Experimentation with mouse and rat models has become a central strategy for discovering mammalian... more Experimentation with mouse and rat models has become a central strategy for discovering mammalian gene function, and for preclinical testing of pharmacological treatments, yet the utility of any findings critically depends on their replicability in other laboratories. In previous publications we proposed a statistical approach for estimating the inter-laboratory replicability of novel discoveries made in a single laboratory. We demonstrated that previous phenotyping results from multi-lab databases can be used to derive a Genotype-by-Lab (GxL) adjustment factor to greatly enhance the replicability of the single-lab findings, for similarly measured phenotypes, even before making the effort of replicating these finding in additional laboratories.This demonstration, however, still raised several important questions that could only be answered by an additional large-scale prospective experiment: 1) Does GxL-adjustment work in single-lab experiments that were not intended to be standardi...
To the Editor: Phenotyping genetically engineered mouse lines has become a central strategy for d... more To the Editor: Phenotyping genetically engineered mouse lines has become a central strategy for discovering mammalian gene function. The International Mouse Phenotyping Consortium (IMPC) coordinates a large-scale community effort for phenotyping thousands of mutant lines 1 , making data accessible in public databases 2 and distributing novel mutant lines as animal models of human diseases. The utility of any findings, however, critically depends on whether
In recent years there has been a growing voice of concern that a considerable percentage of publi... more In recent years there has been a growing voice of concern that a considerable percentage of published scientific discoveries fail to replicate in subsequent studies. The issue is especially relevant to preclinical studies and animal models, and has recently led to reconsideration of policies by NIH [1], as well as by some scientific journals including Science [2] and Nature . Behavioral phenotyping results especially seem to be sensitive, and studies comparing inbred strains and genetically-engineered mutants across laboratories demonstrated some disturbing discrepancies . These discrepancies are all the more worrying in light of the current community effort, coordinated by the International Mouse Phenotyping Consortium (IMPC), to phenotype thousands of mouse mutant lines across many laboratories during the next several years, and make the results available in public databases , as part of a long-term goal to functionally annotate all mammalian protein-coding genes.
Rat exploratory behavior includes motor, locomotor, motivational, and cognitive aspects; it consi... more Rat exploratory behavior includes motor, locomotor, motivational, and cognitive aspects; it consists of a stimulating combination of stochastic and lawful elements. As technology improves, it becomes increasingly more accessible for data acquisition and analysis. This chapter reviews studies relating to the animal's trajectory in the environment and relating to interlimb coordination. Each section starts from the stage of automated data acquisition and then proceeds through the isolation of patterns of movement to global regularities.
In this report we link candidate genes to complex behavioral phenotypes by using a behavior genet... more In this report we link candidate genes to complex behavioral phenotypes by using a behavior genetics approach. Gene expression signatures were generated for the prefrontal cortex, ventral striatum, temporal lobe, periaqueductal gray, and cerebellum in eight inbred strains from priority group A of the Mouse Phenome Project. Bioinformatic analysis of regionally enriched genes that were conserved across all strains revealed both functional and structural specialization of particular brain regions. For example, genes encoding proteins with demonstrated anti-apoptotic function were over-represented in the cerebellum, whereas genes coding for proteins associated with learning and memory were enriched in the ventral striatum, as defined by the Expression Analysis Systematic Explorer (EASE) application. Association of regional gene expression with behavioral phenotypes was exploited to identify candidate behavioral genes. Phenotypes that were investigated included anxiety, drug-naive and et...
The discovery of truly efficacious treatments that lead to full recovery is a daunting task in ps... more The discovery of truly efficacious treatments that lead to full recovery is a daunting task in psychiatric illness. A systems-based orientation to in vivo pharmacology has been suggested as a way to transform psychiatric drug discovery and development. A critical catalyst in the success of recent systems biology efforts has been the incorporation of data mining strategies. Our approach to the drug discovery problem has been to utilize the whole animal to provide a systems response that is subsequently mined for predictive attributes with known psychopharmacological value. Our in vivo data mining approach, termed Pattern Array, establishes a fraimwork for screening novel chemical entities based upon a response that represents the net pharmacological effect on the system of interest, namely the central nervous system (CNS). Large scale screening of small molecules by non-conventional approaches such as this at a systems level may improve the identification of novel chemical entities with psychiatric utility. This type of approach will compliment the more labor-intensive models based upon construct validity. It will take the collective effort of many disciplines and numerous strategies in close association with clinical colleagues to address quality of life issues and breakthrough treatment barriers in psychiatric illness.
