NINscope a versatile miniscope for multi-region circuit investigations, bioRxiv, 2019-07-01
AbstractMiniaturized fluorescence microscopes (miniscopes) have been instrumental to monitor neural activity during unrestrained behavior and their open-source versions have helped to distribute them at an affordable cost. Generally, the footprint and weight of open-source miniscopes is sacrificed for added functionality. Here, we present NINscope a light-weight, small footprint, open-source miniscope that incorporates a high-sensitivity image sensor, an inertial measurement unit (IMU), and an LED driver for an external optogenetic probe. We highlight the advantages of NINscope by performing the first simultaneous cellular resolution (dual scope) recordings from cerebellum and cerebral cortex in unrestrained mice, revealing that the activity of both regions generally precedes the onset of behavioral acceleration. We further demonstrate the optogenetic stimulation capabilities of NINscope and show that cerebral cortical activity can be driven strongly by cerebellar stimulation. To validate the performance of our miniscope to image from deep-brain regions, we recorded in the dorsal striatum and, using the IMU to assess turning movements, replicate previous studies that show encoding of action space in this subcortical region. Finally, we combine optogenetic stimulation of distinct cortical regions projecting to the dorsal striatum, to probe functional connectivity. In combination with cross-platform control software, NINscope is a versatile addition to the expanding toolbox of open-source miniscopes and will aid multi-region circuit investigations during unrestrained behavior.
biorxiv neuroscience 0-100-users 2019Direct evidence for transport of RNA from the mouse brain to the germline and offspring, bioRxiv, 2019-06-29
AbstractThe traditional concept that heritability occurs exclusively from the transfer of germline-restricted genetics is being challenged by the increasing accumulation of evidence confirming the existence of experience-dependent transgenerational inheritance. Transgenerational inheritance is emerging as a powerful mechanism for robustly transmitting phenotypic adaptations to offspring. However, questions remain unanswered as to how this heritable information is passed from somatic cells. Previous studies have implicated the critical involvement of RNA in heritable transgenerational effects and the high degree of mobility and genomic impact of RNAs in all organisms is an attractive model for the efficient transfer of genetic information. Here we show, for the first time, robust transport of RNA from the brain of an adult male mouse to sperm, and subsequently to offspring. Our observation of heritable genetic information originating from a somatic tissue may reveal a mechanism for how transgenerational effects are transmitted to offspring.
biorxiv evolutionary-biology 0-100-users 2019Identification of type 2 diabetes loci in 433,540 East Asian individuals, bioRxiv, 2019-06-29
SUMMARYMeta-analyses of genome-wide association studies (GWAS) have identified >240 loci associated with type 2 diabetes (T2D), however most loci have been identified in analyses of European-ancestry individuals. To examine T2D risk in East Asian individuals, we meta-analyzed GWAS data in 77,418 cases and 356,122 controls. In the main analysis, we identified 298 distinct association signals at 178 loci, and across T2D association models with and without consideration of body mass index and sex, we identified 56 loci newly implicated in T2D predisposition. Common variants associated with T2D in both East Asian and European populations exhibited strongly correlated effect sizes. New associations include signals innear GDAP1, PTF1A, SIX3, ALDH2, a microRNA cluster, and genes that affect muscle and adipose differentiation. At another locus, eQTLs at two overlapping T2D signals act through two genes, NKX6-3 and ANK1, in different tissues. Association studies in diverse populations identify additional loci and elucidate disease genes, biology, and pathways.Type 2 diabetes (T2D) is a common metabolic disease primarily caused by insufficient insulin production andor secretion by the pancreatic β cells and insulin resistance in peripheral tissues1. Most genetic loci associated with T2D have been identified in populations of European (EUR) ancestry, including a recent meta-analysis of genome-wide association studies (GWAS) of nearly 900,000 individuals of European ancestry that identified >240 loci influencing the risk of T2D2. Differences in allele frequency between ancestries affect the power to detect associations within a population, particularly among variants rare or monomorphic in one population but more frequent in another3,4. Although smaller than studies in European populations, a recent T2D meta-analysis in almost 200,000 Japanese individuals identified 28 additional loci4. The relative contributions of different pathways to the pathophysiology of T2D may also differ between ancestry groups. For example, in East Asian (EAS) populations, T2D prevalence is greater than in European populations among people of similar body mass index (BMI) or waist circumference5. We performed the largest meta-analysis of East Asian individuals to identify new genetic associations and provide insight into T2D pathogenesis.
