Expert web

By placing a component of the marine environment under controlled conditions, mesocosms provide important links between field studies and laboratory experiments. Project Leader Dr Paolo Simonelli and scientific site coordinators Drs Elin Lindehoff, Jamileh Javidpour, Romain Pete, Stella Berger and Tatiana Tsagaraki explain how they are opening up access to these unique resources for European scientist

Colibactin DNA-damage signature indicates mutational impact in colorectal cancer

The mucosal epithelium is a common target of damage by chronic bacterial infections and the accompanying toxins, and most cancers originate from this tissue. We investigated whether colibactin, a potent genotoxin(1) associated with certain strains of Escherichia coli(2), creates a specific DNA-damage signature in infected human colorectal cells. Notably, the genomic contexts of colibactin-induced DNA double-strand breaks were enriched for an AT-rich hexameric sequence motif, associated with distinct DNA-shape characteristics. A survey of somatic mutations at colibactin target sites of several thousand cancer genomes revealed notable enrichment of this motif in colorectal cancers. Moreover, the exact double-strand-break loci corresponded with mutational hot spots in cancer genomes, reminiscent of a trinucleotide signature previously identified in healthy colorectal epithelial cells(3). The present study provides evidence for the etiological role of colibactin in human cancer. Identification of a DNA-damage signature induced by colibactin, a toxin expressed by some strains of Escherichia coli, is enriched in human colorectal cancers.Peer reviewe

Rapid Flow-Based Peptide Synthesis

A flow-based solid-phase peptide synthesis methodology that enables the incorporation of an amino acid residue every 1.8 min under automatic control or every 3 min under manual control is described. This is accomplished by passing a stream of reagent through a heat exchanger into a low volume, low backpressure reaction vessel, and through a UV detector. These features enable continuous delivery of heated solvents and reagents to the solid support at high flow rate, thereby maintaining maximal concentration of reagents in the reaction vessel, quickly exchanging reagents, and eliminating the need to rapidly heat reagents after they have been added to the vessel. The UV detector enables continuous monitoring of the process. To demonstrate the broad applicability and reliability of this method, it was employed in the total synthesis of a small protein, as well as dozens of peptides. The quality of the material obtained with this method is comparable to that for traditional batch methods, and, in all cases, the desired material was readily purifiable by RP-HPLC. The application of this method to the synthesis of the 113-residue Bacillus amyloliquefaciens RNase and the 130-residue DARPin pE59 is described in the accompanying manuscript.MIT Faculty Start-up FundMassachusetts Institute of Technology (Charles E. Reed Faculty Initiative Fund)Deshpande Center for Technological InnovationDamon Runyon-Rachleff (Innovation Award)Sontag Foundation (Distinguished Scientist Award)C. P. Chu and Y. Lai FellowshipDaniel S. Kemp Summer FellowshipNational Institute of General Medical Sciences (U.S.). Biotechnology Training Program (Grant 5T32GM008334-25)National Institutes of Health (U.S.) (Fellowship F32GM101762

Plasma chitotriosidase activity versus CCL18 level for assessing type I Gaucher disease severity: protocol for a systematic review with meta-analysis of individual participant data.

