Dan Valente

Analysis of the Trajectory of Drosophila melanogaster in a Circular Open Field Arena

Background Obtaining a complete phenotypic characterization of a freely moving organism is a difficult task, yet such a description is desired in many neuroethological studies. Many metrics currently used in the literature to describe locomotor and exploratory behavior are typically based on average quantities or subjectively chosen spatial and temporal thresholds. All of these measures are relatively coarse-grained in the time domain. It is advantageous, however, to employ metrics based on the entire trajectory that an organism takes while exploring its environment. Methodology/Principal Findings To characterize the locomotor behavior of Drosophila melanogaster, we used a video tracking system to record the trajectory of a single fly walking in a circular open field arena. The fly was tracked for two hours. Here, we present techniques with which to analyze the motion of the fly in this paradigm, and we discuss the methods of calculation. The measures we introduce are based on spatial and temporal probability distributions and utilize the entire time-series trajectory of the fly, thus emphasizing the dynamic nature of locomotor behavior. Marginal and joint probability distributions of speed, position, segment duration, path curvature, and reorientation angle are examined and related to the observed behavior. Conclusions/Significance The measures discussed in this paper provide a detailed profile of the behavior of a single fly and highlight the interaction of the fly with the environment. Such measures may serve as useful tools in any behavioral study in which the movement of a fly is an important variable and can be incorporated easily into many setups, facilitating high-throughput phenotypic characterization.

An assay for social interaction in Drosophila fragile X mutants

We developed a novel assay to examine social interactions in Drosophila and, as a first attempt, apply it here at examining the behavior of Drosophila Fragile X Mental Retardation gene (dfmr1) mutants. Fragile X syndrome is the most common cause of single gene intellectual disability (ID) and is frequently associated with autism. Our results suggest that dfmr1 mutants are less active than wild-type flies and interact with each other less often. In addition, mutants for one allele of dfmr1, dfmr1B55, are more likely to come in close contact with a wild-type fly than another dfmr1B55 mutant. Our results raise the possibility of defective social expression with preserved receptive abilities. We further suggest that the assay may be applied in a general strategy of examining endophenoypes of complex human neurological disorders in Drosophila, and specifically in order to understand the genetic basis of social interaction defects linked with ID.

The angular interval between the direction of progression and body orientation in normal, alcohol- and cocaine treated fruit flies.

In this study we characterize the coordination between the direction a fruit-fly walks and the direction it faces, as well as offer a methodology for isolating and validating key variables with which we phenotype fly locomotor behavior. Our fundamental finding is that the angular interval between the direction a fly walks and the direction it faces is actively managed in intact animals and modulated in a patterned way with drugs. This interval is small in intact flies, larger with alcohol and much larger with cocaine. The dynamics of this interval generates six coordinative modes that flow smoothly into each other. Under alcohol and much more so under cocaine, straight path modes dwindle and modes involving rotation proliferate. To obtain these results we perform high content analysis of video-tracked open field locomotor behavior. Presently there is a gap between the quality of descriptions of insect behaviors that unfold in circumscribed situations, and descriptions that unfold in extended time and space. While the first describe the coordination between low-level kinematic variables, the second quantify cumulative measures and subjectively defined behavior patterns. Here we reduce this gap by phenotyping extended locomotor behavior in terms of the coordination between low-level kinematic variables, which we quantify, combining into a single field two disparate fields, that of high content phenotyping and that of locomotor coordination. This will allow the study of the genes/brain/locomotor coordination interface in genetically engineered and pharmacologically manipulated animal models of human diseases.

Characterizing Animal Behavior through Audio and Video Signal Processing

This article presents two instances in which multimedia systems and processing have elucidated animal behavior and have been central in developing quantitative descriptions. These examples demonstrate multimedia systems utility and necessity in developing a complete phenotypic description. We hope that this article will spur interest in this subject in the multimedia community, so more advanced processing techniques will enter the field of quantitative neuroethology. You might have noticed that in our two examples, there was nothing very multimodal about the media techniques used. Both of these systems are transparently unimodal. This speaks to the limited crossover between the multimedia community and the behavioral neuroscientists (or neuroethologists). These examples did show, however, that the neuroscientific community can benefit greatly from incorporating multimedia techniques into their experiments and data analysis. As the walls between these disciplines begin to fall, experimental setups that are truly multimedia will likely appear. Such systems will allow complete phenotypic descriptions of animals in ethologically relevant settings, along with methods for analyzing, manipulating, annotating, and storing the resulting data. Combining these phenotypic descriptions with the corresponding genetic and neural network properties will facilitate the connection of these organization levels and lead to a more thorough understanding of brain functioning.

Generative rules of Drosophila locomotor behavior as a candidate homology across phyla

The discovery of shared behavioral processes across phyla is a significant step in the establishment of a comparative study of behavior. We use immobility as an origin and reference for the measurement of fly locomotor behavior; speed, walking direction and trunk orientation as the degrees of freedom shaping this behavior; and cocaine as the parameter inducing progressive transitions in and out of immobility. We characterize and quantify the generative rules that shape Drosophila locomotor behavior, bringing about a gradual buildup of kinematic degrees of freedom during the transition from immobility to normal behavior, and the opposite narrowing down into immobility. Transitions into immobility unfold via sequential enhancement and then elimination of translation, curvature and finally rotation. Transitions out of immobility unfold by progressive addition of these degrees of freedom in the opposite order. The same generative rules have been found in vertebrate locomotor behavior in several contexts (pharmacological manipulations, ontogeny, social interactions) involving transitions in-and-out of immobility. Recent claims for deep homology between arthropod central complex and vertebrate basal ganglia provide an opportunity to examine whether the rules we report also share common descent. Our approach prompts the discovery of behavioral homologies, contributing to the elusive problem of behavioral evolution.