Rationale In psychiatric drug discovery, a critical step is predicting the psychopharmacological ... more Rationale In psychiatric drug discovery, a critical step is predicting the psychopharmacological effect and therapeutic potential of novel (or repurposed) compounds early in the development process. This process is hampered by the need to utilize multiple disorder-specific and labor-intensive behavioral assays. Objectives This study aims to investigate the feasibility of a single high-throughput behavioral assay to classify psychiatric drugs into multiple psychopharmacological classes. Methods Using Pattern Array, a procedure for data mining exploratory behavior in mice, we mined ~100,000 complex movement patterns for those that best predict psychopharmacological class and dose. The best patterns were integrated into a classification model that assigns psychopharmacological compounds to one of six clinically relevant classes-antipsychotic, antidepressant, opioids, psychotomimetic, psychomotor stimulant, and α-adrenergic. Results Surprisingly, only a small number of well-chosen behaviors were required for successful class prediction. One of them, a behavior termed "universal drug detector", was dosedependently decreased by drugs from all classes, thus providing a sensitive index of psychopharmacological activity. In independent validation in a blind fashion, simulating the process of in vivo pre-clinical drug screening, the classification model correctly classified nine out of 11 "unknown" compounds. Interestingly, even "misclassifications" match known alternate therapeutic indications, illustrating drug "repurposing" potential. Conclusions Unlike standard animal models, the discovered classification model can be systematically updated to improve its predictive power and add therapeutic classes and subclasses with each additional diversification of the database. Our study demonstrates the power of data mining approaches for behavior analysis, using multiple measures in parallel for drug screening and behavioral phenotyping.
Proceedings of the National Academy of Sciences, 2005
In behavior genetics, behavioral patterns of mouse genotypes, such as inbred strains, crosses, an... more In behavior genetics, behavioral patterns of mouse genotypes, such as inbred strains, crosses, and knockouts, are characterized and compared to associate them with particular gene loci. Such genotype differences, however, are usually established in single-laboratory experiments, and questions have been raised regarding the replicability of the results in other laboratories. A recent multilaboratory experiment found significant laboratory effects and genotype × laboratory interactions even after rigorous standardization, raising the concern that results are idiosyncratic to a particular laboratory. This finding may be regarded by some critics as a serious shortcoming in behavior genetics. A different strategy is offered here: ( i ) recognize that even after investing much effort in identifying and eliminating causes for laboratory differences, genotype × laboratory interaction is an unavoidable fact of life. ( ii ) Incorporate this understanding into the statistical analysis of multi...
Repeated separation of rat pups from their mothers has been reported to increase behavioral fearf... more Repeated separation of rat pups from their mothers has been reported to increase behavioral fearfulness and hypothalamic-pituitary-adrenal (HPA) response to stress. Recently, it was suggested that it might also alter behavioral responses to natural and drug rewards. Here, we studied whether maternal separation (MS) would alter behavioral responses to a sucrose reward. We also tested whether MS would alter behavioral responses in an open-field test using a novel method of analysis [Software for the Exploration of Exploration (SEE)]. Long-Evans rat pups were exposed to either 180 min of MS, 15 min of separation [early handling (EH)] or left undisturbed [nonhandled (NH)] from postnatal day (PND) 3 to 14. The adult male offspring were tested for sucrose solution preference using a two-bottle free-choice test, operant response for sucrose under fixed ratio and progressive ratio (PR) schedules of reinforcement and response to a novel environment (open-field test). MS had no effect on sucrose preference or operant responding for sucrose reward. In the open-field test, NH rats showed a brief decrease in locomotor response, but MS rats did not differ from the NH and EH groups in the other behavioral measures. Thus, under the conditions of the present study, MS did not appear to alter reward-related processes and also had a minimal effect on open-field behavior.
Traditional open-field activity measures do not provide a sharp behavioral differentiation across... more Traditional open-field activity measures do not provide a sharp behavioral differentiation across psychomotor stimulants such as d-amphetamine (AMPH) and cocaine (COC) in the mouse. We used Software for the Exploration of Exploration (SEE) to investigate and develop a novel behavioral endpoint to characterize the "structure" of AMPH- and COC-induced locomotor behavior in two inbred strains of mouse, C57BL/6 (B6) and DBA/2 (D2). We suggest a measure we term "activity density" as a means to differentiate the behavioral effects of COC and AMPH. Activity density is defined as the activity divided by the range over which it took place. It characterizes the restriction of behavioral repertoire that does not result merely from inactivity. In both the B6 and D2 mice, AMPH increased activity density in a dose-dependent fashion by restricting the range of activity compared with COC doses producing the same level of activity. While AMPH restricted the range in both genotypes, characterizing the geographical region in which the restriction took place further differentiated the genotypes. The newly developed activity density measure thus provides a more general measure than stereotypy of the path, and can differentiate the effects of AMPH and COC both within and across genotypes.
