Helicobacter hepaticus infection in mice: models for understanding lower bowel inflammation and cancer

Pioneering work in the 1990s first linked a novel microaerobic bacterium, Helicobacter hepaticus, with chronic active hepatitis and inflammatory bowel disease in several murine models. Targeted H. hepaticus infection experiments subsequently demonstrated its ability to induce colitis, colorectal cancer, and extraintestinal diseases in a number of mouse strains with defects in immune function and/or regulation. H. hepaticus is now widely utilized as a model system to dissect how intestinal microbiota interact with the host to produce both inflammatory and tolerogenic responses. This model has been used to make important advances in understanding factors that regulate both acquired and innate immune response within the intestine. Further, it has been an effective tool to help define the function of regulatory T cells, including their ability to directly inhibit the innate inflammatory response to gut microbiota. The complete genomic sequence of H. hepaticus has advanced the identification of several virulence factors and aided in the elucidation of H. hepaticus pathogenesis. Delineating targets of H. hepaticus virulence factors could facilitate novel approaches to treating microbially induced lower bowel inflammatory diseases.National Institutes of Health (U.S.) (grant R01-DK052413)National Institutes of Health (U.S.) (grant P01-CA026731)National Institutes of Health (U.S.) (grant R01-CA067529)National Institutes of Health (U.S.) (grant P30-ES02109)National Institutes of Health (U.S.) (grant R01-A1052267)National Institutes of Health (U.S.) (grantR01-CA108854

Deep Markov Random Field for Image Modeling

Markov Random Fields (MRFs), a formulation widely used in generative image modeling, have long been plagued by the lack of expressive power. This issue is primarily due to the fact that conventional MRFs formulations tend to use simplistic factors to capture local patterns. In this paper, we move beyond such limitations, and propose a novel MRF model that uses fully-connected neurons to express the complex interactions among pixels. Through theoretical analysis, we reveal an inherent connection between this model and recurrent neural networks, and thereon derive an approximated feed-forward network that couples multiple RNNs along opposite directions. This formulation combines the expressive power of deep neural networks and the cyclic dependency structure of MRF in a unified model, bringing the modeling capability to a new level. The feed-forward approximation also allows it to be efficiently learned from data. Experimental results on a variety of low-level vision tasks show notable improvement over state-of-the-arts.Comment: Accepted at ECCV 201

<i>Campylobacter jejuni</i> Type VI Secretion System: Roles in Adaptation to Deoxycholic Acid, Host Cell Adherence, Invasion, and <i>In Vivo</i> Colonization

The recently identified type VI secretion system (T6SS) of proteobacteria has been shown to promote pathogenicity, competitive advantage over competing microorganisms, and adaptation to environmental perturbation. By detailed phenotypic characterization of loss-of-function mutants, in silico, in vitro and in vivo analyses, we provide evidence that the enteric pathogen, Campylobacter jejuni, possesses a functional T6SS and that the secretion system exerts pleiotropic effects on two crucial processes – survival in a bile salt, deoxycholic acid (DCA), and host cell adherence and invasion. The expression of T6SS during initial exposure to the upper range of physiological levels of DCA (0.075%–0.2%) was detrimental to C. jejuni proliferation, whereas down-regulation or inactivation of T6SS enabled C. jejuni to resist this effect. The C. jejuni multidrug efflux transporter gene, cmeA, was significantly up-regulated during the initial exposure to DCA in the wild type C. jejuni relative to the T6SS-deficient strains, suggesting that inhibition of proliferation is the consequence of T6SS-mediated DCA influx. A sequential modulation of the efflux transporter activity and the T6SS represents, in part, an adaptive mechanism for C. jejuni to overcome this inhibitory effect, thereby ensuring its survival. C. jejuni T6SS plays important roles in host cell adhesion and invasion as T6SS inactivation resulted in a reduction of adherence to and invasion of in vitro cell lines, while over-expression of a hemolysin co-regulated protein, which encodes a secreted T6SS component, greatly enhanced these processes. When inoculated into B6.129P2-IL-10tm1Cgn mice, the T6SS-deficient C. jejuni strains did not effectively establish persistent colonization, indicating that T6SS contributes to colonization in vivo. Taken together, our data demonstrate the importance of bacterial T6SS in host cell adhesion, invasion, colonization and, for the first time to our knowledge, adaptation to DCA, providing new insights into the role of T6SS in C. jejuni pathogenesis.</p

