectives: We examined whether co-rumination with online friends buffered the link between social anxiety and depressive symptoms over time in a community sample. Methods: In a sample of 526 participants (358 girls; Mage = 14.05) followed at three time points, we conducted a latent cross-lagged model with social anxiety, depressive symptoms, and co-rumination, controlling for friendship stability and friendship quality, and adding a latent interaction between social anxiety and co-rumination predicting depressive symptoms. Results: Social anxiety predicted depressive symptoms, but no direct links between social anxiety and co-rumination emerged. Instead, co-rumination buffered the link between social anxiety and depressive symptoms for adolescents with higher but not lower levels of social anxiety. Conclusions: These findings indicate that co-rumination exerted a positive influence on interpersonal relationships by diminishing the influence from social anxiety on depressive symptoms over time