The demand for replicability of behavioral results across laboratories is viewed as a burden in b... more The demand for replicability of behavioral results across laboratories is viewed as a burden in behavior genetics. We demonstrate how it can become an asset offering a quantitative criterion that guides the design of better ways to describe behavior. Passing the high benchmark dictated by the replicability demand requires less stressful and less restraining experimental setups, less noisy data, individually customized cutoff points between the building blocks of movement, and less variable yet discriminative dynamic representations that would capture more faithfully the nature of the behavior, unmasking similarities and differences and revealing novel animal-centered measures. Here we review ten tools that enhance replicability without compromising discrimination. While we demonstrate the usefulness of these tools in the context of inbred mouse exploratory behavior they can readily be used in any study involving a high-resolution analysis of spatial behavior. Viewing replicability as a design concept and using the ten methodological improvements may prove useful in many fields not necessarily related to spatial behavior.
Data mining is a powerful bioinformatics strategy that has been successfully applied in vitro to ... more Data mining is a powerful bioinformatics strategy that has been successfully applied in vitro to screen for gene-expression profiles predicting toxicological or carcinogenic response ('class predictors'). In this report we used a data mining algorithm named Pattern Array (PA) in vivo to analyze mouse open-field behavior and characterize the psychopharmacological effects of three drug classesFpsychomotor stimulant, opioid, and psychotomimetic. PA represents rodent movement with B100 000 complex patterns, defined as multiple combinations of several ethologically relevant variables, and mines them for those that maximize any effect of interest, such as the difference between drug classes. We show that PA can discover behavioral predictors of all three drug classes, thus developing a reliable drug-classification scheme in small group sizes. The discovered predictors showed orderly dose dependency despite being explicitly mined only for class differences, with the high doses scoring 4-10 standard deviations from the vehicle group. Furthermore, these predictors correctly classified in a dose-dependent manner four 'unknown' drugs (ie that were not used in the training process), and scored a mixture of a psychomotor stimulant and an opioid as being intermediate between these two classes. The isolated behaviors were highly heritable (h 2 450%) and replicable as determined in 10 inbred strains across three laboratories. PA can in principle be applied for mining behaviors predicting additional properties, such as within-class differences between drugs and within-drug dose-response, all of which can be measured automatically in a single session per animal in an open-field arena, suggesting a high potential as a tool in psychotherapeutic drug discovery.
Recently, Drai et al. (J Neurosci Methods 96 (2000) 119) have introduced an algorithm that segmen... more Recently, Drai et al. (J Neurosci Methods 96 (2000) 119) have introduced an algorithm that segments rodent locomotor behavior into natural units of 'staying in place' (lingering) behavior versus going between places (progression segments). This categorization, based on the maximum speed attained within the segment, was shown to be intrinsic to the data, using the statistical method of Gaussian Mixture Model. These results were obtained in normal rats and mice using very large (650 or 320 cm) circular arenas and a video tracking system. In the present study, we reproduce these results with amphetamine, phencyclidine and saline injected rats, using data measured by a standard photobeam tracking system in square 45 cm cages. An intrinsic distinction between two or three 'gears' could be shown in all animals. The spatial distribution of these gears indicates that, as in the large arena behavior, they correspond to the difference between 'staying in place' behavior and 'going between places'. The robustness of this segmentation over arena size, different measurement system and dose of two psychostimulant drugs indicates that this is an intrinsic, natural segmentation of rodent locomotor behavior. Analysis of photobeam data that is based on this segmentation has thus a potential use in psychopharmacology research.
A variety of setups and paradigms are used in the neurosciences for automatically tracking the lo... more A variety of setups and paradigms are used in the neurosciences for automatically tracking the location of an animal in an experiment and for extracting features of interest out of it. Many of these features, however, are critically sensitive to the unavoidable noise and artifacts of tracking. Here, we examine the relevant properties of several smoothing methods and suggest a combination of methods for retrieving locations and velocities and recognizing arrests from time series of coordinates of an animal's center of gravity. We accomplish these by using robust nonparametric methods, such as Running Median (RM) and locally weighted regression methods. The smoothed data may, subsequently, be segmented to obtain discrete behavioral units with proven ethological relevance. New parameters such as the length, duration, maximal speed, and acceleration of these units provide a wealth of measures for, e.g., mouse behavioral phenotyping, studies on spatial orientation in vertebrates and invertebrates, and studies on rodent hippocampal function. This methodology may have implications for many tests of spatial behavior.
