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FXR agonists are used to treat non-alcoholic fatty liver disease (NAFLD), in part because they reduce hepatic lipids. Here, we show that FXR activation with the FXR agonist GSK2324 controls hepatic lipids via reduced absorption and selective decreases in fatty acid synthesis. Using comprehensive lipidomic analyses, we show that FXR activation in mice or humans specifically reduces hepatic levels of mono- and polyunsaturated fatty acids (MUFA and PUFA). Decreases in MUFA are due to FXR-dependent repression of Scd1, Dgat2, and Lpin1 expression, which is independent of SHP and SREBP1c. FXR-dependent decreases in PUFAs are mediated by decreases in lipid absorption. Replenishing bile acids in the diet prevented decreased lipid absorption in GSK2324-treated mice, suggesting that FXR reduces absorption via decreased bile acids. We used tissue-specific FXR KO mice to show that hepatic FXR controls lipogenic genes, whereas intestinal FXR controls lipid absorption. Together, our studies establish two distinct pathways by which FXR regulates hepatic lipids.

BackgroundCoronary artery disease (CAD) is a multifactorial condition with both genetic and exogenous causes. The contribution of tissue-specific functional networks to the development of atherosclerosis remains largely unclear. The aim of this study was to identify and characterize central regulators and networks leading to atherosclerosis.MethodsBased on several hundred genes known to affect atherosclerosis risk in mouse (as demonstrated in knockout models) and human (as shown by genome-wide association studies), liver gene regulatory networks were modeled. The hierarchical order and regulatory directions of genes within the network were based on Bayesian prediction models, as well as experimental studies including chromatin immunoprecipitation DNA-sequencing, chromatin immunoprecipitation mass spectrometry, overexpression, small interfering RNA knockdown in mouse and human liver cells, and knockout mouse experiments. Bioinformatics and correlation analyses were used to clarify associations between central genes and CAD phenotypes in both human and mouse.ResultsThe transcription factor MAFF (MAF basic leucine zipper transcription factor F) interacted as a key driver of a liver network with 3 human genes at CAD genome-wide association studies loci and 11 atherosclerotic murine genes. Most importantly, expression levels of the low-density lipoprotein receptor (LDLR) gene correlated with MAFF in 600 CAD patients undergoing bypass surgery (STARNET [Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task]) and a hybrid mouse diversity panel involving 105 different inbred mouse strains. Molecular mechanisms of MAFF were tested in noninflammatory conditions and showed positive correlation between MAFF and LDLR in vitro and in vivo. Interestingly, after lipopolysaccharide stimulation (inflammatory conditions), an inverse correlation between MAFF and LDLR in vitro and in vivo was observed. Chromatin immunoprecipitation mass spectrometry revealed that the human CAD genome-wide association studies candidate BACH1 (BTB domain and CNC homolog 1) assists MAFF in the presence of lipopolysaccharide stimulation with respective heterodimers binding at the MAF recognition element of the LDLR promoter to transcriptionally downregulate LDLR expression.ConclusionsThe transcription factor MAFF was identified as a novel central regulator of an atherosclerosis/CAD-relevant liver network. MAFF triggered context-specific expression of LDLR and other genes known to affect CAD risk. Our results suggest that MAFF is a missing link between inflammation, lipid and lipoprotein metabolism, and a possible treatment target.

Ozone is a crucial air pollutant that damages human health and vegetation. As it is related to the photo-oxidation of the nitrogen oxides and volatile organic compounds, the summertime reduction of these precursors is the primary focus of current ozone mitigation strategies. During ozone pollution episodes in eastern China, an observed accumulation of daily total oxidants (Ox=NO2+O3) in cool seasons (spring and autumn: 60 ppb and winter 40 ppb) is comparable to that in summer (60 ppb), indicating fast photochemical production of secondary pollutants including ozone over the year. Unrecognized fast radical primary productions are found to counteract the increased termination of hydroxyl radical and unfavorable meteorological conditions to maintain the rapid total oxidant formations in cool seasons. Elucidating and regulating the primary radical sources may be critical for the secondary air pollution control in cool seasons.

