Mutant Generation in Vertebrate Model Organisms by TILLING

2011 ◽  
pp. 475-504 ◽  
Author(s):  
Sylke Winkler ◽  
Nicola Gscheidel ◽  
Michael Brand
Keyword(s):  
Model Organisms ◽  
Vertebrate Model

scholarly journals An automated feeding system for the African killifish reveals effects of dietary restriction on lifespan and allows scalable assessment of associative learning

2021 ◽  
Author(s):  
Andrew McKay ◽  
Chi-Kuo Hu ◽  
Sharon Chen ◽  
Claire Nicole Bedbrook ◽  
Mike Thielvoldt ◽  
...  
Keyword(s):  
Associative Learning ◽  
Dietary Restriction ◽  
Model Organism ◽  
Video Camera ◽  
Food Delivery ◽  
Automated System ◽  
Model Organisms ◽  
Feeding Time ◽  
Feeding System ◽  
Vertebrate Model

AbstractThe African turquoise killifish is an exciting new vertebrate model for aging studies. A significant challenge for any model organism is control over its diet in space and time. To address this challenge, we created an automated and networked fish feeding system. Our automated feeder is designed to be open-source, easily transferable, and built from widely available components. Compared to manual feeding, our automated system is highly precise and flexible. As a proof-of-concept for the feeding schedule flexibility of these automated feeders, we define a favorable regimen for growth and fertility for the African killifish and a dietary restriction regimen where both feeding time and quantity are reduced. We show that this dietary restriction regimen extends lifespan in males. Moreover, combining our automated feeding system with a video camera, we establish an associative learning assay for the killifish. This learning assay provides an integrative measure of cognitive decline during aging. The ability to precisely control food delivery in the killifish opens new areas to assess lifespan and cognitive behavior dynamics and to screen for dietary interventions and drugs in a high-throughput manner previously impossible with traditional vertebrate model organisms.

Zebrafish as an animal model for the antiviral RNA interference pathway

2021 ◽  
Author(s):  
Yanxin Ren ◽  
Xueyu Li ◽  
Zhonghui Tian ◽  
Yan Xu ◽  
Ruilin Zhang ◽  
...  
Keyword(s):  
Rna Interference ◽  
Sindbis Virus ◽  
Rna Virus ◽  
Model Organism ◽  
Model Organisms ◽  
Rnai Pathway ◽  
Small Interfering Rnas ◽  
Argonaute 2 ◽  
Larval Zebrafish ◽  
Vertebrate Model

The zebrafish (Danio rerio) possesses evolutionarily conserved innate and adaptive immunity as a mammal and has recently become a popular vertebrate model to exploit infection and immunity. Antiviral RNA interference (RNAi) has been illuminated in various model organisms, including Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans and mice. However, to date, there is no report on the antiviral RNAi pathway of zebrafish. Here, we have evaluated the possible use of zebrafish to study antiviral RNAi with Sindbis virus (SINV), vesicular stomatitis virus (VSV) and Nodamura virus (NoV). We find that SINVs and NoVs induce the production of virus-derived small interfering RNAs (vsiRNAs), the hallmark of antiviral RNAi, with a preference for a length of 22 nucleotides, after infection of larval zebrafish. Meanwhile, the suppressor of RNAi (VSR) protein, NoV B2, may affect the accumulation of the NoV in zebrafish. Furthermore, taking advantage of the fact that zebrafish argonaute-2 (Ago2) protein is naturally deficient in cleavage compared with that of mammals, we provide evidence that the slicing activity of human Ago2 can virtually inhibit the accumulation of RNA virus after being ectopically expressed in larval zebrafish. Thus, zebrafish may be a unique model organism to study the antiviral RNAi pathway.

scholarly journals Gelsolin and Related Proteins in Vertebrate Model Organisms

2019 ◽  
Vol 67 (4) ◽  
pp. 159-167
Author(s):  
Marta MIGOCKA-PATRZAŁEK ◽  
Joanna NIEDBALSKA-TARNOWSKA ◽  
Arnold GARBIEC ◽  
Magda DUBIŃSKA-MAGIERA ◽  
Małgorzata DACZEWSKA
Keyword(s):  
Actin Binding ◽  
Model Organisms ◽  
Potential Candidate ◽  
Research Directions ◽  
Main Research ◽  
Founding Member ◽  
Vertebrate Model ◽  
Eukaryotic Organisms ◽  
Apoptosis Regulation ◽  
Related Proteins

Gelsolin, encoded by the Gsn gene, is a highly conserved actin-binding protein detected in all studied eukaryotic organisms. Gelsolin is the founding member of the gelsolin superfamily of proteins, whose main functions are binding, severing, and capping actin filaments. Moreover, gelsolin is engaged in apoptosis regulation, signal transduction, and embryonic development. Gelsolin is also implicated in some human diseases such as Alzheimer disease and familial amyloidosis of the Finnish type (FAF). Because of its multifunctionality, gelsolin is a potential candidate for diverse therapeutic applications. Most of our knowledge about gelsolin superfamily proteins comes from investigations conducted on vertebrate model organisms such as zebrafish (Danio rerio), African clawed frogs (Xenopus laevis), chickens (Gallus gallus), and mice (Mus musculus). Here, we present fundamental findings as well as new knowledge to indicate main research directions and future possibilities. Different model organisms provide specific possibilities and present particular advantages. However, all of them give useful data, which allow us to gain a better understanding of the function of gelsolin and related proteins.

