MEROPS: the peptidase database

Peptidases (proteolytic enzymes) and their natural, protein inhibitors are of great relevance to biology, medicine and biotechnology. The MEROPS database () aims to fulfil the need for an integrated source of information about these proteins. The organizational principle of the database is a hierarchical classification in which homologous sets of proteins of interest are grouped into families and the homologous families are grouped in clans. The most important addition to the database has been newly written, concise text annotations for each peptidase family. Other forms of information recently added include highlighting of active site residues (or the replacements that render some homologues inactive) in the sequence displays and BlastP search results, dynamically generated alignments and trees at the peptidase or inhibitor level, and a curated list of human and mouse homologues that have been experimentally characterized as active. A new way to display information at taxonomic levels higher than species has been devised. In the Literature pages, references have been flagged to draw attention to particularly ‘hot’ topics

Expression of KOC, S100P, mesothelin and MUC1 in pancreatico-biliary adenocarcinomas: development and utility of a potential diagnostic immunohistochemistry panel

<b>Background</b> Pancreatico-biliary adenocarcinomas (PBA) have a poor prognosis. Diagnosis is usually achieved by imaging and/or endoscopy with confirmatory cytology. Cytological interpretation can be difficult especially in the setting of chronic pancreatitis/cholangitis. Immunohistochemistry (IHC) biomarkers could act as an adjunct to cytology to improve the diagnosis. Thus, we performed a meta-analysis and selected KOC, S100P, mesothelin and MUC1 for further validation in PBA resection specimens.<p></p> <b>Methods</b> Tissue microarrays containing tumour and normal cores in a ratio of 3:2, from 99 surgically resected PBA patients, were used for IHC. IHC was performed on an automated platform using antibodies against KOC, S100P, mesothelin and MUC1. Tissue cores were scored for staining intensity and proportion of tissue stained using a Histoscore method (range, 0–300). Sensitivity and specificity for individual biomarkers, as well as biomarker panels, were determined with different cut-offs for positivity and compared by summary receiver operating characteristic (ROC) curve.<p></p> <b>Results</b> The expression of all four biomarkers was high in PBA versus normal ducts, with a mean Histoscore of 150 vs. 0.4 for KOC, 165 vs. 0.3 for S100P, 115 vs. 0.5 for mesothelin and 200 vs. 14 for MUC1 (p < .0001 for all comparisons). Five cut-offs were carefully chosen for sensitivity/specificity analysis. Four of these cut-offs, namely 5%, 10% or 20% positive cells and Histoscore 20 were identified using ROC curve analysis and the fifth cut-off was moderate-strong staining intensity. Using 20% positive cells as a cut-off achieved higher sensitivity/specificity values: KOC 84%/100%; S100P 83%/100%; mesothelin 88%/92%; and MUC1 89%/63%. Analysis of a panel of KOC, S100P and mesothelin achieved 100% sensitivity and 99% specificity if at least 2 biomarkers were positive for 10% cut-off; and 100% sensitivity and specificity for 20% cut-off.<p></p> <b>Conclusion</b> A biomarker panel of KOC, S100P and mesothelin with at least 2 biomarkers positive was found to be an optimum panel with both 10% and 20% cut-offs in resection specimens from patients with PBA.<p></p&gt

Classification of long-term condition patterns in rheumatoid arthritis and associations with adverse health events: a UK Biobank cohort study

Purpose: We aimed to classify individuals with RA and ≥2 additional long-term conditions (LTCs) and describe the association between different LTC classes, number of LTCs and adverse health outcomes. Methods: We used UK Biobank participants who reported RA (n=5,625) and employed latent class analysis (LCA) to create classes of LTC combinations for those with ≥2 additional LTCs. Cox-proportional hazard and negative binomial regression were used to compare the risk of all-cause mortality, major adverse cardiac events (MACE), and number of emergency hospitalisations over an 11-year follow-up across the different LTC classes and in those with RA plus one additional LTC. Persons with RA without LTCs were the reference group. Analyses were adjusted for demographic characteristics, smoking, BMI, alcohol consumption and physical activity. Results: A total of 2,566 (46%) participants reported ≥2 LTCs in addition to RA. This involved 1,138 distinct LTC combinations of which 86% were reported by ≤2 individuals. LCA identified 5 morbidity-classes. The distinctive condition in the class with the highest mortality was cancer (class 5; HR 2.66 95%CI (1.91-3.70)). The highest MACE (HR 2.95 95%CI (2.11-4.14)) and emergency hospitalisations (rate ratio 3.01 (2.56-3.54)) were observed in class 3 which comprised asthma, COPD & CHD. There was an increase in mortality, MACE and emergency hospital admissions within each class as the number of LTCs increased. Conclusions: The risk of adverse health outcomes in RA varied with different patterns of multimorbidity. The pattern of multimorbidity should be considered in risk assessment and formulating management plans in patients with RA

Human umbilical cord perivascular cells improve human pancreatic islet transplant function by increasing vascularization