ObjectiveIn a recent article in Arteriosclerosis, Thrombosis, and Vascular Biology, it was reported that ATP-binding cassette transporter G1 (ABCG1) containing leucine at position 550 (ABCG1-L550) was localized to the plasma membrane, whereas ABCG1-P550 (proline at position 550) was intracellular. Because the published data on the subcellular localization of ABCG1 are controversial, we performed additional experiments to determine the importance of leucine or proline at amino acid 550.Approach and resultsWe transfected multiple cell lines (CHO-K1, Cos-7, and HEK293 [human embryonic kidney]) with untagged or FLAG-tagged ABCG1 containing either leucine or proline at position 550. Immunofluorescence studies demonstrated that in all cases, ABCG1 localized to intracellular endosomal vesicles. We also show that both ABCG1-L550 and ABCG1-P550 are equally active in both promoting the efflux of cellular cholesterol to exogenous high-density lipoprotein and in inducing the activity of sterol regulatory element-binding protein-2, presumably as a result of redistributing intracellular sterols away from the endoplasmic reticulum. Importantly, we treated nontransfected primary peritoneal macrophages with a liver X receptor agonist and demonstrate, using immunofluorescence, that although endogenous ABCG1 localizes to intracellular endosomes, none was detectable at the cell surface/plasma membrane.ConclusionsABCG1, irrespective of either a leucine or proline at position 550, is an intracellular protein that localizes to vesicles of the endosomal pathway where it functions to mobilize sterols away from the endoplasmic reticulum and out of the cell.

Specific bile acids are potent signaling molecules that modulate metabolic pathways affecting lipid, glucose and bile acid homeostasis, and the microbiota. Bile acids are synthesized from cholesterol in the liver, and the key enzymes involved in bile acid synthesis (Cyp7a1, Cyp8b1) are regulated transcriptionally by the nuclear receptor FXR. We have identified an FXR-regulated pathway upstream of a transcriptional repressor that controls multiple bile acid metabolism genes. We identify MafG as an FXR target gene and show that hepatic MAFG overexpression represses genes of the bile acid synthetic pathway and modifies the biliary bile acid composition. In contrast, loss-of-function studies using MafG(+/-) mice causes de-repression of the same genes with concordant changes in biliary bile acid levels. Finally, we identify functional MafG response elements in bile acid metabolism genes using ChIP-seq analysis. Our studies identify a molecular mechanism for the complex feedback regulation of bile acid synthesis controlled by FXR.

The secondary organic aerosol (SOA) mass yields from NO3 oxidation of a series of biogenic volatile organic compounds (BVOCs), consisting of five monoterpenes and one sesquiterpene (α-pinene, β-pinene, Δ-3-carene, limonene, sabinene, and β-caryophyllene), were investigated in a series of continuous flow experiments in a 10 m(3) indoor Teflon chamber. By making in situ measurements of the nitrate radical and employing a kinetics box model, we generate time-dependent yield curves as a function of reacted BVOC. SOA yields varied dramatically among the different BVOCs, from zero for α-pinene to 38-65% for Δ-3-carene and 86% for β-caryophyllene at mass loading of 10 μg m(-3), suggesting that model mechanisms that treat all NO3 + monoterpene reactions equally will lead to errors in predicted SOA depending on each location's mix of BVOC emissions. In most cases, organonitrate is a dominant component of the aerosol produced, but in the case of α-pinene, little organonitrate and no aerosol is formed.

