Role of Src phosphorylation of FXR in bile acid regulation

Bile acids are physiological detergents which aid in the absorption of dietary lipids and lipid soluble vitamins but also function as fed state signaling molecules. Elevated bile acid levels in the liver can lead to cholestatic injury, primary biliary cirrhosis, fibrosis, and liver cancer; therefore, these levels must be tightly regulated. The farnesoid X receptor (FXR) is the primary bile acid nuclear receptor and acts as the master regulator of bile acid homeostasis, preventing liver damage caused by bile acid accumulation. FXR does this by regulating the expression of many target genes in the gut and liver including the intestinal hormone fibroblast growth factor 19 (FGF19) and orphan nuclear receptor small heterodimer partner (SHP). In response to elevated hepatic bile acid levels FXR, acting directly as well as through FGF19 and SHP, inhibits the synthesis of bile acids, downregulates bile acid importers, upregulates bile acid exporters along with genes involved in bile acid conjugation and detoxification. These important roles of FXR are highlighted by the phenotypic effects observed in FXR knockout (FXR-/-) mice. FXR-/- mice display elevated bile acid pool size as well as elevated serum bile acid levels. Additionally, FXR-/- mice show signs of liver damage and develop spontaneous tumors as they age. Understanding how FXR receives signals and translates them into transcriptional responses to mediate these diverse cellular effects will be important for the development of therapeutic agents to treat cholestatic liver disorders. One mechanism through which FXR activity is regulated is signal-induced post-translational modifications. FXR has been shown to undergo multiple types of post-translational modifications including phosphorylation, methylation, acetylation and sumoylation in response to physiological and pathological signals. These modifications affect FXR in many ways including modulating subcellular localization, stability, DNA binding, interaction with transcriptional coregulators and affecting the expression of FXR target genes in a gene selective manner. Mutation of a single amino acid, disrupting one of these post-translational modifications, has been shown to dramatically alter FXR function. Interestingly, some of these post-translational modifications have been shown to be misregulated in models of disease, which highlights the importance of understanding the molecular mechanisms through which FXR is post-translationally modified. In this study a new post-translational modification of FXR was identified which profoundly impacts FXR transcriptional activity. Unbiased mass spectrometry based proteomic analysis showed that tyrosine-67 of FXR is rapidly phosphorylated in liver hepatocytes in response to treatment with either natural bile acids or FGF19. Biochemical analysis paired with bioinformatic tools identified Src as the kinase responsible for this post-translational modification. Feeding mice a diet supplemented with the primary bile acid cholic acid (CA) led to interaction between FXR and Src as well as phosphorylation of FXR. Further studies showed that Src interacts with the DNA binding domain of FXR specifically. In vitro kinase assays utilizing purified Src protein coupled with studies utilizing siRNA knockdown of Src demonstrated that Src is both necessary and sufficient for FXR phosphorylation. Adenoviral reconstitution of wild type and tyrosine-67 phosphorylation deficient mutant (Y67F) FXR in isolated primary mouse hepatocytes (PMH) showed that disruption of this phosphorylation site led to a decrease in FXR/RXR interaction and decreased expression of a subset of FXR target genes involved in bile acid regulation, particularly bile salt export pump (BSEP) and SHP. Disruption of this site in vivo also led to elevated bile acid levels, elevated liver enzyme levels, and increased macrophage infiltration; all signs of liver damage. Additionally, when challenged in models simulating cholestasis, these signs of liver damage are dramatically elevated in mice expressing Y67F-FXR. These in vivo studies demonstrate that disruption of the FXR tyrosine-67 site drastically impairs FXR’s ability to regulate its target genes, maintain bile acid homeostasis, and protect the liver from bile acid induced toxicity. In conclusion, this study identified a previously unknown phosphorylation site of FXR which is mediated by Src. We further showed that this phosphorylation is critical for FXR function, maintenance of bile acid homeostasis, and protecting the liver against bile toxicity; with loss of this phosphorylation site leading to the development of liver damage in vivo. The profound effects FXR tyrosine-67 phosphorylation has on FXR transcriptional activity and metabolic outcomes suggest that this site and the kinase leading to its phosphorylation may prove to be innovative targets for the treatment of hepatobiliary and cholestatic diseases

