Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray

BACKGROUND: Unravelling the path from genotype to phenotype, as it is influenced by an organism's environment, is one of the central goals in biology. Gene expression profiling by means of microarrays has become very prominent in this endeavour, although resources exist only for relatively few model systems. As genomics has matured into a comparative research program, expression profiling now also provides a powerful tool for non-traditional model systems to elucidate the molecular basis of complex traits. RESULTS: Here we present a microarray constructed with ~4500 features, derived from a brain-specific cDNA library for the African cichlid fish Astatotilapia burtoni (Perciformes). Heterologous hybridization, targeting RNA to an array constructed for a different species, is used for eight different fish species. We quantified the concordance in gene expression profiles across these species (number of genes and fold-changes). Although most robust when target RNA is derived from closely related species (<10 MA divergence time), our results showed consistent profiles for other closely related taxa (~65 MA divergence time) and, to a lesser extent, even very distantly related species (>200 MA divergence time). CONCLUSION: This strategy overcomes some of the restrictions imposed on model systems that are of importance for evolutionary and ecological studies, but for which only limited sequence information is available. Our work validates the use of expression profiling for functional genomics within a comparative framework and provides a foundation for the molecular and cellular analysis of complex traits in a wide range of organisms

Are some individuals generally more behaviorally plastic than others? An experiment with sailfin mollies

Individuals within the same population generally differ among each other not only in their behavioral traits but also in their level of behavioral plasticity (i.e., in their propensity to modify their behavior in response to changing conditions). If the proximate factors underlying individual differences in behavioral plasticity were the same for any measure of plasticity, as commonly assumed, one would expect plasticity to be repeatable across behaviors and contexts. However, this assumption remains largely untested. Here, we conducted an experiment with sailfin mollies (Poecilia latipinna) whose behavioral plasticity was estimated both as the change in their personality traits or mating behavior across a social gradient and using their performance on a reversal-learning task. We found that the correlations between pairwise measures of plasticity were weak and non-significant, thus indicating that the most plastic individuals were not the same in all the tests. This finding might arise because either individuals adjust the magnitude of their behavioral responses depending on the benefits of plasticity, and/or individuals expressing high behavioral plasticity in one context are limited by neural and/or physiological constraints in the amount of plasticity they can express in other contexts. Because the repeatability of behavioral plasticity may have important evolutionary consequences, additional studies are needed to assess the importance of trade-offs between conflicting selection pressures on the maintenance of intra-individual variation in behavioral plasticity

Evolutionary conserved neural signature of early life stress affects animal social competence

In vertebrates, the early social environment can persistently influence behaviour and social competence later in life. However, the molecular mechanisms underlying variation in animal social competence are largely unknown. In rats, high-quality maternal care causes an upregulation of hippocampal glucocorticoid receptors (gr) and reduces offspring stress responsiveness. This identifies gr regulation as a candidate mechanism for maintaining variation in animal social competence. We tested this hypothesis in a highly social cichlid fish, Neolamprologus pulcher, reared with or without caring parents. We find that the molecular pathway translating early social experience into later-life alterations of the stress axis is homologous across vertebrates: fish reared with parents expressed the glucocorticoid receptor gr1 more in the telencephalon. Furthermore, expression levels of the transcription factor egr-1 (early growth response 1) were associated with gr1 expression in the telencephalon and hypothalamus. When blocking glucocorticoid receptors (GR) with an antagonist, mifepristone (RU486), parent-reared individuals showed more socially appropriate, submissive behaviour when intruding on a larger conspecific's territory. Remarkably, mifepristone-treated fish were less attacked by territory owners and had a higher likelihood of territory takeover. Our results indicate that early social-environment effects on stress axis programming are mediated by an evolutionary conserved molecular pathway, which is causally involved in environmentally induced variation of animal social competence

Effect of the early social environment on behavioural and genomic responses to a social challenge in a cooperatively breeding vertebrate

The early social environment can have substantial, lifelong effects on vertebrate social behaviour, which can be mediated by developmental plasticity of brain gene expression. Early-life effects can influence immediate behavioural responses towards later-life social challenges and can activate different gene expression responses. However, while genomic responses to social challenges have been reported frequently, how developmental experience influences the shape of these genomic reaction norms remains largely unexplored. We tested how manipulating the early social environment of juvenile cooperatively breeding cichlids, Neolamprologus pulcher, affects their behavioural and brain genomic responses when competing over a resource. Juveniles were reared either with or without a breeder pair and a helper. Fish reared with family members behaved more appropriately in the competition than when reared without. We investigated whether the different social rearing environments also affected the genomic responses to the social challenge. A set of candidate genes, coding for hormones and receptors influencing social behaviour, were measured in the telencephalon and hypothalamus. Social environment and social challenge both influenced gene expression of egr-1 (early growth response 1) and gr1 (glucocorticoid receptor 1) in the telencephalon and of bdnf (brain-derived neurotrophic factor) in the hypothalamus. A global analysis of the 11 expression patterns in the two brain areas showed that neurogenomic states diverged more strongly between intruder fish and control fish when they had been reared in a natural social setting. Our results show that same molecular pathways may be used differently in response to a social challenge depending on early-life experiences

Balancing selection on size: effects on the incidence of an alternative reproductive tactic

