A new version of the Community Atmosphere Model (CAM) has been developed and released to the climate community. CAM Version 3 (CAM3) is an atmospheric general circulation model that includes the ...Community Land Model (CLM3), an optional slab ocean model, and a thermodynamic sea ice model. The dynamics and physics in CAM3 have been changed substantially compared to implementations in previous versions. CAM3 includes options for Eulerian spectral, semi-Lagrangian, and finite-volume formulations of the dynamical equations. It supports coupled simulations using either finite-volume or Eulerian dynamics through an explicit set of adjustable parameters governing the model time step, cloud parameterizations, and condensation processes. The model includes major modifications to the parameterizations of moist processes, radiation processes, and aerosols. These changes have improved several aspects of the simulated climate, including more realistic tropical tropopause temperatures, boreal winter land surface temperatures, surface insolation, and clear-sky surface radiation in polar regions. The variation of cloud radiative forcing during ENSO events exhibits much better agreement with satellite observations. Despite these improvements, several systematic biases reduce the fidelity of the simulations. These biases include underestimation of tropical variability, errors in tropical oceanic surface fluxes, underestimation of implied ocean heat transport in the Southern Hemisphere, excessive surface stress in the storm tracks, and offsets in the 500-mb height field and the Aleutian low.
Since its discovery, the protein regulated in development and DNA damage 1 (REDD1) has been implicated in the cellular response to various stressors. Most notably, its role as a repressor of ...signaling through the central metabolic regulator, the mechanistic target of rapamycin in complex 1 (mTORC1) has gained considerable attention. Not surprisingly, changes in REDD1 mRNA and protein have been observed in skeletal muscle under various physiological conditions (e.g., nutrient consumption and resistance exercise) and pathological conditions (e.g., sepsis, alcoholism, diabetes, obesity) suggesting a role for REDD1 in regulating mTORC1-dependent skeletal muscle protein metabolism. Our understanding of the causative role of REDD1 in skeletal muscle metabolism is increasing mostly due to the availability of genetically modified mice in which the REDD1 gene is disrupted. Results from such studies provide support for an important role for REDD1 in the regulation of mTORC1 as well as reveal unexplored functions of this protein in relation to other aspects of skeletal muscle metabolism. The goal of this work is to provide a comprehensive review of the role of REDD1 (and its paralog REDD2) in skeletal muscle during both physiological and pathological conditions.
Diabetic cardiomyopathy is associated with increased risk of heart failure in type 1 diabetic patients. Mitochondrial dysfunction is suggested as an underlying contributor to diabetic cardiomyopathy. ...Cardiac mitochondria are characterized by subcellular spatial locale, including mitochondria located beneath the sarcolemma, subsarcolemmal mitochondria (SSM), and mitochondria situated between the myofibrils, interfibrillar mitochondria (IFM). The goal of this study was to determine whether type 1 diabetic insult in the heart influences proteomic make-up of spatially distinct mitochondrial subpopulations and to evaluate the role of nuclear encoded mitochondrial protein import. Utilizing multiple proteomic approaches (iTRAQ and two-dimensional-differential in-gel electrophoresis), IFM proteomic make-up was impacted by type 1 diabetes mellitus to a greater extent than SSM, as evidenced by decreased abundance of fatty acid oxidation and electron transport chain proteins. Mitochondrial phosphate carrier and adenine nucleotide translocator, as well as inner membrane translocases, were decreased in the diabetic IFM (P < 0.05 for both). Mitofilin, a protein involved in cristae morphology, was diminished in the diabetic IFM (P < 0.05). Posttranslational modifications, including oxidations and deamidations, were most prevalent in the diabetic IFM. Mitochondrial heat shock protein 70 (mtHsp70) was significantly decreased in diabetic IFM (P < 0.05). Mitochondrial protein import was decreased in the diabetic IFM with no change in the diabetic SSM (P < 0.05). Taken together, these results indicate that mitochondrial proteomic alterations in the type 1 diabetic heart are more pronounced in the IFM. Further, proteomic alterations are associated with nuclear encoded mitochondrial protein import dysfunction and loss of an essential mitochondrial protein import constituent, mtHsp70, implicating this process in the pathogenesis of the diabetic heart.