Long-Term Measurements of Ground Motions Offshore

Long-Term measurements of earthquake ground motions offshore, using the Sandia National Laboratories\u27 SEMS device which records only the strongest motions and transmits them upon command to a boat at the surface, have shown that offshore ground motions may in certain cases be substantially different from empirically predicted ground motions based on onshore data. In particular, the attenuation effects of soft and/or gassy soils, the wedging of offshore deposits as a function of direction to and distance from the source, and sharp velocity-depth profiles, are shown to be possible actors contributing to such differences. For the well constrained recording to date, the offshore ground motions are only 13 to 23 percent of those which would be calculated using empirical predictions based on onshore data. To address this situation, Sandia has installed a net of three long-lived (SEMS), two of them in the vicinity of instrumented platforms, in the Sandia Barbara Channel. The results are intended to evaluate the earthquake hazards of offshore energy developments and to provide firm data on the design parameters required for the harvesting of 0ffshore energy resources

Emission estimates of HCFCs and HFCs in California from the 2010 CalNex study

The CalNex 2010 (California Research at the Nexus of Air Quality and Climate Change) study was designed to evaluate the chemical composition of air masses over key source regions in California. During May to June 2010, air samples were collected on board a National Oceanic and Atmospheric Administration (NOAA) WP-3D aircraft over the South Coast Air Basin of California (SoCAB) and the Central Valley (CV). This paper analyzes six effective greenhouse gases - chlorodifluoromethane (HCFC-22), 1,1-dichloro-1-fluoroethane (HCFC-141b), 1-chloro-1,1-difluoroethane (HCFC-142b), 2-chloro-1,1,1,2-tetrafluoroethane (HCFC-124), 1,1,1,2- tetrafluoroethane (HFC-134a), and 1,1-difluoroethane (HFC-152a) - providing the most comprehensive characterization of chlorofluorocarbon (CFC) replacement compound emissions in California. Concentrations of measured HCFCs and HFCs are enhanced greatly throughout the SoCAB and CV, with highest levels observed in the SoCAB: 310 ± 92 pptv for HCFC-22, 30.7 ± 18.6 pptv for HCFC-141b, 22.9 ± 2.0 pptv for HCFC-142b, 4.86 ± 2.56 pptv for HCFC-124, 109 ± 46.4 pptv for HFC-134a, and 91.2 ± 63.9 pptv for HFC-152a. Annual emission rates are estimated for all six compounds in the SoCAB using the measured halocarbon to carbon monoxide (CO) mixing ratios and CO emissions inventories. Emission rates of 3.05 ± 0.70 Gg for HCFC-22, 0.27 ± 0.07 Gg for HCFC-141b, 0.06 ± 0.01 Gg for HCFC-142b, 0.11 ± 0.03 Gg for HCFC-124, 1.89 ± 0.43 Gg for HFC-134a, and 1.94 ± 0.45 Gg for HFC-152b for the year 2010 are calculated for the SoCAB. These emissions are extrapolated from the SoCAB region to the state of California using population data. Results from this study provide a baseline emission rate that will help future studies determine if HCFC and HFC mitigation strategies are successful. Key PointsHCFC and HFC emissions are calculated for the year 2010 for the SoCABEmissions are extrapolated to the state of CaliforniaEmissions are calculated using CalNex field measurements © 2013. American Geophysical Union. All Rights Reserved

Use of ERTS-1 data to access and monitor change in the west side of the San Joaquin Valley and central coastal zone of California

