High-Resolution Mutational Profiling Suggests the Genetic Validity of Glioblastoma Patient-Derived Pre-Clinical Models

Recent advances in the ability to efficiently characterize tumor genomes is enabling targeted drug development, which requires rigorous biomarker-based patient selection to increase effectiveness. Consequently, representative DNA biomarkers become equally important in pre-clinical studies. However, it is still unclear how well these markers are maintained between the primary tumor and the patient-derived tumor models. Here, we report the comprehensive identification of somatic coding mutations and copy number aberrations in four glioblastoma (GBM) primary tumors and their matched pre-clinical models: serum-free neurospheres, adherent cell cultures, and mouse xenografts. We developed innovative methods to improve the data quality and allow a strict comparison of matched tumor samples. Our analysis identifies known GBM mutations altering PTEN and TP53 genes, and new actionable mutations such as the loss of PIK3R1, and reveals clear patient-to-patient differences. In contrast, for each patient, we do not observe any significant remodeling of the mutational profile between primary to model tumors and the few discrepancies can be attributed to stochastic errors or differences in sample purity. Similarly, we observe ∼96% primary-to-model concordance in copy number calls in the high-cellularity samples. In contrast to previous reports based on gene expression profiles, we do not observe significant differences at the DNA level between in vitro compared to in vivo models. This study suggests, at a remarkable resolution, the genome-wide conservation of a patient’s tumor genetics in various pre-clinical models, and therefore supports their use for the development and testing of personalized targeted therapies.     

Neighboring Parenchyma Cells Contribute to Arabidopsis Xylem Lignification,while Lignification of Interfascicular Fibers Is Cell Autonomous

Lignin is a critical structural component of plants, providing vascular integrity and mechanical strength. Lignin precursors (monolignols) must be exported to the extracellular matrix where random oxidative coupling produces a complex lignin polymer. The objectives of this study were twofold: to determine the timing of lignification with respect to programmed cell death and to test if nonlignifying xylary parenchyma cells can contribute to the lignification of tracheary elements and fibers. This study demonstrates that lignin deposition is not exclusively a postmortem event, but also occurs prior to programmed cell death. Radiolabeled monolignols were not detected in the cytoplasm or vacuoles of tracheary elements or neighbors. To experimentally define which cells in lignifying tissues contribute to lignification in intact plants, a microRNA against CINNAMOYL CoA-REDUCTASE1 driven by the promoter from CELLULOSE SYNTHASE7 (ProCESA7:miRNA CCR1) was used to silence monolignol biosynthesis specifically in cells developing lignified secondary cell walls. When monolignol biosynthesis in ProCESA7:miRNA CCR1 lines was silenced in the lignifying cells themselves, but not in the neighboring cells, lignin was still deposited in the xylem secondary cell walls. Surprisingly, a dramatic reduction in cell wall lignification of extraxylary fiber cells demonstrates that extraxylary fibers undergo cell autonomous lignification.     

Structural Basis for Auto-Inhibition of the NDR1 Kinase Domain by an Atypically Long Activation Segment

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Does uptake of Alexandrium fundyense cysts contribute to the levels of PSP toxin found in the sea scallop, Placopecten magellanicus?

Atlantic sea scallops, Placopecten magellanicus, in most areas of the Bay of Fundy, New Brunswick, Canada, have year-round concentrations of paralytic shellfish posioning (PSP) toxins greater than the regulatory concentration of 80 μg STX eq. 100 g⁻¹ wet weight. Scallops (mean shell height of 10.7 cm, age 3–5 years) were collected by SCUBA and individually tagged near Parker Island, Bay of Fundy. Half were hung 2 m below the low tide water level and the remainder were placed on the bottom (11 m depth at low tide) under the scallops held at 2 m. Scallop, water and sediment samples were collected monthly for determination of concentrations of PSP toxins and Alexandrium fundyense.In October, 1993, mean concentrations of PSP toxins in digestive gland, and mantle were 3205 and 1018 μg STX eq. 100 g⁻¹ wet weight, respectively. Eight months later (June 1994), PSP concentrations in digestive glands from the surface and bottom had declined to 504 and 682 μg STX eq. 100 g⁻¹ wet weight, respectively, whereas those in the mantle had declined to 802 and 681 μg STX eq. 100 g⁻¹ wet weight. During July 1994, A. fundyense concentrations observed at Parker Island and offshore were 320 cells l⁻¹ and 14,200 cells l⁻¹, respectively. Subsequently, toxin concentrations in surface and bottom scallop digestive glands increased to 12,720 and 11,408 μg STX eq. 100 g⁻¹ wet weight, whereas concentrations in mantles increased to 2126 and 1748 μg STX eq. 100 g⁻¹ wet weight, respectively. Concentrations of PSP toxins in these tissues in October 1994 were similar to those measured in October 1993. Concentrations of PSP toxin were less than the regulatory concentration in the gonads and non-detectable in adductor muscles of all scallops sampled.There were no statistically significant differences in profiles for uptake and depuration of PSP toxins in scallops held at the surface compared to those from bottom, suggesting that A. fundyense cysts at the concentrations found in the sediment (45 cysts cm⁻³) did not contribute significantly to the year-round presence of PSP toxins within scallop tissues. The year-round occurrence of PSP toxin is probably due to accumulation during summer blooms followed by a very slow rate of depuration.     

