High-throughput in vivo vertebrate screening

Pardo-Martín, Carlos; Chang, Tsung-Yao; Koo, Bryan Kyo; Gilleland, Cody L.; Wasserman, Steven C.; Yanik, Mehmet Fatih

doi:10.1038/nmeth.1481

Cited by 308 publications

(303 citation statements)

References 15 publications

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“…As our system was capable to manipulate larvae without using anesthetics or rigid gels, this enabled us to perform analysis correlating sophisticated molecular phenotypes with behavioral change in awake larvae, which was not feasible in most existing strategies. 17,19 Using this system, we studied ethanol-induced acute responses in behaving larvae from different aspects including behavioral changes, cardiac, and neurological physiology. We found that the motor function of a larva was significantly affected by ethanol treatment, especially at a high concentration of 3%, which induced a biphasic effect on specific type of eye movements; and the behavioral changes were temporally coincided with the dynamic responses in cardiac and nervous system.…”

Section: Discussionmentioning

confidence: 99%

“…Even though some microfluidic systems were developed to study the behaviors or morphological development of zebrafish embryos, these platforms were difficult to resolve sophisticated organ-specific information at cellular level. [16][17][18] On the other hand, cellularresolution imaging of zebrafish typically requires manual or automatic manipulation and orientation of larvae using rigid gel or physical restrictions, [19][20][21][22][23] which are not permissive to behavioral analysis. Even though partial restriction may be applied to allow high-resolution imaging of brain activity and observation of associated motor behaviors, 11,24 such experiments are quite laborious and not versatile enough for high-throughput applications.…”

Section: Introductionmentioning

confidence: 99%

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Autonomous system for cross-organ investigation of ethanol-induced acute response in behaving larval zebrafish

Lin

Chen

et al. 2016

Biomicrofluidics

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Ethanol is widely consumed and has been associated with various diseases in different organs. It is therefore important to study ethanol-induced responses in living organisms with the capability to address specific organs in an integrative manner. Here, we developed an autonomous system based on a series of microfluidic chips for cross-organ investigation of ethanol-induced acute response in behaving larval zebrafish. This system enabled high-throughput, gel-free, and anesthetic-free manipulation of larvae, and thus allowed real-time observation of behavioral responses, and associated physiological changes at cellular resolution within specific organs in response to acute ethanol stimuli, which would otherwise be impossible by using traditional methods for larva immobilization and orientation. Specifically, three types of chips ("motion," "lateral," and "dorsal"), based on a simple hydrodynamic design, were used to perform analysis in animal behavior, cardiac, and brain physiology, respectively. We found that ethanol affected larval zebrafish in a dose-dependent manner. The motor function of different body parts was significantly modulated by ethanol treatment, especially at a high dose of 3%. These behavioral changes were temporally associated with a slow-down of heart-beating and a stereotyped activation of certain brain regions. As we demonstrated in this proof-of-concept study, this versatile Fish-on-Chip platform could potentially be adopted for systematic cross-organ investigations involving chemical or genetic manipulations in zebrafish model. Published by AIP Publishing. [http://dx

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Autonomous system for cross-organ investigation of ethanol-induced acute response in behaving larval zebrafish

Lin

Chen

et al. 2016

Biomicrofluidics

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“…The approach has already been successfully applied to diverse areas of research such as the identification of drug targets in cancer 9,[31][32][33] and embryonic development [34][35][36] and even has potential for application in deciphering the pathways involved in neuropsychiatric disorders 37,38 . However implementation of such a system requires a significant investment of time and effort with process optimization often taking a minimum of 6 months.…”

