Advancing Behavioural Genomics by Considering Timescale

Animal behavioural traits often covary with gene expression, pointing towards a genomic constraint on organismal responses to environmental cues. This pattern highlights a gap in our understanding of the time course of environmentally responsive gene expression, and moreover, how these dynamics are regulated. Advances in behavioural genomics explore how gene expression dynamics are correlated with behavioural traits that range from stable to highly labile. We consider the idea that certain genomic regulatory mechanisms may predict the timescale of an environmental effect on behaviour. This temporally minded approach could inform both organismal and evolutionary questions ranging from the remediation of early life social trauma to understanding the evolution of trait plasticity

Age, but Not Experience, Affects Courtship Gene Expression in Male Drosophila melanogaster

Mutation screens in model organisms have helped identify the foundation of many fundamental organismal phenotypes. An emerging question in evolutionary and behavioral biology is the extent to which these “developmental” genes contribute to the subtle individual variation that characterizes natural populations. A related question is whether individual differences arise from static differences in gene expression that arose during previous life stages, or whether they are due to dynamic regulation of expression during the life stage under investigation. Here, we address these questions using genes that have been discovered to control the development of normal courtship behavior in male Drosophila melanogaster. We examined whether these genes have static or dynamic expression in the heads of adult male flies of different ages and with different levels of social experience. We found that 16 genes of the 25 genes examined were statically expressed, and 9 genes were dynamically expressed with changes related to adult age. No genes exhibited rapid dynamic expression changes due to social experience or age*experience interaction. We therefore conclude that a majority of fly “courtship” genes are statically expressed, while a minority are regulated in adults with respect to age, but not with respect to relevant social experience. These results are consistent with those from a recent microarray analysis that found none of the canonical courtship genes changed expression in male flies after brief exposure to females

Sleep, aging, and lifespan in Drosophila

<p>Abstract</p> <p>Background</p> <p>Epidemiological studies in humans suggest that a decrease in daily sleep duration is associated with reduced lifespan, but this issue remains controversial. Other studies in humans also show that both sleep quantity and sleep quality decrease with age. <it>Drosophila melanogaster </it>is a useful model to study aging and sleep, and inheriting mutations affecting the potassium current Shaker results in flies that sleep less and have a shorter lifespan. However, whether the link between short sleep and reduced longevity exists also in wild-type flies is unknown. Similarly, it is unknown whether such a link depends on sleep amount per se, rather than on other factors such as waking activity. Also, sleep quality has been shown to decrease in old flies, but it remains unclear whether aging-related sleep fragmentation is a generalized phenomenon.</p> <p>Results</p> <p>We compared 3 short sleeping mutant lines (<it>Hk</it>¹, <it>Hk</it>^{<it>Y </it>}and <it>Hk</it>²) carrying a mutation in Hyperkinetic, which codes for the beta subunit of the Shaker channel, to wild-type siblings throughout their entire lifespan (all flies kept at 20°C). <it>Hk</it>¹and <it>Hk</it>^{<it>Y </it>}mutants were short sleeping relative to wild-type controls from day 3 after eclosure, and <it>Hk</it>²flies became short sleepers about two weeks later. All 3 <it>Hk </it>mutant lines had reduced lifespan relative to wild-type flies. Total sleep time showed a trend to increase in all lines with age, but the effect was most pronounced in <it>Hk</it>¹and <it>Hk</it>^{<it>Y </it>}flies. In both mutant and wild-type lines sleep quality did not decay with age, but the strong preference for sleep at night declined starting in "middle age". Using Cox regression analysis we found that in <it>Hk</it>¹and <it>Hk</it>^{<it>Y </it>}mutants and their control lines there was a negative relationship between total sleep amount during the first 2 and 4 weeks of age and hazard (individual risk of death), while no association was found in <it>Hk</it>²flies and their wild-type controls. <it>Hk</it>¹and <it>Hk</it>^{<it>Y </it>}mutants and their control lines also showed an association between total daily wake activity over the first 2 and 4 weeks of age and hazard. However, when both sleep duration and wake activity were used in the same regression, the effects of activity were much reduced, while most of the sleep effects remained significant. Finally, <it>Hk</it>¹flies and wild-type siblings were also tested at 25°C, and results were similar to those at 20°C. Namely, <it>Hk</it>¹mutants were short sleeping, hyperactive, and short lived relative to controls, and sleep quality in both groups did not decrease with age.</p> <p>Conclusions</p> <p>Different <it>Hk </it>mutations affect the sleep phenotype, and do so in an age-dependent manner. In 4 of the 6 lines tested sleep associates significantly with lifespan variation even after any effect of activity is removed, but activity does not associate significantly with lifespan after the effects of sleep are removed. Thus, in addition to environmental factors and genetic background, sleep may also affect longevity. Sleep quality does not necessarily decay as flies age, suggesting that aging-related sleep fragmentation may also depend on many factors, including genetic background and rearing conditions.</p

Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome

Background: Next-generation sequencing is providing researchers with a relatively fast and affordable option for developing genomic resources for organisms that are not among the traditional genetic models. Here we present a de novo assembly of the guppy (Poecilia reticulata) transcriptome using 454 sequence reads, and we evaluate potential uses of this transcriptome, including detection of sex-specific transcripts and deployment as a reference for gene expression analysis in guppies and a related species. Guppies have been model organisms in ecology, evolutionary biology, and animal behaviour for over 100 years. An annotated transcriptome and other genomic tools will facilitate understanding the genetic and molecular bases of adaptation and variation in a vertebrate species with a uniquely well known natural history. Results: We generated approximately 336 Mbp of mRNA sequence data from male brain, male body, female brain, and female body. The resulting 1,162,670 reads assembled into 54,921 contigs, creating a reference transcriptome for the guppy with an average read depth of 28×. We annotated nearly 40% of this reference transcriptome by searching protein and gene ontology databases. Using this annotated transcriptome database, we identified candidate genes of interest to the guppy research community, putative single nucleotide polymorphisms (SNPs), and male-specific expressed genes. We also showed that our reference transcriptome can be used for RNA- sequencing-based analysis of differential gene expression. We identified transcripts that, in juveniles, are regulated differently in the presence and absence of an important predator, Rivulus hartii, including two genes implicated in stress response. For each sample in the RNA-seq study, >50% of high-quality reads mapped to unique sequences in the reference database with high confidence. In addition, we evaluated the use of the guppy reference transcriptome for gene expression analyses in a congeneric species, the sailfin molly (Poecilia latipinna). Over 40% of reads from the sailfin molly sample aligned to the guppy transcriptome. Conclusions: We show that next-generation sequencing provided a reliable and broad reference transcriptome. This resource allowed us to identify candidate gene variants, SNPs in coding regions, and sex-specific gene expression, and permitted quantitative analysis of differential gene expression

Closure between aerosol particles and cloud condensation nuclei at Kaashidhoo Climate Observatory

Predicting the cloud condensation nuclei (CCN) supersaturation spectrum from aerosol properties is a fairly straightforward matter, as long as those properties are simple. During the Indian Ocean Experiment we measured CCN spectra, size-resolved aerosol chemical composition, and aerosol number distributions and attempted to reconcile them using a modified form of Köhler theory. We obtained general agreement between our measured and modeled CCN spectra. However, the agreement was not as good during a time period when organic carbon comprised a quarter of the total mass of the aerosol in the submicron size range. The modeled concentrations overpredict those actually measured during that time period. This suggests that some component, presumably organic material, can inhibit the uptake of water by the electrolytic fraction of the mass

Very Extended X-ray and H-alpha Emission in M82: Implications for the Superwind Phenomenon

We discuss the properties and implications of a 3.7x0.9 kpc region of spatially-coincident X-ray and H-alpha emission about 11.6 kpc to the north of the galaxy M82 previously discussed by Devine and Bally (1999). The PSPC X-ray spectrum is fit by thermal plasma (kT=0.80+-0.17 keV) absorbed by only the Galactic foreground column density. We evaluate the relationship of the X-ray/H-alpha ridge to the M82 superwind. The main properties of the X-ray emission can all be explained as being due to shock-heating driven as the superwind encounters a massive ionized cloud in the halo of M82. This encounter drives a slow shock into the cloud, which contributes to the excitation of the observed H-alpha emission. At the same time, a fast bow-shock develops in the superwind just upstream of the cloud, and this produces the observed X-ray emission. This interpretation would imply that the superwind has an outflow speed of roughly 800 km/s, consistent with indirect estimates based on its general X-ray properties and the kinematics of the inner kpc-scale region of H-alpha filaments. The gas in the M82 ridge is roughly two orders-of-magnitude hotter than the minimum "escape temperature" at this radius, so this gas will not be retained by M82. (abridged)Comment: 24 pages (latex), 3 figures (2 gif files and one postscript), accepted for publication in Part 1 of The Astrophysical Journa

