Adding function to the genome of African Salmonella ST313, bioRxiv, 2018-10-22
AbstractSalmonella Typhimurium ST313 causes invasive nontyphoidal Salmonella (iNTS) disease in sub-Saharan Africa, targeting susceptible HIV+, malarial or malnourished individuals. An in-depth genomic comparison between the ST313 isolate D23580, and the well-characterized ST19 isolate 474 that causes gastroenteritis across the globe, revealed extensive synteny. To understand how the 856 nucleotide variations generated phenotypic differences, we devised a large-scale experimental approach that involved the global gene expression analysis of strains D23580 and 474 grown in sixteen infection-relevant growth conditions. Comparison of transcriptional patterns identified virulence and metabolic genes that were differentially expressed between D23580 versus 474, many of which were validated by proteomics. We also uncovered the S. Typhimurium D23580 and 474 genes that showed expression differences during infection of murine macrophages. Our comparative transcriptomic data are presented in a new enhanced version of the Salmonella expression compendium SalComD23580 <jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpbioinf.gen.tcd.iecgi-binsalcom_v2.pl>bioinf.gen.tcd.iecgi-binsalcom_v2.pl<jatsext-link>. We discovered that the ablation of melibiose utilization was caused by 3 independent SNP mutations in D23580 that are shared across ST313 lineage 2, suggesting that the ability to catabolise this carbon source has been negatively selected during ST313 evolution. The data revealed a novel plasmid maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase, highlighting the power of large-scale comparative multi-condition analyses to pinpoint key phenotypic differences between bacterial pathovariants.
biorxiv microbiology 0-100-users 2018Navigome Navigating the Human Phenome, bioRxiv, 2018-10-22
AbstractWe now have access to a sufficient number of genome-wide association studies (GWAS) to cluster phenotypes into genetic-informed categories and to navigate the “phenome” space of human traits. Using a collection of 465 GWAS, we generated genetic correlations, pathways, gene-wise and tissue-wise associations using MAGMA and S-PrediXcan for 465 human traits. Testing 7267 biological pathways, we found that only 898 were significantly associated with any trait. Similarly, out of ~20,000 tested protein-coding genes, 12,311 genes exhibited an association. Based on the genetic correlations between all traits, we constructed a phenome map using t-distributed stochastic neighbor embedding (t-SNE), where each of the 465 traits can be visualized as an individual point. This map reveals well-defined clusters of traits such as educationhigh longevity, lower longevity, height, body composition, and depressionanxietyneuroticism. These clusters are enriched in specific groups of pathways, such as lipid pathways in the lower longevity cluster, and neuronal pathways for body composition or education clusters. The map and all other analyses are available in the Navigome web interface (<jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpsphenviz.navigome.com>httpsphenviz.navigome.com<jatsext-link>).
biorxiv bioinformatics 0-100-users 2018Predicting the Future with Multi-scale Successor Representations, bioRxiv, 2018-10-22
AbstractThe successor representation (SR) is a candidate principle for generalization in reinforcement learning, computational accounts of memory, and the structure of neural representations in the hippocampus. Given a sequence of states, the SR learns a predictive representation for every given state that encodes how often, on average, each upcoming state is expected to be visited, even if it is multiple steps ahead. A discount or scale parameter determines how many steps into the future SR’s generalizations reach, enabling rapid value computation, subgoal discovery, and flexible decision-making in large trees. However, SR with a single scale could discard information for predicting both the sequential order of and the distance between states, which are common problems in navigation for animals and artificial agents. Here we propose a solution an ensemble of SRs with multiple scales. We show that the derivative of multi-scale SR can reconstruct both the sequence of expected future states and estimate distance to goal. This derivative can be computed linearly we show that a multi-scale SR ensemble is the Laplace transform of future states, and the inverse of this Laplace transform is a biologically plausible linear estimation of the derivative. Multi-scale SR and its derivative could lead to a common principle for how the medial temporal lobe supports both map-based and vector-based navigation.