Mutations in copper/zinc superoxide dismutase 1 (SOD1), primary causes of human amyotrophic lateral sclerosis (ALS), provoke motor neuron death through an unidentified toxic property. The known ...neurofilament-dependent slowing of axonal transport, combined with the prominent misaccumulation of neurofilaments in ALS, suggests that an important aspect of toxicity may arise from damage to transport. Here we verify this hypothesis for two SOD1 mutations linked to familial ALS. Reduced transport of selective cargoes of slow transport, especially tubulin, arises months before neurodegeneration. For one mutant, this represents the earliest detectable abnormality. Thus, damage to the cargoes or machinery of slow transport is an early feature of toxicity mediated by mutant SOD1.
Global Synthetic Aperture Radar (SAR) measurements made over the past decades provide insights into the lateral extent of magmatic domains, and capture volcanic process on scales useful for volcano ...monitoring. Satellite-based SAR imagery has great potential for monitoring topographic change, the distribution of eruptive products and surface displacements (InSAR) at subaerial volcanoes. However, there are challenges in applying it routinely, as would be required for the reliable operational assessment of hazard. The deformation detectable depends upon satellite repeat time and swath widths, relative to the spatial and temporal scales of volcanological processes. We describe the characteristics of InSAR-measured volcano deformation over the past two decades, highlighting both the technique’s capabilities and its limitations as a monitoring tool. To achieve this, we draw on two global datasets of volcano deformation: the Smithsonian Institution Volcanoes of the World database and the Centre for the Observation and Modelling of Earthquakes, Volcanoes and Tectonics volcano deformation catalogue, as well as compiling some measurement characteristics and interpretations from the primary literature.
We find that a higher proportion of InSAR observations capture non-eruptive and non-magmatic processes than those from ground-based instrument networks, and that both transient (< month) and long-duration (> 5 years) deformation episodes are under-represented. However, satellite radar is already used to assess the development of extended periods of unrest and long-lasting eruptions, and improved spatial resolution and coverage have resulted in the detection of previously unrecognised deformation at both ends of the spatial scale (~ 10 to > 1000 km
2
). ‘Baseline’ records of past InSAR measurements, including ‘null’ results, are fundamental for any future interpretation of interferograms in terms of hazard‚ both by providing information about past deformation at an individual volcano, and for assessing the characteristics of deformation that are likely to be detectable (and undetectable) using InSAR.
More than half of all InSAR deformation signals attributed to magmatic processes have sources in the shallow crust (< 5 km depth). While the depth distribution of InSAR-derived deformation sources is affected by measurement limitations, their lateral distribution provides information about the extent of active magmatic domains. Deformation is common (24% of all potentially magmatic events) at loci ≥5 km away from the nearest active volcanic vent. This demonstrates that laterally extensive active magmatic domains are not exceptional, but can comprise the shallowest part of trans-crustal magmatic systems in a range of volcanic settings.
This study tested the hypothesis that resveratrol supplementation would lower oxidative stress in exercised muscles of aged mice. Young (3 months) and aged (27 months) C57BL/6 mice received a control ...or a 0.05% trans-resveratrol-supplemented diet for 10 days. After 7 days of dietary intervention, 20 maximal electrically evoked isometric contractions were obtained from the plantar flexors of one limb in anesthetized mice. Exercise was conducted for three consecutive days. Resveratrol supplementation blunted the exercise-induced increase in xanthine oxidase activity in muscles from young (25%) and aged (53%) mice. Resveratrol lowered H2O2 levels in control (13%) and exercised (38%) muscles from aged animals, reduced Nox4 protein in both control and exercised muscles of young (30%) and aged mice (40%), and increased the ratio of reduced glutathione to oxidized glutathione in exercised muscles from young (38%) and aged (135%) mice. Resveratrol prevented the increase in lipid oxidation, increased catalase activity, and increased MnSOD activity in exercised muscles from aged mice. These data show that dietary resveratrol suppresses muscle indicators of oxidative stress in response to isometric contractions in aged mice.
