Microbiome-derived bile acids contribute to elevated antigenic response and bone erosion in rheumatoid arthritis

Rheumatoid arthritis (RA) is a chronic, disabling and incurable autoimmune disease. It has been widely recognized that gut microbial dysbiosis is an important contributor to the pathogenesis of RA, although distinct alterations in microbiota have been associated with this disease. Yet, the metabolites that mediate the impacts of the gut microbiome on RA are less well understood. Here, with microbial profiling and non-targeted metabolomics, we revealed profound yet diverse perturbation of the gut microbiome and metabolome in RA patients in a discovery set. In the Bacteroides-dominated RA patients, differentiation of gut microbiome resulted in distinct bile acid profiles compared to healthy subjects. Predominated Bacteroides species expressing BSH and 7a-HSDH increased, leading to elevated secondary bile acid production in this subgroup of RA patients. Reduced serum fibroblast growth factor-19 and dysregulated bile acids were evidence of impaired farnesoid X receptor-mediated signaling in the patients. This gut microbiota-bile acid axis was correlated to ACPA. The patients from the validation sets demonstrated that ACPA-positive patients have more abundant bacteria expressing BSH and 7a-HSDH but less Clostridium scindens expressing 7a-dehydroxylation enzymes, together with dysregulated microbial bile acid metabolism and more severe bone erosion than ACPA-negative ones. Mediation analyses revealed putative causal relationships between the gut microbiome, bile acids, and ACPA-positive RA, supporting a potential causal effect of Bacteroides species in increasing levels of ACPA and bone erosion mediated via disturbing bile acid metabolism. These results provide insights into the role of gut dysbiosis in RA in a manifestation-specific manner, as well as the functions of bile acids in this gut-joint axis, which may be a potential intervention target for precisely controlling RA conditions.Comment: 38 pages, 6 figure

Ssk1p-Independent Activation of Ssk2p Plays an Important Role in the Osmotic Stress Response in Saccharomyces cerevisiae: Alternative Activation of Ssk2p in Osmotic Stress

In Saccharomyces cerevisiae, external high osmolarity activates the HOG MAPK pathway, which controls various aspects of osmoregulation. MAPKKK Ssk2 is activated by Ssk1 in the SLN1 branch of the osmoregulatory HOG MAPK pathway under hyperosmotic stress. We observed that Ssk2 can be activated independent of Ssk1 upon osmotic shock by an unidentified mechanism. The domain for the Ssk1p-independent activation was identified to be located between the amino acids 177,240. This region might be involved in the binding of an unknown regulator to Ssk2 which in turn activates Ssk2p without Ssk1p under hyperosmotic stress. The osmotic stress response through the Ssk1p-independent Ssk2p activation is strong, although its duration is short compared with the Ssk1p-dependent activation. The alternative Ssk2p activation is also important for the salt resistance

Terrace sizes in molecular beam epitaxy

The order of magnitude of the typical distance $\ell$ between steps in MBE-grown crystal surfaces in calculated from simple scaling assumptions in the absence of evaporation. This distance is measurable by diffraction methods and yields access to the surface diffusion constant $D$. At the lowest non trivial temperatures the characteristic distance is of order $(D/F)^{1/6}$ where $F$ is the beam flux. At slightly higher temperature, $\ell$ is given by an algebraic formula which depends on the lifetime $\tau_2$ of a bound pair of adatoms at the surface, as well as of the diffusion constant $D_2$ of these pairs. In certain ranges, $\ell$ varies as $F^{-1/4}$ or $F^{-1/5}$. At higher temperatures yet, $\ell$ is given by a formula which depends on a larger number of parameters. In special cases, our results are in agreement with the classical formulae of Stoyanov and Kashchiev, but disagree with certain recents works. $\ell$ is found to increase with temperature more rapidly than an Arrhenius exponential. Monte-Carlo simulations are reported and the discrepancy with certain other authors is clarified

7×7 RMSD matrix: A new method for quantitative comparison of the transmembrane domain structures in the G-protein coupled receptors

The G-protein coupled receptors (GPCRs) share a conserved heptahelical fold in the transmembrane (TM) region, but the exact arrangements of the seven TM helices vary with receptors and their activation states. The differences or the changes have been observed in the experimentally solved structures, but have not been systematically and quantitatively investigated due to lack of suitable methods. In this work, we describe a novel method, called 7×7 RMSD matrix that is proposed specifically for comparing the characteristic 7TM bundle structures of GPCRs. Compared to the commonly used overall TM bundle RMSD as a single parameter, a 7×7 RMSD matrix contains 49 parameters, which reveal changes of the relative orientations of the seven TMs. We demonstrate the novelty and advantages of this method by tackling two problems that are challenging for the existing methods. With this method, we are able to identify and quantify the helix movements in the activated receptor structures and reveal structural conservation and divergence as well as the structural relationships of different GPCRs in terms of the relative orientations of the seven TMs

A receiver domain (amino acids 177∼240) near the N-terminus of SSK2 is needed for the activation of SSK2 independent of SSK1.

<p>A. Three mutants <i>ssk2Δ^(1–176)</i>, <i>ssk2Δ^(1–240)</i>, <i>ssk2Δ^(177–239)</i> and wild type Ssk2 were expressed in <i>ste11Δssk1Δssk2Δ</i> mutant, and the Hog1p phosphorylation was determined under osmotic stress. B. Three mutants <i>ssk2Δ^(1–176), ssk2Δ^(1–240), ssk2Δ^(177–239)</i> and wild type Ssk2 were expressed in <i>ste11Δssk2Δssk22Δ</i> mutant, and the Hog1p phosphorylation was determined under osmotic stress. C. The osmosensitivity of the mutants of Ssk2p. D. N- terminal portion of Ssk2p (amino acid 177–240) is required for the activation of Ssk2p by the X factor under osmotic stress.</p

Plasmids used in this study.

<p>Plasmids used in this study.</p

Three MAPKKKs involved in HOG pathway have different properties.

<p>A. Hog1p phosphorylation pattern of <i>ssk2Δssk22Δ</i> mutant. B. Hog1p phosphorylation pattern of <i>ssk22Δste11Δ</i> mutant. C. Hog1p phosphorylation pattern of <i>ssk2Δste11Δ</i> mutant. D. Hog1p phosphorylation pattern of <i>ste11Δssk22Δssk2 Δ^(1–240)</i>. E. Scheme of HOG pathway.</p

Hog1p phosphorylation level and growth phenotypes for the wild type (WT) and mutant yeast cells under various osmotic and salt stress conditions.

<p>A. Hog1p MAPK phosphorylation (P-Hog1p) was detected in the <i>ssk1Δste11Δ</i> mutant under hyperosmotic stress. Cells were exposed to different level of osmotic stress induced by sorbitol (concentration shown) in YPD medium for the time indicated. B. Same experiment as in A but for the wild type strain which shows higher sensitivity and a longer duration of the response. C. Hog1p phosphorylation was not detected in the <i>ste11Δssk2Δssk22Δ</i> mutant. D. Hog1p phosphorylation assay under ionic osmotic stress in the <i>ssk1Δste11Δ</i> double mutant. Cells were exposed to a different levels of salt stress induced by NaCl (concentration shown) in YPD medium for the time indicated. E. Same as in D but for the wild type cells. F. The <i>ssk1Δste11Δ</i> mutant exhibited better growth than <i>hog1Δ</i> mutant under osmotic stress. Serial dilutions (from left to right in each panel) of indicated strains were spotted onto YPD and salt plates and growth was scored after 3 days.</p