Selecting particles from digital micrographs is an essential step in single-particle electron cryomicroscopy (cryo-EM). As manual selection of complete datasets—typically comprising thousands of particles—is a tedious and time-consuming process, numerous automatic particle pickers have been developed. However, non-ideal datasets pose a challenge to particle picking. Here we present the particle picking software crYOLO which is based on the deep-learning object detection system You Only Look Once (YOLO). After training the network with 200–2500 particles per dataset it automatically recognizes particles with high recall and precision while reaching a speed of up to five micrographs per second. Further, we present a general crYOLO network able to pick from previously unseen datasets, allowing for completely automated on-the-fly cryo-EM data preprocessing during data acquisition. crYOLO is available as a standalone program under http://sphire.mpg.de/ and is distributed as part of the image processing workflow in SPHIRE.

Selecting particles from digital micrographs is an essential step in single particle electron cryomicroscopy (cryo-EM). Since manual selection of complete datasets typically comprising many thousands of particles is a tedious and time-consuming process, many automatic particle pickers have been developed in the past few decades.However, non-ideal datasets pose a challenge to particle picking. Here, we present a novel automated particle picking software called crYOLO, which is based on the deep learning object detection system "You Only Look Once" (YOLO). After training the network with 500 -2,500 particles per dataset, it automatically recognizes particles with high recall and precision reaching a speed of up to five micrographs per second.Importantly, we demonstrate a powerful general network trained on more than 40 datasets to select previously unseen datasets, thus paving the way for completely automated "on-the-fly" cryo-EM data pre-processing during data acquisition. CrYOLO is available as a standalone program under http://sphire.mpg.de/ and will be part of the image processing workflow in SPHIRE.

The obligatory intracellular bacterium Chlamydophila psittaci is the causative agent of psittacosis in birds and humans. The capability of this zoonotic pathogen to develop a persistent phase is likely to play a role in chronicity of infections, as well as in failure of antibiotic therapy and immunoprophylaxis. To elucidate three different in vitro models for transition of C. psittaci to persistence (iron depletion, penicillin G treatment, and gamma interferon [IFN-␥] exposure), a set of 27 genes was examined by mRNA expression analysis using quantitative real-time PCR. While the phenotypical characteristics were the same as in other chlamydiae, i.e., aberrant morphology of reticulate bodies, loss of cultivability, and rescue of infectivity upon removal of inducers, the transcriptional response of C. psittaci to persistence-inducing factors included several new and distinctive features. Consistent downregulation of membrane proteins, chlamydial sigma factors, cell division protein, and reticulate body-elementary body differentiation proteins from 24 h postinfection onward proved to be a general feature of C. psittaci persistence. However, other genes displayed considerable variations in response patterns from one model to another, which suggests that there is no persistence model per se. In contrast to results for Chlamydia trachomatis, late shutdown of essential genes in C. psittaci was more comprehensive with IFN-␥-induced persistence, which is probably due to the absence of a functional tryptophan synthesis operon.

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In 2005, an outbreak of severe respiratory disease in a mixed poultry flock that was infected with Chlamydophila (C.) psittaci led to dissemination of the infection to at least 100 small poultry farms in 11 districts of Central Germany. At the same time, a total of 24 persons in contact with poultry from one of the flocks reported flu-like symptoms to their physician, thus suggesting zoonotic transmission. Within 3 weeks, seven individuals had to be hospitalized, with three of them requiring intensive care. Analysis of ompA sequences from chlamydial isolates and directly from clinical samples revealed the presence of both genotype A and E/B of C. psittaci at the source of the outbreak and in contact flocks. Genotype A was also detected in the three severely ill patients. The findings of the present study demonstrate the high zoonotic potential of avian chlamydiae. To ensure speedy eradication of psittacosis in poultry flocks and effective treatment of infected humans, fast, sensitive and species-specific detection of the causative agent is essential, as well as close collaboration between regional public health services, attending physicians and the diagnostic laboratories involved.