E pluribus unum, ex uno plura: quantitative and single-gene perspectives on the study of behavior

Natural variation in codon bias and mRNA folding strength interact synergistically to modify protein expression in Saccharomyces cerevisiae

Codon bias and mRNA folding strength (mF) are hypothesized molecular mechanisms by which polymorphisms in genes modify protein expression. Natural patterns of codon bias and mF across genes as well as effects of altering codon bias and mF suggest that the influence of these 2 mechanisms may vary depending on the specific location of polymorphisms within a transcript. Despite the central role codon bias and mF may play in natural trait variation within populations, systematic studies of how polymorphic codon bias and mF relate to protein expression variation are lacking. To address this need, we analyzed genomic, transcriptomic, and proteomic data for 22 Saccharomyces cerevisiae isolates, estimated protein accumulation for each allele of 1,620 genes as the log of protein molecules per RNA molecule (logPPR), and built linear mixed-effects models associating allelic variation in codon bias and mF with allelic variation in logPPR. We found that codon bias and mF interact synergistically in a positive association with logPPR, and this interaction explains almost all the effects of codon bias and mF. We examined how the locations of polymorphisms within transcripts influence their effects and found that codon bias primarily acts through polymorphisms in domain-encoding and 3' coding sequences, while mF acts most significantly through coding sequences with weaker effects from untranslated regions. Our results present the most comprehensive characterization to date of how polymorphisms in transcripts influence protein expression.

Learning about quantitative genetics from Marla Sokolowski

Marla Sokolowski is a true pioneer in behavioral genetics, having made the first molecular delineation of a naturally occurring behavioral polymorphism in her work on the foraging locus in Drosophila melanogaster. The gene was subsequently found to be responsible for behavioral variants and types in many other species, both invertebrate and mammal (human). The path to get there is a paradigmatic example of how to use the power of genetic analysis, including some rather esoteric techniques, to zero in on a gene and delineate its molecular identity and its pleiotropic roles.

Of what use is connectomics? A personal perspective on the Drosophila connectome

The brain is a network of neurons and its biological output is behaviour. This is an exciting age, with a growing acknowledgement that the comprehensive compilation of synaptic circuits densely reconstructed in the brains of model species is now both technologically feasible and a scientifically enabling possibility in neurobiology, much as 30 years ago genomics was in molecular biology and genetics. Implemented by huge advances in electron microscope technology, especially focused ion beam-scanning electron microscope (FIB-SEM) milling (see Glossary), image capture and alignment, and computer-aided reconstruction of neuron morphologies, enormous progress has been made in the last decade in the detailed knowledge of the actual synaptic circuits formed by real neurons, in various brain regions of the fly Drosophila It is useful to distinguish synaptic pathways that are major, with 100 or more presynaptic contacts, from those that are minor, with fewer than about 10; most neurites are both presynaptic and postsynaptic, and all synaptic sites have multiple postsynaptic dendrites. Work on Drosophila has spearheaded these advances because cell numbers are manageable, and neuron classes are morphologically discrete and genetically identifiable, many confirmed by reporters. Recent advances are destined within the next few years to reveal the complete connectome in an adult fly, paralleling advances in the larval brain that offer the same prospect possibly within an even shorter time frame. The final amendment and validation of segmented bodies by human proof-readers remains the most time-consuming step, however. The value of a complete connectome in Drosophila is that, by targeting to specific neurons transgenes that either silence or activate morphologically identified circuits, and then identifying the resulting behavioural outcome, we can determine the causal mechanism for behaviour from its loss or gain. More importantly, the connectome reveals hitherto unsuspected pathways, leading us to seek novel behaviours for these. Circuit information will eventually be required to understand how differences between brains underlie differences in behaviour, and especially to herald yet more advanced connectomic strategies for the vertebrate brain, with an eventual prospect of understanding cognitive disorders having a connectomic basis. Connectomes also help us to identify common synaptic circuits in different species and thus to reveal an evolutionary progression in candidate pathways.

Assessing the Genetic Landscape of Animal Behavior

Recent years have seen an increase in studies that associate genomic loci with behavioral variation both within and across animal species. Ryan York compiles and analyzes over 1,000 of these loci, finding that the genetic...

