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Jonathan M Cachat

Jonathan M Cachat
CCV Research

Neuroscience & Psychopharmacology; Data Science & Data Engineering
Involved w several projects moving legacy data collection & analysis away from stale, legacy hardware into GCP

About

76
Publications
69,949
Reads
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6,163
Citations
Introduction
Strategic vision for neuroscience data management, neuroinformatics and open science, open data
Additional affiliations
January 1970 - December 2012
Tulane University
Education
August 2008 - August 2010
Tulane University
Field of study
  • Neuroscience, Psychopharmacology
August 2004 - May 2008
Denison University
Field of study

Publications

Publications (76)
Article
Full-text available
The use of adult zebrafish (Danio rerio) in neurobehavioral research is rapidly expanding. The present large-scale study applied the newest video-tracking and data-mining technologies to further examine zebrafish anxiety-like phenotypes. Here, we generated temporal and spatial three-dimensional (3D) reconstructions of zebrafish locomotion, globally...
Thesis
Full-text available
Zebrafish (Danio rerio) are offering novel perspectives to investigate the nervous system as a genetically and molecularly tractable in-vivo model of complex vertebrate behavior. The balance of low cost, experimental agility and phenotypic complexity, unique to zebrafish, empowers researchers to study biochemical regulators of development, behavior...
Article
Full-text available
Since various behavioral movement patterns are likely to be valid within different, unique ranges of spatial and temporal scales (e.g., instantaneous, diurnal, or seasonal) with the corresponding spatial extents, a cross-scale approach is needed for accurate classification of behaviors expressed in movement. Here, we introduce a methodology for the...
Preprint
Full-text available
This agricultural research examined how Tubular Daylighting Devices (TDDs), manufactured by Solatube International, Inc., can support indoor cannabis cultivation. TDDs are daylight harvesting systems that use optics to capture outdoor sunlight and transfer it indoors via highly engineered and reflective internal mirrored films. While the economic i...
Chapter
Full-text available
The serotonergic system is highly conserved in vertebrate species, including zebrafish. In spite of a genome duplication in teleost fish (which altered the number of genes encoding proteins related to synthesis, transport and signaling within the serotonergic system), the expression pattern of these proteins in zebrafish is similar to other vertebr...
Article
Full-text available
The first volume in the new Cambridge Handbooks in Behavioral Genetics series, Behavioral Genetics of the Mouse provides baseline information on normal behaviors, essential in both the design of experiments using genetically modified or pharmacologically treated animals and in the interpretation and analyses of the results obtained. The book offers...
Data
The NIF Registry is available to download in a couple of ways. The version attached to this paper is a snapshot and we recommend that you use an up-to date version. The places to view the updated registry are: 1. The main NIF site https://neuinfo.org/mynif/search.php?q=*&t=registry&b=0&r=20 *download the registry from here by looking at the "sour...
Article
Full-text available
Zebrafish (Danio rerio) are rapidly gaining popularity in translational neuroscience and behavioral research. Physiological similarity to mammals, ease of genetic manipulations, sensitivity to pharmacological and genetic factors, robust behavior, low cost, and potential for high-throughput screening contribute to the growing utility of zebrafish mo...
Article
Full-text available
The number of available neuroscience resources (databases, tools, materials, and networks) available via the Web continues to expand, particularly in light of newly implemented data sharing policies required by funding agencies and journals. However, the nature of dense, multifaceted neuroscience data and the design of classic search engine systems...
Article
Full-text available
An indole alkaloid, ibogaine is the principal psychoactive component of the iboga plant, used by indigenous peoples in West Africa for centuries. Modulating multiple neurotransmitter systems, the drug is a potent hallucinogen in humans, although its psychotropic effects remain poorly understood. Expanding the range of model species is an important...
Article
Intra-session habituation to novelty reflects spatial working memory (related to exploration and cognition), and is observed in various species, including zebrafish (Danio rerio). With the growing understanding of complex zebrafish behaviors, the extent to which they habituate remains unclear. Here we perform a large-scale characterization of zebra...
Article
Serotonin transporter (SERT) and brain-derived neurotrophic factor (BDNF) are key modulators of molecular signaling, cognition and behavior. Although SERT and BDNF mutant mouse phenotypes have been extensively characterized, little is known about their self-grooming behavior. Grooming represents an important behavioral domain sensitive to environme...
