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Article
Open AccessCombining OSMAC, metabolomic and genomic methods for the production and annotation of halogenated azaphilones and ilicicolins in termite symbiotic fungi
We gathered a collection of termite mutualistic strains from French Guiana to explore the metabolites of symbiotic microorganisms. Molecular networks reconstructed from a metabolomic analysis using LC–ESI–MS/M...
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Article
Open AccessTranscriptomic analysis of the trade-off between endurance and burst-performance in the frog Xenopus allofraseri
Variation in locomotor capacity among animals often reflects adaptations to different environments. Despite evidence that physical performance is heritable, the molecular basis of locomotor performance and per...
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Protocol
A New Method for Sequencing the Mitochondrial Genome by Using Long Read Technology
We describe a protocol to prepare a multiplexed mtDNA library from a blood sample for performing a long read sequencing of the mitochondrial genome. All steps are carefully described to get a high enrichment o...
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Article
Open AccessA new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants
Mitochondrial DNA is remarkably polymorphic. This is why animal geneticists survey mitochondrial genomes variations for fundamental and applied purposes. We present here an approach to sequence whole mitochond...
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Article
Open AccessIdentification of novel cis-regulatory elements of Eya1 in Xenopus laevis using BAC recombineering
The multifunctional Eya1 protein plays important roles during the development of cranial sensory organs and ganglia, kidneys, hypaxial muscles and several other organs in vertebrates. Eya1 is encoded by a comp...
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Chapter
Designing Non-viral Targeted Integrating Vectors for Genome Engineering in Vertebrates
Genome engineering for biomedicine and biotechnology requires the integration of transgenes at specific sites in safe genomic environments. These specific integrations are needed to avoid position effects, ins...
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Article
Open AccessncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins
Inverted repeat genes encode precursor RNAs characterized by hairpin structures. These RNA hairpins are then metabolized by biosynthetic pathways to produce functional small RNAs. In eukaryotic genomes, short ...
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Protocol
Databases of Gene Expression in Xenopus Development
Gene expression data for Xenopus are collected and curated in diverse forms and locations. The intention of this chapter is to give the reader a guide to the publicly accessible databases where these data can be ...
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Article
Reduced levels of survival motor neuron protein leads to aberrant motoneuron growth in a Xenopus model of muscular atrophy
Spinal muscular atrophy (SMA) is a neurodegenerative disease characterized by motor neuron loss and skeletal muscle atrophy. The loss of function of the smn1 gene, the main supplier of survival motor neuron prote...
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Article
Open AccessEvading the annotation bottleneck: using sequence similarity to search non-sequence gene data
Non-sequence gene data (images, literature, etc.) can be found in many different public databases. Access to these data is mostly by text based methods using gene names; however, gene annotation is neither com...
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Article
Open AccessAn ontology for Xenopus anatomy and development
The frogs Xenopus laevis and Xenopus (Silurana) tropicalis are model systems that have produced a wealth of genetic, genomic, and developmental information. Xenbase is a model organism database that provides cent...
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Article
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)
One purpose of the biomedical literature is to report results in sufficient detail that the methods of data collection and analysis can be independently replicated and verified. Here we present reporting guide...
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Article
Open AccessEvaluation of time profile reconstruction from complex two-color microarray designs
As an alternative to the frequently used "reference design" for two-channel microarrays, other designs have been proposed. These designs have been shown to be more profitable from a theoretical point of view (...
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Article
Open AccessExploring nervous system transcriptomes during embryogenesis and metamorphosis in Xenopus tropicalis using EST analysis
The western African clawed frog Xenopus tropicalis is an anuran amphibian species now used as model in vertebrate comparative genomics. It provides the same advantages as Xenopus laevis but is diploid and has a s...
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Article
The mariner Transposons Belonging to the irritans Subfamily Were Maintained in Chordate Genomes by Vertical Transmission
Mariner-like elements (MLEs) belong to the Tc1-mariner superfamily of DNA transposons, which is very widespread in animal genomes. We report here the first complete description of a MLE, Xtmar1, within the genome...
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Article
The transmembrane protein XFLRT3 forms a complex with FGF receptors and promotes FGF signalling
Fibroblast growth factors (FGFs) signal through high-affinity tyrosine kinase receptors to regulate a diverse range of cellular processes, including cell growth, differentiation and migration, as well as cell ...
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Chapter
Large Scale Expression Screening Identifies Molecular Pathways and Predicts Gene function
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Protocol
Expression Profiling by Systematic High-Throughput In Situ Hybridization to Whole-Mount Embryos
The genome of a given organism is considered in biology as the fundamental invariant (1). It is virtually the same throughout lifetime and, to a lesser extent, over generations. By contrast, genetic information i...
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Article
Features of the mammal mar1 transposons in the human, sheep, cow, and mouse genomes and implications for their evolution
Mariner-like elements (MLE) belong to the Tc1/mariner superfamily of class II transposons. We have analyzed the mariner related to the cecropia subfamily, and called mammal mar1, in four mammalian genomes, Bos t...
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Article
Synexpression groups in eukaryotes
In 1960, Jacob and Monod described the bacterial operon, a cluster of functionally interacting genes whose expression is tightly coordinated. Global expression analysis has shown that the highly coordinate exp...
