Coronavirus 3CL(pro )proteinase cleavage sites: Possible relevance to SARS virus pathology

BACKGROUND: Despite the passing of more than a year since the first outbreak of Severe Acute Respiratory Syndrome (SARS), efficient counter-measures are still few and many believe that reappearance of SARS, or a similar disease caused by a coronavirus, is not unlikely. For other virus families like the picornaviruses it is known that pathology is related to proteolytic cleavage of host proteins by viral proteinases. Furthermore, several studies indicate that virus proliferation can be arrested using specific proteinase inhibitors supporting the belief that proteinases are indeed important during infection. Prompted by this, we set out to analyse and predict cleavage by the coronavirus main proteinase using computational methods. RESULTS: We retrieved sequence data on seven fully sequenced coronaviruses and identified the main 3CL proteinase cleavage sites in polyproteins using alignments. A neural network was trained to recognise the cleavage sites in the genomes obtaining a sensitivity of 87.0% and a specificity of 99.0%. Several proteins known to be cleaved by other viruses were submitted to prediction as well as proteins suspected relevant in coronavirus pathology. Cleavage sites were predicted in proteins such as the cystic fibrosis transmembrane conductance regulator (CFTR), transcription factors CREB-RP and OCT-1, and components of the ubiquitin pathway. CONCLUSIONS: Our prediction method NetCorona predicts coronavirus cleavage sites with high specificity and several potential cleavage candidates were identified which might be important to elucidate coronavirus pathology. Furthermore, the method might assist in design of proteinase inhibitors for treatment of SARS and possible future diseases caused by coronaviruses. It is made available for public use at our website:

Phospho.ELM:a database of experimentally verified phosphorylation sites in eukaryotic proteins

BACKGROUND: Post-translational phosphorylation is one of the most common protein modifications. Phosphoserine, threonine and tyrosine residues play critical roles in the regulation of many cellular processes. The fast growing number of research reports on protein phosphorylation points to a general need for an accurate database dedicated to phosphorylation to provide easily retrievable information on phosphoproteins.DESCRIPTION: Phospho.ELM http://phospho.elm.eu.org is a new resource containing experimentally verified phosphorylation sites manually curated from the literature and is developed as part of the ELM (Eukaryotic Linear Motif) resource. Phospho.ELM constitutes the largest searchable collection of phosphorylation sites available to the research community. The Phospho.ELM entries store information about substrate proteins with the exact positions of residues known to be phosphorylated by cellular kinases. Additional annotation includes literature references, subcellular compartment, tissue distribution, and information about the signaling pathways involved as well as links to the molecular interaction database MINT. Phospho.ELM version 2.0 contains 1703 phosphorylation site instances for 556 phosphorylated proteins.CONCLUSION: Phospho.ELM will be a valuable tool both for molecular biologists working on protein phosphorylation sites and for bioinformaticians developing computational predictions on the specificity of phosphorylation reactions.</p

Description of call handling in emergency medical dispatch centres in Scandinavia: recognition of out-of-hospital cardiac arrests and dispatcher-assisted CPR

Background The European resuscitation council have highlighted emergency medical dispatch centres as an important key player for early recognition of Out-of-Hospital Cardiac Arrest (OHCA) and in providing dispatcher assisted cardiopulmonary resuscitation (CPR) before arrival of emergency medical services. Early recognition is associated with increased bystander CPR and improved survival rates. The aim of this study is to describe OHCA call handling in emergency medical dispatch centres in Copenhagen (Denmark), Stockholm (Sweden) and Oslo (Norway) with focus on sensitivity of recognition of OHCA, provision of dispatcher-assisted CPR and time intervals when CPR is initiated during the emergency call (NO-CPRprior), and to describe OHCA call handling when CPR is initiated prior to the emergency call (CPRprior). Methods Baseline data of consecutive OHCA eligible for inclusion starting January 1st 2016 were collected from respective cardiac arrest registries. A template based on the Cardiac Arrest Registry to Enhance Survival definition catalogue was used to extract data from respective cardiac arrest registries and from corresponding audio files from emergency medical dispatch centres. Cases were divided in two groups: NO-CPRprior and CPRprior and data collection continued until 200 cases were collected in the NO-CPRprior-group. Results NO-CPRprior OHCA was recognised in 71% of the calls in Copenhagen, 83% in Stockholm, and 96% in Oslo. Abnormal breathing was addressed in 34, 7 and 98% of cases and CPR instructions were started in 50, 60, and 80%, respectively. Median time (mm:ss) to first chest compression was 02:35 (Copenhagen), 03:50 (Stockholm) and 02:58 (Oslo). Assessment of CPR quality was performed in 80, 74, and 74% of the cases. CPRprior comprised 71 cases in Copenhagen, 9 in Stockholm, and 38 in Oslo. Dispatchers still started CPR instructions in 41, 22, and 40% of the calls, respectively and provided quality assessment in 71, 100, and 80% in these respective instances. Conclusions We observed variations in OHCA recognition in 71–96% and dispatcher assisted-CPR were provided in 50–80% in NO-CPRprior calls. In cases where CPR was initiated prior to emergency calls, dispatchers were less likely to start CPR instructions but provided quality assessments during instructions.publishedVersio

Bacterial diversity in snow on North Pole ice floes

The microbial abundance and diversity in snow on ice floes at three sites near the North Pole was assessed using quantitative PCR and 454 pyrosequencing. Abundance of 16S rRNA genes in the samples ranged between 43 and 248 gene copies per millilitre of melted snow. A total of 291,331 sequences were obtained through 454 pyrosequencing of 16S rRNA genes, resulting in 984 OTUs at 97 % identity. Two sites were dominated by Cyanobacteria (72 and 61 %, respectively), including chloroplasts. The third site differed by consisting of 95 % Proteobacteria. Principal component analysis showed that the three sites clustered together when compared to the underlying environments of sea ice and ocean water. The Shannon indices ranged from 2.226 to 3.758, and the Chao1 indices showed species richness between 293 and 353 for the three samples. The relatively low abundances and diversity found in the samples indicate a lower rate of microbial input to this snow habitat compared to snow in the proximity of terrestrial and anthropogenic sources of microorganisms. The differences in species composition and diversity between the sites show that apparently similar snow habitats contain a large variation in biodiversity, although the differences were smaller than the differences to the underlying environment. The results support the idea that a globally distributed community exists in snow and that the global snow community can in part be attributed to microbial input from the atmosphere. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00792-014-0660-y) contains supplementary material, which is available to authorized users