Although most animal behaviors are associated with some form of heritable genetic variation, we do not yet understand how genes sculpt behavior across evolution, either directly or indirectly. To address this, I here compile a data set comprised of over 1000 genomic loci representing a spectrum of behavioral variation across animal taxa. Comparative analyses reveal that courtship and feeding behaviors are associated with genomic regions of significantly greater effect than other traits, on average threefold greater than other behaviors. Investigations of whole-genome sequencing and phenotypic data for 87 behavioral traits from the Drosophila Genetics Reference Panel indicate that courtship and feeding behaviors have significantly greater genetic contributions and that, in general, behavioral traits overlap little in individual base pairs but increasingly interact at the levels of genes and traits. These results provide evidence that different types of behavior are associated with variable genetic bases and suggest that, across animal evolution, the genetic landscape of behavior is more rugged, yet predictable, than previously thought.

Natural variability in Drosophila larval and pupal NaCl tolerance

The regulation of NaCl is essential for the maintenance of cellular tonicity and functionality, and excessive salt exposure has many adverse effects. The fruit fly, Drosophila melanogaster, is a good osmoregulator and some strains can survive on media with very low or high NaCl content. Previous analyses of mutant alleles have implicated various stress signaling cascades in NaCl sensitivity or tolerance; however, the genes influencing natural variability of NaCl tolerance remain for the most part unknown. Here, we use two approaches to investigate natural variation in D. melanogaster NaCl tolerance. We describe four D. melanogaster lines that were selected for different degrees of NaCl tolerance, and present data on their survival, development, and pupation position when raised on varying NaCl concentrations. After finding evidence for natural variation in salt tolerance, we present the results of Quantitative Trait Loci (QTL) mapping of natural variation in larval and pupal NaCl tolerance, and identify different genomic regions associated with NaCl tolerance during larval and pupal development.

“Altruism: a saga”

Recently, a number of prominent evolutionary biologists have contested the theory of kin selection and have in turn been strongly challenged by the majority of their colleagues. The heated nature of the argument over the role of kin and group selection in the evolution of altruism is a testament to the ways in which vested interests and intellectual territory disputes play out in scientific proceedings. However, a closer look at the history of attempts to understand the evolution of altruism, going back to Darwin, suggests that something more than mere academic sword-fighting is going on. There is a long history of social and biological thought intermingling and influencing each other when it comes to the study of social behavior. A consideration of this history, alongside a consideration of possible significant parallels in the evolution of sociality in nature and in man, may help to make better sense of why an entire community is up in arms about ants.

Genes involved in sex pheromone discrimination in Drosophila melanogaster and their background-dependent effect

Mate choice is based on the comparison of the sensory quality of potential mating partners, and sex pheromones play an important role in this process. In Drosophila melanogaster, contact pheromones differ between male and female in their content and in their effects on male courtship, both inhibitory and stimulatory. To investigate the genetic basis of sex pheromone discrimination, we experimentally selected males showing either a higher or lower ability to discriminate sex pheromones over 20 generations. This experimental selection was carried out in parallel on two different genetic backgrounds: wild-type and desat1 mutant, in which parental males showed high and low sex pheromone discrimination ability respectively. Male perception of male and female pheromones was separately affected during the process of selection. A comparison of transcriptomic activity between high and low discrimination lines revealed genes not only that varied according to the starting genetic background, but varied reciprocally. Mutants in two of these genes, Shaker and quick-to-court, were capable of producing similar effects on discrimination on their own, in some instances mimicking the selected lines, in others not. This suggests that discrimination of sex pheromones depends on genes whose activity is sensitive to genetic context and provides a rare, genetically defined example of the phenomenon known as “allele flips,” in which interactions have reciprocal effects on different genetic backgrounds.

Thinking about visual behavior; learning about photoreceptor function

Visual behavioral assays in Drosophila melanogaster were initially developed to explore the genetic control of behavior, but have a rich history of providing conceptual openings into diverse questions in cell and developmental biology. Here, we briefly summarize the early efforts to employ three of these behaviors: phototaxis, the UV-visible light choice, and the optomotor response. We then discuss how each of these assays has expanded our understanding of neuronal connection specificity and synaptic function. All of these studies have contributed to the development of sophisticated tools for manipulating gene expression, assessing cell fate specification, and visualizing neuronal development. With these tools in hand, the field is now poised to return to the original goal of understanding visual behavior using genetic approaches.

