scholarly journals Housing, Husbandry and Welfare of a “Classic” Fish Model, the Paradise Fish (Macropodus opercularis)

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 786
Author(s):  
Anita Rácz ◽  
Gábor Adorján ◽  
Erika Fodor ◽  
Boglárka Sellyei ◽  
Mohammed Tolba ◽  
...  
Keyword(s):  
Genetic Model ◽  
Behavioral Genetics ◽  
Breeding Population ◽  
Model Organisms ◽  
Behavioral Repertoire ◽  
Model Species ◽  
External Fertilization ◽  
Fish Model ◽  
Model Animal ◽  
Paradise Fish

Thanks to its small size, external fertilization and fecundity, over the past four decades, zebrafish (Danio rerio) has become the dominant fish model species in biological and biomedical research. Multiple lines of evidence, however, suggest that the reliance on only a handful of genetic model organisms is problematic, as their unique evolutionary histories makes them less than ideal to study biological questions unrelated to their historically contingent adaptations. Therefore, a need has emerged to develop novel model species, better suited for studying particular problems. The paradise fish (Macropodus opercularis) has a much more complex behavioral repertoire than zebrafish and has been a favored model animal in ethological research during the last decades of the previous century. We believe that with currently available, easily adaptable genetic toolkits, this species could be easily developed into a popular model of behavioral genetics. Despite its earlier popularity, however, the description of a detailed housing and husbandry protocol for this species is still missing from scientific literature. We present here a detailed description of how to raise and breed paradise fish successfully under laboratory conditions, and also discuss some of the challenges we faced while creating a stable breeding population for this species in our facility.

scholarly journals In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2226
Author(s):  
Sazia Kunvar ◽  
Sylwia Czarnomska ◽  
Cino Pertoldi ◽  
Małgorzata Tokarska
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Bos Taurus ◽  
Model Organism ◽  
Genotyping By Sequencing ◽  
Model Organisms ◽  
European Bison ◽  
Model Animal ◽  
Pcr Duplicates ◽  
Species Specific

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

scholarly journals Insights into mammalian biology from the wild house mouse Mus musculus

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Megan Phifer-Rixey ◽  
Michael W Nachman
Keyword(s):  
House Mouse ◽  
Mus Musculus ◽  
Genetic Model ◽  
Inbred Strains ◽  
Mendelian Inheritance ◽  
Model Organisms ◽  
House Mice ◽  
Small Subset ◽  
Wild Mice ◽  
Wide Range

The house mouse, Mus musculus, was established in the early 1900s as one of the first genetic model organisms owing to its short generation time, comparatively large litters, ease of husbandry, and visible phenotypic variants. For these reasons and because they are mammals, house mice are well suited to serve as models for human phenotypes and disease. House mice in the wild consist of at least three distinct subspecies and harbor extensive genetic and phenotypic variation both within and between these subspecies. Wild mice have been used to study a wide range of biological processes, including immunity, cancer, male sterility, adaptive evolution, and non-Mendelian inheritance. Despite the extensive variation that exists among wild mice, classical laboratory strains are derived from a limited set of founders and thus contain only a small subset of this variation. Continued efforts to study wild house mice and to create new inbred strains from wild populations have the potential to strengthen house mice as a model system.

scholarly journals A circadian clock in Saccharomyces cerevisiae

2010 ◽  
Vol 107 (5) ◽  
pp. 2043-2047 ◽  
Author(s):  
Zheng Eelderink-Chen ◽  
Gabriella Mazzotta ◽  
Marcel Sturre ◽  
Jasper Bosman ◽  
Till Roenneberg ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Model ◽  
Circadian Clocks ◽  
Model Systems ◽  
Model Organisms ◽  
Biological Clocks ◽  
Experimental Systems ◽  
Fundamental Biological Process ◽  
Free Running ◽  
And Behavior

Circadian timing is a fundamental biological process, underlying cellular physiology in animals, plants, fungi, and cyanobacteria. Circadian clocks organize gene expression, metabolism, and behavior such that they occur at specific times of day. The biological clocks that orchestrate these daily changes confer a survival advantage and dominate daily behavior, for example, waking us in the morning and helping us to sleep at night. The molecular mechanism of circadian clocks has been sketched out in genetic model systems from prokaryotes to humans, revealing a combination of transcriptional and posttranscriptional pathways, but the clock mechanism is far from solved. Although Saccharomyces cerevisiae is among the most powerful genetic experimental systems and, as such, could greatly contribute to our understanding of cellular timing, it still remains absent from the repertoire of circadian model organisms. Here, we use continuous cultures of yeast, establishing conditions that reveal characteristic clock properties similar to those described in other species. Our results show that metabolism in yeast shows systematic circadian entrainment, responding to cycle length and zeitgeber (stimulus) strength, and a (heavily damped) free running rhythm. Furthermore, the clock is obvious in a standard, haploid, auxotrophic strain, opening the door for rapid progress into cellular clock mechanisms.

scholarly journals The Neurotransmitters Involved in Drosophila Alcohol-Induced Behaviors

2020 ◽  
Vol 14 ◽  
Author(s):  
Maggie M. Chvilicek ◽  
Iris Titos ◽  
Adrian Rothenfluh
Keyword(s):  
Drosophila Melanogaster ◽  
Behavioral Response ◽  
Recent Progress ◽  
Mammalian Species ◽  
Health And Safety ◽  
Model Organisms ◽  
Negative Consequences ◽  
Behavioral Repertoire ◽  
Significant Research ◽  
Alcohol Response

