Correction:A study of the structural properties of sites modified by the O-linked 6-N-acetylglucosamine transferase

[This corrects the article DOI: 10.1371/journal.pone.0184405.]

A unified analysis of evolutionary and population constraint in protein domains highlights structural features and pathogenic sites

Protein evolution is constrained by structure and function, creating patterns in residue conservation that are routinely exploited to predict structure and other features. Similar constraints should affect variation across individuals, but it is only with the growth of human population sequencing that this has been tested at scale. Now, human population constraint has established applications in pathogenicity prediction, but it has not yet been explored for structural inference. Here, we map 2.4 million population variants to 5885 protein families and quantify residue-level constraint with a new Missense Enrichment Score (MES). Analysis of 61,214 structures from the PDB spanning 3661 families shows that missense depleted sites are enriched in buried residues or those involved in small-molecule or protein binding. MES is complementary to evolutionary conservation and a combined analysis allows a new classification of residues according to a conservation plane. This approach finds functional residues that are evolutionarily diverse, which can be related to specificity, as well as family-wide conserved sites that are critical for folding or function. We also find a possible contrast between lethal and non-lethal pathogenic sites, and a surprising clinical variant hot spot at a subset of missense enriched positions

Evaluation of soil-water parameters of a Red Latosol under pasture and 'cerrado'

O objetivo primeiro neste trabalho foi avaliar a qualidade fisico-hídrica do solo em áreas sob pastejo, em relação a um cerrado natural. Os tratamentos foram: cerrado natural, cerrado antropizado (pastejado na estação seca) e três pastagens cultivadas, com diferentes graus de cobertura do solo. O estudo foi realizado na Embrapa Cerrados em um Latossolo Vermelho, nas camadas de 0-5, 10-15, 40-55 e 70-80 cm, cujos parâmetros avaliados foram condutividade hidráulica saturada (Ks), capacidade de água disponível (CAD), densidade do solo (Ds) e macroporosidade (Ma). A qualidade fisico-hídrica do solo nas áreas sob pastejo foi analisada tendo-se como referência os parâmetros medidos no cerrado natural. Observou-se semelhança estatística da CAD na camada 0-5 cm para todas as áreas mas ocorreu drástica redução da saturação efetiva nas áreas sob pastejo, explicada principalmente pela queda na macroporosidade. A redução média da Ma foi de 70,8%, ocasionando um decréscimo da ordem de 73,6% da Ks nos primeiros 15 cm das áreas sob pastejo, podendo-se concluir que a camada superficial do solo foi a mais afetada pelo pastejo, com perda significativa da qualidade fisico-hídrica e previsível redução na capacidade de infiltração da água no solo. _________________________________________________________________________________ ABSTRACTThe objective of this study was to evaluate the soil-water quality under grazing pastures in comparison to a natural 'cerrado' (savanna). The treatments were: natural 'cerrado', grazed 'cerrado' during the dry season, and three cultivated pastures with different degrees of soil covering. The research was conducted at the Embrapa Cerrados, on a Red Latosol in the 0-5, 10-15, 40-55, and 70-80 cm soil layers, in which the following parameters were quantified: saturated hydraulic conductivity (Ks), available water capacity (CAD), soil bulk density (Ds), and macroporosity (Ma). The soil-water quality was determined by taking as references the corresponding parameters measured in the natural 'cerrado'. Statistical similarity of CAD values in the 0-5 cm soil layer for all treatments was observed. However, there was a drastic reduction of the effective saturation in the treatments of grazed areas, mainly explained by the reduction in macroporosity. The mean decrease in Ma was 70.8%, causing a 73.6% decline in Ks in the 15 cm upper soil layer of the grazed areas, which led to the conclusion that the surface soil layers were the most affected by the grazing activity, with significant deterioration of their soil-water quality and a predictable reduction in water-infiltration capacity

The anti-inflammatory mechanisms of Hsp70

Immune responses to heat shock proteins (Hsp) develop in virtually all inflammatory diseases; however, the significance of such responses is only now becoming clear. In experimental disease models, Hsp administration can prevent or arrest inflammatory damage, and in initial clinical trials in patients with chronic inflammatory diseases, Hsp peptides have been shown to promote the production of anti-inflammatory cytokines, indicating immunoregulatory potential of Hsp. Therefore, the presence of immune responses to Hsp in inflammatory diseases can be seen as an attempt of the immune system to correct the inflammatory condition. Hsp70 can modulate inflammatory responses in models of arthritis, colitis and graft rejection, and the mechanisms underlying this effect are now being elucidated. Incubation with microbial Hsp70 was seen to induce tolerogenic dendritic cells (DCs) and to promote a suppressive phenotype in myeloid-derived suppressor cells and monocytes. These DC could induce regulatory T cells (Tregs), independently of the antigens they presented. Some Hsp70 family members are associated with autophagy, leading to a preferential uploading of Hsp70 peptides in MHC class II molecules of stressed cells. Henceforth, conserved Hsp70 peptides may be presented in these situations and constitute targets of Tregs, contributing to downregulation of inflammation. Finally, an interfering effect in multiple intracellular inflammatory signaling pathways is also known for Hsp70. Altogether it seems attractive to use Hsp70, or its derivative peptides, for modulation of inflammation. This is a physiological immunotherapy approach, without the immediate necessity of defining disease-specific auto-antigens. In this article, we present the evidence on anti-inflammatory effects of Hsp70 and discuss the need for experiments that will be crucial for the further exploration of the immunosuppressive potential of this protein