There are no author-identified significant results in this report

Bromine measurements in ozone depleted air over the Arctic Ocean

In situ measurements of ozone, photochemically active bromine compounds, and other trace gases over the Arctic Ocean in April 2008 are used to examine the chemistry and geographical extent of ozone depletion in the arctic marine boundary layer (MBL). Data were obtained from the NOAA WP-3D aircraft during the Aerosol, Radiation, and Cloud Processes affecting Arctic Climate (ARCPAC) study and the NASA DC-8 aircraft during the Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS) study. Fast (1 s) and sensitive (detection limits at the low pptv level) measurements of BrCl and BrO were obtained from three different chemical ionization mass spectrometer (CIMS) instruments, and soluble bromide was measured with a mist chamber. The CIMS instruments also detected Br2. Subsequent laboratory studies showed that HOBr rapidly converts to Br2 on the Teflon instrument inlets. This detected Br2 is identified as active bromine and represents a lower limit of the sum HOBr + Br2. The measured active bromine is shown to likely be HOBr during daytime flights in the arctic. In the MBL over the Arctic Ocean, soluble bromide and active bromine were consistently elevated and ozone was depleted. Ozone depletion and active bromine enhancement were confined to the MBL that was capped by a temperature inversion at 200–500 m altitude. In ozone-depleted air, BrO rarely exceeded 10 pptv and was always substantially lower than soluble bromide that was as high as 40 pptv. BrCl was rarely enhanced above the 2 pptv detection limit, either in the MBL, over Alaska, or in the arctic free troposphere

Quantifying sources of methane using light alkanes in the Los Angeles basin, California

Methane (CH4), carbon dioxide (CO2), carbon monoxide (CO), and C2-C5 alkanes were measured throughout the Los Angeles (L.A.) basin in May and June 2010. We use these data to show that the emission ratios of CH4/CO and CH4/CO2 in the L.A. basin are larger than expected from population-apportioned bottom-up state inventories, consistent with previously published work. We use experimentally determined CH4/CO and CH4/CO2 emission ratios in combination with annual State of California CO and CO2 inventories to derive a yearly emission rate of CH4 to the L.A. basin. We further use the airborne measurements to directly derive CH4 emission rates from dairy operations in Chino, and from the two largest landfills in the L.A. basin, and show these sources are accurately represented in the California Air Resources Board greenhouse gas inventory for CH4. We then use measurements of C2-C5 alkanes to quantify the relative contribution of other CH4 sources in the L.A. basin, with results differing from those of previous studies. The atmospheric data are consistent with the majority of CH4 emissions in the region coming from fugitive losses from natural gas in pipelines and urban distribution systems and/or geologic seeps, as well as landfills and dairies. The local oil and gas industry also provides a significant source of CH4 in the area. The addition of CH4 emissions from natural gas pipelines and urban distribution systems and/or geologic seeps and from the local oil and gas industry is sufficient to account for the differences between the top-down and bottom-up CH4 inventories identified in previously published work. Key PointsTop-down estimates of CH4 emissions in L.A. are greater than inventory estimatesEstimates of CH4 emissions from landfills in L.A. agree with CARB inventoryPipeline natural gas and/or seeps, and landfills are main sources of CH4 in L.A. ©2013. American Geophysical Union. All Rights Reserved

Sensitivity to grid resolution in the ability of a chemical transport model to simulate observed oxidant chemistry under high-isoprene conditions

Formation of ozone and organic aerosol in continental atmospheres depends on whether isoprene emitted by vegetation is oxidized by the high-NOx pathway (where peroxy radicals react with NO) or by low-NOx pathways (where peroxy radicals react by alternate channels, mostly with HO2). We used mixed layer observations from the SEAC4RS aircraft campaign over the Southeast US to test the ability of the GEOS-Chem chemical transport model at different grid resolutions (0.25°  ×  0.3125°, 2°  ×  2.5°, 4°  ×  5°) to simulate this chemistry under high-isoprene, variable-NOx conditions. Observations of isoprene and NOx over the Southeast US show a negative correlation, reflecting the spatial segregation of emissions; this negative correlation is captured in the model at 0.25°  ×  0.3125° resolution but not at coarser resolutions. As a result, less isoprene oxidation takes place by the high-NOx pathway in the model at 0.25°  ×  0.3125° resolution (54 %) than at coarser resolution (59 %). The cumulative probability distribution functions (CDFs) of NOx, isoprene, and ozone concentrations show little difference across model resolutions and good agreement with observations, while formaldehyde is overestimated at coarse resolution because excessive isoprene oxidation takes place by the high-NOx pathway with high formaldehyde yield. The good agreement of simulated and observed concentration variances implies that smaller-scale non-linearities (urban and power plant plumes) are not important on the regional scale. Correlations of simulated vs. observed concentrations do not improve with grid resolution because finer modes of variability are intrinsically more difficult to capture. Higher model resolution leads to decreased conversion of NOx to organic nitrates and increased conversion to nitric acid, with total reactive nitrogen oxides (NOy) changing little across model resolutions. Model concentrations in the lower free troposphere are also insensitive to grid resolution. The overall low sensitivity of modeled concentrations to grid resolution implies that coarse resolution is adequate when modeling continental boundary layer chemistry for global applications

