Patterns of behavior exhibited by mice in their home cages reflect the function and interaction of numerous behavioral and physiological systems. Detailed assessment of these patterns thus has the potential to provide a powerful tool for understanding basic aspects of behavioral regulation and their perturbation by disease processes. However, the capacity to identify and examine these patterns in terms of their discrete levels of organization across diverse behaviors has been difficult to achieve and automate. Here, we describe an automated approach for the quantitative characterization of fundamental behavioral elements and their patterns in the freely behaving mouse. We demonstrate the utility of this approach by identifying unique features of home cage behavioral structure and changes in distinct levels of behavioral organization in mice with single gene mutations altering energy balance. The robust, automated, reproducible quantification of mouse home cage behavioral structure detailed here should have wide applicability for the study of mammalian physiology, behavior, and disease.circadian ͉ ingestion ͉ obesity ͉ phenotyping M olecular genetic approaches for manipulating gene expression and neural activity in mice, combined with the elucidation of the mouse genome, provide unprecedented opportunities for the investigation of diverse behavioral processes in the context of a mammalian system. While substantial insights have been gained through the application of existing behavioral assays, many of these examine behavior over a limited time window and focus on a single behavioral domain (1, 2). To complement such approaches, we developed an automated, readily-standardized quantitative approach for elucidating the complex organization of diverse behaviors exhibited by mice in their home cages.We focused on mice in their home cages because the organization of behavior in freely acting animals provides a window into the central integration of numerous behavioral and physiological systems (e.g., energy balance, thermal status, osmotic/volume status, sleep, reproduction, defense, and environmental entrainment). The functions and interactions of these systems result in the coordinated organization of multiple behaviors (3-5). Although several sophisticated approaches for automated behavioral data collection and home cage monitoring exist, they do not employ algorithms that quantitatively capture the rich temporal and spatial structure of diverse behaviors that occur over multiple time scales (1,(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19).As a first step in examining this structure, we made use of the observation that in natural environments animals typically alternate between two major discrete states, active and inactive (20)(21)(22). During active states (ASs), animals engage in behaviors such as foraging and patrolling within a regularly traversed home range. During inactive states (ISs), animals return to a refuge (nest, burrow, or home base) and engage in behaviors such as rest and sleep (23-26). These...

The intracellular endosymbiotic bacterium Wolbachia can protect insects against viral infection, and is being introduced into mosquito populations in the wild to block the transmission of arboviruses that infect humans and are a major public health concern. To investigate the mechanisms underlying this antiviral protection, we have developed a new model system combining Wolbachia-infected Drosophila melanogaster cell culture with the model mosquito-borne Semliki Forest virus (SFV; Togaviridae, Alphavirus). Wolbachia provides strong antiviral protection rapidly after infection, suggesting that an early stage post-infection is being blocked. Wolbachia does appear to have major effects on events distinct from entry, assembly or exit as it inhibits the replication of an SFV replicon transfected into the cells. Furthermore, it causes a far greater reduction in the expression of proteins from the 3´ open reading frame than the 5´ non-structural protein open reading frame, indicating that it is blocking the replication of viral RNA. Further to this separation of the replicase proteins and viral RNA in transreplication assays shows that uncoupling of viral RNA and replicase proteins does not overcome Wolbachia’s antiviral activity. This further suggests that replicative processes are disrupted, such as translation or replication, by Wolbachia infection. This may occur by Wolbachia mounting an active antiviral response, but the virus did not cause any transcriptional response by the bacterium, suggesting that this is not the case. Host microRNAs (miRNAs) have been implicated in protection, but again we found that host cell miRNA expression was unaffected by the bacterium and neither do our findings suggest any involvement of the antiviral siRNA pathway. We conclude that Wolbachia may directly interfere with early events in virus replication such as translation of incoming viral RNA or RNA transcription, and this likely involves an intrinsic (as opposed to an induced) mechanism.

Multiple isolates of the genus Providencia were obtained from the haemolymph of wild-caught Drosophila melanogaster fruit flies. Sixteen isolates were distinguished from the six previously described species based on 16S rRNA gene sequences. These isolates belonged to two distinct groups, which we propose each comprise previously undescribed species. Two isolates, designated A T and B

The mosquito Aedes aegypti transmits some of the most important human arboviruses, including dengue, yellow fever and chikungunya viruses. It has a large genome containing many repetitive sequences, which has resulted in the genome being poorly assembled — there are 4,758 scaffolds, few of which have been assigned to a chromosome. To allow the mapping of genes affecting disease transmission, we have improved the genome assembly by scoring a large number of SNPs in recombinant progeny from a cross between two strains of Ae. aegypti, and used these to generate a genetic map. This revealed a high rate of misassemblies in the current genome, where, for example, sequences from different chromosomes were found on the same scaffold. Once these were corrected, we were able to assign 60% of the genome sequence to chromosomes and approximately order the scaffolds along the chromosome. We found that there are very large regions of suppressed recombination around the centromeres, which can extend to as much as 47% of the chromosome. To illustrate the utility of this new genome assembly, we mapped a gene that makes Ae. aegypti resistant to the human parasite Brugia malayi, and generated a list of candidate genes that could be affecting the trait.

BackgroundOrganisms can rapidly adapt to their environment when colonizing a new habitat, and this could occur by changing protein sequences or by altering patterns of gene expression. The importance of gene expression in driving local adaptation is increasingly being appreciated, and cis-regulatory elements (CREs), which control and modify the expression of the nearby genes, are predicted to play an important role. Here we investigate genetic variation in gene expression in immune-challenged Drosophila melanogaster from temperate and tropical or sub-tropical populations in Australia and United States.ResultsWe find parallel latitudinal changes in gene expression, with genes involved in immunity, insecticide resistance, reproduction, and the response to the environment being especially likely to differ between latitudes. By measuring allele-specific gene expression (ASE), we show that cis-regulatory variation also shows parallel latitudinal differences between the two continents and contributes to the latitudinal differences in gene expression.ConclusionsBoth Australia and United States were relatively recently colonized by D. melanogaster, and it was recently shown that introductions of both African and European flies occurred, with African genotypes contributing disproportionately to tropical populations. Therefore, both the demographic history of the populations and local adaptation may be causing the patterns that we see.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3333-7) contains supplementary material, which is available to authorized users.