Lineage calling can identify antibiotic resistant clones within minutes, bioRxiv, 2018-08-29
Introductory ParagraphSurveillance of circulating drug resistant bacteria is essential for healthcare providers to deliver effective empiric antibiotic therapy. However, the results of surveillance may not be available on a timescale that is optimal for guiding patient treatment. Here we present a method for inferring characteristics of an unknown bacterial sample by identifying the presence of sequence variation across the genome that is linked to a phenotype of interest, in this case drug resistance. We demonstrate an implementation of this principle using sequence k-mer content, matched to a database of known genomes. We show this technique can be applied to data from an Oxford Nanopore device in real time and is capable of identifying the presence of a known resistant strain in 5 minutes, even from a complex metagenomic sample. This flexible approach has wide application to pathogen surveillance and may be used to greatly accelerate diagnoses of resistant infections.
biorxiv bioinformatics 200-500-users 2018Rapid heuristic inference of antibiotic resistance and susceptibility by genomic neighbor typing, bioRxiv, 2018-08-29
AbstractSurveillance of drug-resistant bacteria is essential for healthcare providers to deliver effective empiric antibiotic therapy. However, traditional molecular epidemiology does not typically occur on a timescale that could impact patient treatment and outcomes. Here we present a method called ‘genomic neighbor typing’ for inferring the phenotype of a bacterial sample by identifying its closest relatives in a database of genomes with metadata. We show that this technique can infer antibiotic susceptibility and resistance for both S. pneumoniae and N. gonorrhoeae. We implemented this with rapid k-mer matching, which, when used on Oxford Nanopore MinION data, can run in real time. This resulted in determination of resistance within ten minutes (sensspec 91%100% for S. pneumoniae and 81%100% N. gonorrhoeae from isolates with a representative database) of sequencing starting, and for clinical metagenomic sputum samples (75%100% for S. pneumoniae), within four hours of sample collection. This flexible approach has wide application to pathogen surveillance and may be used to greatly accelerate appropriate empirical antibiotic treatment.
biorxiv bioinformatics 200-500-users 2018SABER enables highly multiplexed and amplified detection of DNA and RNA in cells and tissues, bioRxiv, 2018-08-28
SUMMARYFluorescent in situ hybridization (FISH) reveals the abun-dance and positioning of nucleic acid sequences in fixed sam-ples and can be combined with cell segmentation to produce a powerful single cell gene expression assay. However, it re-mains difficult to label more than a few targets and to visu-alize nucleic acids in environments such as thick tissue sam-ples using conventional FISH technologies. Recently, meth-ods have been developed for multiplexed amplification of FISH signals, yet it remains challenging to achieve high lev-els of simultaneous multiplexing combined with high sam-pling efficiency and simple workflows. Here, we introduce signal amplification by exchange reaction (SABER), which endows oligo-based FISH probes with long, single-stranded DNA concatemers that serve as targets for sensitive fluores-cent detection. We establish that SABER effectively ampli-fies the signal of probes targeting nucleic acids in fixed cells and tissues, can be deployed against at least 17 targets si-multaneously, and detects mRNAs with high efficiency. As a demonstration of the utility of SABER in assays involv-ing genetic manipulations, we apply multiplexed FISH of reporters and cell type markers to the identification of en-hancers with cell type-specific activity in the mouse retina. SABER represents a simple and versatile molecular toolkit to allow rapid and cost effective multiplexed imaging.
biorxiv genetics 200-500-users 2018The deadly touch protein denaturation at the water-air interface and how to prevent it, bioRxiv, 2018-08-26
ABSTRACTElectron cryo-microscopy analyzes the structure of proteins and protein complexes in vitrified solution. Proteins tend to adsorb to the air-water interface in unsupported films of aqueous solution, which can result in partial or complete denaturation of the protein. We investigated the structure of yeast fatty acid synthase at the air-water interface by electron cryo-tomography and single-particle image processing. Around 90% of complexes adsorbed to the air-water interface are partly denatured. We show that the unfolded regions are those facing the air-water interface. Denaturation by contact with air may happen at any stage of specimen preparation. Denaturation at the air-water interface is completely avoided when the complex is plunge-frozen on a substrate of hydrophilized graphene.
biorxiv biophysics 0-100-users 2018Widespread methane formation by Cyanobacteria in aquatic and terrestrial ecosystems, bioRxiv, 2018-08-25
AbstractEvidence is accumulating to challenge the paradigm that biogenic methanogenesis, traditionally considered a strictly anerobic process, is exclusive to Archaea. Here we demonstrate that Cyanobacteria living in marine, freshwater and terrestrial environments produce methane at substantial rates under light and dark oxic and anoxic conditions, forming a link between light driven primary productivity and methane production in globally relevant group of phototrophs. Biogenic methane production was enhanced during oxygenic photosynthesis and directly attributed to the cyanobacteria by applying stable isotope labelling techniques. We suggest that formation of methane by Cyanobacteria may contribute to methane accumulation in oxygen-saturated surface waters of marine and freshwater ecosystems. Moreover, in these environments, cyanobacterial blooms already do, and might further occur more frequently during future global warming and thus have a direct feedback on climate change. We further highlight that cyanobacterial methane production not only affects recent and future global methane budgets, but also has implications for inferences on Earth’s methane budget for the last 3.5 billion years, when this phylum is thought to have first evolved.
biorxiv microbiology 200-500-users 2018Fast Batch Alignment of Single Cell Transcriptomes Unifies Multiple Mouse Cell Atlases into an Integrated Landscape, bioRxiv, 2018-08-21
AbstractIncreasing numbers of large scale single cell RNA-Seq projects are leading to a data explosion, which can only be fully exploited through data integration. Therefore, efficient computational tools for combining diverse datasets are crucial for biology in the single cell genomics era. A number of methods have been developed to assist data integration by removing technical batch effects, but most are computationally intensive. To overcome the challenge of enormous datasets, we have developed BBKNN, an extremely fast graph-based data integration method. We illustrate the power of BBKNN for dimensionalityreduced visualisation and clustering in multiple biological scenarios, including a massive integrative study over several murine atlases. BBKNN successfully connects cell populations across experimentally heterogeneous mouse scRNA-Seq datasets, which reveals global markers of cell type and organspecificity and provides the foundation for inferring the underlying transcription factor network. BBKNN is available at <jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpsgithub.comTeichlabbbknn>httpsgithub.comTeichlabbbknn<jatsext-link>.
biorxiv bioinformatics 0-100-users 2018