ABSTRACT Question: Does fluctuating natural selection on body size of fish among years (balancing selection) influence the frequency of an alternative male reproductive tactic? Hypothesis: When the surviving juveniles of a cohort are larger because of selection, a higher proportion of the population will develop as mature &apos;sneaker&apos; males than expected in the absence of selection. In the case where selection favours smaller individuals, a lower proportion will develop as mature &apos;sneaker&apos; males. Organisms: Juvenile Atlantic salmon (Salmo salar) from a naturally sustained population in the Ste-Marguerite River, Centre Interuniversitaire de Recherche sur le Saumon Atlantique, Province of Québec, Canada. Methods: The presence of balancing size-selection was examined by measuring the proportional shift of the mean size and variance of juvenile salmon sampled in the autumn and following spring at multiple sites for each of three annual cohorts. The proportional shift in mean size of individuals over winter was then correlated with the incidence of early male maturity (sneakers) observed at the same sites for each cohort the following fall. Conclusions: Winter mortality decreased the size of surviving fish in one cohort by 7.8% on average, increased size by 2.7% on average in another and had little effect on the third. Proportionally more juvenile males adopted the sneaker tactic when juveniles surviving winter were larger, whereas fewer juvenile males adopted the sneaker tactic when surviving juveniles were smaller. The fluctuating nature of selection on body size indirectly maintains life-cycle divergence through a direct effect on size frequencies within a cohort

Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains

BACKGROUND: Sinorhizobium meliloti is a soil bacterium that forms nitrogen-fixing nodules on the roots of leguminous plants such as alfalfa (Medicago sativa). This species occupies different ecological niches, being present as a free-living soil bacterium and as a symbiont of plant root nodules. The genome of the type strain Rm 1021 contains one chromosome and two megaplasmids for a total genome size of 6 Mb. We applied comparative genomic hybridisation (CGH) on an oligonucleotide microarrays to estimate genetic variation at the genomic level in four natural strains, two isolated from Italian agricultural soil and two from desert soil in the Aral Sea region. RESULTS: From 4.6 to 5.7 percent of the genes showed a pattern of hybridisation concordant with deletion, nucleotide divergence or ORF duplication when compared to the type strain Rm 1021. A large number of these polymorphisms were confirmed by sequencing and Southern blot. A statistically significant fraction of these variable genes was found on the pSymA megaplasmid and grouped in clusters. These variable genes were found to be mainly transposases or genes with unknown function. CONCLUSION: The obtained results allow to conclude that the symbiosis-required megaplasmid pSymA can be considered the major hot-spot for intra-specific differentiation in S. meliloti

Stability of palm oil-based emulsion liquid membrane for succinic acid extraction from aqueous solution

Emulsion liquid membrane (ELM) process has high potential in the separation of succinic from the fermentation broth. However, the major drawback of this technology is the stability of emulsion globules during the extraction process and the chemical involve d in the liquid membrane formulation. This study investigate the stability of ELM using a greener formulation containing Amberlite LA - 2 as a carrier, Span 80 and Tween 80 as a surfactant, palm oil as a diluent and sodium carbonate (Na 2 CO 3 ) as an aqueous st ripping agent. The emulsion stability was evaluated by observing the water - oil separation of the emulsion and microscopic image of emulsion droplets count and size. Several operating parameters including the organic to internal ratio, homogenizer speed, ho mogenizing time, and surfactant concentration, and surfactant blend were investigated. The results show the most stable water - in - oil emulsion was observed at 3:1 organic to internal ratio; 7000rpm homogenizer speed; 5 minute emulsification time; 3% (w/v) s urfactant at HLB 8. Besides, the extraction study shows 70% of the succinic acid was extracted at 0.01M Na 2 CO 3 , 1:3 treat ratio, and 0.7M Amberlite in palm oil at optimum primary emulsion stability conditions. This indicates the potential of using palm oil based ELM for the extraction of succinic acid

A test of the coupling of predator defense morphology and behavior variation in two threespine stickleback populations

Among-population differences in morphology and behaviors such as boldness have been shown to co-vary with ecological conditions, including predation regime. However, between- and within-population covariation of predator defense morphology with variation in behaviors relevant to ecology and evolution (boldness, exploration, activity, sociability and aggressiveness, often defined as personality traits when they are consistent across time and contexts) have never been quantified together in a single study in juvenile fish from populations found in contrasting environments. We measured predator defense morphology differences between adults from two freshwater populations of threespine sticklebacks with different ecological conditions. We then quantified five behaviors in juveniles from both populations raised in a common environment. Wild-caught adults showed significant differences in predator defense morphology. One population had significantly lower lateral plate number, shorter dorsal spine, pelvic spine and pelvic girdle. Furthermore, 61% of individuals from that population showed an absence of pelvic spine and girdle. At the population level, we found that differences in defense morphology in adults between the two lakes were coupled with differences in behaviors in juveniles raised in a common environment. Levels of activity, aggressiveness and boldness were higher in juveniles from the population lacking predator defense structures. At the individual level, anti-predator morphology of adult females could not predict their offspring’s behavior, but juvenile coloration predicted individual boldness in a population-specific manner. Our results suggest that ecological conditions, as reflected in adult predator defense morphology, also affect juvenile behavior in threespine sticklebacks, resulting in trait co-specialization, and that there is a genetic or epigenetic component to these behavioral differences [Current Zoology 58 (1): 53–65, 2012]