Article
Zebrafish (Danio rerio) are rapidly becoming an important model organism in neuroscience research, representing an excellent species to study complex social phenotypes. Zebrafish actively form shoals, which can be used to quantify their shoaling behaviors, highly sensitive to various experimental manipulations. Recent advances in video-tracking tec...
Article
Full-text available
The breadth of information resources available to researchers on the Internet continues to expand, particularly in light of recently implemented data-sharing policies required by funding agencies. However, the nature of dense, multifaceted neuroscience data and the design of contemporary search engine systems makes efficient, reliable and relevant...
Article
Widely used in biomedical research, zebrafish (Danio rerio) are steadily gaining popularity as a model organism for studying neurobehavioral phenomena. Here, we focus on to the growing spec-trum of zebrafish behavioral phenotypes and the 'bigger' biological problems these models help to address. Emphasizing the developing potential of zebrafish as...
Article
Full-text available
Widely used in biomedical research, zebrafish (Danio rerio) are steadily gaining popularity as a model organism for studying neurobehavioral phenomena. Here, we focus on to the growing spectrum of zebrafish behavioral phenotypes and the ‘bigger’ biological problems these models help to address. Emphasizing the developing potential of zebrafish as a...
Chapter
Full-text available
Animal behavioral tests are useful tools for modeling complex human brain disorders. The Suok test (ST) is a relatively new behavioral paradigm that simultaneously examines anxiety and neurological/vestibular phenotypes in rodents. The novelty and instability of the ST apparatus induces anxiety-related behavior in mice, whereas the elevation of the...
Article
3,4-methylenedioxymethamphetamine (MDMA, 'ecstasy') is a potent psychedelic drug inducing euphoria and hypersociability in humans, as well as hyperactivity and anxiety in rodents. Adult zebrafish (Danio rerio) have become a widely used species in neurobehavioral research. Here, we explore the effects of a wide range (0.25-120 mg/l) of acute MDMA do...
Article
The zebrafish (Danio rerio) has emerged as a promising model organism for affective or cognitive neuroscience research, and may be useful to study the interplay between memory and anxiety-related states. To assess the effects of acute psychological stress on spatial and cued memory, adult zebrafish were trained in an aquatic plus-maze for 14 days u...
Article
Here, we integrated manual observations, computerized event‐based scoring and automated video analysis of zebrafish traces to generate three‐dimensional (3D) swim path reconstruction of general behavioral patterns, thereby improving the characterization and interpretation of complex, anxiety‐related adult zebrafish behavior. Drugs known to evoke a...
Data
Original behavioral data for experimental manipulations summarized in Fig. 3 of the manuscript. Analysis of traditional endpoints shows that anxiogenic (panel a) and anxiolytic (panel b) treatments significantly affect the behavior of adult zebrafish in standardized 6-min novel tank tests. Additionally, high- and low-anxiety-like behavioral profile...
Data
Optimization of automated movement parameters to improve correlation with observed behavioral states (also see Fig. S2 for examples). Raw track data (used here to generate 3D swim path reconstructions in fish presented in Fig. 6) consists of exact expression values of automatically-generated movement parameters. Precisely integrating manually obser...
Data
Optimization of behavioral data based on computer-generated values and their global analysis using our approach. Erratic movements and freezing bouts are used here as examples. (DOCX)
Data
A comprehensive catalogue of traditional (manual) and automated (EthoVision XT7-generated) behavioral parameters characterizing adult zebrafish behavior in the novel tank test (see [50] for details). (DOCX)
Data
Correlation analysis of manual, event-based and automated behavioral quantification techniques on various endpoints assessed for all fish used in the present study. Our study integrated three approaches to quantify zebrafish behavior: manual observation (performed during the novel tank test), event-based scoring (performed by trained observers duri...
Data
Spearman correlation coefficients generated by unsupervised, hierarchical cluster analysis. The cluster analysis performed in our study resulted in several meaningful sub-groups of related experimental treatments or behavioral endpoints. With a correlation coefficient of 0.652, anxiogenic treatments grouped within Cluster I, whereas strongly correl...
Article
Full-text available
Mounting evidence implicates the zebrafish (Danio rerio) as a promising model species for reward and addiction research. Modeling drug abuse-related behavior in both adult and larval zebrafish produced a wealth of clinically translatable data, also demonstrating their sensitivity to various drugs of abuse and the ability to develop tolerance. Sever...