Campylobacter jejuni Type VI Secretion System: Roles in Adaptation to Deoxycholic Acid, Host Cell Adherence, Invasion, and In Vivo Colonization

The recently identified type VI secretion system (T6SS) of proteobacteria has been shown to promote pathogenicity, competitive advantage over competing microorganisms, and adaptation to environmental perturbation. By detailed phenotypic characterization of loss-of-function mutants, in silico, in vitro and in vivo analyses, we provide evidence that the enteric pathogen, Campylobacter jejuni, possesses a functional T6SS and that the secretion system exerts pleiotropic effects on two crucial processes – survival in a bile salt, deoxycholic acid (DCA), and host cell adherence and invasion. The expression of T6SS during initial exposure to the upper range of physiological levels of DCA (0.075%–0.2%) was detrimental to C. jejuni proliferation, whereas down-regulation or inactivation of T6SS enabled C. jejuni to resist this effect. The C. jejuni multidrug efflux transporter gene, cmeA, was significantly up-regulated during the initial exposure to DCA in the wild type C. jejuni relative to the T6SS-deficient strains, suggesting that inhibition of proliferation is the consequence of T6SS-mediated DCA influx. A sequential modulation of the efflux transporter activity and the T6SS represents, in part, an adaptive mechanism for C. jejuni to overcome this inhibitory effect, thereby ensuring its survival. C. jejuni T6SS plays important roles in host cell adhesion and invasion as T6SS inactivation resulted in a reduction of adherence to and invasion of in vitro cell lines, while over-expression of a hemolysin co-regulated protein, which encodes a secreted T6SS component, greatly enhanced these processes. When inoculated into B6.129P2-IL-10[superscript tm1Cgn] mice, the T6SS-deficient C. jejuni strains did not effectively establish persistent colonization, indicating that T6SS contributes to colonization in vivo. Taken together, our data demonstrate the importance of bacterial T6SS in host cell adhesion, invasion, colonization and, for the first time to our knowledge, adaptation to DCA, providing new insights into the role of T6SS in C. jejuni pathogenesis

Clinical and molecular genetic features of pulmonary hypertension in patients with hereditary hemorrhagic telangiectasia

BACKGROUND: Most patients with familial primary pulmonary hypertension have defects in the gene for bone morphogenetic protein receptor II (BMPR2), a member of the transforming growth factor beta (TGF-beta) superfamily of receptors. Because patients with hereditary hemorrhagic telangiectasia may have lung disease that is indistinguishable from primary pulmonary hypertension, we investigated the genetic basis of lung disease in these patients. METHODS: We evaluated members of five kindreds plus one individual patient with hereditary hemorrhagic telangiectasia and identified 10 cases of pulmonary hypertension. In the two largest families, we used microsatellite markers to test for linkage to genes encoding TGF-beta-receptor proteins, including endoglin and activin-receptor-like kinase 1 (ALK1), and BMPR2. In subjects with hereditary hemorrhagic telangiectasia and pulmonary hypertension, we also scanned ALK1 and BMPR2 for mutations. RESULTS: We identified suggestive linkage of pulmonary hypertension with hereditary hemorrhagic telangiectasia on chromosome 12q13, a region that includes ALK1. We identified amino acid changes in activin-receptor-like kinase 1 that were inherited in subjects who had a disorder with clinical and histologic features indistinguishable from those of primary pulmonary hypertension. Immunohistochemical analysis in four subjects and one control showed pulmonary vascular endothelial expression of activin-receptor-like kinase 1 in normal and diseased pulmonary arteries. CONCLUSIONS: Pulmonary hypertension in association with hereditary hemorrhagic telangiectasia can involve mutations in ALK1. These mutations are associated with diverse effects, including the vascular dilatation characteristic of hereditary hemorrhagic telangiectasia and the occlusion of small pulmonary arteries that is typical of primary pulmonary hypertension

Bayesian Constraints on theta_{13} from Solar and KamLAND Neutrino Data

We present the results of a Bayesian analysis of solar and KamLAND neutrino data in the framework of three-neutrino mixing. We adopt two approaches for the prior probability distribution of the oscillation parameters Delta m^2_{21}, sin^2 theta_{12}, sin^2 theta_{13}: 1) a traditional flat uninformative prior; 2) an informative prior which describes the limits on sin^2 theta_{13} obtained in atmospheric and long-baseline accelerator and reactor neutrino experiments. In both approaches, we present the allowed regions in the sin^2 theta_{13} - Delta m^2_{21} and sin^2 theta_{12} - sin^2 theta_{13} planes, as well as the marginal posterior probability distribution of sin^2 theta_{13}. We confirm the 1.2 sigma hint of theta_{13} > 0 found in hep-ph/0806.2649 from the analysis of solar and KamLAND neutrino data. We found that the statistical significance of the hint is reduced to about 0.8 sigma by the constraints on sin^2 theta_{13} coming from atmospheric and long-baseline accelerator and reactor neutrino data, in agreement with arXiv:0808.2016.Comment: 21 pages. Final version published in Phys. Rev. D 80 (2009) 05300

