Global tropospheric ozone modelling:quantifying errors due to grid resolution.

Ozone production in global chemical models is dependent on model resolution because ozone chemistry is inherently nonlinear, the timescales for chemical production are short, and precursors are artificially distributed over the spatial scale of the model grid. In this study we examine the sensitivity of ozone, its precursors, and its production to resolution by running a global chemical transport model at four different resolutions between T21 (5.6° × 5.6°) and T106 (1.1° × 1.1°) and by quantifying the errors in regional and global budgets. The sensitivity to vertical mixing through the parameterization of boundary layer turbulence is also examined. We find less ozone production in the boundary layer at higher resolution, consistent with slower chemical production in polluted emission regions and greater export of precursors. Agreement with ozonesonde and aircraft measurements made during the NASA TRACE-P campaign over the western Pacific in spring 2001 is consistently better at higher resolution. We demonstrate that the numerical errors in transport processes on a given resolution converge geometrically for a tracer at successively higher resolutions. The convergence in ozone production on progressing from T21 to T42, T63, and T106 resolution is likewise monotonic but indicates that there are still large errors at 120 km scales, suggesting that T106 resolution is too coarse to resolve regional ozone production. Diagnosing the ozone production and precursor transport that follow a short pulse of emissions over east Asia in springtime allows us to quantify the impacts of resolution on both regional and global ozone. Production close to continental emission regions is overestimated by 27% at T21 resolution, by 13% at T42 resolution, and by 5% at T106 resolution. However, subsequent ozone production in the free troposphere is not greatly affected. We find that the export of short-lived precursors such as NO x by convection is overestimated at coarse resolution

Lipidomic profiling of rat hepatic stellate cells during activation reveals a two-stage process accompanied by increased levels of lysosomal lipids

Hepatic stellate cells (HSCs) are liver-resident cells best known for their role in vitamin A storage under physiological conditions. Upon liver injury, HSCs activate into myofibroblast-like cells, a key process in the onset of liver fibrosis. Lipids play an important role during HSC activation. Here, we provide a comprehensive characterization of the lipidomes of primary rat HSCs during 17 days of activation in vitro. For lipidomic data interpretation, we expanded our previously described Lipid Ontology (LION) and associated web application (LION/Web) with the LION-PCA heatmap module, which generates heatmaps of the most typical LION-signatures in lipidomic datasets. Furthermore, we used LION to perform pathway analysis to determine the significant metabolic conversions in lipid pathways. Together, we identify two distinct stages of HSC activation. In the first stage, we observe a decrease of saturated phosphatidylcholine, sphingomyelin, and phosphatidic acid and an increase in phosphatidylserine and polyunsaturated bis(monoacylglycero)phosphate (BMP), a lipid class typically localized at endosomes and lysosomes. In the second activation stage, BMPs, hexosylceramides, and ether-linked phosphatidylcholines are elevated, resembling a lysosomal lipid storage disease profile. The presence of isomeric structures of BMP in HSCs was confirmed ex vivo in MS-imaging datasets of steatosed liver sections. Finally, treatment with pharmaceuticals targeting the lysosomal integrity led to cell death in primary HSCs but not in HeLa cells. In summary, our combined data suggest that lysosomes play a critical role during a two-stage activation process of HSCs

Inhibition of polyploidization in Pten-deficient livers reduces steatosis

The tumour suppressor PTEN is a negative regulator of the PI3K/AKT signalling pathway. Liver-specific deletion of Pten in mice results in the hyper-activation PI3K/AKT signalling accompanied by enhanced genome duplication (polyploidization), marked lipid accumulation (steatosis) and formation of hepatocellular carcinomas. However, it is unknown whether polyploidization in this model has an impact on the development of steatosis and the progression towards liver cancer. Here, we used a liver-specific conditional knockout approach to delete Pten in combination with deletion of E2f7/8, known key inducers of polyploidization. As expected, Pten deletion caused severe steatosis and liver tumours accompanied by enhanced polyploidization. Additional deletion of E2f7/8 inhibited polyploidization, alleviated Pten-induced steatosis without affecting lipid species composition and accelerated liver tumour progression. Global transcriptomic analysis showed that inhibition of polyploidization in Pten-deficient livers resulted in reduced expression of genes involved in energy metabolism, including PPAR-gamma signalling. However, we find no evidence that deregulated genes in Pten-deficient livers are direct transcriptional targets of E2F7/8, supporting that reduction in steatosis and progression towards liver cancer are likely consequences of inhibiting polyploidization. Lastly, flow cytometry and image analysis on isolated primary wildtype mouse hepatocytes provided further support that polyploid cells can accumulate more lipid droplets than diploid hepatocytes. Collectively, we show that polyploidization promotes steatosis and function as an important barrier against liver tumour progression in Pten-deficient livers