Section: Discussionmentioning

confidence: 99%

High Content Screening in Neurodegenerative Diseases

Jain¹,

Kesteren²,

Heutink³

2012

JoVE

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The functional annotation of genomes, construction of molecular networks and novel drug target identification, are important challenges that need to be addressed as a matter of great urgency [1][2][3][4] . Multiple complementary 'omics' approaches have provided clues as to the genetic risk factors and pathogenic mechanisms underlying numerous neurodegenerative diseases, but most findings still require functional validation 5. For example, a recent genome wide association study for Parkinson's Disease (PD), identified many new loci as risk factors for the disease, but the underlying causative variant(s) or pathogenic mechanism is not known 6,7 . As each associated region can contain several genes, the functional evaluation of each of the genes on phenotypes associated with the disease, using traditional cell biology techniques would take too long.There is also a need to understand the molecular networks that link genetic mutations to the phenotypes they cause. It is expected that disease phenotypes are the result of multiple interactions that have been disrupted. Reconstruction of these networks using traditional molecular methods would be time consuming. Moreover, network predictions from independent studies of individual components, the reductionism approach, will probably underestimate the network complexity 8 . This underestimation could, in part, explain the low success rate of drug approval due to undesirable or toxic side effects. Gaining a network perspective of disease related pathways using HT/HC cellular screening approaches, and identifying key nodes within these pathways, could lead to the identification of targets that are more suited for therapeutic intervention.High-throughput screening (HTS) is an ideal methodology to address these issues [9][10][11][12] . but traditional methods were one dimensional whole-well cell assays, that used simplistic readouts for complex biological processes. They were unable to simultaneously quantify the many phenotypes observed in neurodegenerative diseases such as axonal transport deficits or alterations in morphology properties 13,14 . This approach could not be used to investigate the dynamic nature of cellular processes or pathogenic events that occur in a subset of cells. To quantify such features one has to move to multi-dimensional phenotypes termed high-content screening (HCS) 4,[15][16][17] . HCS is the cell-based quantification of several processes simultaneously, which provides a more detailed representation of the cellular response to various perturbations compared to HTS. HCS has many advantages over HTS 18,19 , but conducting a high-throughput (HT)-high-content (HC) screen in neuronal models is problematic due to high cost, environmental variation and human error. In order to detect cellular responses on a 'phenomics' scale using HC imaging one has to reduce variation and error, while increasing sensitivity and reproducibility.Herein we describe a method to accurately and reliably conduct shRNA screens using automated cell culturing 20 and H...

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“…2A) include multiharmonic (Evanko et al, 2010) and fluorescence imaging by confocal, multiphoton laser scanning microscopy (Abbott, 2009;Pardo-Martin et al, 2010) or lightsheet fluorescence microscopy (LSFM) (Huisken and Stainier, 2009;Keller et al, 2010), combined with newly developed fluorescent proteins and biological sensors (Chudakov et al, 2005;Giepmans et al, 2006) and in situ hybridization (ISH) techniques (Welten et al, 2006;Brend and Holley, 2009). These advances opened new perspectives for the construction of high resolution anatomical and gene expression atlases.…”

Section: Imaging Modalitiesmentioning

confidence: 99%

Assembling models of embryo development: Image analysis and the construction of digital atlases

Castro-González

Ledesma-Carbayo

Peyriéras

et al. 2012

Birth Defects Research Pt C

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Digital atlases of animal development provide a quantitative description of morphogenesis, opening the path toward processes modeling. Prototype atlases offer a data integration framework where to gather information from cohorts of individuals with phenotypic variability. Relevant information for further theoretical reconstruction includes measurements in time and space for cell behaviors and gene expression. The latter as well as data integration in a prototypic model, rely on image processing strategies. Developing the tools to integrate and analyze biological multidimensional data are highly relevant for assessing chemical toxicity or performing drugs preclinical testing. This article surveys some of the most prominent efforts to assemble these prototypes, categorizes them according to salient criteria and discusses the key questions in the field and the future challenges toward the reconstruction of multiscale dynamics in model organisms.

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High-throughput in vivo vertebrate screening

Cited by 308 publications

References 15 publications

Autonomous system for cross-organ investigation of ethanol-induced acute response in behaving larval zebrafish

Autonomous system for cross-organ investigation of ethanol-induced acute response in behaving larval zebrafish

High Content Screening in Neurodegenerative Diseases

Assembling models of embryo development: Image analysis and the construction of digital atlases

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