Global Budget and Radiative Forcing of Black Carbon Aerosol: Constraints from Pole-to-Pole (HIPPO) Observations across the Pacific

We use a global chemical transport model (GEOS-Chem) to interpret aircraft curtain observations of black carbon (BC) aerosol over the Pacific from 85°N to 67°S during the 2009–2011 HIAPER (High-Performance Instrumented Airborne Platform for Environmental Research) Pole-to-Pole Observations (HIPPO) campaigns. Observed concentrations are very low, implying much more efficient scavenging than is usually implemented in models. Our simulation with a global source of $6.5 Tg a^{−1}$ and mean tropospheric lifetime of 4.2 days (versus 6.8 ± 1.8 days for the Aerosol Comparisons between Observations and Models (AeroCom) models) successfully simulates BC concentrations in source regions and continental outflow and captures the principal features of the HIPPO data but is still higher by a factor of 2 (1.48 for column loads) over the Pacific. It underestimates BC absorbing aerosol optical depths (AAODs) from the Aerosol Robotic Network by 32% on a global basis. Only 8.7% of global BC loading in GEOS-Chem is above 5 km, versus 21 ± 11% for the AeroCom models, with important implications for radiative forcing estimates. Our simulation yields a global BC burden of 77 Gg, a global mean BC AAOD of 0.0017, and a top-of-atmosphere direct radiative forcing (TOA DRF) of $0.19 W m^{−2}$, with a range of $0.17–0.31 W m^{−2}$ based on uncertainties in the BC atmospheric distribution. Our TOA DRF is lower than previous estimates $(0.27 \pm 0.06 W m^{−2}$ in AeroCom, $0.65–0.9 W m^{−2}$ in more recent studies). We argue that these previous estimates are biased high because of excessive BC concentrations over the oceans and in the free troposphere.Engineering and Applied Science

The divergent DSL ligand Dll3 does not activate Notch signaling but cell autonomously attenuates signaling induced by other DSL ligands

Mutations in the DSL (Delta, Serrate, Lag2) Notch (N) ligand Delta-like (Dll) 3 cause skeletal abnormalities in spondylocostal dysostosis, which is consistent with a critical role for N signaling during somitogenesis. Understanding how Dll3 functions is complicated by reports that DSL ligands both activate and inhibit N signaling. In contrast to other DSL ligands, we show that Dll3 does not activate N signaling in multiple assays. Consistent with these findings, Dll3 does not bind to cells expressing any of the four N receptors, and N1 does not bind Dll3-expressing cells. However, in a cell-autonomous manner, Dll3 suppressed N signaling, as was found for other DSL ligands. Therefore, Dll3 functions not as an activator as previously reported but rather as a dedicated inhibitor of N signaling. As an N antagonist, Dll3 promoted Xenopus laevis neurogenesis and inhibited glial differentiation of mouse neural progenitors. Finally, together with the modulator lunatic fringe, Dll3 altered N signaling levels that were induced by other DSL ligands

The host metabolite D-serine contributes to bacterial niche specificity through gene selection

Escherichia coli comprise a diverse array of both commensals and niche-specific pathotypes. The ability to cause disease results from both carriage of specific virulence factors and regulatory control of these via environmental stimuli. Moreover, host metabolites further refine the response of bacteria to their environment and can dramatically affect the outcome of the host–pathogen interaction. Here, we demonstrate that the host metabolite, D-serine, selectively affects gene expression in E. coli O157:H7. Transcriptomic profiling showed exposure to D-serine results in activation of the SOS response and suppresses expression of the Type 3 Secretion System (T3SS) used to attach to host cells. We also show that concurrent carriage of both the D-serine tolerance locus (dsdCXA) and the locus of enterocyte effacement pathogenicity island encoding a T3SS is extremely rare, a genotype that we attribute to an ‘evolutionary incompatibility’ between the two loci. This study demonstrates the importance of co-operation between both core and pathogenic genetic elements in defining niche specificity