Inhibition of polyploidization in Pten-deficient livers reduces steatosis

The tumour suppressor PTEN is a negative regulator of the PI3K/AKT signalling pathway. Liver-specific deletion of Pten in mice results in the hyper-activation PI3K/AKT signalling accompanied by enhanced genome duplication (polyploidization), marked lipid accumulation (steatosis) and formation of hepatocellular carcinomas. However, it is unknown whether polyploidization in this model has an impact on the development of steatosis and the progression towards liver cancer. Here, we used a liver-specific conditional knockout approach to delete Pten in combination with deletion of E2f7/8, known key inducers of polyploidization. As expected, Pten deletion caused severe steatosis and liver tumours accompanied by enhanced polyploidization. Additional deletion of E2f7/8 inhibited polyploidization, alleviated Pten-induced steatosis without affecting lipid species composition and accelerated liver tumour progression. Global transcriptomic analysis showed that inhibition of polyploidization in Pten-deficient livers resulted in reduced expression of genes involved in energy metabolism, including PPAR-gamma signalling. However, we find no evidence that deregulated genes in Pten-deficient livers are direct transcriptional targets of E2F7/8, supporting that reduction in steatosis and progression towards liver cancer are likely consequences of inhibiting polyploidization. Lastly, flow cytometry and image analysis on isolated primary wildtype mouse hepatocytes provided further support that polyploid cells can accumulate more lipid droplets than diploid hepatocytes. Collectively, we show that polyploidization promotes steatosis and function as an important barrier against liver tumour progression in Pten-deficient livers.</p

Hepatic stellate cells retain the capacity to synthesize retinyl esters and to store neutral lipids in small lipid droplets in the absence of LRAT

Hepatic stellate cells (HSCs) play an important role in liver physiology and under healthy conditions they have a quiescent and lipid-storing phenotype. Upon liver injury, HSCs are activated and rapidly lose their retinyl ester-containing lipid droplets. To investigate the role of lecithin:retinol acyltransferase (LRAT) and acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1) in retinyl ester synthesis and lipid droplet dynamics, we modified LC–MS/MS procedures by including multiple reaction monitoring allowing unambiguous identification and quantification of all major retinyl ester species. Quiescent primary HSCs contain predominantly retinyl palmitate. Exogenous fatty acids are a major determinant in the retinyl ester species synthesized by activated HSCs and LX-2 cells, indicating that HSCs shift their retinyl ester synthesizing capacity from LRAT to DGAT1 during activation. Quiescent LRAT−/− HSCs retain the capacity to synthesize retinyl esters and to store neutral lipids in lipid droplets ex vivo. The median lipid droplet size in LRAT−/− HSCs (1080 nm) is significantly smaller than in wild type HSCs (1618 nm). This is a consequence of an altered lipid droplet size distribution with 50.5 ± 9.0% small (≤ 700 nm) lipid droplets in LRAT−/− HSCs and 25.6 ± 1.4% large (1400–2100 nm) lipid droplets in wild type HSC cells. Upon prolonged (24 h) incubation, the amounts of small (≤ 700 nm) lipid droplets strongly increased both in wild type and in LRAT−/− HSCs, indicating a dynamic behavior in both cell types. The absence of retinyl esters and reduced number of lipid droplets in LRAT-deficient HSCs in vivo will be discussed

The vertical distribution of ozone instantaneous radiative forcing from satellite and chemistry climate models

We evaluate the instantaneous radiative forcing (IRF) of tropospheric ozone predicted by four state-of-the-art global chemistry climate models (AM2-Chem, CAM-Chem, ECHAM5-MOZ, and GISS-PUCCINI) against ozone distribution observed from the NASA Tropospheric Emission Spectrometer (TES) during August 2006. The IRF is computed through the application of an observationally constrained instantaneous radiative forcing kernels (IRFK) to the difference between TES and model-predicted ozone. The IRFK represent the sensitivity of outgoing longwave radiation to the vertical and spatial distribution of ozone under all-sky condition. Through this technique, we find total tropospheric IRF biases from -0.4 to + 0.7 W/m(2) over large regions within the tropics and midlatitudes, due to ozone differences over the region in the lower and middle troposphere, enhanced by persistent bias in the upper troposphere-lower stratospheric region. The zonal mean biases also range from -30 to + 50 mW/m(2) for the models. However, the ensemble mean total tropospheric IRF bias is less than 0.2 W/m(2) within the entire troposphere

