scholarly journals microCT-Based Phenomics in the Zebrafish Skeleton Reveals Virtues of Deep Phenotyping in a Distributed Organ System

2017 ◽  
Author(s):  
Matthew Hur ◽  
Charlotte A. Gistelinck ◽  
Philippe Huber ◽  
Jane Lee ◽  
Marjorie H. Thompson ◽  
...  
Keyword(s):  
Axial Skeleton ◽  
Thyroid Stimulating Hormone ◽  
Effect Sizes ◽  
Genetic Screens ◽  
Spatially Distributed ◽  
Functional Understanding ◽  
Increase Productivity ◽  
Brittle Bone Disease ◽  
Mutant Phenotypes ◽  
Deep Phenotyping

ABSTRACTPhenomics, which ideally involves in-depth phenotyping at the whole-organism scale, may enhance our functional understanding of genetic variation. Here, we demonstrate methods to profile hundreds of measures comprised of morphological and densitometric traits from a large number sites in the axial skeleton of adult zebrafish. We show the potential for vertebral patterns to confer heightened sensitivity, with similar specificity, in discriminating mutant populations compared to analyzing individual vertebrae in isolation. We identify phenotypes associated with human brittle bone disease and thyroid stimulating hormone receptor hyperactivity. Finally, we develop allometric models and show their potential to aid in the discrimination of mutant phenotypes masked by alterations in growth. Our studies demonstrate virtues of deep phenotyping in a spatially distributed organ. Analyzing phenotypic patterns may increase productivity in genetic screens, and could facilitate the study of genetic variants associated with smaller effect sizes, such as those that underlie complex diseases.

scholarly journals MicroCT-based phenomics in the zebrafish skeleton reveals virtues of deep phenotyping in a distributed organ system

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Matthew Hur ◽  
Charlotte A Gistelinck ◽  
Philippe Huber ◽  
Jane Lee ◽  
Marjorie H Thompson ◽  
...  
Keyword(s):  
Axial Skeleton ◽  
Thyroid Stimulating Hormone ◽  
Organ System ◽  
Genetic Screens ◽  
Spatially Distributed ◽  
Functional Understanding ◽  
Increase Productivity ◽  
Brittle Bone Disease ◽  
Mutant Phenotypes ◽  
Deep Phenotyping

Phenomics, which ideally involves in-depth phenotyping at the whole-organism scale, may enhance our functional understanding of genetic variation. Here, we demonstrate methods to profile hundreds of phenotypic measures comprised of morphological and densitometric traits at a large number of sites within the axial skeleton of adult zebrafish. We show the potential for vertebral patterns to confer heightened sensitivity, with similar specificity, in discriminating mutant populations compared to analyzing individual vertebrae in isolation. We identify phenotypes associated with human brittle bone disease and thyroid stimulating hormone receptor hyperactivity. Finally, we develop allometric models and show their potential to aid in the discrimination of mutant phenotypes masked by alterations in growth. Our studies demonstrate virtues of deep phenotyping in a spatially distributed organ system. Analyzing phenotypic patterns may increase productivity in genetic screens, and facilitate the study of genetic variants associated with smaller effect sizes, such as those that underlie complex diseases.

scholarly journals A simple and effective F0 knockout method for rapid screening of behaviour and other complex phenotypes

2020 ◽  
Author(s):  
François Kroll ◽  
Gareth T Powell ◽  
Marcus Ghosh ◽  
Paride Antinucci ◽  
Timothy J Hearn ◽  
...  
Keyword(s):  
Neurological Diseases ◽  
Rapid Screening ◽  
Genetic Screens ◽  
Behavioural Phenotype ◽  
Larval Zebrafish ◽  
Complex Phenotypes ◽  
Human Genes ◽  
Behavioural Phenotypes ◽  
Mutant Phenotypes ◽  
Genetic Contributions

ABSTRACTHundreds of human genes are associated with neurological diseases, but translation into tractable biological mechanisms is lagging. Larval zebrafish are an attractive model to investigate genetic contributions to neurological diseases. However, current CRISPR-Cas9 methods are difficult to apply to large genetic screens studying behavioural phenotypes. To facilitate rapid genetic screening, we developed a simple sequencing-free tool to validate gRNAs and a highly effective CRISPR-Cas9 method capable of converting >90% of injected embryos directly into F0 biallelic knockouts. We demonstrate that F0 knockouts reliably recapitulate complex mutant phenotypes, such as altered molecular rhythms of the circadian clock, escape responses to irritants, and multi-parameter day-night locomotor behaviours. The technique is sufficiently robust to knockout multiple genes in the same animal, for example to create the transparent triple knockout crystal fish for imaging. Our F0 knockout method cuts the experimental time from gene to behavioural phenotype in zebrafish from months to one week.