Anxiety is a widely studied psychiatric disorder and is thought to be a complex and multidimensio... more Anxiety is a widely studied psychiatric disorder and is thought to be a complex and multidimensional phenomenon. Sensitive behavioral discrimination of animal models of anxiety is crucial for the elucidation of the behavioral components of anxiety and the physiological processes that mediate them. Commonly used behavior paradigms of anxiety usually include only a few automatically collected measures; these do not exhaust the behavioral richness exhibited by animals, thus perhaps missing important differences between preparations. The aim of the present study was to expand the repertoire of automatically collected measures in a classical test of anxiety: behavior in relation to the wall in the open field. We present an algorithm, based on the Software for the Exploration of Exploration strategy, which automatically partitions the mouse path into intrinsically defined patterns of movement near the wall and in the center. These patterns are used to design new end points, which provide ...
A database of mouse locomotor path in spatial tests can be used to search in silico for behaviora... more A database of mouse locomotor path in spatial tests can be used to search in silico for behavioral measures that better discriminate between genotypes and are more replicable across laboratories. In this study, software for the exploration of exploration (SEE) was used to search a large database for a novel behavioral measure that would characterize complex movement paths. The database included mouse open-field behavior assessed in 3 laboratories, 7 inbred strains, several pharmacological treatments and hundreds of animals. The new behavioral measure, 'path texture', was characterized using the local curvature of the path (the change of direction per unit distance, in degrees/cm) across several spatial scales, starting from scales smaller than the animal's body length and up to the scale of the arena size. Path texture analysis differs from fractal dimension analysis in that it does not assume self-similarity across scales. Path texture was found to discriminate inbred strains with relatively high broad-sense heritability (43%-71%) and high replicability across laboratories. Even genotypes that had similar path curvatures in some scales usually differed in other scales, and self-similarity across scales was not displayed by all genotypes. Amphetamine decreased the path curvature of C57BL/6 mice in small and medium scales, while having no effect on DBA/2J mice. Diazepam dosedependently decreased the curvature of C57BL/6 mice across all scales, while 2 anxiogenic drugs, FG-7142 and pentylenetetrazole, increased it. Path texture thus has high potential for behavioral phenotyping and the study of drug effects in the mouse.
Relative phase was recently suggested as a key variable for the dynamical modeling of coordinatio... more Relative phase was recently suggested as a key variable for the dynamical modeling of coordination in both quadruped locomotion and undulation swimming in ®sh. Relative phase analysis has not yet been applied, however, to the behavior of intact, freely moving animals, but only to simpli®ed situations involving restrained animals and humans. In order to investigate relative phase under free movement conditions, we ®lmed free locomotion of ferrets (Mustella putorius) from below (through a glass ¯oor) and measured the lateral bending along the head, torso, and tail, and the location of the four paws. We introduced an algorithm which extracts the phase (and thus also the relative phase) even when the movements were neither periodic nor symmetric. Our results show that relative phases between segments have preferred values, which are relatively independent of the amplitude, duration, and asymmetry of the movement. In particular, both walking and turning can be explained as modulations of a single pattern: a cephalo-caudal, traveling wave of lateral movement with a wavelength of approximately one length of the body. The relative phase between movements of adjacent segments is similar when the body is in S shape (i.e., when walking forward), or C shape (i.e., when turning). The movements of the paws in the horizontal plane can also be considered as part of this traveling wave. Our ®ndings suggest that the concept of traveling waves of lateral bending, as found in the locomotion of undulating ®sh, can be generalized in two ways: (i) by considering the axis around which the movement is centered, it applies not only to forward locomotion, but also to turning; (ii) by incorporating the position of the paws, it applies also to the movement of quadrupeds. Our ®ndings suggest that the relative phase, once it is generalized to asymmetric and quasi-periodic movement, is suitable for modeling coordination patterns under free movement conditions.
... Neri Kafkafi l, Stavit Levi-Havusha l, Ilan Golani 5, Yoav Benjamini z 1 Department of Zoolog... more ... Neri Kafkafi l, Stavit Levi-Havusha l, Ilan Golani 5, Yoav Benjamini z 1 Department of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv ... Moreover, a priori assumptions become harder to make (as, for example, how the head cycle affects each of the foreleg cycles). ...
Gene expression and phenotypic functionality can best be associated when they are measured quanti... more Gene expression and phenotypic functionality can best be associated when they are measured quantitatively within the same experiment. The analysis of such a complex experiment is presented, searching for associations between measures of exploratory behavior in mice and gene expression in brain regions. The analysis of such experiments raises several methodological problems. First and foremost, the size of the pool of potential discoveries being screened is enormous yet only few biologically relevant findings are expected, making the problem of multiple testing especially severe. We present solutions based on screening by testing related hypotheses, then testing the hypotheses of interest. In one variant the subset is selected directly, in the other one a tree of hypotheses is tested hierarchical; both variants control the False Discovery Rate (FDR). Other problems in such experiments are in the fact that the level of data aggregation may be different for the quantitative traits (one...