Islet transplantation is an efficacious therapy for type 1 diabetes; however, islets from multiple donor pancreata are required, and a gradual attrition in transplant function is seen. Here, we manufactured human umbilical cord perivascular mesenchymal stromal cells (HUCPVCs) to Good Manufacturing Practice (GMP) standards. HUCPVCs showed a stable phenotype while undergoing rapid ex vivo expansion at passage 2 (p2) to passage 4 (p4) and produced proregenerative factors, strongly suppressing T cell responses in the resting state and in response to inflammation. Transplanting an islet equivalent (IEQ):HUCPVC ratio of 1:30 under the kidney capsule in diabetic NSG mice demonstrated the fastest return to normoglycemia by 3 days after transplant: Superior glycemic control was seen at both early (2.7 weeks) and later stages (7, 12, and 16 weeks) versus ratios of 1:0, 1:10, and 1:50, respectively. Syngeneic islet transplantation in immunocompetent mice using the clinically relevant hepatic portal route with a marginal islet mass showed that mice transplanted with an IEQ:HUCPVC ratio of 1:150 had superior glycemic control versus ratios of 1:0, 1:90, and 1:210 up to 6 weeks after transplant. Immunodeficient mice transplanted with human islets (IEQ:HUCPVC ratio of 1:150) exhibited better glycemic control for 7 weeks after transplant versus islet transplant alone, and islets transplanted via the hepatic portal vein in an allogeneic mouse model using a curative islet mass demonstrated delayed rejection of islets when cotransplanted with HUCPVCs (IEQ:HUCPVC ratio of 1:150). The immunosuppressive and proregenerative properties of HUCPVCs demonstrated long-term positive effects on graft function in vivo, indicating that they may improve long-term human islet allotransplantation outcomes

Association between risk, duration and cause of hospitalisations in people with rheumatoid arthritis and multimorbidity in the UK Biobank and Scottish Early Rheumatoid Arthritis (SERA) cohorts: longitudinal observational study

Objectives: To investigate association between presence of multimorbidity in people with established and early rheumatoid arthritis (RA) and risk, duration and cause of hospitalisations. Design: Longitudinal observational study. Setting: UK Biobank, population-based cohort recruited between 2006 and 2010, and the Scottish Early Rheumatoid Arthritis (SERA), inception cohort recruited between 2011 and 2015. Both linked to mortality and hospitalisation data. Participants: 4757 UK Biobank participants self-reporting established RA; 825 SERA participants with early RA meeting the 2010 ACR/EULAR classification criteria. Participants stratified by number of long-term conditions (LTCs) in addition to RA (RA only, RA + 1 LTC and RA + ≥ 2 LTCs) and matched to five non-RA controls. Main outcome measures: Number and duration of hospitalisations and their causes. Incidence rate ratios (IRR) and 95% confidence intervals (CI) calculated using negative binomial regression models. Results: Participants with RA + ≥ 2 LTCs experienced higher hospitalisation rates compared to those with RA alone (UK Biobank: IRR 2.10, 95% CI 1.91 to 2.30; SERA: IRR 1.74, 95% CI 1.23 to 2.48). Total duration of hospitalisation in RA + ≥ 2 LTCs was also higher (UK Biobank: IRR 2.48, 95% CI 2.17 to 2.84; SERA: IRR 1.90, 95% CI 1.07 to 3.38) than with RA alone. Rate and total duration of hospitalisations was higher in UK Biobank RA participants than non-RA controls with equivalent number of LTCs. Hospitalisations for respiratory infection were higher in early RA than established RA and were the commonest cause of hospital admission in early RA. Conclusions: Participants with established or early RA with multimorbidity experienced a higher rate and duration of hospitalisations than those with RA alone and with non-RA matched controls

A novel metabolomic approach used for the comparison of Staphylococcus aureus planktonic cells and biofilm samples

Introduction: Bacterial cell characteristics change significantly during differentiation between planktonic and biofilm states. While established methods exist to detect and identify transcriptional and proteomic changes, metabolic fluctuations that distinguish these developmental stages have been less amenable to investigation. Objectives: The objectives of the study were to develop a robust reproducible sample preparation methodology for high throughput biofilm analysis and to determine differences between Staphylococcus aureus in planktonic and biofilm states. Methods: The method uses bead beating in a chloroform/methanol/water extraction solvent to both disrupt cells and quench metabolism. Verification of the method was performed using liquid-chromatography-mass spectrometry. Raw mass-spectrometry data was analysed using an in-house bioinformatics pipe-line incorporating XCMS, MzMatch and in-house R-scripts, with identifications matched to internal standards and metabolite data-base entries. Results: We have demonstrated a novel mechanical bead beating method that has been optimised for the extraction of the metabolome from cells of a clinical Staphylococcus aureus strain existing in a planktonic or biofilm state. This high-throughput method is fast and reproducible, allowing for direct comparison between different bacterial growth states. Significant changes in arginine biosynthesis were identified between the two cell populations. Conclusions: The method described herein represents a valuable tool in studying microbial biochemistry at a molecular level. While the methodology is generally applicable to the lysis and extraction of metabolites from Gram positive bacteria, it is particularly applicable to biofilms. Bacteria that exist as a biofilm are shown to be highly distinct metabolically from their ‘free living’ counterparts, thus highlighting the need to study microbes in different growth states. Metabolomics can successfully distinguish between a planktonic and biofilm growth state. Importantly, this study design, incorporating metabolomics, could be optimised for studying the effects of antimicrobials and drug modes of action, potentially providing explanations and mechanisms of antibiotic resistance and to help devise new antimicrobials