scholarly journals A simple and effective F0 knockout method for rapid screening of behaviour and other complex phenotypes

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
François Kroll ◽  
Gareth T Powell ◽  
Marcus Ghosh ◽  
Gaia Gestri ◽  
Paride Antinucci ◽  
...  
Keyword(s):  
Neurological Diseases ◽  
Rapid Screening ◽  
Genetic Screens ◽  
Behavioural Phenotype ◽  
Larval Zebrafish ◽  
Complex Phenotypes ◽  
Human Genes ◽  
Behavioural Phenotypes ◽  
Mutant Phenotypes ◽  
Genetic Contributions

Hundreds of human genes are associated with neurological diseases, but translation into tractable biological mechanisms is lagging. Larval zebrafish are an attractive model to investigate genetic contributions to neurological diseases. However, current CRISPR-Cas9 methods are difficult to apply to large genetic screens studying behavioural phenotypes. To facilitate rapid genetic screening, we developed a simple sequencing-free tool to validate gRNAs and a highly effective CRISPR-Cas9 method capable of converting >90% of injected embryos directly into F0 biallelic knockouts. We demonstrate that F0 knockouts reliably recapitulate complex mutant phenotypes, such as altered molecular rhythms of the circadian clock, escape responses to irritants, and multi-parameter day-night locomotor behaviours. The technique is sufficiently robust to knockout multiple genes in the same animal, for example to create the transparent triple knockout crystal fish for imaging. Our F0 knockout method cuts the experimental time from gene to behavioural phenotype in zebrafish from months to one week.

scholarly journals Integration of Odor-Induced Activity of Kenyon Cells in an Electrotonically Compact Drosophila Mushroom Body Output Neuron (MBON)

2019 ◽  
Author(s):  
Omar Hafez ◽  
Benjamin Escribano ◽  
Jan Pielage ◽  
Ernst Niebur
Keyword(s):  
Mushroom Body ◽  
Behavioral Outcomes ◽  
Dendritic Structure ◽  
Internal Representation ◽  
Kenyon Cell ◽  
Sensory Stimuli ◽  
Output Neuron ◽  
Spatially Distributed ◽  
Functional Understanding ◽  
Distributed Cluster

AbstractThe formation of an ecologically useful lasting memory requires that the brain has an accurate internal representation of the surrounding environment. In addition, it must have the ability to integrate a variety of different sensory stimuli and associate them with rewarding and aversive behavioral outcomes. Over the previous years, a number of studies have dissected the anatomy and elucidated some of the working principles of the Drosophila mushroom body (MB), the fly’s center for learning and memory. As a consequence, we now have a functional understanding of where and how in the MB sensory stimuli converge and are associated. However, the molecular and cellular dynamics at the critical synaptic intersection for this process, the Kenyon cell-mushroom body output neuron (KC-MBON) synapse, are largely unknown. Here, we introduce a first approach to understand this integration process and the physiological changes occurring at the KC-MBON synapse during Kenyon cell (KC) activation. We use the published connectome of the Drosophila MB to construct a functional computational model of the MBON-α3-A dendritic structure. We simulate synaptic input by individual KC-MBON synapses by current injections into precisely (μm) identified local dendritic sections, and the input from a model population of KCs representing an odor by a spatially distributed cluster of current injections. By recording the effect of the simulated current injections on the membrane potential of the neuron, we show that the MBON-α3-A is electrotonically compact. This suggests that odor-induced MBON activity is likely governed by input strength while the positions of KC input synapses are largely irrelevant.

scholarly journals Eukaryotic MCM Proteins: Beyond Replication Initiation

2004 ◽  
Vol 68 (1) ◽  
pp. 109-131 ◽  
Author(s):  
Susan L. Forsburg
Keyword(s):  
Genome Stability ◽  
Dna Helicase ◽  
Replication Initiation ◽  
Genetic Screens ◽  
Minichromosome Maintenance ◽  
Experimental Systems ◽  
Damage Response ◽  
Mcm Proteins ◽  
Mutant Phenotypes ◽  
Related Proteins

SUMMARY The minichromosome maintenance (or MCM) protein family is composed of six related proteins that are conserved in all eukaryotes. They were first identified by genetic screens in yeast and subsequently analyzed in other experimental systems using molecular and biochemical methods. Early data led to the identification of MCMs as central players in the initiation of DNA replication. More recent studies have shown that MCM proteins also function in replication elongation, probably as a DNA helicase. This is consistent with structural analysis showing that the proteins interact together in a heterohexameric ring. However, MCMs are strikingly abundant and far exceed the stoichiometry of replication origins; they are widely distributed on unreplicated chromatin. Analysis of mcm mutant phenotypes and interactions with other factors have now implicated the MCM proteins in other chromosome transactions including damage response, transcription, and chromatin structure. These experiments indicate that the MCMs are central players in many aspects of genome stability.