Book
Animal models have traditionally played a crucial role in improving our understanding of brain pathogenesis. Zebrafish (Danio rerio) have generated considerable discoveries in the areas of genetics, embryology, endocrinology, and neuroscience. Zebrafish Models in Neurobehavioral Research emphasizes the growing importance of zebrafish in neurobehavi...
Book
As a model organism, zebrafish (Danio rerio) offer an opportunity to perform steadfast scientific investigations in a robust and high-throughput manner. In Zebrafish Neurobehavioral Protocols, experts in the field provide a series of detailed behavioral protocols dealing with the major current research areas in the field of behavioral neuroscience....
Article
Lysergic acid diethylamide (LSD) is a potent hallucinogenic drug that strongly affects animal and human behavior. Although adult zebrafish (Danio rerio) are emerging as a promising neurobehavioral model, the effects of LSD on zebrafish have not been investigated previously. Several behavioral paradigms (the novel tank, observation cylinder, light-d...
Chapter
Full-text available
Depression, as part of a larger class of affective disorders, is one of the world’s most deleterious and widespread neurobehavioral diseases. However, much remains to be discovered concerning depression, due to the daunting complexity of its pathological mechanisms and etiology. Various animal models have been proposed over the years, some of which...
Chapter
Full-text available
Zebrafish have traditionally been used as effective genetic and developmental models in biomedical research. Recently, the scope and utility of zebrafish in biomedical research has been further expanded with the implementation of new genetic techniques aimed at developing translational models of human pathogenesis. Additionally, screens measuring s...
Article
Full-text available
Zebrafish (Danio rerio) are becoming increasingly popular in neurobehavioral research. Here, we summarize recent data on behavioral responses of adult zebrafish to a wide spectrum of putative anxiolytic and anxiogenic agents. Using the novel tank test as a sensitive and efficient behavioral assay, zebrafish anxiety-like behavior can be bi-direction...
Chapter
Full-text available
Three-dimensional reconstruction is a method of qualifying the behavioral activity of several animals including mice, rats, and zebrafish. This method allows for measuring behavioral endpoint data on two types of tracking planes (temporal and spatial). Temporal tracking measures the activity of a subject across time while spatial tracking measures...
Chapter
Full-text available
The zebrafish (Danio rerio) is rapidly becoming a popular model species in stress and neuroscience research. Their behavior, robustly affected by environmental and pharmacological manipulations, can be paralleled by physiological (endocrine) analysis. Zebrafish have a hypothalamic-pituitary-interrenal (HPI) axis, which is homologous to the human hy...
Chapter
Full-text available
Due to physiological and anatomical similarities to other vertebrates, zebrafish are becoming a widely used model in neurobehavioral research. With the growing popularity of zebrafish as experimental subjects, it is important to develop tools that accurately record their behavioral phenotypes. Video-aided analysis of zebrafish behavior offers an in...
Chapter
Full-text available
The development of reliable pharmacological screening assays is an important task. However, it is based upon the ability of animal models, such as the zebrafish, to demonstrate predictive validity for a specific set of drug classes. A popular assay used for this purpose is the novel tank diving paradigm, where zebrafish behavior can easily be modul...
Chapter
Full-text available
The light/dark box test, traditionally used to quantify rodent anxiety-like behavior, has recently been applied to the adult zebrafish (Danio rerio). Utilizing the fish’s scototaxis (aversion to bright areas and natural preference for the dark), this paradigm can be used to assess levels of anxiety in adult zebrafish. The light/dark box is a simple...
Chapter
Full-text available
Various novelty-based assays used to quantify zebrafish (Danio rerio) behavior show a striking similarity to behavioral responses in rodents. Exposed to the open field test, zebrafish establish overt homebases demonstrating clear preference for a particular area of the tank. This behavior aims to establish a “safe zone” that zebrafish can familiari...
Chapter
Full-text available
While zebrafish (Danio rerio) are widely utilized as a model species for neuroscience research, they also possess several qualities that make them particularly useful for studying stress and anxiety-related behaviors. Zebrafish neuroendocrine responses are robust, and correlate strongly with behavioral endpoints. These fish are also highly sensitiv...
Article