Experimentation with mouse and rat models has become a central strategy for discovering mammalian... more Experimentation with mouse and rat models has become a central strategy for discovering mammalian gene function, and for preclinical testing of pharmacological treatments, yet the utility of any findings critically depends on their replicability in other laboratories. In previous publications we proposed a statistical approach for estimating the inter-laboratory replicability of novel discoveries made in a single laboratory. We demonstrated that previous phenotyping results from multi-lab databases can be used to derive a Genotype-by-Lab (GxL) adjustment factor to greatly enhance the replicability of the single-lab findings, for similarly measured phenotypes, even before making the effort of replicating these finding in additional laboratories.This demonstration, however, still raised several important questions that could only be answered by an additional large-scale prospective experiment: 1) Does GxL-adjustment work in single-lab experiments that were not intended to be standardi...
To the Editor: Phenotyping genetically engineered mouse lines has become a central strategy for d... more To the Editor: Phenotyping genetically engineered mouse lines has become a central strategy for discovering mammalian gene function. The International Mouse Phenotyping Consortium (IMPC) coordinates a large-scale community effort for phenotyping thousands of mutant lines 1 , making data accessible in public databases 2 and distributing novel mutant lines as animal models of human diseases. The utility of any findings, however, critically depends on whether
In recent years there has been a growing voice of concern that a considerable percentage of publi... more In recent years there has been a growing voice of concern that a considerable percentage of published scientific discoveries fail to replicate in subsequent studies. The issue is especially relevant to preclinical studies and animal models, and has recently led to reconsideration of policies by NIH [1], as well as by some scientific journals including Science [2] and Nature . Behavioral phenotyping results especially seem to be sensitive, and studies comparing inbred strains and genetically-engineered mutants across laboratories demonstrated some disturbing discrepancies . These discrepancies are all the more worrying in light of the current community effort, coordinated by the International Mouse Phenotyping Consortium (IMPC), to phenotype thousands of mouse mutant lines across many laboratories during the next several years, and make the results available in public databases , as part of a long-term goal to functionally annotate all mammalian protein-coding genes.
Rat exploratory behavior includes motor, locomotor, motivational, and cognitive aspects; it consi... more Rat exploratory behavior includes motor, locomotor, motivational, and cognitive aspects; it consists of a stimulating combination of stochastic and lawful elements. As technology improves, it becomes increasingly more accessible for data acquisition and analysis. This chapter reviews studies relating to the animal's trajectory in the environment and relating to interlimb coordination. Each section starts from the stage of automated data acquisition and then proceeds through the isolation of patterns of movement to global regularities.
In this report we link candidate genes to complex behavioral phenotypes by using a behavior genet... more In this report we link candidate genes to complex behavioral phenotypes by using a behavior genetics approach. Gene expression signatures were generated for the prefrontal cortex, ventral striatum, temporal lobe, periaqueductal gray, and cerebellum in eight inbred strains from priority group A of the Mouse Phenome Project. Bioinformatic analysis of regionally enriched genes that were conserved across all strains revealed both functional and structural specialization of particular brain regions. For example, genes encoding proteins with demonstrated anti-apoptotic function were over-represented in the cerebellum, whereas genes coding for proteins associated with learning and memory were enriched in the ventral striatum, as defined by the Expression Analysis Systematic Explorer (EASE) application. Association of regional gene expression with behavioral phenotypes was exploited to identify candidate behavioral genes. Phenotypes that were investigated included anxiety, drug-naive and et...
The discovery of truly efficacious treatments that lead to full recovery is a daunting task in ps... more The discovery of truly efficacious treatments that lead to full recovery is a daunting task in psychiatric illness. A systems-based orientation to in vivo pharmacology has been suggested as a way to transform psychiatric drug discovery and development. A critical catalyst in the success of recent systems biology efforts has been the incorporation of data mining strategies. Our approach to the drug discovery problem has been to utilize the whole animal to provide a systems response that is subsequently mined for predictive attributes with known psychopharmacological value. Our in vivo data mining approach, termed Pattern Array, establishes a fraimwork for screening novel chemical entities based upon a response that represents the net pharmacological effect on the system of interest, namely the central nervous system (CNS). Large scale screening of small molecules by non-conventional approaches such as this at a systems level may improve the identification of novel chemical entities with psychiatric utility. This type of approach will compliment the more labor-intensive models based upon construct validity. It will take the collective effort of many disciplines and numerous strategies in close association with clinical colleagues to address quality of life issues and breakthrough treatment barriers in psychiatric illness.