Using unmanned aerial vehicle‐based multispectral,RGB and thermal imagery for phenotyping of forest genetic trials: A case study in Pinus halepensis

The assessment of genetic differentiation in functional traits is fundamental towards understanding the adaptive characteristics of forest species. While traditional phenotyping techniques are costly and time‐consuming, remote sensing data derived from cameras mounted on unmanned aerial vehicles (UAVs) provide potentially valid high‐throughput information for assessing morphophysiological differences among tree populations. In this work, we test for genetic variation in vegetation indices (VIs) and canopy temperature among populations of Pinus halepensis as proxies for canopy architecture, leaf area, photosynthetic pigments, photosynthetic efficiency and water use. The interpopulation associations between vegetation properties and above‐ground growth (stem volume) were also assessed. Three flights (July 2016, November 2016 and May 2017) were performed in a genetic trial consisting of 56 populations covering a large part of the species range. Multispectral (visible and near infrared wavelengths), RGB (red, green, blue) and thermal images were used to estimate canopy temperature and vegetation cover (VC) and derive several VIs. Differences among populations emerged consistently across flights for VC and VIs related to leaf area, indicating genetic divergence in crown architecture. Population differences in indices related to photosynthetic pigments emerged only in May 2017 and were probably related to a contrasting phenology of needle development. Conversely, the low population differentiation for the same indices in July 2016 and November 2016 suggested weak interpopulation variation in the photosynthetic machinery of mature needles of P. halepensis. Population differences in canopy temperature found in July 2016 were indicative of variation in stomatal regulation under drought stress. Stem volume correlated with indices related to leaf area (positively) and with canopy temperature (negatively), indicating a strong influence of canopy properties and stomatal conductance on above‐ground growth at the population level. Specifically, a combination of VIs and canopy temperature accounted for about 60% of population variability in stem volume of adult trees. This is the first study to propose UAV remote sensing as an effective tool for screening genetic variation in morphophysiological traits of adult forest trees.     

Climate change reduces resilience to fire in subalpine rainforests

Climate change is affecting the distribution of species and the functioning of ecosystems. For species that are slow growing and poorly dispersed, climate change can force a lag between the distributions of species and the geographic distributions of their climatic envelopes, exposing species to the risk of extinction. Climate also governs the resilience of species and ecosystems to disturbance, such as wildfire. Here we use species distribution modelling and palaeoecology to assess and test the impact of vegetation–climate disequilibrium on the resilience of an endangered fire‐sensitive rainforest community to fires. First, we modelled the probability of occurrence of Athrotaxis spp. and Nothofagus gunnii rainforest in Tasmania (hereon “montane rainforest”) as a function of climate. We then analysed three pollen and charcoal records spanning the last 7,500 cal year BP from within both high (n = 1) and low (n = 2) probability of occurrence areas. Our study indicates that climatic change between 3,000 and 4,000 cal year bp induced a disequilibrium between montane rainforests and climate that drove a loss of resilience of these communities. Current and future climate change are likely to shift the geographic distribution of the climatic envelopes of this plant community further, suggesting that current high‐resilience locations will face a reduction in resilience. Coupled with the forecast of increasing fire activity in southern temperate regions, this heralds a significant threat to this and other slow growing, poorly dispersed and fire sensitive forest systems that are common in the southern mid to high latitudes.     

Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques

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Effects of Pharmacotherapy on Combat-Related PTSD,Anxiety, and Depression: A Systematic Review and Meta-Regression Analysis

ObjectivesTo estimate the effect of pharmacotherapy on PTSD, anxiety, and depression among combat veterans; to determine whether the effects varied according to patient and intervention characteristics; and to examine differential effects of pharmacotherapy on outcomes.ResultsPharmacotherapy significantly reduced (Δ, 95%CI) PTSD (0.38, 0.23-0.52), anxiety (0.42, 0.30-0.54), and depressive symptoms (0.52, 0.35-0.70). The effects of SSRIs and tricyclic antidepressants on PTSD were greater than other medications independent of treatment duration. The effect of SSRIs and tricyclic antidepressants were greater than other medications up to 5.2 and 13.6 weeks for anxiety and depression, respectively. The magnitude of the effect of pharmacotherapy on concurrently-measured PTSD, anxiety, and depression did not significantly differ.ConclusionsPharmacotherapy reduced PTSD, anxiety, and depressive symptoms in combat veterans. The effects of SSRIs and tricyclic antidepressants were greater for PTSD and occurred quicker for anxiety and depression than other medications.     

Contrasting primary successional trajectories of fungi and bacteria in retreating glacier soils

Early community assembly of soil microbial communities is essential for pedogenesis and development of organic legacies. We examined fungal and bacterial successions along a well‐established temperate glacier forefront chronosequence representing ~70 years of deglaciation to determine community assembly. As microbial communities may be heavily structured by establishing vegetation, we included nonvegetated soils as well as soils from underneath four plant species with differing mycorrhizal ecologies (Abies lasiocarpa, ectomycorrhizal; Luetkea pectinata, arbuscular mycorrhizal; Phyllodoce empetriformis, ericoid mycorrhizal; Saxifraga ferruginea, nonmycorrhizal). Our main objectives were to contrast fungal and bacterial successional dynamics and community assembly as well as to decouple the effects of plant establishment and time since deglaciation on microbial trajectories using high‐throughput sequencing. Our data indicate that distance from glacier terminus has large effects on biomass accumulation, community membership, and distribution for both fungi and bacteria. Surprisingly, presence of plants rather than their identity was more important in structuring bacterial communities along the chronosequence and played only a very minor role in structuring the fungal communities. Further, our analyses suggest that bacterial communities may converge during assembly supporting determinism, whereas fungal communities show no such patterns. Although fungal communities provided little evidence of convergence in community structure, many taxa were nonrandomly distributed across the glacier foreland; similar taxon‐level responses were observed in bacterial communities. Overall, our data highlight differing drivers for fungal and bacterial trajectories during early primary succession in recently deglaciated soils.