Generative adversarial networks for reconstructing natural images from brain activity, bioRxiv, 2017-12-09
AbstractWe explore a method for reconstructing visual stimuli from brain activity. Using large databases of natural images we trained a deep convolutional generative adversarial network capable of generating gray scale photos, similar to stimUli presented during two functional magnetic resonance imaging experiments. Using a linear model we learned to predict the generative model’s latent space from measured brain activity. The objective was to create an image similar to the presented stimulus image through the previously trained generator. Using this approach we were able to reconstruct structural and some semantic features of a proportion of the natural images sets. A behavioral test showed that subjects were capable of identifying a reconstruction of the original stimuhis in 67.2% and 66.4% of the cases in a pairwise comparison for the two natural image datasets respectively. our approach does not require end-to-end training of a large generative model on limited neuroimaging data. Rapid advances in generative modeling promise further improvements in reconstruction performance.
biorxiv neuroscience 0-100-users 2017High-efficiency optogenetic silencing with soma-targeted anion-conducting channelrhodopsins, bioRxiv, 2017-12-09
AbstractOptogenetic silencing allows time-resolved functional interrogation of defined neuronal populations. However, the limitations of inhibitory optogenetic tools impose stringent constraints on experimental paradigms. The high light power requirement of light-driven ion pumps and their effects on intracellular ion homeostasis pose unique challenges, particularly in experiments that demand inhibition of a widespread neuronal population in vivo. Guillardia theta anion-conducting channelrhodopsins (GtACRs) are promising in this regard, due to their high single-channel conductance and favorable photon-ion stoichiometry. However, GtACRs show poor membrane targeting in mammalian cells, and the activity of such channels can cause transient excitation in the axon due to an excitatory chloride reversal potential in this compartment. Here we address both problems by enhancing membrane targeting and subcellular compartmentalization of GtACRs. The resulting GtACR-based optogenetic tools show improved photocurrents, greatly reduced axonal excitation, high light sensitivity and rapid kinetics, allowing highly efficient inhibition of neuronal activity in the mammalian brain.
biorxiv neuroscience 100-200-users 2017Insular Celtic population structure and genomic footprints of migration, bioRxiv, 2017-12-09
AbstractPrevious studies of the genetic landscape of Ireland have suggested homogeneity, with population substructure undetectable using single-marker methods. Here we have harnessed the haplotype-based method fineSTRUCTURE in an Irish genome-wide SNP dataset, identifying 23 discrete genetic clusters which segregate with geographical provenance. Cluster diversity is pronounced in the west of Ireland but reduced in the east where older structure has been eroded by historical migrations. Accordingly, when populations from the neighbouring island of Britain are included, a west-east cline of Celtic-British ancestry is revealed along with a particularly striking correlation between haplotypes and geography across both islands. A strong relationship is revealed between subsets of Northern Irish and Scottish populations, where discordant genetic and geographic affinities reflect major migrations in recent centuries. Additionally, Irish genetic proximity of all Scottish samples likely reflects older strata of communication across the narrowest inter-island crossing. Using GLOBETROTTER we detected Irish admixture signals from Britain and Europe and estimated dates for events consistent with the historical migrations of the Norse-Vikings, the Anglo-Normans and the British Plantations. The influence of the former is greater than previously estimated from Y chromosome haplotypes. In all, we paint a new picture of the genetic landscape of Ireland, revealing structure which should be considered in the design of studies examining rare genetic variation and its association with traits.Author summaryA recent genetic study of the UK (People of the British Isles; PoBI) expanded our understanding of population history of the islands, using newly-developed, powerful techniques that harness the rich information embedded in chunks of genetic code called haplotypes. These methods revealed subtle regional diversity across the UK, and, using genetic data alone, timed key migration events into southeast England and Orkney. We have extended these methods to Ireland, identifying regional differences in genetics across the island that adhere to geography at a resolution not previously reported. Our study reveals relative western diversity and eastern homogeneity in Ireland owing to a history of settlement concentrated on the east coast and longstanding Celtic diversity in the west. We show that Irish Celtic diversity enriches the findings of PoBI; haplotypes mirror geography across Britain and Ireland, with relic Celtic populations contributing greatly to haplotypic diversity. Finally, we used genetic information to date migrations into Ireland from Europe and Britain consistent with historical records of Viking and Norman invasions, demonstrating the signatures of these migrations the on modern Irish genome. Our findings demonstrate that genetic structure exists in even small isolated populations, which has important implications for population-based genetic association studies.