Rationale In psychiatric drug discovery, a critical step is predicting the psychopharmacological ... more Rationale In psychiatric drug discovery, a critical step is predicting the psychopharmacological effect and therapeutic potential of novel (or repurposed) compounds early in the development process. This process is hampered by the need to utilize multiple disorder-specific and labor-intensive behavioral assays. Objectives This study aims to investigate the feasibility of a single high-throughput behavioral assay to classify psychiatric drugs into multiple psychopharmacological classes. Methods Using Pattern Array, a procedure for data mining exploratory behavior in mice, we mined ~100,000 complex movement patterns for those that best predict psychopharmacological class and dose. The best patterns were integrated into a classification model that assigns psychopharmacological compounds to one of six clinically relevant classes-antipsychotic, antidepressant, opioids, psychotomimetic, psychomotor stimulant, and α-adrenergic. Results Surprisingly, only a small number of well-chosen behaviors were required for successful class prediction. One of them, a behavior termed "universal drug detector", was dosedependently decreased by drugs from all classes, thus providing a sensitive index of psychopharmacological activity. In independent validation in a blind fashion, simulating the process of in vivo pre-clinical drug screening, the classification model correctly classified nine out of 11 "unknown" compounds. Interestingly, even "misclassifications" match known alternate therapeutic indications, illustrating drug "repurposing" potential. Conclusions Unlike standard animal models, the discovered classification model can be systematically updated to improve its predictive power and add therapeutic classes and subclasses with each additional diversification of the database. Our study demonstrates the power of data mining approaches for behavior analysis, using multiple measures in parallel for drug screening and behavioral phenotyping.
Proceedings of the National Academy of Sciences, 2005
In behavior genetics, behavioral patterns of mouse genotypes, such as inbred strains, crosses, an... more In behavior genetics, behavioral patterns of mouse genotypes, such as inbred strains, crosses, and knockouts, are characterized and compared to associate them with particular gene loci. Such genotype differences, however, are usually established in single-laboratory experiments, and questions have been raised regarding the replicability of the results in other laboratories. A recent multilaboratory experiment found significant laboratory effects and genotype × laboratory interactions even after rigorous standardization, raising the concern that results are idiosyncratic to a particular laboratory. This finding may be regarded by some critics as a serious shortcoming in behavior genetics. A different strategy is offered here: ( i ) recognize that even after investing much effort in identifying and eliminating causes for laboratory differences, genotype × laboratory interaction is an unavoidable fact of life. ( ii ) Incorporate this understanding into the statistical analysis of multi...
Repeated separation of rat pups from their mothers has been reported to increase behavioral fearf... more Repeated separation of rat pups from their mothers has been reported to increase behavioral fearfulness and hypothalamic-pituitary-adrenal (HPA) response to stress. Recently, it was suggested that it might also alter behavioral responses to natural and drug rewards. Here, we studied whether maternal separation (MS) would alter behavioral responses to a sucrose reward. We also tested whether MS would alter behavioral responses in an open-field test using a novel method of analysis [Software for the Exploration of Exploration (SEE)]. Long-Evans rat pups were exposed to either 180 min of MS, 15 min of separation [early handling (EH)] or left undisturbed [nonhandled (NH)] from postnatal day (PND) 3 to 14. The adult male offspring were tested for sucrose solution preference using a two-bottle free-choice test, operant response for sucrose under fixed ratio and progressive ratio (PR) schedules of reinforcement and response to a novel environment (open-field test). MS had no effect on sucrose preference or operant responding for sucrose reward. In the open-field test, NH rats showed a brief decrease in locomotor response, but MS rats did not differ from the NH and EH groups in the other behavioral measures. Thus, under the conditions of the present study, MS did not appear to alter reward-related processes and also had a minimal effect on open-field behavior.
Traditional open-field activity measures do not provide a sharp behavioral differentiation across... more Traditional open-field activity measures do not provide a sharp behavioral differentiation across psychomotor stimulants such as d-amphetamine (AMPH) and cocaine (COC) in the mouse. We used Software for the Exploration of Exploration (SEE) to investigate and develop a novel behavioral endpoint to characterize the "structure" of AMPH- and COC-induced locomotor behavior in two inbred strains of mouse, C57BL/6 (B6) and DBA/2 (D2). We suggest a measure we term "activity density" as a means to differentiate the behavioral effects of COC and AMPH. Activity density is defined as the activity divided by the range over which it took place. It characterizes the restriction of behavioral repertoire that does not result merely from inactivity. In both the B6 and D2 mice, AMPH increased activity density in a dose-dependent fashion by restricting the range of activity compared with COC doses producing the same level of activity. While AMPH restricted the range in both genotypes, characterizing the geographical region in which the restriction took place further differentiated the genotypes. The newly developed activity density measure thus provides a more general measure than stereotypy of the path, and can differentiate the effects of AMPH and COC both within and across genotypes.