Gene expression profiling of early intervertebral disc degeneration reveals a down-regulation of canonical Wnt signaling and caveolin-1 expression: implications for development of regenerative strategies

INTRODUCTION: Early degeneration of the intervertebral disc (IVD) involves a change in cellular differentiation from notochordal cells (NCs) in the nucleus pulposus (NP) to chondrocyte-like cells (CLCs). The purpose of this study was to investigate the gene expression profiles involved in this process using NP tissue from non-chondrodystrophic and chondrodystrophic dogs, a species with naturally occurring IVD degeneration. METHODS: Dual channel DNA microarrays were used to compare 1) healthy NP tissue containing only NCs (NC-rich), 2) NP tissue with a mixed population of NCs and CLCs (Mixed), and 3) NP tissue containing solely CLCs (CLC-rich) in both non-chondrodystrophic and chondrodystrophic dogs. Based on previous reports and the findings of the microarray analyses, canonical Wnt signaling was further evaluated using qPCR of relevant Wnt target genes. We hypothesized that caveolin-1, a regulator of Wnt signaling that showed significant changes in gene expression in the microarray analyses, played a significant role in early IVD degeneration. Caveolin-1 expression was investigated in IVD tissue sections and in cultured NCs. To investigate the significance of Caveolin-1 in IVD health and degeneration, the NP of 3-month-old Caveolin-1 knock-out mice was histopathologically evaluated and compared with the NP of wild-type mice of the same age. RESULTS: Early IVD degeneration involved significant changes in numerous pathways, including Wnt/β-catenin signaling. With regard to Wnt/β-catenin signaling, axin2 gene expression was significantly higher in chondrodystrophic dogs compared with non-chondrodystrophic dogs. IVD degeneration involved significant down-regulation of axin2 gene expression. IVD degeneration involved significant down-regulation in Caveolin-1 gene and protein expression. NCs showed abundant caveolin-1 expression in vivo and in vitro, whereas CLCs did not. The NP of wild-type mice was rich in viable NCs, whereas the NP of Caveolin-1 knock-out mice contained chondroid-like matrix with mainly apoptotic, small, rounded cells. CONCLUSIONS: Early IVD degeneration involves down-regulation of canonical Wnt signaling and Caveolin-1 expression, which appears to be essential to the physiology and preservation of NCs. Therefore, Caveolin-1 may be regarded an exciting target for developing strategies for IVD regeneration

Space-based formaldehyde measurements as constrains on volatile organic compound emissions in east and south Asia and implications for ozone

We use a continuous 6-year record (1996–2001) of GOME satellite measurements of formaldehyde (HCHO) columns over east and south Asia to improve regional emission estimates of reactive nonmethane volatile organic compounds (NMVOCs), including isoprene, alkenes, HCHO, and xylenes. Mean monthly HCHO observations are compared to simulated HCHO columns from the GEOS-Chem chemical transport model using state-of-science, “bottom-up” emission inventories from Streets et al. (2003a) for anthropogenic and biomass burning emissions and Guenther et al. (2006) for biogenic emissions (MEGAN). We find that wintertime GOME observations can diagnose anthropogenic reactive NMVOC emissions from China, leading to an estimate 25% higher than Streets et al. (2003a). We attribute the difference to vehicular emissions. The biomass burning source for east and south Asia is almost 5 times the estimate of Streets et al. (2003a). GOME reveals a large source from agricultural burning in the North China Plain in June missing from current inventories. This source may reflect a recent trend toward in-field burning of crop residues as the need for biofuels diminishes. Biogenic isoprene emission in east and south Asia derived from GOME is 56 ± 30 Tg yr−1, similar to 52 Tg yr−1 from MEGAN. We find, however, that MEGAN underestimates emissions in China and overestimates emissions in the tropics. The higher Chinese biogenic and biomass burning emissions revealed by GOME have important implications for ozone pollution. We find 5 to 20 ppb seasonal increases in surface ozone in GEOS-Chem for central and northern China when using GOME-derived versus bottom-up emissions. Our methodology can be adapted for other regions of the world to provide top-down constraints on NMVOC emissions where multiple emission source types overlap in space and time.Earth and Planetary SciencesEngineering and Applied Science

Expression analysis of limb element markers during mouse embryonic development

The authors declare no conflicts of interest. The authors thank Yolanda Ramirez Casas and J. Martin Collinson for technical advice and past and present lab staff for helpful discussions.Peer reviewedPublisher PD