CRISPR antiphage defence mediated by the cyclic nucleotide-binding membrane protein Csx23

Biotechnology and Biological Sciences Research Council [BB/T004789/1 to M.F.W., T.M.G.]; European Research Council Advanced Grant [101018608 to M.F.W.]; Engineering and Physical Sciences Research Council [EP/X016455/1 to K.A., B.E.B., M.F.W.]; BBSRC equipment grants [BB/R013780/1, BB/T017740/1 to B.E.B.]. Funding for open access charge: University of St Andrews block grant.CRISPR-Cas provides adaptive immunity in prokaryotes. Type III CRISPR systems detect invading RNA and activate the catalytic Cas10 subunit, which generates a range of nucleotide second messengers to signal infection. These molecules bind and activate a diverse range of effector proteins that provide immunity by degrading viral components and/or by disturbing key aspects of cellular metabolism to slow down viral replication. Here, we focus on the uncharacterised effector Csx23, which is widespread in Vibrio cholerae. Csx23 provides immunity against plasmids and phage when expressed in Escherichia coli along with its cognate type III CRISPR system. The Csx23 protein localises in the membrane using an N-terminal transmembrane α-helical domain and has a cytoplasmic C-terminal domain that binds cyclic tetra-adenylate (cA4), activating its defence function. Structural studies reveal a tetrameric structure with a novel fold that binds cA4 specifically. Using pulse EPR, we demonstrate that cA4 binding to the cytoplasmic domain of Csx23 results in a major perturbation of the transmembrane domain, consistent with the opening of a pore and/or disruption of membrane integrity. This work reveals a new class of cyclic nucleotide binding protein and provides key mechanistic detail on a membrane-associated CRISPR effector.Many anti-viral defence systems generate a cyclic nucleotide signal that activates cellular defences in response to infection. Type III CRISPR systems use a specialised polymerase to make cyclic oligoadenylate (cOA) molecules from ATP. These can bind and activate a range of effector proteins that slow down viral replication. In this study, we focussed on the Csx23 effector from the human pathogen Vibrio cholerae – a trans-membrane protein that binds a cOA molecule, leading to anti-viral immunity. Structural studies revealed a new class of nucleotide recognition domain, where cOA binding is transmitted to changes in the trans-membrane domain, most likely resulting in membrane depolarisation. This study highlights the diversity of mechanisms for anti-viral defence via nucleotide signalling.Peer reviewe

Development of machine learning models to predict cancer-related fatigue in Dutch breast cancer survivors up to 15 years after diagnosis

Purpose: To prevent (chronic) cancer-related fatigue (CRF) after breast cancer, it is important to identify survivors at risk on time. In literature, factors related to CRF are identified, but not often linked to individual risks. Therefore, our aim was to predict individual risks for developing CRF.Methods: Two pre-existing datasets were used. The Nivel-Primary Care Database and the Netherlands Cancer Registry (NCR) formed the Primary Secondary Cancer Care Registry (PSCCR). NCR data with Patient Reported Outcomes Following Initial treatment and Long-term Evaluation of Survivorship (PROFILES) data resulted in the PSCCR-PROFILES dataset. Predictors were patient, tumor and treatment characteristics, and pre-diagnosis health. Fatigue was GP-reported (PSCCR) or patient-reported (PSCCR-PROFILES). Machine learning models were developed, and performances compared using the C-statistic.Results: In PSCCR, 2224/12813 (17%) experienced fatigue up to 7.6 ± 4.4 years after diagnosis. In PSCCR-PROFILES, 254 (65%) of 390 patients reported fatigue 3.4 ± 1.4 years after diagnosis. For both, models predicted fatigue poorly with best C-statistics of 0.561 ± 0.006 (PSCCR) and 0.669 ± 0.040 (PSCCR-PROFILES).Conclusion: Fatigue (GP-reported or patient-reported) could not be predicted accurately using available data of the PSCCR and PSCCR-PROFILES datasets.Implications for Cancer Survivors: CRF is a common but underreported problem after breast cancer. We aimed to develop a model that could identify individuals with a high risk of developing CRF, ideally to help them prevent (chronic) CRF. As our models had poor predictive abilities, they cannot be used for this purpose yet. Adding patient-reported data as predictor could lead to improved results. Until then, awareness for CRF stays crucial

Gegenüberstellung der Simulationsfunktionalitäten von Werkzeugen zur Geschäftsprozessmodellierung