BACKGROUND: Gaucher disease (GD) is an autosomal recessive lysosomal storage disorder caused by deficiency in acid beta-glucosidase. GD exhibits a wide clinical spectrum of disease severity with an unpredictable natural course. Plasma chitotriosidase activity and CC chemokine ligand 18 (CCL18) have been exchangeably used for monitoring GD activity and response to enzyme replacement therapy in conjunction with clinical assessment. Yet, a large-scale head-to-head comparison of these two biomarkers is currently lacking. We propose a collaborative systematic review with meta-analysis of individual participant data (IPD) to compare the accuracy of plasma chitotriosidase activity and CCL18 in assessing type I (i.e., non-neuropathic) GD severity. METHODS: Eligible studies include cross-sectional, cohort, and randomized controlled studies recording both plasma chitotriosidase activity and CCL18 level at baseline and/or at follow-up in consecutive children or adult patients with type I GD. Pre-specified surrogate outcomes reflecting GD activity include liver and spleen volume, hemoglobin concentration, platelet count, and symptomatic bone events with imaging confirmation. Primary studies will be identified by searching Medline (1995 onwards), EMBASE (1995 onwards), and Cochrane Central Register of Controlled Trials (CENTRAL). Electronic search will be complemented by contacting research groups in order to identify unpublished relevant studies. Where possible, IPD will be extracted from published articles. Corresponding authors will be invited to collaborate by supplying IPD. The methodological quality of retrieved studies will be appraised for each study outcome, using a checklist adapted from the Quality Assessment of Diagnostic Accuracy Studies-2 tool. The primary outcome will be a composite of liver volume >1.25 multiple of normal (MN), spleen volume >5 MN, hemoglobin concentration <11 g/dL, or platelet count <100 × 109/L. Effect size estimates for biomarker comparative accuracy in predicting outcomes will be reported as differences in areas under receiver operating characteristic curves along with 95% confidence intervals. Effect size estimates will be reported as (weighted) mean differences along with 95% confidence intervals for each biomarker according to outcomes. IPD meta-analysis will be conducted with both one- and two-stage approaches. DISCUSSION: Valid and precise accuracy estimates will be derived for CCL18 relative to plasma chitotriosidase activity in discriminating patients according to GD severity. SYSTEMATIC REVIEW REGISTRATION: PROSPERO 2015 CRD42015027243

How to Keep it Adequate: A Validation Protocol for Agent-Based Simulation

Agent-based models are used in a huge diversity of contexts, which complicates the establishment of a shared understanding of model validity and adequate methods for model construction, inference and validation. Starting from the tenet that model validity can only be judged with respect to a well-defined purpose and context, we conceptualise validation as systematically substantiating the premises on which conclusions from simulation analysis for a specific context are built. We revisit the premises of empirical and structural validation and argue that validation should not be understood as an isolated step in the modelling process. Rather, sound conclusions from simulation analysis require context-adequate choices at all steps of simulation analysis. To facilitate communication, we develop a protocol of guiding questions to analyse the modelling context, choose appropriate methods at each step, document the premises involved in a specific simulation analysis, and demonstrate the adequacy of the model for its context

Severe cutaneous reactions to drugs in the setting of a general hospital

Abstract: BACKGROUND: Cutaneous drug reactions are frequently found. Assessing the clinical and epidemiological profile of severe forms is extremely relevant for their better recognition and management. Few studies have assessed the severe forms of cutaneous drug reactions in patients hospitalized in our setting. OBJECTIVES: To assess the clinical and epidemiological aspects of severe cutaneous adverse reactions to drugs in a tertiary hospital in Porto Alegre, Brazil. METHODS: All cases of severe cutaneous adverse reactions to drugs in patients hospitalized from January/2005 to December/2010 were retrospectively analyzed for clinical and epidemiological variables. Cases of Stevens- Johnson Syndrome, Toxic Epidermal Necrolysis, drug hypersensitivity syndrome or Drug Reaction with Eosinophilia and Systemic Symptoms and acute generalized exanthematous pustulosis were included. RESULTS: An occurrence rate of 1 serious reaction for every 3,048 inpatients was found (total of 173,767 inpatients admitted in the period). Drug Reaction with Eosinophilia and Systemic Symptoms was the most frequent presentation. The drugs most frequently involved were anticonvulsants (40.4%), antibiotics (26.3%), and analgesics/anti-inflammatory drugs (10.5%). Thirty seven patients (64.9%) were admitted to hospital because of the cutaneous drug reaction. Ten patients (17.5%) died and in most of those (60%), the drug causing the reaction could not be determined. CONCLUSIONS: The frequency of severe cutaneous adverse reactions to drugs in our setting is significant. Drug Reaction with Eosinophilia and Systemic Symptoms seems to be the most frequent presentation of severe cutaneous drug reactions. Most patients developed cutaneous drug reactions outside the hospital. Mortality rates were higher for Toxic Epidermal Necrolysis and this presentation significantly affected older people. Not knowing the drug causing the reaction was related to mortality