biorxiv genetics 100-200-users 2019Mutational signatures are jointly shaped by DNA damage and repair, bioRxiv, 2019-06-29
SummaryMutations arise when DNA lesions escape DNA repair. To delineate the contributions of DNA damage and DNA repair deficiency to mutagenesis we sequenced 2,721 genomes of 54 C. elegans strains, each deficient for a specific DNA repair gene and wild-type, upon exposure to 12 different genotoxins. Combining genotoxins and repair deficiency leads to differential mutation rates or new mutational signatures in more than one third of experiments. Translesion synthesis polymerase deficiencies show dramatic and diverging effects. Knockout of Polκ dramatically exacerbates the mutagenicity of alkylating agents; conversely, Polζ deficiency reduces alkylation- and UV-induced substitution rates. Examples of DNA damage-repair deficiency interactions are also found in cancer genomes, although cases of hypermutation are surprisingly rare despite signs of positive selection in a number of DNA repair genes. Nevertheless, cancer risk may be substantially elevated even by small increases in mutagenicity according to evolutionary multi-hit theory. Overall, our data underscore how mutagenesis is a joint product of DNA damage and DNA repair, implying that mutational signatures may be more variable than currently anticipated.Highlights<jatslist list-type=bullet><jatslist-item>Combining exposure to DNA damaging agents and DNA repair deficiency in C. elegans leads to altered mutation rates and new mutational signatures<jatslist-item><jatslist-item>Mutagenic effects of genotoxic exposures are generally exacerbated by DNA repair deficiency<jatslist-item><jatslist-item>Mutagenesis of UVB and alkylating agents is reduced in translesion synthesis polymerase deficiencies<jatslist-item><jatslist-item>Human cancer genomes contain examples of DNA damagerepair interactions, but mutations in DNA repair genes usually only associate with moderate mutator phenotypes, in line with evolutionary theory<jatslist-item>
biorxiv genomics 100-200-users 2019Insights into human genetic variation and population history from 929 diverse genomes, bioRxiv, 2019-06-28
AbstractGenome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented private genetic variation in southern and central Africa and in Oceania and the Americas, but an absence of fixed, private variants between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the last 10,000 years, a potentially major population growth episode after the peopling of the Americas, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations. We also demonstrate benefits to the study of population relationships of genome sequences over ascertained array genotypes. These genome sequences are freely available as a resource with no access or analysis restrictions.
biorxiv genomics 200-500-users 2019MitoFinder efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics, bioRxiv, 2019-06-28
AbstractThanks to the development of high-throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routinely inferring phylogenetic relationships from thousands of genomic markers. Recently, it has been shown that mitochondrial DNA (mtDNA) is frequently sequenced alongside the targeted loci in such capture experiments. Despite its broad evolutionary interest, mtDNA is rarely assembled and used in conjunction with nuclear markers in capture-based studies. Here, we developed MitoFinder, a user-friendly bioinformatic pipeline, to efficiently assemble and annotate mitogenomic data from hundreds of UCE libraries. As a case study, we used ants (Formicidae) for which 501 UCE libraries have been sequenced whereas only 29 mitogenomes are available. We compared the efficiency of four different assemblers (IDBA-UD, MEGAHIT, MetaSPAdes, and Trinity) for assembling both UCE and mtDNA loci. Using MitoFinder, we show that metagenomic assemblers, in particular MetaSPAdes, are well suited to assemble both UCEs and mtDNA. Mitogenomic signal was successfully extracted from all 501 UCE libraries allowing confirming species identification using COI barcoding. Moreover, our automated procedure retrieved 296 cases in which the mitochondrial genome was assembled in a single contig, thus increasing the number of available ant mitogenomes by an order of magnitude. By leveraging the power of metagenomic assemblers, MitoFinder provides an efficient tool to extract complementary mitogenomic data from UCE libraries, allowing testing for potential mito-nuclear discordance. Our approach is potentially applicable to other sequence capture methods, transcriptomic data, and whole genome shotgun sequencing in diverse taxa.
biorxiv evolutionary-biology 0-100-users 2019