Simultaneous mesoscopic and two-photon imaging of neuronal activity in cortical circuits, bioRxiv, 2018-11-12
AbstractSpontaneous and sensory-evoked activity propagates across spatial scales in the mammalian cortex but technical challenges have generally precluded establishing conceptual links between the function of local circuits of neurons and brain-wide network dynamics. To solve this problem, we developed a method for simultaneous cellular-resolution two-photon calcium imaging of a local microcircuit and mesoscopic widefield calcium imaging of the entire cortical mantle in awake, behaving mice. Our method employs an orthogonal axis design whereby the mesoscopic objective is oriented downward directly above the brain and the two-photon objective is oriented horizontally, with imaging performed through a glass right angle microprism implanted in the skull. In support of this method, we introduce a suite of analysis tools for relating the activity of individual cells to distal cortical areas, as well as a viral method for robust and widespread gene delivery in the juvenile mouse brain. We use these methods to characterize the diversity of associations of individual, genetically-defined neurons with cortex-wide network motifs.
biorxiv neuroscience 0-100-users 2018A polyploid admixed origin of beer yeasts derived from European and Asian wine populations, bioRxiv, 2018-11-09
AbstractStrains of Saccharomyces cerevisiae used to make beer, bread and wine are genetically and phenotypically distinct from wild populations associated with trees. The origins of these domesticated populations are not always clear; human-associated migration and admixture with wild populations have had a strong impact on S. cerevisiae population structure. We examined the population genetic history of beer strains and find that ale strains and the S. cerevisiae portion of allotetraploid lager strains were derived from admixture between populations closely related to European grape wine strains and Asian rice wine strains. Similar to both lager and baking strains, ale strains are polyploid, providing them with a passive means of remaining isolated from other populations and providing us with a living relic of their ancestral hybridization. To reconstruct their polyploid origin we phased the genomes of two ale strains and found ale haplotypes to both be recombinants between European and Asian alleles and to also contain novel alleles derived from extinct or as yet uncharacterized populations. We conclude that modern beer strains are the product of a historical melting pot of fermentation technology.
biorxiv evolutionary-biology 0-100-users 2018Rate variation in the evolution of non-coding DNA associated with social evolution in bees, bioRxiv, 2018-11-08
The evolutionary origins of eusociality represent increases in complexity from individual to caste-based, group reproduction. These behavioral transitions have been hypothesized to go hand-in-hand with an increased ability to regulate when and where genes are expressed. Bees have convergently evolved eusociality up to five times, providing a framework to test this hypothesis. To examine potential links between putative gene regulatory elements and social evolution, we compare alignable, non-coding sequences in eleven diverse bee species, encompassing three independent origins of reproductive division of labor and two elaborations of eusocial complexity. We find that rates of evolution in a number of non-coding sequences correlate with key social transitions in bees. Interestingly, while we find little evidence for convergent rate changes associated with independent origins of social behavior, a number of molecular pathways exhibit convergent rate changes in conjunction with subsequent elaborations of social organization. We also present evidence that many novel non-coding regions may have been recruited alongside the origin of sociality in corbiculate bees; these loci could represent gene regulatory elements associated with division of labor within this group. Thus, our findings are consistent with the hypothesis that gene regulatory innovations are associated with the evolution of eusociality and illustrate how a thorough examination of both coding and non-coding sequence can provide a more complete understanding of the molecular mechanisms underlying behavioral evolution.
