Elina L. Niño

Parallel epigenomic and transcriptomic responses to viral infection in honey bees (Apis mellifera).

Populations of honey bees are declining throughout the world, with US beekeepers losing 30% of their colonies each winter. Though multiple factors are driving these colony losses, it is increasingly clear that viruses play a major role. However, information about the molecular mechanisms mediating antiviral immunity in honey bees is surprisingly limited. Here, we examined the transcriptional and epigenetic (DNA methylation) responses to viral infection in honey bee workers. One-day old worker honey bees were fed solutions containing Israeli Acute Paralysis Virus (IAPV), a virus which causes muscle paralysis and death and has previously been associated with colony loss. Uninfected control and infected, symptomatic bees were collected within 20–24 hours after infection. Worker fat bodies, the primary tissue involved in metabolism, detoxification and immune responses, were collected for analysis. We performed transcriptome- and bisulfite-sequencing of the worker fat bodies to identify genome-wide gene expression and DNA methylation patterns associated with viral infection. There were 753 differentially expressed genes (FDR<0.05) in infected versus control bees, including several genes involved in epigenetic and antiviral pathways. DNA methylation status of 156 genes (FDR<0.1) changed significantly as a result of the infection, including those involved in antiviral responses in humans. There was no significant overlap between the significantly differentially expressed and significantly differentially methylated genes, and indeed, the genomic characteristics of these sets of genes were quite distinct. Our results indicate that honey bees have two distinct molecular pathways, mediated by transcription and methylation, that modulate protein levels and/or function in response to viral infections.

Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens

BackgroundOrganisms typically face infection by diverse pathogens, and hosts are thought to have developed specific responses to each type of pathogen they encounter. The advent of transcriptomics now makes it possible to test this hypothesis and compare host gene expression responses to multiple pathogens at a genome-wide scale. Here, we performed a meta-analysis of multiple published and new transcriptomes using a newly developed bioinformatics approach that filters genes based on their expression profile across datasets. Thereby, we identified common and unique molecular responses of a model host species, the honey bee (Apis mellifera), to its major pathogens and parasites: the Microsporidia Nosema apis and Nosema ceranae, RNA viruses, and the ectoparasitic mite Varroa destructor, which transmits viruses.ResultsWe identified a common suite of genes and conserved molecular pathways that respond to all investigated pathogens, a result that suggests a commonality in response mechanisms to diverse pathogens. We found that genes differentially expressed after infection exhibit a higher evolutionary rate than non-differentially expressed genes. Using our new bioinformatics approach, we unveiled additional pathogen-specific responses of honey bees; we found that apoptosis appeared to be an important response following microsporidian infection, while genes from the immune signalling pathways, Toll and Imd, were differentially expressed after Varroa/virus infection. Finally, we applied our bioinformatics approach and generated a gene co-expression network to identify highly connected (hub) genes that may represent important mediators and regulators of anti-pathogen responses.ConclusionsOur meta-analysis generated a comprehensive overview of the host metabolic and other biological processes that mediate interactions between insects and their pathogens. We identified key host genes and pathways that respond to phylogenetically diverse pathogens, representing an important source for future functional studies as well as offering new routes to identify or generate pathogen resilient honey bee stocks. The statistical and bioinformatics approaches that were developed for this study are broadly applicable to synthesize information across transcriptomic datasets. These approaches will likely have utility in addressing a variety of biological questions.

Differential effects of insemination volume and substance on reproductive changes in honey bee queens (Apis mellifera L.)

Mating causes dramatic changes in female insects at the behavioural, physiological and molecular level. The factors driving these changes (e.g. seminal proteins, seminal volume) and the molecular pathways by which these factors are operating have been characterized only in a handful of insect species. In the present study, we use instrumental insemination of honey bee queens to examine the role of the insemination substance and volume in triggering post‐mating changes. We also examine differences in gene expression patterns in the fat bodies of queens with highly activated ovaries to determine if events during copulation can cause long‐term changes in gene expression. We found that the instrumental insemination procedure alone caused cessation of mating flights and triggered ovary activation, with high‐volume inseminated queens having the greatest ovary activation. Hierarchical clustering grouped queens primarily by insemination substance and then insemination volume, suggesting that while volume may trigger short‐term physiological changes (i.e. ovary activation) substance plays a greater role in regulating long‐term transcriptional changes. The results of gene ontology analysis and comparison with previous studies suggest that both insemination substance and volume trigger molecular post‐mating changes by altering overlapping gene pathways involved in honey bee reproduction. We also discuss the effects on two genes (vitellogenin and transferrin) involved in reproduction and defence responses.