Genotoxic stress induces Sca‐1‐expressing metastatic mammary cancer cells

We describe a cell damage‐induced phenotype in mammary carcinoma cells involving acquisition of enhanced migratory and metastatic properties. Induction of this state by radiation required increased activity of the Ptgs2 gene product cyclooxygenase 2 (Cox2), secretion of its bioactive lipid product prostaglandin E2 (PGE2), and the activity of the PGE2 receptor EP4. Although largely transient, decaying to low levels in a few days to a week, this phenotype was cumulative with damage and levels of cell markers Sca‐1 and ALDH1 increased with treatment dose. The Sca‐1+, metastatic phenotype was inhibited by both Cox2 inhibitors and PGE2 receptor antagonists, suggesting novel approaches to radiosensitization

The atypical chemokine receptor ACKR2 is protective against sepsis

Sepsis is a systemic inflammatory response as a result of uncontrolled infections. Neutrophils are the first cells to reach the primary sites of infection and chemokines play a key role in recruiting neutrophils. However, in sepsis chemokines could also contribute to neutrophil infiltration to vital organs leading to multiple organ failure. ACKR2 is an atypical chemokine receptor, which can remove and degrade inflammatory CC chemokines. The role of ACK2 in sepsis is unknown. Using a model of cecal ligation and puncture (CLP), we demonstrate here that ACKR2 deficient (−/−) mice exhibited a significant reduction in the survival rate compared to similarly treated wild type (WT) mice. However, neutrophil migration to the peritoneal cavity and bacterial load were similar between WT and ACKR2−/− mice during CLP. In contrast, ACKR2−/− mice showed increased neutrophil infiltration and elevated CC chemokine levels in the lung, kidney and heart compared to the WT mice. In addition, ACKR2−/− mice also showed more severe lesions in the lung and kidney than those in the WT mice. Consistent with these results, WT mice under non-severe sepsis (90% survival) had higher expression of ACKR2 in these organs than mice under severe sepsis (no survival). Finally, the lungs from septic patients showed increased number of ACKR2+ cells compared to those of non-septic patients. Our data indicate that ACKR2 may have a protective role during sepsis, and the absence of ACKR2 leads to exacerbated chemokine accumulation, neutrophil infiltration and damage to vital organs

March1-dependent modulation of donor MHC II on CD103+ dendritic cells mitigates alloimmunity.

In transplantation, donor dendritic cells (do-DCs) initiate the alloimmune response either by direct interaction with host T cells or by transferring intact donor MHC to host DCs. However, how do-DCs can be targeted for improving allograft survival is still unclear. Here we show CD103+ DCs are the major do-DC subset involved in the acute rejection of murine skin transplants. In the absence of CD103+ do-DCs, less donor MHC-II is carried to host lymph nodes, fewer allogenic T cells are primed and allograft survival is prolonged. Incubation of skin grafts with the anti-inflammatory mycobacterial protein DnaK reduces donor MHC-II on CD103+DCs and prolongs graft survival. This effect is mediated through IL-10-induced March1, which ubiquitinates and decreases MHC-II levels. Importantly, in vitro pre-treatment of human DCs with DnaK reduces their ability to prime alloreactive T cells. Our findings demonstrate a novel therapeutic approach to dampen alloimmunity by targeting donor MHC-II on CD103+DCs

miR-155 in the progression of lung fibrosis in systemic sclerosis

Background\ud MicroRNA (miRNA) control key elements of mRNA stability and likely contribute to the dysregulated lung gene expression observed in systemic sclerosis associated interstitial lung disease (SSc-ILD). We analyzed the miRNA gene expression of tissue and cells from patients with SSc-ILD. A chronic lung fibrotic murine model was used.\ud \ud Methods\ud RNA was isolated from lung tissue of 12 patients with SSc-ILD and 5 controls. High-resolution computed tomography (HRCT) was performed at baseline and 2–3 years after treatment. Lung fibroblasts and peripheral blood mononuclear cells (PBMC) were isolated from healthy controls and patients with SSc-ILD. miRNA and mRNA were analyzed by microarray, quantitative polymerase chain reaction, and/or Nanostring; pathway analysis was performed by DNA Intelligent Analysis (DIANA)-miRPath v2.0 software. Wild-type and miR-155 deficient (miR-155ko) mice were exposed to bleomycin.\ud \ud Results\ud Lung miRNA microarray data distinguished patients with SSc-ILD from healthy controls with 185 miRNA differentially expressed (q < 0.25). DIANA-miRPath revealed 57 Kyoto Encyclopedia of Genes and Genomes pathways related to the most dysregulated miRNA. miR-155 and miR-143 were strongly correlated with progression of the HRCT score. Lung fibroblasts only mildly expressed miR-155/miR-21 after several stimuli. miR-155 PBMC expression strongly correlated with lung function tests in SSc-ILD. miR-155ko mice developed milder lung fibrosis, survived longer, and weaker lung induction of several genes after bleomycin exposure compared to wild-type mice.\ud \ud Conclusions\ud miRNA are dysregulated in the lungs and PBMC of patients with SSc-ILD. Based on mRNA-miRNA interaction analysis and pathway tools, miRNA may play a role in the progression of the disease. Our findings suggest that targeting miR-155 might provide a novel therapeutic strategy for SSc-ILD