biorxiv evolutionary-biology 0-100-users 2018A genome-wide algal mutant library reveals a global view of genes required for eukaryotic photosynthesis, bioRxiv, 2018-11-07
Photosynthetic organisms provide food and energy for nearly all life on Earth, yet half of their protein-coding genes remain uncharacterized1,2. Characterization of these genes could be greatly accelerated by new genetic resources for unicellular organisms that complement the use of multicellular plants by enabling higher-throughput studies. Here, we generated a genome-wide, indexed library of mapped insertion mutants for the flagship unicellular alga Chlamydomonas reinhardtii (Chlamydomonas hereafter). The 62,389 mutants in the library, covering 83% of nuclear, protein-coding genes, are available to the community. Each mutant contains unique DNA barcodes, allowing the collection to be screened as a pool. We leveraged this feature to perform a genome-wide survey of genes required for photosynthesis, which identified 303 candidate genes. Characterization of one of these genes, the conserved predicted phosphatase CPL3, showed it is important for accumulation of multiple photosynthetic protein complexes. Strikingly, 21 of the 43 highest-confidence genes are novel, opening new opportunities for advances in our understanding of this biogeochemically fundamental process. This library is the first genome-wide mapped mutant resource in any unicellular photosynthetic organism, and will accelerate the characterization of thousands of genes in algae, plants and animals.
biorxiv genomics 0-100-users 2018Comparative analysis of sequencing technologies platforms for single-cell transcriptomics, bioRxiv, 2018-11-06
AbstractAll single-cell RNA-seq protocols and technologies require library preparation prior to sequencing on a platform such as Illumina. Here, we present the first report to utilize the BGISEQ-500 platform for scRNA-seq, and compare the sensitivity and accuracy to Illumina sequencing. We generate a scRNA-seq resource of 468 unique single-cells and 1,297 matched single cDNA samples, performing SMARTer and Smart-seq2 protocols on mESCs and K562 cells with RNA spike-ins. We sequence these libraries on both BGISEQ-500 and Illumina HiSeq platforms using single- and paired-end reads. The two platforms have comparable sensitivity and accuracy in terms of quantification of gene expression, and low technical variability. Our study provides a standardised scRNA-seq resource to benchmark new scRNA-seq library preparation protocols and sequencing platforms.
biorxiv genomics 0-100-users 2018Investigating causal relationships between sleep traits and risk of breast cancer a Mendelian randomization study, bioRxiv, 2018-11-06
AbstractObjectiveTo examine whether sleep traits have a causal effect on risk of breast cancer.DesignMultivariable regression, one- and two-sample Mendelian randomization.SettingThe UK Biobank prospective cohort study and the Breast Cancer Association Consortium (BCAC) case-control genome-wide association study.Participants156,848 women in the multivariable regression and one-sample Mendelian randomization analysis in UK Biobank (7,784 with a breast cancer diagnosis) and 122,977 breast cancer cases and 105,974 controls from BCAC in the two-sample Mendelian randomization analysis.ExposuresSelf-reported chronotype (morningevening preference), insomnia symptoms and sleep duration in multivariable regression, and genetic variants robustly associated with these sleep traits.Main outcome measuresBreast cancer (prevalent and incident cases in UK Biobank, prevalent cases only in BCAC).ResultsIn multivariable regression analysis using data on breast cancer incidence in UK Biobank, morning preference was inversely associated with breast cancer (HR 0.95, 95% CI 0.93, 0.98 per category increase) while there was little evidence for an association with sleep duration and insomnia symptoms. Using 341 single nucleotide polymorphisms (SNPs) associated with chronotype, 91 SNPs associated sleep duration and 57 SNPs associated with insomnia symptoms, one-sample MR analysis in UK Biobank provided some supportive evidence for a protective effect of morning preference on breast cancer risk (HR 0.85, 95% 0.70, 1.03 per category increase) but imprecise estimates for sleep duration and insomnia symptoms. Two-sample MR using data from BCAC supported findings for a protective effect of morning preference (OR 0.88, 95% CI 0.82, 0.93 per category increase) and adverse effect of increased sleep duration (OR 1.19, 95% CI 1.02, 1.39 per hour increase) on breast cancer (both estrogen receptor positive and negative), while there was inconsistent evidence for insomnia symptoms. Results were largely robust to sensitivity analyses accounting for horizontal pleiotropy.ConclusionsWe found consistent evidence for a protective effect of morning preference and suggestive evidence for an adverse effect of sleep duration on breast cancer risk.
biorxiv epidemiology 0-100-users 2018