Geschäftsprozesse beschreiben, über die Darstellung von Aktivitäten respektive Vorgängen, die Abläufe der Leistungserstellung in einer Unternehmung. Ziel bei der Planung ist es, die Prozesse so effizient und effektiv wie möglich zu gestalten, um mit möglichst wenig eingesetzten Ressourcen ein vordefiniertes Ziel zu erreichen. Effizienz und Effektivität der Prozesse sind dabei entscheidende Faktoren für die Wettbewerbsposition einer Unternehmung, da die realen Kosten der Leistungserstellung aus den Abläufen, die wiederum Ressourcen beanspruchen, resultieren. Um Geschäftsprozesse zu optimieren, können mathematisch - analytische Verfahren angewandt werden. Diese mathematischen Verfahren erlauben es, Geschäftsprozesse und -ketten als geschlossene Ausdrücke zu formulieren und optimal zu lösen. Die analytischen Verfahren scheitern allerdings, sobald die Geschäftsprozesse eine gewisse Komplexität aufweisen. Gemeint sind hochflexible Geschäftsprozesse, die sich dadurch auszeichnen, dass sie entweder nicht vollständig planbar sind, da prozessrelevante Bezugsgrößen unbekannt oder variabel sind, oder diese nicht losgelöst vom Anwendungskontext betrachtet werden können. Zusätzlich komplexitätssteigernd wirkt sich eine zeitliche Überlappung zwischen Planung und Ausführung des Prozesses aus. Um diese komplexen Geschäftsprozesse nachvollziehen und untersuchen zu können und somit einen Ansatz für die Optimierung zu schaffen, bietet sich hier eine Simulation dieser Prozesse an. Ein Simulationsmodell besteht aus einer möglichst realitätsnahen Nachbildung eines Ablaufs in einem Modell und dient der Entscheidungsunterstützung

Limit on the Radiative Neutrinoless Double Electron Capture of 36^{36}Ar from GERDA Phase I

Neutrinoless double electron capture is a process that, if detected, would give evidence of lepton number violation and the Majorana nature of neutrinos. A search for neutrinoless double electron capture of $^{36}$Ar has been performed with germanium detectors installed in liquid argon using data from Phase I of the GERmanium Detector Array (GERDA) experiment at the Gran Sasso Laboratory of INFN, Italy. No signal was observed and an experimental lower limit on the half-life of the radiative neutrinoless double electron capture of $^{36}$Ar was established: $T_{1/2} >$ 3.6 $\times$ 10$^{21}$ yr at 90 % C.I.Comment: 7 pages, 3 figure

The diagnosis and management of patients with idiopathic osteolysis

Idiopathic osteolysis or disappearing bone disease is a condition characterized by the spontaneous onset of rapid destruction and resorption of a single bone or multiple bones. Disappearing bone disorder is a disease of several diagnostic types. We are presenting three patients with osteolysis who have different underlying pathological features. Detailed phenotypic assessment, radiologic and CT scanning, and histological and genetic testing were the baseline diagnostic tools utilized for diagnosis of each osteolysis syndrome. The first patient was found to have Gorham-Stout syndrome (non-heritable). The complete destruction of pelvic bones associated with aggressive upward extension to adjacent bones (vertebral column and skull base) was notable and skeletal angiomatosis was detected. The second patient showed severe and aggressive non-hereditary multicentric osteolysis with bilateral destruction of the hip bones and the tarsal bones as well as a congenital unilateral solitary kidney and nephropathy. The third patient was phenotypically and genotypically compatible with Winchester syndrome resulting in multicentric osteolysis (autosomal recessive). Proven mutation of the (MMP2-Gen) was detected in this third patient that was associated with 3MCC deficiency (3-Methylcrontonyl CoA Carboxylase deficiency). The correct diagnoses in our 3 patients required the exclusion of malignant osteoclastic tumours, inflammatory disorders of bone, vascular disease, and neurogenic arthropathies using history, physical exam, and appropriate testing and imaging. This review demonstrates how to evaluate and treat these complex and difficult patients. Lastly, we described the various management procedures and treatments utilized for these patients

Flux Modulations seen by the Muon Veto of the GERDA Experiment

The GERDA experiment at LNGS of INFN is equipped with an active muon veto. The main part of the system is a water Cherenkov veto with 66~PMTs in the water tank surrounding the GERDA cryostat. The muon flux recorded by this veto shows a seasonal modulation. Two effects have been identified which are caused by secondary muons from the CNGS neutrino beam (2.2 %) and a temperature modulation of the atmosphere (1.4 %). A mean cosmic muon rate of $I^0_{\mu} = (3.477 \pm 0.002_{\textrm{stat}} \pm 0.067_{\textrm{sys}}) \times 10^{-4}$/(s$\cdot$m$^2$) was found in good agreement with other experiments at LNGS at a depth of 3500~meter water equivalent.Comment: 7 pages, 6 figure

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

ReSurveyGermany: Vegetation-plot time-series over the past hundred years in Germany

Vegetation-plot resurvey data are a main source of information on terrestrial biodiversity change, with records reaching back more than one century. Although more and more data from re-sampled plots have been published, there is not yet a comprehensive open-access dataset available for analysis. Here, we compiled and harmonised vegetation-plot resurvey data from Germany covering almost 100 years. We show the distribution of the plot data in space, time and across habitat types of the European Nature Information System (EUNIS). In addition, we include metadata on geographic location, plot size and vegetation structure. The data allow temporal biodiversity change to be assessed at the community scale, reaching back further into the past than most comparable data yet available. They also enable tracking changes in the incidence and distribution of individual species across Germany. In summary, the data come at a level of detail that holds promise for broadening our understanding of the mechanisms and drivers behind plant diversity change over the last century