Comparison of mesospheric and lower thermospheric residual wind with High Resolution Doppler Imager, medium frequency, and meteor radar winds

The objective of this study is to compare observed mean meridional winds with those deduced from theory. The diabatic circulation is computed from High Resolution Dopper Imager (HRDI) mesospheric and lower thermospheric temperatures during January and July conditions. The meridional wind component is compared with HRDI Eulerian mean meridional winds near 95 km and with seasonal averages of meridional winds at a number of radar medium-frequency (MF) and meteor wind (MW) sites. The diabatic wind is directed from the summer toward the winter hemisphere. Peak values exceed 20 m s−1 and are observed at 105 km near 20° in the summer hemisphere. A secondary maximum of about 10 m s−1 is observed in the wintertime lower mesosphere during the July case. The diabatic wind is qualitatively consistent with HRDI 95-km mean meridional winds at latitudes equatorward of 50°. Time-averaged summertime radar winds are consistent with HRDI and diabatic winds between 50°S and 20°N. At winter midlatitudes, MF radar winds are directed oppositely to the diabatic wind, while one available MW measurement is directed with the diabatic wind. The zonal acceleration implied by the diabatic wind is about 150–200 m s−1 d−1 in the midlatitude summer lower thermosphere.R. S. Lieberman, A. K. Smith, S. J. Franke, R. A. Vincent, J. R. Isler, A. H. Manson, C. E. Meek, G. J. Fraser, A. Fahrutdinova, T. Thayaparan, W. Hocking, J. MacDougall, T. Nakamura, and T. Tsud

A primary electron beam facility at CERN -- eSPS Conceptual design report

The design of a primary electron beam facility at CERN is described. The study has been carried out within the framework of the wider Physics Beyond Colliders study. It re-enables the Super Proton Synchrotron (SPS) as an electron accelerator, and leverages the development invested in Compact Linear Collider (CLIC) technology for its injector and as an accelerator research and development infrastructure. The facility would be relevant for several of the key priorities in the 2020 update of the European Strategy for Particle Physics, such as an electron-positron Higgs factory, accelerator R\&D, dark sector physics, and neutrino physics. In addition, it could serve experiments in nuclear physics. The electron beam delivered by this facility would provide access to light dark matter production significantly beyond the targets predicted by a thermal dark matter origin, and for natures of dark matter particles that are not accessible by direct detection experiments. It would also enable electro-nuclear measurements crucial for precise modelling the energy dependence of neutrino-nucleus interactions, which is needed to precisely measure neutrino oscillations as a function of energy. The implementation of the facility is the natural next step in the development of X-band high-gradient acceleration technology, a key technology for compact and cost-effective electron/positron linacs. It would also become the only facility with multi-GeV drive bunches and truly independent electron witness bunches for plasma wakefield acceleration. A second phase capable to deliver positron witness bunches would make it a complete facility for plasma wakefield collider studies. [...

The mannose receptor (CD206) identifies a population of colonic macrophages in health and inflammatory bowel disease

To understand the contribution of mononuclear phagocytes (MNP), which include monocyte-derived intestinal macrophages, to the pathogenesis of inflammatory bowel disease (IBD), it is necessary to identify functionally-different MNP populations. We aimed to characterise intestinal macrophage populations in patients with IBD. We developed 12-parameter flow cytometry protocols to identify and human intestinal MNPs. We used these protocols to purify and characterize colonic macrophages from colonic tissue from patients with Crohn’s disease (CD), ulcerative colitis (UC), or non-inflamed controls, in a cross-sectional study. We identify macrophage populations (CD45+CD64+ HLA-DR+) and describe two distinct subsets, differentiated by their expression of the mannose receptor, CD206. CD206+ macrophages expressed markers consistent with a mature phenotype: high levels of CD68 and CD163, higher transcription of IL-10 and lower expression of TREM1. CD206− macrophages appear to be less mature, with features more similar to their monocytic precursors. We identified and purified macrophage populations from human colon. These appear to be derived from a monocytic precursor with high CCR2 and low CD206 expression. As these cells mature, they acquire expression of IL-10, CD206, CD63, and CD168. Targeting the newly recruited monocyte-derived cells may represent a fruitful avenue to ameliorate chronic inflammation in IBD