biorxiv genetics 100-200-users 2017Long Read Annotation (LoReAn) automated eukaryotic genome annotation based on long-read cDNA sequencing, bioRxiv, 2017-12-09
AbstractSingle-molecule full-length cDNA sequencing can aid genome annotation by revealing transcript structure and alternative splice-forms, yet current annotation pipelines do not incorporate such information. Here we present LoReAn (Long Read Annotation) software, an automated annotation pipeline utilizing short- and long-read cDNA sequencing, protein evidence, and ab initio prediction to generate accurate genome annotations. Based on annotations of two fungal and two plant genomes, we show that LoReAn outperforms popular annotation pipelines by integrating single-molecule cDNA sequencing data generated from either the PacBio or MinION sequencing platforms, and correctly predicting gene structure and capturing genes missed by other annotation pipelines.
biorxiv bioinformatics 0-100-users 2017LRX- and FER-dependent extracellular sensing coordinates vacuolar size for cytosol homeostasis, bioRxiv, 2017-12-09
Cellular elongation requires the defined coordination of intra- and extracellular processes. The vacuole is the biggest plant organelle and its dimension has a role in limiting cell expansion (Löfke et al., 2015; Scheuring et al., 2016). We reveal that the increase in vacuolar occupancy enables cellular elongation with relatively little enlargement of the cytosole. It remains, however, completely unknown how the vacuolar size is coordinated with other growth-relevant processes. Intriguingly, we show that extracellular constraints impact on the intracellular expansion of the vacuole. The underlying cell wall sensing mechanism requires the interaction of the extracellular leucine-rich repeat extensin (LRX) with the receptor-like kinase Feronia (FER). Our data suggests that LRX links the plasma membrane localised FER with the cell wall, allowing this module to jointly sense and convey extracellular signals to the underlying cell. This mechanism coordinates cell wall acidificationloosening with the increase in vacuolar size, contributing cytosol homeostasis during plant cell expansion.
biorxiv plant-biology 0-100-users 2017Resolving the Full Spectrum of Human Genome Variation using Linked-Reads, bioRxiv, 2017-12-09
AbstractLarge-scale population based analyses coupled with advances in technology have demonstrated that the human genome is more diverse than originally thought. To date, this diversity has largely been uncovered using short read whole genome sequencing. However, standard short-read approaches, used primarily due to accuracy, throughput and costs, fail to give a complete picture of a genome. They struggle to identify large, balanced structural events, cannot access repetitive regions of the genome and fail to resolve the human genome into its two haplotypes. Here we describe an approach that retains long range information while harnessing the advantages of short reads. Starting from only ∼1ng of DNA, we produce barcoded short read libraries. The use of novel informatic approaches allows for the barcoded short reads to be associated with the long molecules of origin producing a novel datatype known as ‘Linked-Reads’. This approach allows for simultaneous detection of small and large variants from a single Linked-Read library. We have previously demonstrated the utility of whole genome Linked-Reads (lrWGS) for performing diploid, de novo assembly of individual genomes (Weisenfeld et al. 2017). In this manuscript, we show the advantages of Linked-Reads over standard short read approaches for reference based analysis. We demonstrate the ability of Linked-Reads to reconstruct megabase scale haplotypes and to recover parts of the genome that are typically inaccessible to short reads, including phenotypically important genes such as STRC, SMN1 and SMN2. We demonstrate the ability of both lrWGS and Linked-Read Whole Exome Sequencing (lrWES) to identify complex structural variations, including balanced events, single exon deletions, and single exon duplications. The data presented here show that Linked-Reads provide a scalable approach for comprehensive genome analysis that is not possible using short reads alone.
biorxiv genomics 0-100-users 2017