Characterization of animal behavior through the use of audio and video signal processing

Quantifiying animal behavior is a challenge at the forefront of research in neuroscience. This type of objective description is essential for proper interpretation of results, ensures reproducibility of experiments across laboratories, and presents the researcher with a more complete picture of the genotype-phenotype relationship in the context of the nervous system. Because high-throughput experimental setups increasingly require automated acquisition and analysis of long series of behavioral data, multimedia systems are becoming a vital part of the behavioral neuroscientist’s toolkit. In this article we present two examples in which audio and video acquisition and processing have been used to quantify animal behavior, ranging from mammal locomotor activity to birdsong.

Laboratory evolution of adenylyl cyclase independent learning in Drosophila and missing heritability

Gene interactions are acknowledged to be a likely source of missing heritability in large‐scale genetic studies of complex neurological phenotypes. However, involvement of rare variants, de novo mutations, genetic lesions that are not easily detected with commonly used methods and epigenetic factors also are possible explanations. We used a laboratory evolution study to investigate the modulatory effects of background genetic variation on the phenotypic effect size of a null mutation with known impact on olfactory learning. To accomplish this, we first established a population that contained variation at just 23 loci and used selection to evolve suppression of the learning defect seen with null mutations in the rutabaga adenylyl cyclase. We thus biased the system to favor relatively simplified outcomes by choosing a Mendelian trait and by restricting the genetic variation segregating in the population. This experimental design also assures that the causal effects are among the known 23 segregating loci. We observe a robust response to selection that requires the presence of the 23 variants. Analyses of the underlying genotypes showed that interactions between more than two loci are likely to be involved in explaining the selection response, with implications for the missing heritability problem.

Shared generative rules of locomotor behavior in arthropods and vertebrates

The discovery of shared behavioral processes across phyla is an essential step in the establishment of a comparative study of behavior. We use immobility as an origin and reference for the measurement of locomotor behavior; speed, direction of walking and direction of facing as the three degrees of freedom shaping fly locomotor behavior; and cocaine as the parameter inducing a progressive transition in and out of immobility. In this way we expose and quantify the generative rules that shape part of fruit fly locomotor behavior, bringing about a gradual buildup of freedom during the transition from immobility to normal behavior and a precisely opposite narrowing down during the transition into immobility. During buildup the fly exhibits enhancement and then reduction to normal values of movement along each degree of freedom: first, body rotation in the horizontal plane, then path curvature and then speed of translation. Transition into immobility unfolds by narrowing down of the repertoire in the opposite sequential order, showing reciprocal relations during both buildup and narrowing down. The same generative rules apply to vertebrate locomotor behavior in a variety of contexts involving transition out and into immobility. Recent claims for deep homology between the arthropod central complex and the vertebrate basal ganglia provide an opportunity to examine whether the generative rules we discovered also share common descent. Neurochemical processes mediating the buildup of locomotor behavior in vertebrates could guide the search for equivalent processes in arthropods. The measurement methodology we use prompts the discovery of candidate behavioral homologies. Significance Statement Do flies and mice share the same behavior? By defining immobility as an intrinsic reference point for locomotor behavior we show that the rules that generate the transition from immobility to full blown normal behavior, and from full blown behavior to immobility are shared by fruit flies and mice. These rules constitute a much desired aim of evolutionary biology: the discovery of behavioral homologies across distant phyla. The methodology we use facilitates the discovery of cross-phyletic behavioral homologies, shedding light on the problem of the evolution of behavior.

Multimedia signal processing for behavioral quantification in neuroscience

While there have been great advances in quantification of the genotype of organisms, including full genomes for many species, the quantification of phenotype is at a comparatively primitive stage. Part of the reason is technical difficulty: the phenotype covers a wide range of characteristics, ranging from static morphological features, to dynamic behavior. The latter poses challenges that are in the area of multimedia signal processing. Automated analysis of video and audio recordings of animal and human behavior is a growing area of research, ranging from the behavioral phenotyping of genetically modified mice or drosophila to the study of song learning in birds and speech acquisition in human infants. This paper reviews recent advances and identifies key problems for a range of behavior experiments that use audio and video recording. This research area offers both research challenges and an application domain for advanced multimedia signal processing. There are a number of MMSP tools that now exist which are directly relevant for behavioral quantification, such as speech recognition, video analysis and more recently, wired and wireless sensor networks for surveillance. The research challenge is to adapt these tools and to develop new ones required for studying human and animal behavior in a high throughput manner while minimizing human intervention. In contrast with consumer applications, in the research arena there is less of a penalty for computational complexity, so that algorithmic quality can be maximized through the utilization of larger computational resources that are available to the biomedical researcher.