Chemical profiles of two pheromone glands are differentially regulated by distinct mating factors in honey bee queens (Apis mellifera L.).

Pheromones mediate social interactions among individuals in a wide variety of species, from yeast to mammals. In social insects such as honey bees, pheromone communication systems can be extraordinarily complex and serve to coordinate behaviors among many individuals. One of the primary mediators of social behavior and organization in honey bee colonies is queen pheromone, which is produced by multiple glands. The types and quantities of chemicals produced differ significantly between virgin and mated queens, and recent studies have suggested that, in newly mated queens, insemination volume or quantity can affect pheromone production. Here, we examine the long-term impact of different factors involved during queen insemination on the chemical composition of the mandibular and Dufours glands, two of the major sources of queen pheromone. Our results demonstrate that carbon dioxide (an anesthetic used in instrumental insemination), physical manipulation of genital tract (presumably mimicking the act of copulation), insemination substance (saline vs. semen), and insemination volume (1 vs. 8 µl) all have long-term effects on mandibular gland chemical profiles. In contrast, Dufours gland chemical profiles were changed only upon insemination and were not influenced by exposure to carbon dioxide, manipulation, insemination substance or volume. These results suggest that the chemical contents of these two glands are regulated by different neuro-physiological mechanisms. Furthermore, workers responded differently to the different mandibular gland extracts in a choice assay. Although these studies must be validated in naturally mated queens of varying mating quality, our results suggest that while the chemical composition of Dufours gland is associated with mating status, that of the mandibular glands is associated with both mating status and insemination success. Thus, the queen appears to be signaling both status and reproductive quality to the workers, which may impact worker behavior and physiology as well as social organization and productivity of the colony.

Genome‐wide analysis of brain transcriptional changes in honey bee (Apis mellifera L.) queens exposed to carbon dioxide and physical manipulation

Mating is a complex process causing many behavioural and physiological changes, but the factors triggering them and the underlying molecular processes are not well characterized. In the present study we examine the effects of CO2 (a commonly used anaesthetic in instrumental insemination that causes changes similar to those occurring after mating) and physical manipulation (which may mimic certain aspects of copulation) on the behavioural, physiological and brain transcriptional changes in honey bee queens. We show that while CO2 causes cessation of mating flights and ovary activation, physical manipulation has additional effects on ovary activation and brain transcriptional changes. Comparisons with previous studies of honey bees and female Drosophila indicate that common molecular mechanisms may be responsible for regulating reproductive changes across different mating regimes and insect orders.

Genomic analysis of the interactions between social environment and social communication systems in honey bees (Apis mellifera)

Social context is often a primary regulator of social behavior, but genes that affect or are affected by social context have rarely been investigated. In social insects, caste specific pheromones are key modulators of social behavior, e.g., in honey bees the queen mandibular gland (MG) pheromone mediates reproductive dominance, its absence prompting ovary activation and queen pheromone production in workers. Here, we investigate the effect of social environment on genome-wide expression patterns in the MG, to determine how social context modulates expression of genes that, in turn alter social environment. We used microarrays to examine the MGs of virgin and mated queens, and queenright (QR) and queenless (QL) workers with or without activated ovaries. Approximately 2554 transcripts were significantly differentially expressed among these groups, with caste and social context being the main regulators of gene expression patterns, while physiological state (ovary activation) only minimally affecting gene expression. Thus, social context strongly regulates expression of genes, which, in turn, shape social environment. Among these, 25 genes that are putatively involved in caste selective production of the fatty-acid derived MG pheromone were differentially expressed in queens and workers. These genes whose functions correspond with enzymatic or transport processes emphasize the occurrence of disparate pheromone biosynthetic pathways for queens and workers, adding another dimension regarding the regulation of these important pheromones. Gene ontology analysis also revealed genes of different functional categories whose expression was impacted by caste or by the social environment, suggesting that the MG has broader functions than pheromone biosynthesis.