Abstract Semantic Associative Network Training: A Replication and Update of an Abstract Word Retrieval Therapy Program

2020 ◽  
Vol 29 (3) ◽  
pp. 1574-1595
Author(s):  
Chaleece W. Sandberg ◽  
Teresa Gray
Keyword(s):  
Concrete Word ◽  
Abstract Word ◽  
Distinct Pattern ◽  
Word Retrieval ◽  
Effect Sizes ◽  
Associative Network ◽  
Direct Training ◽  
Network Training ◽  
Abstract Words ◽  
Concrete Words

Purpose We report on a study that replicates previous treatment studies using Abstract Semantic Associative Network Training (AbSANT), which was developed to help persons with aphasia improve their ability to retrieve abstract words, as well as thematically related concrete words. We hypothesized that previous results would be replicated; that is, when abstract words are trained using this protocol, improvement would be observed for both abstract and concrete words in the same context-category, but when concrete words are trained, no improvement for abstract words would be observed. We then frame the results of this study with the results of previous studies that used AbSANT to provide better evidence for the utility of this therapeutic technique. We also discuss proposed mechanisms of AbSANT. Method Four persons with aphasia completed one phase of concrete word training and one phase of abstract word training using the AbSANT protocol. Effect sizes were calculated for each word type for each phase. Effect sizes for this study are compared with the effect sizes from previous studies. Results As predicted, training abstract words resulted in both direct training and generalization effects, whereas training concrete words resulted in only direct training effects. The reported results are consistent across studies. Furthermore, when the data are compared across studies, there is a distinct pattern of the added benefit of training abstract words using AbSANT. Conclusion Treatment for word retrieval in aphasia is most often aimed at concrete words, despite the usefulness and pervasiveness of abstract words in everyday conversation. We show the utility of AbSANT as a means of improving not only abstract word retrieval but also concrete word retrieval and hope this evidence will help foster its application in clinical practice.

The Role of Zinc in Thyroid Hormones Metabolism

2019 ◽  
Vol 89 (1-2) ◽  
pp. 80-88 ◽  
Author(s):  
Juliana Soares Severo ◽  
Jennifer Beatriz Silva Morais ◽  
Taynáh Emannuelle Coelho de Freitas ◽  
Ana Letícia Pereira Andrade ◽  
Mayara Monte Feitosa ◽  
...  
Keyword(s):  
Thyroid Hormones ◽  
Scientific Evidence ◽  
Thyroid Stimulating Hormone ◽  
Zinc Transporters ◽  
Serum Concentrations ◽  
Metabolic Adaptations ◽  
Serum T3 ◽  
Regulatory Effects ◽  
Shed Light

Abstract. Thyroid hormones play an important role in body homeostasis by facilitating metabolism of lipids and glucose, regulating metabolic adaptations, responding to changes in energy intake, and controlling thermogenesis. Proper metabolism and action of these hormones requires the participation of various nutrients. Among them is zinc, whose interaction with thyroid hormones is complex. It is known to regulate both the synthesis and mechanism of action of these hormones. In the present review, we aim to shed light on the regulatory effects of zinc on thyroid hormones. Scientific evidence shows that zinc plays a key role in the metabolism of thyroid hormones, specifically by regulating deiodinases enzymes activity, thyrotropin releasing hormone (TRH) and thyroid stimulating hormone (TSH) synthesis, as well as by modulating the structures of essential transcription factors involved in the synthesis of thyroid hormones. Serum concentrations of zinc also appear to influence the levels of serum T3, T4 and TSH. In addition, studies have shown that Zinc transporters (ZnTs) are present in the hypothalamus, pituitary and thyroid, but their functions remain unknown. Therefore, it is important to further investigate the roles of zinc in regulation of thyroid hormones metabolism, and their importance in the treatment of several diseases associated with thyroid gland dysfunction.

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