Computational haplotype recovery and long-read validation identifies novel isoforms of industrially relevant enzymes from natural microbial communities, bioRxiv, 2017-11-23
AbstractPopulation-level diversity of natural microbiomes represent a biotechnological resource for biomining, biorefining and synthetic biology but requires the recovery of the exact DNA sequence (or “haplotype”) of the genes and genomes of every individual present. Computational haplotype reconstruction is extremely difficult, complicated by environmental sequencing data (metagenomics). Current approaches cannot choose between alternative haplotype reconstructions and fail to provide biological evidence of correct predictions. To overcome this, we present Hansel and Gretel a novel probabilistic framework that reconstructs the most likely haplotypes from complex microbiomes, is robust to sequencing error and uses all available evidence from aligned reads, without altering or discarding observed variation. We provide the first formalisation of this problem and propose “metahaplome” as a definition for the set of haplotypes for any genomic region of interest within a metagenomic dataset. Finally, we demonstrate using long-read sequencing, biological evidence of novel haplotypes of industrially important enzymes computationally predicted from a natural microbiome.
biorxiv bioinformatics 0-100-users 2017Spliceosome profiling visualizes the operations of a dynamic RNP in vivo at nucleotide resolution, bioRxiv, 2017-11-23
SummaryTools to understand how the spliceosome functions in vivo have lagged behind advances in its structural biology. We describe methods to globally profile spliceosome-bound precursor, intermediates and products at nucleotide resolution. We apply these tools to three divergent yeast species that span 600 million years of evolution. The sensitivity of the approach enables detection of novel cases of non-canonical catalysis including interrupted, recursive and nested splicing. Employing statistical modeling to understand the quantitative relationships between RNA features and the data, we uncover independent roles for intron size, position and number in substrate progression through the two catalytic stages. These include species-specific inputs suggestive of spliceosome-transcriptome coevolution. Further investigations reveal ATP-dependent discard of numerous endogenous substrates at both the precursor and lariat-intermediate stages and connect discard to intron retention, a form of splicing regulation. Spliceosome profiling is a quantitative, generalizable global technology to investigate an RNP central to eukaryotic gene expression.Highlights<jatslist list-type=bullet><jatslist-item>Measurement of spliceosome-bound precursor and intermediate in three species<jatslist-item><jatslist-item>Non-canonical splicing events revealed<jatslist-item><jatslist-item>Statistical modeling uncovers substrate features that predict catalytic efficiency<jatslist-item><jatslist-item>Discard of suboptimal substrates occurs in vivo and predicts intron-retained mRNAs<jatslist-item>
biorxiv molecular-biology 0-100-users 2017Dynamics of the upper airway microbiome in the pathogenesis of asthma-associated persistent wheeze in preschool children, bioRxiv, 2017-11-21
ABSTRACTRepeated cycles of infection-associated lower airway inflammation drives the pathogenesis of persistent wheezing disease in children. Tracking these events across a birth cohort during their first five years, we demonstrate that >80% of infectious events indeed involve viral pathogens, but are accompanied by a shift in the nasopharyngeal microbiome (NPM) towards dominance by a small range of pathogenic bacterial genera. Unexpectedly, this change in NPM frequently precedes the appearance of viral pathogens and acute symptoms. In non-sensitized children these events are associated only with “transient wheeze” that resolves after age three. In contrast, in children developing early allergic sensitization, they are associated with ensuing development of persistent wheeze, which is the hallmark of the asthma phenotype. This suggests underlying pathogenic interactions between allergic sensitization and antibacterial mechanisms.
biorxiv genetics 0-100-users 2017Eye movement-related confounds in neural decoding of visual working memory representations, bioRxiv, 2017-11-21
AbstractThe study of visual working memory (VWM) has recently seen revitalization with the emergence of new insights and theories regarding its neural underpinnings. One crucial ingredient responsible for this progress is the rise of neural decoding techniques. These techniques promise to uncover the representational contents of neural signals, as well as the underlying code and the dynamic profile thereof. Here, we aimed to contribute to the field by subjecting human volunteers to a combined VWMimagery task, while recording and decoding their neural signals as measured by MEG. At first sight, the results seem to provide evidence for a persistent, stable representation of the memorandum throughout the delay period. However, control analyses revealed that these findings can be explained by subtle, VWM-specific eye movements. As a potential remedy, we demonstrate the use of a functional localizer, which was specifically designed to target bottom-up sensory signals and as such avoids eye movements, to train the neural decoders. This analysis revealed a sustained representation for approximately 1 second, but no longer throughout the entire delay period. We conclude by arguing for more awareness of the potentially pervasive and ubiquitous effects of eye movement-related confounds.Significance statementVisual working memory is an important aspect of higher cognition and has been subject of much investigation within the field of cognitive neuroscience. Over recent years, these studies have increasingly relied on the use of neural decoding techniques. Here, we show that neural decoding may be susceptible to confounds induced by stimulus-specific eye movements. Such eye movements during working memory have been reported before, and may in fact be a common phenomenon. Given the widespread use of neural decoding and the potentially contaminating effects of eye movements, we therefore believe that our results are of significant relevance for the field.
biorxiv neuroscience 0-100-users 2017The Generation and Propagation of the Human Alpha Rhythm, bioRxiv, 2017-11-19
AbstractThe alpha rhythm is the longest studied brain oscillation and has been theorized to play a key role in cognition. Still, its physiology is poorly understood. In this study, we used micro and macro electrodes in surgical epilepsy patients to measure the intracortical and thalamic generators of the alpha rhythm during quiet wakefulness. We first found that alpha in posterior cortex propagates from higher-order anterosuperior areas towards the occipital pole, consistent with alpha effecting top-down processing. This cortical alpha leads pulvinar alpha, complicating prevailing theories of a thalamic pacemaker. Finally, alpha is dominated by currents and firing in supragranular cortical layers. Together, these results suggest that the alpharhythm likely reflects short-range supragranular feedback which propagates from higher to lower-order cortex and cortex to thalamus. These physiological insights suggest how alpha could mediate feedback throughout the thalamocortical system.
biorxiv neuroscience 0-100-users 2017Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities, bioRxiv, 2017-11-19
ABSTRACTMammalian gene promoters and enhancers share many properties. They are composed of a unified promoter architecture of divergent transcripton initiation and gene promoters may exhibit enhancer function. However, it is currently unclear how expression strength of a regulatory element relates to its enhancer strength and if the unifying architecture is conserved across Metazoa. Here we investigate the transcription initiation landscape and its associated RNA decay in D. melanogaster. Surprisingly, we find that the majority of active gene-distal enhancers and a considerable fraction of gene promoters are divergently transcribed. We observe quantitative relationships between enhancer potential, expression level and core promoter strength, providing an explanation for indirectly related histone modifications that are reflecting expression levels. Lowly abundant unstable RNAs initiated from weak core promoters are key characteristics of gene-distal developmental enhancers, while the housekeeping enhancer strengths of gene promoters reflect their expression strengths. The different layers of regulation mediated by gene-distal enhancers and gene promoters are also reflected in chromatin interaction data. Our results suggest a unified promoter architecture of many D. melanogaster regulatory elements, that is universal across Metazoa, whose regulatory functions seem to be related to their core promoter elements.
biorxiv genomics 0-100-users 2017