Pro-apoptotic BH3-only Bcl-2 family members in vertebrate model organisms suitable for genetic experimentation

2002 ◽  
Vol 9 (11) ◽  
pp. 1163-1166 ◽  
Author(s):  
L Coultas ◽  
D C S Huang ◽  
J M Adams ◽  
A Strasser
Keyword(s):  
Family Members ◽  
Model Organisms ◽  
Vertebrate Model

scholarly journals New Findings on LMO7 Transcripts, Proteins and Regulatory Regions in Human and Vertebrate Model Organisms and the Intracellular Distribution in Skeletal Muscle Cells

2021 ◽  
Vol 22 (23) ◽  
pp. 12885
Author(s):  
Geyse Gomes ◽  
Mariana Juliani do Amaral ◽  
Kayo Moreira Bagri ◽  
Larissa Melo Vasconcellos ◽  
Marcius da Silva Almeida ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Regulatory Element ◽  
Muscle Cells ◽  
Intracellular Distribution ◽  
Skeletal Muscle Cells ◽  
Model Organisms ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
New Findings ◽  
Vertebrate Model

LMO7 is a multifunctional PDZ–LIM protein that can interact with different molecular partners and is found in several intracellular locations. The aim of this work was to shed light on LMO7 evolution, alternative transcripts, protein structure and gene regulation through multiple in silico analyses. We also explored the intracellular distribution of the LMO7 protein in chicken and zebrafish embryonic skeletal muscle cells by means of confocal fluorescence microscopy. Our results revealed a single LMO7 gene in mammals, sauropsids, Xenopus and in the holostean fish spotted gar while two lmo7 genes (lmo7a and lmo7b) were identified in teleost fishes. In addition, several different transcripts were predicted for LMO7 in human and in major vertebrate model organisms (mouse, chicken, Xenopus and zebrafish). Bioinformatics tools revealed several structural features of the LMO7 protein including intrinsically disordered regions. We found the LMO7 protein in multiple intracellular compartments in chicken and zebrafish skeletal muscle cells, such as membrane adhesion sites and the perinuclear region. Curiously, the LMO7 protein was detected within the nuclei of muscle cells in chicken but not in zebrafish. Our data showed that a conserved regulatory element may be related to muscle-specific LMO7 expression. Our findings uncover new and important information about LMO7 and open new challenges to understanding how the diverse regulation, structure and distribution of this protein are integrated into highly complex vertebrate cellular milieux, such as skeletal muscle cells.

scholarly journals The Xenopus Phenotype Ontology: bridging model organism phenotype data to human health and development.

2021 ◽  
Author(s):  
Malcolm E Fisher ◽  
Erik J Segerdell ◽  
Nicolas Matentzoglu ◽  
Mardi J Nenni ◽  
Joshua D Fortriede ◽  
...  
Keyword(s):  
Design Patterns ◽  
Model Organism ◽  
Model Organisms ◽  
Phenotype Ontology ◽  
Phenotypic Data ◽  
Anatomy Ontology ◽  
Ontology Language ◽  
Phenotype Data ◽  
Vertebrate Model ◽  
Research Continuum

Background: Ontologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are interoperable across the biomedical research continuum. There is also an increasing need for methods to interrelate phenotypic data easily and accurately from experiments in animal models with human development and disease. Results: Here we present the Xenopus Phenotype Ontology (XPO) to annotate phenotypic data from experiments in Xenopus, one of the major vertebrate model organisms used to study gene function in development and disease. The XPO implements design patterns from the Unified Phenotype Ontology (uPheno), and the principles outlined by the Open Biological and Biomedical Ontologies (OBO Foundry) to maximize interoperability with other species and facilitate ongoing ontology management. Constructed in Web Ontology Language (OWL) the XPO combines the existing uPheno library of ontology design patterns with additional terms from the Xenopus Anatomy Ontology (XAO), the Phenotype and Trait Ontology (PATO) and the Gene Ontology (GO). The integration of these different ontologies into the XPO enables rich phenotypic curation, whilst the uPheno bridging axioms allows phenotypic data from Xenopus experiments to be related to phenotype data from other model organisms and human disease. Moreover, the simple post-composed uPheno design patterns facilitate ongoing XPO development as the generation of new terms and classes of terms can be substantially automated. Conclusions: The XPO serves as an example of current best practices to help overcome many of the inherent challenges in harmonizing phenotype data between different species. The XPO currently consists of approximately 22,000 terms and is being used to curate phenotypes by Xenbase, the Xenopus Model Organism Knowledgebase, forming a standardized corpus of genotype-phenotype data that can be directly related to other uPheno compliant resources.