Perceived psychosocial impacts of legalized same-sex marriage: A scoping review of sexual minority adults’ experiences

A growing body of literature provides important insights into the meaning and impact of the right to marry a same-sex partner among sexual minority people. We conducted a scoping review to 1) identify and describe the psychosocial impacts of equal marriage rights among sexual minority adults, and 2) explore sexual minority women (SMW) perceptions of equal marriage rights and whether psychosocial impacts differ by sex. Using Arksey and O’Malley’s framework we reviewed peer-reviewed English-language publications from 2000 through 2019. We searched six databases (PubMed, PsycINFO, CINAHL, Web of Science, JSTOR, and Sociological Abstracts) to identify English language, peer-reviewed journal articles reporting findings from empirical studies with an explicit focus on the experiences and perceived impact of equal marriage rights among sexual minority adults. We found 59 studies that met our inclusion criteria. Studies identified positive psychosocial impacts of same-sex marriage (e.g., increased social acceptance, reduced stigma) across individual, interpersonal (dyad, family), community (sexual minority), and broader societal levels. Studies also found that, despite equal marriage rights, sexual minority stigma persists across these levels. Only a few studies examined differences by sex, and findings were mixed. Research to date has several limitations; for example, it disproportionately represents samples from the U.S. and White populations, and rarely examines differences by sexual or gender identity or other demographic characteristics. There is a need for additional research on the impact of equal marriage rights and same-sex marriage on the health and well-being of diverse sexual minorities across the globe

Spatial correlation between submillimetre and Lyman-alpha galaxies in the SSA 22 protocluster

Lyman-alpha emitters are thought to be young, low-mass galaxies with ages of ~10^8 yr. An overdensity of them in one region of the sky (the SSA 22 field) traces out a filamentary structure in the early Universe at a redshift of z = 3.1 (equivalent to 15 per cent of the age of the Universe) and is believed to mark a forming protocluster. Galaxies that are bright at (sub)millimetre wavelengths are undergoing violent episodes of star formation, and there is evidence that they are preferentially associated with high-redshift radio galaxies, so the question of whether they are also associated with the most significant large-scale structure growing at high redshift (as outlined by Lyman-alpha emitters) naturally arises. Here we report an imaging survey of 1,100-um emission in the SSA 22 region. We find an enhancement of submillimetre galaxies near the core of the protocluster, and a large-scale correlation between the submillimetre galaxies and the low-mass Lyman-alpha emitters, suggesting synchronous formation of the two very different types of star-forming galaxy within the same structure at high redshift. These results are in general agreement with our understanding of the formation of cosmic structure.Comment: Published in Nature (7th May 2009 issue). The astro-ph paper includes the main text (10 pages, 2 figures, 1 table) and supplementary material (6 pages, 4 figures, 1 table

Evaluation of an Air Quality Model for the Size and Composition of Source-Oriented Particle Classes

Air quality model predictions of the size and composition of atmospheric particle classes are evaluated by comparison with aerosol time-of-flight mass spectrometry (ATOFMS) measurements of single-particle size and composition at Long Beach and Riverside, CA, during September 1996. The air quality model tracks the physical diameter, chemical composition, and atmospheric concentration of thousands of representative particles from different emissions classes as they are transported from sources to receptors while undergoing atmospheric chemical reactions. In the model, each representative particle interacts with a common gas phase but otherwise evolves separately from all other particles. The model calculations yield an aerosol population, in which particles of a given size may exhibit different chemical compositions. ATOFMS data are adjusted according to the known particle detection efficiencies of the ATOFMS instruments, and model predictions are modified to simulate the chemical sensitivities and compositional detection limits of the ATOFMS instruments. This permits a direct, semiquantitative comparison between the air quality model predictions and the single-particle ATOFMS measurements to be made. The air quality model accurately predicts the fraction of atmospheric particles containing sodium, ammonium, nitrate, carbon, and mineral dust, across all particle sizes measured by ATOFMS at the Long Beach site, and in the coarse particle size range (D_a ≥ 1.8 μm) at the Riverside site. Given that this model evaluation is very likely the most stringent test of any aerosol air quality model to date, the model predictions show impressive agreement with the single-particle ATOFMS measurements