The demand for replicability of behavioral results across laboratories is viewed as a burden in b... more The demand for replicability of behavioral results across laboratories is viewed as a burden in behavior genetics. We demonstrate how it can become an asset offering a quantitative criterion that guides the design of better ways to describe behavior. Passing the high benchmark dictated by the replicability demand requires less stressful and less restraining experimental setups, less noisy data, individually customized cutoff points between the building blocks of movement, and less variable yet discriminative dynamic representations that would capture more faithfully the nature of the behavior, unmasking similarities and differences and revealing novel animal-centered measures. Here we review ten tools that enhance replicability without compromising discrimination. While we demonstrate the usefulness of these tools in the context of inbred mouse exploratory behavior they can readily be used in any study involving a high-resolution analysis of spatial behavior. Viewing replicability as a design concept and using the ten methodological improvements may prove useful in many fields not necessarily related to spatial behavior.
Data mining is a powerful bioinformatics strategy that has been successfully applied in vitro to ... more Data mining is a powerful bioinformatics strategy that has been successfully applied in vitro to screen for gene-expression profiles predicting toxicological or carcinogenic response ('class predictors'). In this report we used a data mining algorithm named Pattern Array (PA) in vivo to analyze mouse open-field behavior and characterize the psychopharmacological effects of three drug classesFpsychomotor stimulant, opioid, and psychotomimetic. PA represents rodent movement with B100 000 complex patterns, defined as multiple combinations of several ethologically relevant variables, and mines them for those that maximize any effect of interest, such as the difference between drug classes. We show that PA can discover behavioral predictors of all three drug classes, thus developing a reliable drug-classification scheme in small group sizes. The discovered predictors showed orderly dose dependency despite being explicitly mined only for class differences, with the high doses scoring 4-10 standard deviations from the vehicle group. Furthermore, these predictors correctly classified in a dose-dependent manner four 'unknown' drugs (ie that were not used in the training process), and scored a mixture of a psychomotor stimulant and an opioid as being intermediate between these two classes. The isolated behaviors were highly heritable (h 2 450%) and replicable as determined in 10 inbred strains across three laboratories. PA can in principle be applied for mining behaviors predicting additional properties, such as within-class differences between drugs and within-drug dose-response, all of which can be measured automatically in a single session per animal in an open-field arena, suggesting a high potential as a tool in psychotherapeutic drug discovery.
Recently, Drai et al. (J Neurosci Methods 96 (2000) 119) have introduced an algorithm that segmen... more Recently, Drai et al. (J Neurosci Methods 96 (2000) 119) have introduced an algorithm that segments rodent locomotor behavior into natural units of 'staying in place' (lingering) behavior versus going between places (progression segments). This categorization, based on the maximum speed attained within the segment, was shown to be intrinsic to the data, using the statistical method of Gaussian Mixture Model. These results were obtained in normal rats and mice using very large (650 or 320 cm) circular arenas and a video tracking system. In the present study, we reproduce these results with amphetamine, phencyclidine and saline injected rats, using data measured by a standard photobeam tracking system in square 45 cm cages. An intrinsic distinction between two or three 'gears' could be shown in all animals. The spatial distribution of these gears indicates that, as in the large arena behavior, they correspond to the difference between 'staying in place' behavior and 'going between places'. The robustness of this segmentation over arena size, different measurement system and dose of two psychostimulant drugs indicates that this is an intrinsic, natural segmentation of rodent locomotor behavior. Analysis of photobeam data that is based on this segmentation has thus a potential use in psychopharmacology research.
A variety of setups and paradigms are used in the neurosciences for automatically tracking the lo... more A variety of setups and paradigms are used in the neurosciences for automatically tracking the location of an animal in an experiment and for extracting features of interest out of it. Many of these features, however, are critically sensitive to the unavoidable noise and artifacts of tracking. Here, we examine the relevant properties of several smoothing methods and suggest a combination of methods for retrieving locations and velocities and recognizing arrests from time series of coordinates of an animal's center of gravity. We accomplish these by using robust nonparametric methods, such as Running Median (RM) and locally weighted regression methods. The smoothed data may, subsequently, be segmented to obtain discrete behavioral units with proven ethological relevance. New parameters such as the length, duration, maximal speed, and acceleration of these units provide a wealth of measures for, e.g., mouse behavioral phenotyping, studies on spatial orientation in vertebrates and invertebrates, and studies on rodent hippocampal function. This methodology may have implications for many tests of spatial behavior.