biorxiv neuroscience 0-100-users 2018Transduction of the Geomagnetic Field as Evidenced from Alpha-band Activity in the Human Brain, bioRxiv, 2018-10-20
AbstractMagnetoreception, the perception of the geomagnetic field, is a sensory modality well-established across all major groups of vertebrates and some invertebrates, but its presence in humans has been tested rarely, yielding inconclusive results. We report here a strong, specific human brain response to ecologically-relevant rotations of Earth-strength magnetic fields. Following geomagnetic stimulation, a drop in amplitude of EEG alpha oscillations (8-13 Hz) occurred in a repeatable manner. Termed alpha event-related desynchronization (alpha-ERD), such a response is associated with sensory and cognitive processing of external stimuli. Biophysical tests showed that the neural response was sensitive to the dynamic components and axial alignment of the field but also to the static components and polarity of the field. This pattern of results implicates ferromagnetism as the biophysical basis for the sensory transduction and provides a basis to start the behavioral exploration of human magnetoreception.
biorxiv biophysics 0-100-users 2018Transposon accumulation lines uncover histone H2A.Z-driven integration bias towards environmentally responsive genes, bioRxiv, 2018-10-19
Inherited transposition events are important drivers of genome evolution but because transposable element (TE) mobilization is usually rare, its impact on the creation of genetic variation remains poorly characterized. Here, we used a population of A. thaliana epigenetic recombinant inbred lines (epiRILs) to characterize >8000 de novo insertions produced by several TEs families also active in nature. Integration was strongly biased towards genes, with evident deleterious effects. Biases were TE family-specific and associated with distinct chromatin features. Notably, we demonstrate that the histone variant H2A.Z guides the preferential integration of Ty1Copia LTR-retrotransposons within environmentally responsive genes and that this guiding function is evolutionary conserved. Finally, we uncover an important role for epigenetic silencing in exacerbating or alleviating the effects of TE insertions on target genes. These findings establish chromatin as a major determinant of the spectrum and functional impact of TE-generated mutations, with important implications for adaptation and evolution.
biorxiv genomics 0-100-users 2018Diversification and collapse of a telomere elongation mechanism, bioRxiv, 2018-10-18
AbstractIn virtually all eukaryotes, telomerase counteracts chromosome erosion by adding repetitive sequence to terminal ends. Drosophila melanogaster instead relies on specialized retrotransposons that insert preferentially at telomeres. This exchange of goods between host and mobile element—wherein the mobile element provides an essential genome service and the host provides a hospitable niche for mobile element propagation—has been called a ‘genomic symbiosis’. However, these telomere-specialized, ‘jockey’ family elements may actually evolve to selfishly over-replicate in the genomes that they ostensibly serve. Under this intra-genomic conflict model, we expect rapid diversification of telomere-specialized retrotransposon lineages and possibly, the breakdown of this tenuous relationship. Here we report data consistent with both predictions. Searching the raw reads of the 15-million-year-old ‘melanogaster species group’, we generated de novo jockey retrotransposon consensus sequences and used phylogenetic tree-building to delineate four distinct telomere-associated lineages. Recurrent gains, losses, and replacements account for this striking retrotransposon lineage diversity. Moreover, an ancestrally telomere-specialized element has ‘escaped,’ residing now throughout the genome of D. rhopaloa. In D. biarmipes, telomere-specialized elements have disappeared completely. De novo assembly of long-reads and cytogenetics confirmed this species-specific collapse of retrotransposon-dependent telomere elongation. Instead, telomere-restricted satellite DNA and DNA transposon fragments occupy its terminal ends. We infer that D. biarmipes relies instead on a recombination-based mechanism conserved from yeast to flies to humans. Combined with previous reports of adaptive evolution at host proteins that regulate telomere length, telomere-associated retrotransposon diversification and disappearance offer compelling evidence that intra-genomic conflict shapes Drosophila telomere evolution.
biorxiv evolutionary-biology 0-100-users 2018