Genome-wide expression patterns and the genetic architecture of a fundamental social trait

Explaining how interactions between genes and the environment influence social behavior is a fundamental research goal, yet there is limited relevant information for species exhibiting natural variation in social organization. The fire ant Solenopsis invicta is characterized by a remarkable form of social polymorphism, with the presence of one or several queens per colony and the expression of other phenotypic and behavioral differences being completely associated with allelic variation at a single Mendelian factor marked by the gene Gp-9. Microarray analyses of adult workers revealed that differences in the Gp-9 genotype are associated with the differential expression of an unexpectedly small number of genes, many of which have predicted functions, implying a role in chemical communication relevant to the regulation of colony queen number. Even more surprisingly, worker gene expression profiles are more strongly influenced by indirect effects associated with the Gp-9 genotypic composition within their colony than by the direct effect of their own Gp-9 genotype. This constitutes an unusual example of an “extended phenotype” and suggests a complex genetic architecture with a single Mendelian factor, directly and indirectly influencing the individual behaviors that, in aggregate, produce an emergent colony-level phenotype.

Fundamental research goals for scientists interested in social evolution are to determine the numbers and types of genes that directly regulate individual social behaviors as well as to understand how the social environment indirectly influences the expression of socially relevant traits. The fire ant Solenopsis invicta features a remarkable form of social variation in which the occurrence of two distinct social types that differ in colony queen number is associated with genetic differences at a genomic region marked by the gene Gp-9. Our analyses of gene expression profiles in fire ant workers revealed that differences in Gp-9 genotype are associated with the differential expression of an unexpectedly small number of genes, many of which are predicted to function in chemical communication relevant to the regulation of colony queen number. Surprisingly, worker gene expression profiles are more strongly influenced by indirect effects associated with the social environment within their colony than by the direct effect of their own Gp-9 genotype. These results suggest a complex genetic architecture underlying the control of colony queen number in fire ants, with a single Mendelian factor directly regulating, and the social environment indirectly influencing, the expression of the individual behaviors that, in aggregate, yield an emergent colony social organization.

Microarray analysis of replicate populations selected against a wing-shape correlation in Drosophila melanogaster

We selected bidirectionally to change the phenotypic correlation between two wing dimensions in Drosophila melanogaster and measured gene expression differences in late third instar wing disks, using microarrays. We tested an array of 12 selected lines, including 10 from a Massachusetts population (5 divergently selected pairs) and 2 from a California population (1 divergently selected pair). In the Massachusetts replicates, 29 loci showed consistent, significant expression differences in all 5 line-pair comparisons. However, the significant loci in the California lines were almost completely different from these. The disparity between responding genes in different gene pools confirms recent evidence that surprisingly large numbers of loci can affect wing shape. Our results also show that with well-replicated selection lines, of large effective size, the numbers of candidate genes in microarray-based searches can be reduced to realistic levels.

Neuropeptide Y facilitates activity-based-anorexia

The hypothesis that treatment with neuropeptide Y (NPY) can increase running activity and decrease food intake and body weight was tested. Female rats with a running wheel lost more weight than sedentary rats and ran progressively more as the availability of food was gradually reduced. When food was available for only 1h/day, the rats lost control over body weight. Correlatively, the level of NPY mRNA was increased in the hypothalamic arcuate nucleus. This phenomenon, activity-based-anorexia, was enhanced by intracerebroventricular infusion of NPY in rats which had food available during 2h/day. By contrast, NPY stimulated food intake but not wheel running in rats which had food available continuously. These findings are inconsistent with the prevailing theory of the role of the hypothalamus in the regulation of body weight according to which food intake is a homeostatic process controlled by "orexigenic" and "anorexigenic" neural networks. However, the finding that treatment with NPY, generally considered an "orexigen", can increase physical activity and decrease food intake and cause a loss of body weight is in line with the clinical observation that patients with anorexia nervosa are physically hyperactive and eat only little food despite having depleted body fat and up-regulated hypothalamic "orexigenic" peptides.

Theforaging gene ofDrosophila melanogaster: Spatial-expression analysis and sucrose responsiveness

The ability to identify and respond to food is essential for survival, yet little is known about the neural substrates that regulate natural variation in food-related traits. The foraging (for) gene in Drosophila melanogaster encodes a cGMP-dependent protein kinase (PKG) and has been shown to function in food-related traits. To investigate the tissue distribution of FOR protein, we generated an antibody against a common region of the FOR isoforms. In the adult brain we localized FOR to neuronal clusters and projections including neurons that project to the central complex, a cluster within the dorsoposterior region of the brain hemispheres, a separate cluster medial to optic lobes and lateral to brain hemispheres, a broadly distributed frontal-brain cluster, axon bundles of the antennal nerve and of certain subesophageal-ganglion nerves, and the medulla optic lobe. These newly described tissue distribution patterns of FOR protein provide candidate neural clusters and brain regions for investigation of neural networks that govern foraging-related traits. To determine whether FOR has a behavioral function in neurons we expressed UAS-for in neurons using an elav-gal4 driver and measured the effect on adult sucrose responsiveness (SR), known to be higher in rovers than sitters, the two natural variants of foraging. We found that pan-neuronal expression of for caused an increase in the SR of sitters, demonstrating a neural function for PKG in this food-related behavior.

