Systematic loss-of-function screens identify pathway-specific functional circular RNAs.

Circular RNA (circRNA) is covalently closed, single-stranded RNA produced by back-splicing. A few circRNAs have been implicated as functional; however, we lack understanding of pathways that are regulated by circRNAs. Here we generated a pooled short-hairpin RNA library targeting the back-splice junction of 3,354 human circRNAs that are expressed at different levels (ranging from low to high) in humans.

Pathogenomic analysis and characterization of strains recovered from human infections.

is an upper respiratory tract commensal in several mammal and bird species but can also cause severe disease in humans and in production animals such as poultry, cattle, and pigs. In this study, we performed whole-genome sequencing of isolates recovered from a range of human infections, from the mouths of cats, and from wounds on dogs. Together with publicly available genome sequences, we performed phylogenetic and comparative genomic analyses.

The evolutionary mechanism of non-carbapenemase carbapenem-resistant phenotypes in spp.

Antibiotic resistance is driven by selection, but the degree to which a bacterial strain's evolutionary history shapes the mechanism and strength of resistance remains an open question. Here, we reconstruct the genetic and evolutionary mechanisms of carbapenem resistance in a clinical isolate of . A combination of short- and long-read sequencing, machine learning, and genetic and enzymatic analyses established that this carbapenem-resistant strain carries no carbapenemase-encoding genes.

CRISPR screens identify gene targets at breast cancer risk loci.

Background: Genome-wide association studies (GWAS) have identified > 200 loci associated with breast cancer risk. The majority of candidate causal variants are in non-coding regions and likely modulate cancer risk by regulating gene expression. However, pinpointing the exact target of the association, and identifying the phenotype it mediates, is a major challenge in the interpretation and translation of GWAS.

A Structurally Characterized Evolutionary Escape Route from Treatment with the Antibiotic Linezolid.

Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen that presents great health concerns. Treatment requires the use of last-line antibiotics, such as members of the oxazolidinone family, of which linezolid is the first member to see regular use in the clinic. Here, we report a short time scale selection experiment in which strains of MRSA were subjected to linezolid treatment.

Forensic genomics of a novel type from a neonatal intensive care unit in China reveals patterns of colonization, evolution and epidemiology.

During March 2017, a neonatal patient with severe diarrhoea subsequently developed septicaemia and died, with isolated as the causative microorganism. In keeping with infection control protocols, the coincident illness of an attending staff member and three other neonates with infection triggered an outbreak response, leading to microbiological assessment of isolates collected from the staff member and all 21 co-housed neonates. Multilocus sequence typing and genomic sequencing identified that the isolates from the 21 neonates were of a new sequence type, ST2727, and taxonomically belonged to subsp.

First description of antimicrobial resistance in carbapenem-susceptible Klebsiella pneumoniae after imipenem treatment, driven by outer membrane remodeling.

Background: The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a looming threat to human health. Although there are numerous studies regarding porin alteration in association with the production of ESBLs and/or AmpC β-lactamase, a systematic study on the treatment-emergence of porins alteration in antibiotic resistance does not yet exist. The aim of this study was to investigate the underlying mechanism of resistance of K.

A genome-wide scan for correlated mutations detects macromolecular and chromatin interactions in Arabidopsis thaliana.

The concept of exploiting correlated mutations has been introduced and applied successfully to identify interactions within and between biological macromolecules. Its rationale lies in the preservation of physical interactions via compensatory mutations. With the massive increase of available sequence information, approaches based on correlated mutations have regained considerable attention.

A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes.

Background: Cassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding program represents a significant challenge. A reference genome sequence for cassava has been made recently available and community efforts are underway for improving its quality.