The fatty acyl composition of phospholipids determines the biophysical character of membranes and impacts the function of membrane proteins. Here, we define a nuclear receptor pathway for the dynamic modulation of membrane composition in response to changes in cellular lipid metabolism. Ligand activation of liver X receptors (LXRs) preferentially drives the incorporation of polyunsaturated fatty acids into phospholipids through induction of the remodeling enzyme Lpcat3. Promotion of Lpcat3 activity ameliorates endoplasmic reticulum (ER) stress induced by saturated free fatty acids in vitro or by hepatic lipid accumulation in vivo. Conversely, Lpcat3 knockdown in liver exacerbates ER stress and inflammation. Mechanistically, Lpcat3 modulates inflammation both by regulating inflammatory kinase activation through changes in membrane composition and by affecting substrate availability for inflammatory mediator production. These results outline an endogenous mechanism for the preservation of membrane homeostasis during lipid stress and identify Lpcat3 as an important mediator of LXR effects on metabolism.

During the CalNex (California Research at the Nexus of Air Quality and Climate Change) field study in May-June 2010, measurements of volatile organic compounds (VOCs) were performed in the Los Angeles (LA) basin onboard a NOAA research aircraft and at a ground site located in Pasadena. A weekday-weekend effect in ozone, caused by lower NOx emissions due to reduced diesel truck traffic in the weekends, has been previously observed in Los Angeles and other cities. Measurements in the Caldecott tunnel show that emission ratios of VOCs do not vary with the day of the week, but measurements during CalNex2010 show a VOC weekday-weekend effect through faster photochemical processing at lower ambient NOx mixing ratios. Ambient VOC enhancement ratios of long-lived species such as benzene are the same between weekdays and weekends, whereas enhancement ratios of short-lived species, such as trimethyl benzene, are up to a factor of three lower on weekends. Based upon the observed differences in VOC enhancement ratios to CO, we determine that photochemical processing was on average 65%-75% faster on weekends during CalNex2010, which indicates that ambient OH radical concentrations were larger by this factor causing the observed change in VOC composition. A box model calculation based on the Master Chemical Mechanism was used to verify the increase in photochemical processing in the weekends. Key PointsSpatial and temporal photochemical processing in Los AngelesVOC weekday-weekend effectFaster photochemistry in weekends ©2013. American Geophysical Union. All Rights Reserved.

We used mouse hepatic chromatin enriched with an FXR antibody and chromatin immunoprecipitation-sequencing (ChIP-seq) to evaluate FXR binding on a genome-wide scale. This identified 1656 FXR-binding sites and 10% were located within 2 kb of a transcription start site which is much higher than predicted by random occurrence. A motif search uncovered a canonical nuclear receptor IR-1 site, consistent with in vitro DNA-binding studies reported previously. A separate nuclear receptor half-site for monomeric receptors such as LRH-1 was co-enriched and FXR activation of four newly identified promoters was significantly augmented by an LRH-1 expression vector in a co-transfection assay. There were 1038 genes located within 20 kb of a peak and a gene set enrichment analysis showed that genes identified by our ChIP-seq analysis are highly correlated with genes activated by an FXR-VP16 adenovirus in primary mouse hepatocytes providing functional relevance to the genome-wide binding study. Gene Ontology analysis showed FXR-binding sites close to many genes in lipid, fatty acid and steroid metabolism. Other broad gene clusters related to metabolism, transport, signaling and glycolysis were also significantly enriched. Thus, FXR may have a much wider role in cellular metabolism than previously appreciated.

Much previous work in developing computational models of scientific discovery has concentrated on the formation of basic laws. The important role played by additional assumptions in this process is a neglected research topic. W e argue that hypotheses about structure are an important source of such additional assumptions, and that knowledge of this type can be embodied in the notion of Informal Qualitative Models (IQMs). In this paper, we demonstrate that such models can be synthesised by applying a set of operators to the most fundamental model in a domain. Heuristics are employed to control this process, which forms the basis of an architecture for model-driven scientific discovery. Conventional data-driven discovery techniques can be integrated into this architecture, resulting in laws which depend crucially on the model that is applied to a problem. This approach is illustrated by an historical survey of eighteenth and nineteenth century solution chemistry, which focuses on the evolution of the models employed by scientists. A series of models are synthesised which reflect these historical developments, showing the importance of structural models both in understanding certain aspects of the scientific discovery process, and as a basis for practical discovery systems.