Natural variation in Drosophila melanogaster diapause due to the insulin-regulated PI3-kinase

This study links natural variation in a Drosophila melanogaster overwintering strategy, diapause, to the insulin-regulated phosphatidylinositol 3-kinase (PI3-kinase) gene, Dp110. Variation in diapause, a reproductive arrest, was associated with Dp110 by using Dp110 deletions and genomic rescue fragments in transgenic flies. Deletions of Dp110 increased the proportion of individuals in diapause, whereas expression of Dp110 in the nervous system, but not including the visual system, decreased it. The roles of phosphatidylinositol 3-kinase for both diapause in D. melanogaster and dauer formation in Caenorhabditis elegans suggest a conserved role for this kinase in both reproductive and developmental arrests in response to environmental stresses.

Variability, compensation and homeostasis in neuron and network function

Neurons in most animals live a very long time relative to the half-lives of all of the proteins that govern excitability and synaptic transmission. Consequently, homeostatic mechanisms are necessary to ensure stable neuronal and network function over an animal's lifetime. To understand how these homeostatic mechanisms might function, it is crucial to understand how tightly regulated synaptic and intrinsic properties must be for adequate network performance, and the extent to which compensatory mechanisms allow for multiple solutions to the production of similar behaviour. Here, we use examples from theoretical and experimental studies of invertebrates and vertebrates to explore several issues relevant to understanding the precision of tuning of synaptic and intrinsic currents for the operation of functional neuronal circuits.

Comparative plasticity of brain synapses in inbred mouse strains

One niche of experimental biology that has experienced considerable progress is the neurobiology of learning and memory. A key contributor to such progress has been the widespread use of transgenic and `knockout' mice to elucidate the mechanisms of identifiable phenotypes of learning and memory. Inbred mouse strains are needed to generate genetically modified mice. However, genetic variations between inbred strains can confound the interpretation of cellular neurophysiological phenotypes of mutant mice. It is known that altered physiological strength of synaptic transmission (`synaptic plasticity') can modify and regulate learning and memory. Characterization of the synaptic phenotypes of inbred mouse strains is needed to identify the most appropriate strains to use for generating mutant mouse models of memory function. More importantly, comparative electrophysiological analyses of inbred mice per se can also shed light on which forms of synaptic plasticity underlie particular types of learning and memory. Many such analyses have focused on synaptic plasticity in the hippocampus because of the critical roles of this brain structure in the formation and consolidation of long-term memories. Comparative electrophysiological data obtained from several inbred mouse strains are reviewed here to highlight the following key notions: (1) synaptic plasticity is influenced by the genetic backgrounds of inbred mice; (2) the plasticity of hippocampal synapses in inbred mice is`tuned' to particular temporal patterns of activity; (3) long-term potentiation, but not long-term depression, is a cellular correlate of behavioural memory performance in some strains; (4) synaptic phenotyping of inbred mouse strains can identify cellular models of memory impairment that can be used to elucidate mechanisms that may cause specific memory deficits.

A protocol for high-throughput phenotyping, suitable for quantitative trait analysis in mice

Whole-genome genetic association studies in outbred mouse populations represent a novel approach to identifying the molecular basis of naturally occurring genetic variants, the major source of quantitative variation between inbred strains of mice. Measuring multiple phenotypes in parallel on each mouse would make the approach cost effective, but protocols for phenotyping on a large enough scale have not been developed. In this article we describe the development and deployment of a protocol to collect measures on three models of human disease (anxiety, type II diabetes, and asthma) as well as measures of mouse blood biochemistry, immunology, and hematology. We report that the protocol delivers highly significant differences among the eight inbred strains (A/J, AKR/J, BALBc/J, CBA/J, C3H/HeJ, C57BL/6 J, DBA/2 J, and LP/J), the progenitors of a genetically heterogeneous stock (HS) of mice. We report the successful collection of multiple phenotypes from 2000 outbred HS animals. The phenotypes measured in the protocol form the basis of a large-scale investigation into the genetic basis of complex traits in mice designed to examine interactions between genes and between genes and environment, as well as the main effects of genetic variants on phenotypes.