Forecasts of October 2006 are used to investigate southeast Pacific stratocumulus in the Community Atmosphere Model, versions 4 and 5 (CAM4 and CAM5). Both models quickly develop biases similar to ...their climatic biases, suggesting that parameterized physics are the root of the climate errors. An extensive cloud deck is produced in CAM4, but the cloud structure is unrealistic because the boundary layer is too shallow and moist. The boundary layer structure is improved in CAM5, but during the daytime the boundary layer decouples from the cloud layer, causing the cloud layer to break up and transition toward a more trade wind cumulus structure in the afternoon. The cloud liquid water budget shows how different parameterizations contribute to maintaining these different expressions of stratocumulus. Sensitivity experiments help elucidate the origins of the errors. The importance of the diurnal cycle of these clouds for climate simulations is emphasized.
Atoms subject to weak coherent incident light can be treated as coupled classical linear oscillators, supporting subradiant and superradiant collective excitation eigenmodes. We identify the limits ...of validity of this linear classical oscillator model at increasing intensities of the drive by solving the quantum many-body master equation for coherent and incoherent scattering from a chain of trapped atoms. We show that deviations from the linear classical oscillator model depend sensitively on the resonance linewidths υ_{α} of the collective eigenmodes excited by light, with the intensity at which substantial deviation occurs scaling as a power law of υ_{α}. The linear classical oscillator model then becomes inaccurate at much lower intensities for subradiant collective excitations than superradiant ones, with an example system of seven atoms resulting in critical incident light intensities differing by a factor of 30 between the two cases. By individually exciting eigenmodes, we find that this critical intensity has a υ_{α}^{2.5} scaling for narrower resonances and more strongly interacting systems, while it approaches a υ_{α}^{3} scaling for broader resonances and when the dipole-dipole interactions are reduced. The υ_{α}^{3} scaling also corresponds to the semiclassical result whereby quantum fluctuations between the atoms have been neglected. We study both the case of perfectly mode-matched drives and the case of standing-wave drives, with significant differences between the two cases appearing only at very subradiant modes and positions of Fano resonances.
The goal of this study was to design and evaluate a rapid screen to identify metagenomic clones that produce biologically active small molecules. We built metagenomic libraries with DNA from soil on ...the floodplain of the Tanana River in Alaska. We extracted DNA directly from the soil and cloned it into fosmid and bacterial artificial chromosome vectors, constructing eight metagenomic libraries that contain 53,000 clones with inserts ranging from 1 to 190 kb. To identify clones of interest, we designed a high throughput "intracellular" screen, designated METREX, in which metagenomic DNA is in a host cell containing a biosensor for compounds that induce bacterial quorum sensing. If the metagenomic clone produces a quorum-sensing inducer, the cell produces green fluorescent protein (GFP) and can be identified by fluorescence microscopy or captured by fluorescence-activated cell sorting. Our initial screen identified 11 clones that induce and two that inhibit expression of GFP. The intracellular screen detected quorum-sensing inducers among metagenomic clones that a traditional overlay screen would not. One inducing clone carries a LuxI homologue that directs the synthesis of an N-acyl homoserine lactone quorum-sensing signal molecule. The LuxI homologue has 62% amino acid sequence identity to its closest match in GenBank, AmfI from Pseudomonas fluorescens, and is on a 78-kb insert that contains 67 open reading frames. Another inducing clone carries a gene with homology to homocitrate synthase. Our results demonstrate the power of an intracellular screen to identify functionally active clones and biologically active small molecules in metagenomic libraries.
A closed total energy (TE) budget is of utmost importance in coupled climate system modeling; in particular, the dynamical core or physics‐dynamics coupling should ideally not lead to spurious TE ...sources/sinks. To assess this in a global climate model, a detailed analysis of the spurious sources/sinks of TE in National Center for Atmospheric Research's Community Atmosphere Model (CAM) is given. This includes spurious sources/sinks associated with the parameterization suite, the dynamical core, TE definition discrepancies, and physics‐dynamics coupling. The latter leads to a detailed discussion of the pros and cons of various physics‐dynamics coupling methods commonly used in climate/weather modeling.
Key Points
Spurious total energy dissipation in dynamical core is ‐0.3 W/m2 to ‐1 W/m2 at 1 deg
Constant‐pressure assumption in physics leads to 0.3 W/m2 spurious total energy source
There can easily be compensating errors in total energy budget
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