Alcohol is a widely used and abused substance with numerous negative consequences for human health and safety. Historically, alcohol's widespread, non-specific neurobiological effects have made it a challenge to study in humans. Therefore, model organisms are a critical tool for unraveling the mechanisms of alcohol action and subsequent effects on behavior. Drosophila melanogaster is genetically tractable and displays a vast behavioral repertoire, making it a particularly good candidate for examining the neurobiology of alcohol responses. In addition to being experimentally amenable, Drosophila have high face and mechanistic validity: their alcohol-related behaviors are remarkably consistent with humans and other mammalian species, and they share numerous conserved neurotransmitters and signaling pathways. Flies have a long history in alcohol research, which has been enhanced in recent years by the development of tools that allow for manipulating individual Drosophila neurotransmitters. Through advancements such as the GAL4/UAS system and CRISPR/Cas9 mutagenesis, investigation of specific neurotransmitters in small subsets of neurons has become ever more achievable. In this review, we describe recent progress in understanding the contribution of seven neurotransmitters to fly behavior, focusing on their roles in alcohol response: dopamine, octopamine, tyramine, serotonin, glutamate, GABA, and acetylcholine. We chose these small-molecule neurotransmitters due to their conservation in mammals and their importance for behavior. While neurotransmitters like dopamine and octopamine have received significant research emphasis regarding their contributions to behavior, others, like glutamate, GABA, and acetylcholine, remain relatively unexplored. Here, we summarize recent genetic and behavioral findings concerning these seven neurotransmitters and their roles in the behavioral response to alcohol, highlighting the fitness of the fly as a model for human alcohol use.

scholarly journals Unexpected Geographic Variability of the Free Running Period in the Linden Bug Pyrrhocoris apterus

2016 ◽  
Vol 31 (6) ◽  
pp. 568-576 ◽  
Author(s):  
Lenka Pivarciova ◽  
Hanka Vaneckova ◽  
Jan Provaznik ◽  
Bulah Chia-hsiang Wu ◽  
Martin Pivarci ◽  
...  
Keyword(s):  
Technological Progress ◽  
Genetic Basis ◽  
Model Organisms ◽  
Geographic Variability ◽  
Model Species ◽  
Pyrrhocoris Apterus ◽  
Free Running ◽  
Field Lines ◽  
Free Running Period ◽  
Remarkable Progress

Circadian clocks keep organisms in synchrony with external day-night cycles. The free running period (FRP) of the clock, however, is usually only close to—not exactly—24 h. Here, we explored the geographical variation in the FRP of the linden bug, Pyrrhocoris apterus, in 59 field-lines originating from a wide variety of localities representing geographically different environments. We have identified a remarkable range in the FRPs between field-lines, with the fastest clock at ~21 h and the slowest close to 28 h, a range comparable to the collections of clock mutants in model organisms. Similarly, field-lines differed in the percentage of rhythmic individuals, with a minimum of 13.8% and a maximum of 86.8%. Although the FRP correlates with the latitude and perhaps with the altitude of the locality, the actual function of this FRP diversity is currently unclear. With the recent technological progress of massive parallel sequencing and genome editing, we can expect remarkable progress in elucidating the genetic basis of similar geographic variants in P. apterus or in similar emerging model species of chronobiology.

scholarly journals FlyRNAi.org—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2021 update

2020 ◽  
Vol 49 (D1) ◽  
pp. D908-D915
Author(s):  
Yanhui Hu ◽  
Aram Comjean ◽  
Jonathan Rodiger ◽  
Yifang Liu ◽  
Yue Gao ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Functional Genomics ◽  
Protein Interactions ◽  
Protein Modification ◽  
Genetic Model ◽  
Online Resources ◽  
Model Species ◽  
Rnai Screening ◽  
Transcriptomics Data

Abstract The FlyRNAi database at the Drosophila RNAi Screening Center and Transgenic RNAi Project (DRSC/TRiP) provides a suite of online resources that facilitate functional genomics studies with a special emphasis on Drosophila melanogaster. Currently, the database provides: gene-centric resources that facilitate ortholog mapping and mining of information about orthologs in common genetic model species; reagent-centric resources that help researchers identify RNAi and CRISPR sgRNA reagents or designs; and data-centric resources that facilitate visualization and mining of transcriptomics data, protein modification data, protein interactions, and more. Here, we discuss updated and new features that help biological and biomedical researchers efficiently identify, visualize, analyze, and integrate information and data for Drosophila and other species. Together, these resources facilitate multiple steps in functional genomics workflows, from building gene and reagent lists to management, analysis, and integration of data.

Structure and function of two-pore-domain K channels: contributions from genetic model organisms

2005 ◽  
Vol 26 (7) ◽  
pp. 361-367 ◽  
Author(s):  
S BUCKINGHAM ◽  
J KIDD ◽  
R LAW ◽  
C FRANKS ◽  
D SATTELLE
Keyword(s):  
Genetic Model ◽  
Structure And Function ◽  
Model Organisms ◽  
K Channels ◽  
And Function ◽  
Pore Domain

DNA MICROARRAY-BASED ECOTOXICOLOGICAL BIOMARKER DISCOVERY IN A SMALL FISH MODEL SPECIES

2007 ◽  
Vol preprint (2007) ◽  
pp. 1
Author(s):  
Rong-Lin Wang ◽  
David Bencic ◽  
Adam Biales ◽  
David Lattier ◽  
Mitch Kostich ◽  
...  
Keyword(s):  
Dna Microarray ◽  
Biomarker Discovery ◽  
Small Fish ◽  
Model Species ◽  
Fish Model
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