Biomedical subjects

Neri Kafkafi

Publications and source records attributed to Neri Kafkafi.

9 recordsLinked to original sources

PubMed2006

Combined application of behavior genetics and microarray analysis to identify regional expression themes and gene-behavior associations.

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 ethanol-induced distance traveled across a grid floor, and seizure susceptibility. Several genes within the glutamatergic signaling pathway (i.e., NMDA/glutamate receptor subunit 2C, calmodulin, solute carrier family 1 member 2, and glutamine synthetase) were identified in a phenotype-dependent and region-specific manner. In addition to supporting evidence in the literature, many of the genes that were identified could be mapped in silico to surrogate behavior-related quantitative trait loci. The approaches and data set described herein serve as a valuable resource to investigate the genetic underpinning of complex behaviors.

Alcoholism↗

PubMed2005

Genotype-environment interactions in mouse behavior: a way out of the problem.

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 x 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 x laboratory interaction is an unavoidable fact of life. (ii) Incorporate this understanding into the statistical analysis of multilaboratory experiments using the mixed model. Such a statistical approach sets a higher benchmark for finding significant genotype differences. (iii) Develop behavioral assays and endpoints that are able to discriminate genetic differences even over the background of the interaction. (iv) Use the publicly available multilaboratory results in single-laboratory experiments. We use software-based strategy for exploring exploration (see) to analyze the open-field behavior in eight genotypes across three laboratories. Our results demonstrate that replicable behavioral measures can be practically established. Even though we address the replicability problem in behavioral genetics, our strategy is also applicable in other areas where concern about replicability has been raised.

Analysis of Variance↗

PubMed2004

Activity density in the open field: a measure for differentiating the effect of psychostimulants.

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.

Animals↗

PubMed2004

New replicable anxiety-related measures of wall vs center behavior of mice in the open field.

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 an articulated description of various aspects of behavior near the wall and in the center. Sixteen new end points were designed with data from C57BL/6J and DBA/2J mice tested in three laboratories. The strain differences in all end points were evaluated on another data set to assess their validity and were found to remain stable. Ten of the sixteen end points were found to discriminate between the two strains in a replicable manner. The entire set of end points can be used on various genetic and pharmacological models of anxiety with good prospects of providing fine discrimination in a replicable manner.

Algorithms↗

PubMed2004

The dynamics of spatial behavior: how can robust smoothing techniques help?

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.

Algorithms↗

PubMed2003

Darting behavior: a quantitative movement pattern designed for discrimination and replicability in mouse locomotor behavior.

In the open-field behavior of rodents, Software for Exploring Exploration (SEE) can be used for an explicit design of behavioral endpoints with high genotype discrimination and replicability across laboratories. This ability is demonstrated here in the development of a measure for darting behavior. The behavior of two common mouse inbred strains, C57BL/6J (B6) and DBA/2J (D2), was analyzed across three different laboratories, and under the effect of cocaine or amphetamine. "Darting" was defined as having higher acceleration during progression segments while moving less during stops. D2 mice darted significantly more than B6 mice in each laboratory, despite being significantly less active. These differences were maintained following cocaine administration (up to 20mg/kg) and only slightly altered by amphetamine (up to 5mg/kg) despite a several fold increase in activity. The replicability of darting behavior was confirmed in additional experiments distinct from those used for its design. The strategy leading to the darting measure may be used to develop additional discriminative and replicable endpoints of open-field behavior.

Amphetamine↗

PubMed2003

SEE locomotor behavior test discriminates C57BL/6J and DBA/2J mouse inbred strains across laboratories and protocol conditions.

Conventional tests of behavioral phenotyping frequently have difficulties differentiating certain genotypes and replicating these differences across laboratories and protocol conditions. This study explores the hypothesis that automated tests can be designed to quantify ethologically relevant behavior patterns that more readily characterize heritable and replicable phenotypes. It used SEE (Strategy for the Exploration of Exploration) to phenotype the locomotor behavior of the C57BL/6 and DBA/2 mouse inbred strains across 3 laboratories. The 2 genotypes differed in 15 different measures of behavior, none of which had a significant genotype-laboratory interaction. Within the same laboratory, most of these differences were replicated in additional experiments despite the test photoperiod phase being changed and saline being injected. Results suggest that well-designed tests may considerably enhance replicability across laboratories.

Animals↗

PubMed2003

Extending SEE for large-scale phenotyping of mouse open-field behavior.

SEE (Software for the Exploration of Exploration) is a visualization and analysis tool designed for the study of open-field behavior in rodents. In this paper, I present new extensions of SEE that were designed to facilitate its use for mouse behavioral phenotyping and, especially, for the problems of discrimination of genotypes and the replication of results across laboratories and experimental conditions. These extensions were specifically designed to promote a new approach in behavioral phenotyping, reminiscent of the approach that has been successfully employed in bioinformatics during recent years. The path coordinates of all animals from many experiments are stored in a database. SEE can be used to query, visualize, and analyze any desirable subsection of this database and to design new measures (endpoints) with increasingly better discriminative power and replicability. The use of the new extensions is demonstrated here in the analysis of results from several experiments and laboratories, with an emphasis on this approach.

Animals↗

PubMed2002

Repeated maternal separation does not alter sucrose-reinforced and open-field behaviors.

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.

Animals↗