Airborne observations of methane emissions from rice cultivation in the Sacramento Valley of California

Airborne measurements of methane (CH4) and carbon dioxide (CO2) were taken over the rice growing region of California's Sacramento Valley in the late spring of 2010 and 2011. From these and ancillary measurements, we show that CH4 mixing ratios were higher in the planetary boundary layer above the Sacramento Valley during the rice growing season than they were before it, which we attribute to emissions from rice paddies. We derive daytime emission fluxes of CH4 between 0.6 and 2.0% of the CO2 taken up by photosynthesis on a per carbon, or mole to mole, basis. We also use a mixing model to determine an average CH 4/CO2 flux ratio of -0.6% for one day early in the growing season of 2010. We conclude the CH4/CO2 flux ratio estimates from a single rice field in a previous study are representative of rice fields in the Sacramento Valley. If generally true, the California Air Resources Board (CARB) greenhouse gas inventory emission rate of 2.7×1010g CH4/yr is approximately three times lower than the range of probable CH4 emissions (7.8-9.3×10 10g CH4/yr) from rice cultivation derived in this study. We attribute this difference to decreased burning of the residual rice crop since 1991, which leads to an increase in CH4 emissions from rice paddies in succeeding years, but which is not accounted for in the CARB inventory. © 2012. American Geophysical Union. All Rights Reserved

Emissions of organic carbon and methane from petroleum and dairy operations in California's San Joaquin Valley

Petroleum and dairy operations are prominent sources of gas-phase organic compounds in California's San Joaquin Valley. It is essential to understand the emissions and air quality impacts of these relatively understudied sources, especially for oil/gas operations in light of increasing US production. Ground site measurements in Bakersfield and regional aircraft measurements of reactive gas-phase organic compounds and methane were part of the CalNex (California Research at the Nexus of Air Quality and Climate Change) project to determine the sources contributing to regional gas-phase organic carbon emissions. Using a combination of near-source and downwind data, we assess the composition and magnitude of emissions, and provide average source profiles. To examine the spatial distribution of emissions in the San Joaquin Valley, we developed a statistical modeling method using ground-based data and the FLEXPART-WRF transport and meteorological model. We present evidence for large sources of paraffinic hydrocarbons from petroleum operations and oxygenated compounds from dairy (and other cattle) operations. In addition to the small straight-chain alkanes typically associated with petroleum operations, we observed a wide range of branched and cyclic alkanes, most of which have limited previous in situ measurements or characterization in petroleum operation emissions. Observed dairy emissions were dominated by ethanol, methanol, acetic acid, and methane. Dairy operations were responsible for the vast majority of methane emissions in the San Joaquin Valley; observations of methane were well correlated with non-vehicular ethanol, and multiple assessments of the spatial distribution of emissions in the San Joaquin Valley highlight the dominance of dairy operations for methane emissions. The petroleum operations source profile was developed using the composition of non-methane hydrocarbons in unrefined natural gas associated with crude oil. The observed source profile is consistent with fugitive emissions of condensate during storage or processing of associated gas following extraction and methane separation. Aircraft observations of concentration hotspots near oil wells and dairies are consistent with the statistical source footprint determined via our FLEXPART-WRF-based modeling method and ground-based data. We quantitatively compared our observations at Bakersfield to the California Air Resources Board emission inventory and find consistency for relative emission rates of reactive organic gases between the aforementioned sources and motor vehicles in the region. We estimate that petroleum and dairy operations each comprised 22% of anthropogenic non-methane organic carbon at Bakersfield and were each responsible for 8-13% of potential precursors to ozone. Yet, their direct impacts as potential secondary organic aerosol (SOA) precursors were estimated to be minor for the source profiles observed in the San Joaquin Valley