scholarly journals Conserved Vertebrate Chromosome Segments in the Large Salamander Genome

Genetics ◽  
2001 ◽  
Vol 158 (2) ◽  
pp. 735-746 ◽  
Author(s):  
S Randal Voss ◽  
Jeramiah J Smith ◽  
David M Gardiner ◽  
David M Parichy
Keyword(s):  
Small Sample ◽  
Ambystoma Mexicanum ◽  
Model Organisms ◽  
Genetic Linkage Analysis ◽  
Protein Coding ◽  
Mapping Panel ◽  
Organ Systems ◽  
Vertebrate Model ◽  
Ambystomatid Salamanders ◽  
Chromosome Segments

Abstract Urodele amphibians (salamanders) are important models for embryological, physiological, and natural history research and are also a biomedically important group because they are the only vertebrates capable of regenerating entire organ systems. To enhance the utility of salamanders for biomedical research and for understanding genome evolution, genetic linkage analysis was used to identify chromosome segments that are homologous between ambystomatid salamanders and distantly related vertebrate model organisms. A total of 347 loci (AFLPs, RAPDs, and protein-coding loci) were mapped using an interspecific meiotic mapping panel (Ambystoma mexicanum and A. tigrinum tigrinum; family Ambystomatidae). Genome size in Ambystoma was estimated to be 7291 cM, the largest linkage map estimate reported for any organism. However, the relatively large size of the salamander genome did not hinder efforts to map and identify conserved syntenies from a small sample of 24 protein-coding loci. Chromosomal segments that are conserved between fishes and mammals are also conserved in these salamanders. Thus, comparative gene mapping appears to be an efficient strategy for identifying orthologous loci between ambystomatid salamanders and genomically well-characterized vertebrate model organisms.

scholarly journals Identification and Characterization of Two Novel RNA Editing Sites ingrin1bTranscripts of EmbryonicDanio rerio

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Pedro Pozo ◽  
Barry Hoopengardner
Keyword(s):  
Rna Editing ◽  
Model System ◽  
Editing Site ◽  
Model Organisms ◽  
Comparative Approach ◽  
Integrated Models ◽  
Vertebrate Model ◽  
Identification And Characterization ◽  
Insight Into

Discovering RNA editing sites in model organisms provides an insight into their adaptations in addition to finding potential sites for the regulation of neural activity and the basis of integrated models of metazoan editing with a variety of applications, including potential clinical treatments of neural dysregulation. The zebrafish,Danio rerio, is an important vertebrate model system. We focused on thegrin1bgene of zebrafish due to its important function in the nervous tissue as a glutamate receptor. Using a comparative sequence-based approach, we located possible RNA editing events within thegrin1btranscript. Surprisingly, sequence analysis also revealed a new editing site which was not predicted by the comparative approach. We here report the discovery of two novel RNA editing events ingrin1btranscripts of embryonic zebrafish. The frequency of these editing events and their locations within thegrin1btranscript are also described.

scholarly journals Available In Vitro Models for Human Satellite Cells from Skeletal Muscle

2021 ◽  
Vol 22 (24) ◽  
pp. 13221
Author(s):  
Cecilia Romagnoli ◽  
Teresa Iantomasi ◽  
Maria Luisa Brandi
Keyword(s):  
Skeletal Muscle ◽  
Satellite Cells ◽  
3D Models ◽  
In Vitro Models ◽  
Model Organisms ◽  
Disuse Atrophy ◽  
Ethical Implications ◽  
Vertebrate Model ◽  
Muscle Homeostasis

Skeletal muscle accounts for almost 40% of the total adult human body mass. This tissue is essential for structural and mechanical functions such as posture, locomotion, and breathing, and it is endowed with an extraordinary ability to adapt to physiological changes associated with growth and physical exercise, as well as tissue damage. Moreover, skeletal muscle is the most age-sensitive tissue in mammals. Due to aging, but also to several diseases, muscle wasting occurs with a loss of muscle mass and functionality, resulting from disuse atrophy and defective muscle regeneration, associated with dysfunction of satellite cells, which are the cells responsible for maintaining and repairing adult muscle. The most established cell lines commonly used to study muscle homeostasis come from rodents, but there is a need to study skeletal muscle using human models, which, due to ethical implications, consist primarily of in vitro culture, which is the only alternative way to vertebrate model organisms. This review will survey in vitro 2D/3D models of human satellite cells to assess skeletal muscle biology for pre-clinical investigations and future directions.

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