Effects of honey bee (Apis mellifera L.) queen insemination volume on worker behavior and physiology

Honey bee colonies consist of tens of thousands of workers and a single reproductive queen that produces a pheromone blend which maintains colony organization. Previous studies indicated that the insemination quantity and volume alter queen mandibular pheromone profiles. In our 11-month long field study we show that workers are more attracted to high-volume versus low-volume inseminated queens, however, there were no significant differences between treatments in the number of queen cells built by workers in preparation for supersedure. Workers exposed to low-volume inseminated queens initiated production of queen-like esters in their Dufours glands, but there were no significant difference in the amount of methyl farnesoate and juvenile hormone in worker hemolymph. Lastly, queen overwintering survival was unexpectedly lower in high-volume inseminated queens. Our results suggest that the queen insemination volume could ultimately affect colony health and productivity.

Effect of honey bee queen mating condition on worker ovary activation

The presence of the honey bee queen reduces worker ovary activation. When the queen is healthy and fecund, this is interpreted as an adaptive response as workers can gain fitness from helping the queen raise additional offspring, their sisters. However, when the queen is absent, workers activate their ovaries and lay unfertilized eggs that become males. Queen pheromones are recognised as a factor affecting worker ovary activation. Recent work has shown that queen mandibular pheromone composition changes with queen mating condition and workers show different behavioural responses to pheromone extracts from these queens. Here, we tested whether workers reared in colonies with queens of different mating condition varied in level of ovary activation. We also examined the changes in the chemical composition of the queen mandibular glands to determine if the pheromone blend varied among the queens. We found that the workers activated their ovaries when queens were unmated and had lower ovary activation when raised with mated queens, suggesting that workers detect and respond adaptively to queens of differing mating status. Moreover, variation in queen mandibular gland’s chemical composition correlated with the levels of worker ovary activation. Although correlative, this evidence suggests that queen pheromone may act as a signal of queen mating condition for workers, in response to which they alter their level of ovary activation.

Experimental evaluation of Musca domestica (Diptera:Muscidae) as a vector of newcastle disease virus

Abstract House flies, Musca domestica L. (Diptera: Muscidae), were examined for their ability to harbor and transmit Newcastle disease virus (family Paramyxoviridae, genus Avulavirus, NDV) by using a mesogenic NDV strain. Laboratory-reared flies were experimentally exposed to NDV (Roakin strain) by allowing flies to imbibe an inoculum consisting of chicken embryo-propagated virus. NDV was detected in dissected crops and intestinal tissues from exposed flies for up to 96 and 24 h postexposure, respectively; no virus was detected in crops and intestines of sham-exposed flies. The potential of the house fly to directly transmit NDV to live chickens was examined by placing 14-d-old chickens in contact with NDV-exposed house flies 2 h after flies consumed NDV inoculum. NDV-exposed house flies contained ≈104 50% infectious doses (ID50) per fly, but no transmission of NDV was observed in chickens placed in contact with exposed flies at densities as high as 25 flies per bird. Subsequent dose–response studies demonstrated that oral exposure, the most likely route for fly-to-chicken transmission, required an NDV (Roakin) dose ≥106 ID50. These results indicate that house flies are capable of harboring NDV (Roakin) but that they are poor vectors of the virus because they carry an insufficient virus titer to cause infection.

Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools

BackgroundWith the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population dynamics and signatures of selection across the genome using several well-established tests, including FST, pN/pS, and McDonald-Kreitman. We applied these techniques to study populations of honey bees (Apis mellifera) in East Africa. In Kenya, there are several described A. mellifera subspecies, which are thought to be localized to distinct ecological regions.ResultsWe performed whole genome sequencing of 11 worker honey bees from apiaries distributed throughout Kenya and identified 3.6 million putative single-nucleotide polymorphisms. The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome. While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region. We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea.ConclusionsThese results lay the groundwork for future studies of adaptive ecological evolution in honey bees, and demonstrate the use of new, freely available web-based tools and workflows (http://usegalaxy.org/r/kenyanbee) that can be applied to any model system with genomic information.