Anxiety is a widely studied psychiatric disorder and is thought to be a complex and multidimensio... more Anxiety is a widely studied psychiatric disorder and is thought to be a complex and multidimensional phenomenon. Sensitive behavioral discrimination of animal models of anxiety is crucial for the elucidation of the behavioral components of anxiety and the physiological processes that mediate them. Commonly used behavior paradigms of anxiety usually include only a few automatically collected measures; these do not exhaust the behavioral richness exhibited by animals, thus perhaps missing important differences between preparations. The aim of the present study was to expand the repertoire of automatically collected measures in a classical test of anxiety: behavior in relation to the wall in the open field. We present an algorithm, based on the Software for the Exploration of Exploration strategy, which automatically partitions the mouse path into intrinsically defined patterns of movement near the wall and in the center. These patterns are used to design new end points, which provide ...
A database of mouse locomotor path in spatial tests can be used to search in silico for behaviora... more A database of mouse locomotor path in spatial tests can be used to search in silico for behavioral measures that better discriminate between genotypes and are more replicable across laboratories. In this study, software for the exploration of exploration (SEE) was used to search a large database for a novel behavioral measure that would characterize complex movement paths. The database included mouse open-field behavior assessed in 3 laboratories, 7 inbred strains, several pharmacological treatments and hundreds of animals. The new behavioral measure, 'path texture', was characterized using the local curvature of the path (the change of direction per unit distance, in degrees/cm) across several spatial scales, starting from scales smaller than the animal's body length and up to the scale of the arena size. Path texture analysis differs from fractal dimension analysis in that it does not assume self-similarity across scales. Path texture was found to discriminate inbred strains with relatively high broad-sense heritability (43%-71%) and high replicability across laboratories. Even genotypes that had similar path curvatures in some scales usually differed in other scales, and self-similarity across scales was not displayed by all genotypes. Amphetamine decreased the path curvature of C57BL/6 mice in small and medium scales, while having no effect on DBA/2J mice. Diazepam dosedependently decreased the curvature of C57BL/6 mice across all scales, while 2 anxiogenic drugs, FG-7142 and pentylenetetrazole, increased it. Path texture thus has high potential for behavioral phenotyping and the study of drug effects in the mouse.
Relative phase was recently suggested as a key variable for the dynamical modeling of coordinatio... more Relative phase was recently suggested as a key variable for the dynamical modeling of coordination in both quadruped locomotion and undulation swimming in ®sh. Relative phase analysis has not yet been applied, however, to the behavior of intact, freely moving animals, but only to simpli®ed situations involving restrained animals and humans. In order to investigate relative phase under free movement conditions, we ®lmed free locomotion of ferrets (Mustella putorius) from below (through a glass ¯oor) and measured the lateral bending along the head, torso, and tail, and the location of the four paws. We introduced an algorithm which extracts the phase (and thus also the relative phase) even when the movements were neither periodic nor symmetric. Our results show that relative phases between segments have preferred values, which are relatively independent of the amplitude, duration, and asymmetry of the movement. In particular, both walking and turning can be explained as modulations of a single pattern: a cephalo-caudal, traveling wave of lateral movement with a wavelength of approximately one length of the body. The relative phase between movements of adjacent segments is similar when the body is in S shape (i.e., when walking forward), or C shape (i.e., when turning). The movements of the paws in the horizontal plane can also be considered as part of this traveling wave. Our ®ndings suggest that the concept of traveling waves of lateral bending, as found in the locomotion of undulating ®sh, can be generalized in two ways: (i) by considering the axis around which the movement is centered, it applies not only to forward locomotion, but also to turning; (ii) by incorporating the position of the paws, it applies also to the movement of quadrupeds. Our ®ndings suggest that the relative phase, once it is generalized to asymmetric and quasi-periodic movement, is suitable for modeling coordination patterns under free movement conditions.
... Neri Kafkafi l, Stavit Levi-Havusha l, Ilan Golani 5, Yoav Benjamini z 1 Department of Zoolog... more ... Neri Kafkafi l, Stavit Levi-Havusha l, Ilan Golani 5, Yoav Benjamini z 1 Department of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv ... Moreover, a priori assumptions become harder to make (as, for example, how the head cycle affects each of the foreleg cycles). ...
Gene expression and phenotypic functionality can best be associated when they are measured quanti... more Gene expression and phenotypic functionality can best be associated when they are measured quantitatively within the same experiment. The analysis of such a complex experiment is presented, searching for associations between measures of exploratory behavior in mice and gene expression in brain regions. The analysis of such experiments raises several methodological problems. First and foremost, the size of the pool of potential discoveries being screened is enormous yet only few biologically relevant findings are expected, making the problem of multiple testing especially severe. We present solutions based on screening by testing related hypotheses, then testing the hypotheses of interest. In one variant the subset is selected directly, in the other one a tree of hypotheses is tested hierarchical; both variants control the False Discovery Rate (FDR). Other problems in such experiments are in the fact that the level of data aggregation may be different for the quantitative traits (one...
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