Zebrafish (Danio rerio) are emerging as a promising model species in neuroscience research. Many traditional rodent behavioral paradigms may be adapted for zebrafish testing. Exposing zebrafish to three different "open field" tanks for 30 min, we showed that fish display robust homebase behavior, in which one area of the tank is chosen as a preferr...
Article
Full-text available
Several behavioral assays are currently used for high-throughput neurophenotyping and screening of genetic mutations and psychotropic drugs in zebrafish (Danio rerio). In this protocol, we describe a battery of two assays to characterize anxiety-related behavioral and endocrine phenotypes in adult zebrafish. Here, we detail how to use the 'novel ta...
Article
Vitamin D is becoming increasingly recognized as a nontraditional drug target for different brain pathologies. Although widely known for their role in calcium metabolism, vitamin D and its receptor have been linked to several brain disorders, including cognitive decline, epilepsy, affective disorders, and schizophrenia. Here we discuss mounting evi...
Article
Larval zebrafish (Danio rerio) have recently been suggested as a high-throughput experimental model of epilepsy-related pathogenetic states. Here we use adult zebrafish to study behavioral symptoms associated with drug-evoked seizures. Experimental epilepsy-like states were evoked in zebrafish by exposure for 20min to three chemoconvulsant drugs: c...
Article
Full-text available
Analysis of habituation is widely used to characterize animal cognitive phenotypes and their modulation. Although zebrafish (Danio rerio) are increasingly utilized in neurobehavioral research, their habituation responses have not been extensively investigated. Utilizing the novel tank test, we examine intra- and inter-session habituation and demons...
Article
Full-text available
Stress induced by social defeat is a strong modifier of animal anxiety and depression-like phenotypes. Self-grooming is a common rodent behavior, and has an ordered cephalo-caudal progression from licking of the paws to head, body, genitals and tail. Acute stress is known to alter grooming activity levels and disrupt its patterning. Following 15-17...
Article
Full-text available
Animal social defeat stress is a strong modulator of anxiety and depression‐like states. Although grooming is a frequent behavioral marker of stress, little is known about the effects of social stress on grooming. This study explores the effects of chronic social defeat stress on mouse self‐grooming behavior. After exposing mice to 13–15 days of so...
Article
Though widely used to characterize animal cognitive phenotypes and their modulation, habituation phenotypes have not been extensively investigated in zebrafish (Danio rerio). Utilizing the novel tank test, we examined intra‐ and intersession habituation and demonstrated robust habituation responses in zebrafish. Intrasession habituation analysis de...
Article
Full-text available
The zebrafish (Danio rerio) is becoming increasingly popular in the field of neurobehavioral research, including experimental, genetic, and pharmacological models of human brain disorders. While zebrafish research is rapidly expanding, its application as a translational neurobehavioral model is still in its relative infancy. Therefore, further inve...
Article
The zebrafish (Danio rerio) is rapidly becoming a popular model species in behavioral neuroscience research. Zebrafish behavior is robustly affected by environmental and pharmacological manipulations, and can be examined using exploration-based paradigms, paralleled by analysis of endocrine (cortisol) stress responses. Discontinuation of various ps...
Article
This is a mini-review of vitamin D(3), its active metabolites and their functioning in the central nervous system (CNS), especially in relation to nervous system pathologies and aging. The vitamin D(3) endocrine system consists of 3 active calcipherol hormones: calcidiol (25OHD(3)), 1alpha-calcitriol (1alpha,25(OH)2D(3)) and 24-calcitriol (24,25(OH...
Article
Full-text available
The zebrafish (Danio rerio) is emerging as a promising model organism for experimental studies of stress and anxiety. Here we further validate zebrafish models of stress by analyzing how environmental and pharmacological manipulations affect their behavioral and physiological phenotypes. Experimental manipulations included exposure to alarm pheromo...
Article
Experimental models are an important tool for the study of biological mechanisms of psychiatric disorders. Although encouraging progress has been made in biological psychiatry of affective disorders, there remain numerous methodological, conceptual, and translational challenges in this field. Mounting clinical data support the view that psychiatric...
Chapter
Full-text available
Zebrafish behavioral phenotypes are often evaluated in response to pharmacological modulation by various psychotropic drugs. An important step in this process is the method of drug administration. While the most popular drug administration technique in zebrafish research is by immersion, systemic intraperitoneal injection is another effective alter...

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