Comparing Bacterial Genomes by Searching Their Common Intervals

International audienceComparing bacterial genomes implies the use of a dedicated measure. It relies on comparing circular genomes based on a set of conserved genes. Following this assumption, the common interval appears to be a good candidate. For evidences, we propose herein an approach to compute the common intervals between two circular genomes that takes into account duplications. Its application on a concrete case, comparing E. coli and V. cholerae, is accurate. It indeed emphasizes sets of conserved genes that present high impacts on bacterial functions

Ultrastructural Imaging of Activity-Dependent Synaptic Membrane-Trafficking Events in Cultured Brain Slices

Electron microscopy can resolve synapse ultrastructure with nanometer precision, but the capture of time-resolved, activity-dependent synaptic membrane-trafficking events has remained challenging, particularly in functionally distinct synapses in a tissue context. We present a method that combines optogenetic stimulation-coupled cryofixation (“flash-and-freeze”) and electron microscopy to visualize membrane trafficking events and synapse-state-specific changes in presynaptic vesicle organization with high spatiotemporal resolution in synapses of cultured mouse brain tissue. With our experimental workflow, electrophysiological and “flash-and-freeze” electron microscopy experiments can be performed under identical conditions in artificial cerebrospinal fluid alone, without the addition of external cryoprotectants, which are otherwise needed to allow adequate tissue preservation upon freezing. Using this approach, we reveal depletion of docked vesicles and resolve compensatory membrane recycling events at individual presynaptic active zones at hippocampal mossy fiber synapses upon sustained stimulation

Idiopathic pulmonary fibrosis Significance of the usual interstitial pneumonia (UIP) CT-scan patterns defined in new international guidelines

International audienceIntroduction The new 2018 international guidelines for diagnosing usual interstitial pneumonia (UIP)/idiopathic pulmonary fibrosis (IPF) by CT scan split the old pattern possible UIP (2011 IPF guidelines) into two new patterns probable UIP and indeterminate for UIP. However, the proportions and prognoses of these new CT-scan patterns are not clear.Methods We used a monocentric retrospective cohort of 322 patients suspected of having IPF (University Hospital of Rennes; Competence Center for Rare Lung Diseases; 1 January 2012-31 December 2017). All patients initially diagnosed by CT scan as possible UIP were included. The chest CT-scans were then reclassified according to the new 2018 international guidelines by 3 observers. These data were then subjected to survival analysis with multivariate Cox regression using a composite endpoint of death, lung transplantation, a decline of ≥ 10% in forced vital capacity (FVC), or hospitalization.Results Of the 89 possible UIP patients included, 74 (83%) were reclassified as probable UIP and 15 (17%) as indeterminate for UIP. Probable UIP patients were more likely to meet the composite endpoint (56/74 [75.7%] vs. 5/15 [33%] patients; HR [IC 95%] = 3.12 [1.24; 7.83], P = 0.015). Multivariate analysis indicated that the probable UIP pattern was associated with significantly increased risk of reaching the composite endpoint (HR [95% CI] = 2.85[1.00; 8.10], P = 0.049).Conclusion The majority of possible UIP diagnoses corresponded to probable UIP, which was associated with a significantly worse prognosis than indeterminate for UIP. This distinction between these two CT patterns emphasizes the relevance of the new international guidelines for the diagnosis of IPF. © 2020 SPLF and Elsevier Masson SA