Fish scale | EPFL Graph Search

A fish scale is a small rigid plate that grows out of the skin of a fish. The skin of most jawed fishes is covered with these protective scales, which can also provide effective camouflage through the use of reflection and colouration, as well as possible hydrodynamic advantages. The term scale derives from the Old French escale, meaning a shell pod or husk. Scales vary enormously in size, shape, structure, and extent, ranging from strong and rigid armour plates in fishes such as shrimpfishes and boxfishes, to microscopic or absent in fishes such as eels and anglerfishes. The morphology of a scale can be used to identify the species of fish it came from. Scales originated within the jawless ostracoderms, ancestors to all jawed fishes today. Most bony fishes are covered with the cycloid scales of salmon and carp, or the ctenoid scales of perch, or the ganoid scales of sturgeons and gars. Cartilaginous fishes (sharks and rays) are covered with placoid scales. Some species are covered instead by scutes, and others have no outer covering on part or all of the skin. Fish scales are part of the fish's integumentary system, and are produced from the mesoderm layer of the dermis, which distinguishes them from reptile scales. The same genes involved in tooth and hair development in mammals are also involved in scale development. The placoid scales of cartilaginous fishes are also called dermal denticles and are structurally homologous with vertebrate teeth. Most fish are also covered in a layer of mucus or slime which can protect against pathogens such as bacteria, fungi, and viruses, and reduce surface resistance when the fish swims. The bony scales of thelodonts, the most abundant form of fossil fish, are well understood. The scales were formed and shed throughout the organisms' lifetimes, and quickly separated after their death. Bone, a tissue that is both resistant to mechanical damage and relatively prone to fossilization, often preserves internal detail, which allows the histology and growth of the scales to be studied in detail.

Circadian dynamics of RNA localisation in the mammalian liver

Clémence Yumie Syloun Hurni

Gene expression in eukaryotes is a complex multi-step process. It starts in the nucleus with transcription, the synthesis of a mRNA copy from a DNA template. While in the nucleus, the RNA transcript is subject to multiple co- and post-transcriptional modifications, including splicing, capping, polyadenylation, and assembly into ribonucleoprotein complexes. Correctly processed mRNA is exported to the cytoplasm and translated by ribosomes to form a chain of amino acids: the protein. The mRNA lifetime in the cytoplasm is determined by the activity of a distinct set of RNA Binding Proteins, enzymes, and functional RNAs, which promote stability or degradation. Each step of the RNA life cycle is tightly regulated to ensure proper cellular function. The kinetic rates governing these steps are dynamic and notably adapt to the daily fluctuations of the environment related to the alternance of day and night. Indeed, most organisms possess an internal timing system called the circadian clock. The clock is a genetically encoded self-sustained transcriptional-translational feedback loop, which operates in almost every cell and tissue of the body. It controls the temporal gene expression program to synchronise cellular and physiological functions to the external world. In this thesis, I explore the transcriptome of the mouse liver by combining RNA-sequencing, mathematical modelling, and single-molecule RNA-FISH (smFISH), with an emphasis on the spatio-temporal organisation of RNA expression at the subcellular and tissue scales. I first investigate how RNA are differentially localised at the scale of the liver tissue. Hepatocytes are arranged in structural and functional units called lobules, and carry out different physiological functions depending on their spatial position within the lobule. In this collaborative work, we characterised spatio-temporal gene expression profiles, and showed that that while the expression of hundreds of genes is dually orchestrated by time and space, the circadian core clock is expressed uniformly within the liver lobule, and is therefore robust to the heterogeneous microenvironment. Second, I explore the RNA localisation at the scale of a hepatocyte. The subcellular distributions of RNA in different compartments (here, the nucleus and the cytoplasm), are dictated by the balance of a synthesis term and a decay term. To quantify the kinetic parameters driving nuclear and cytoplasmic mRNA accumulation, I sequenced RNA from both cellular fractions from mouse livers sampled at different times of the day. Using a mathematical model describing rhythmic pre-mRNA and mRNA profiles, I could estimate the nuclear export rates and cytoplasmic degradation rates of

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1400 genes. Nuclear export occurs on a much shorter time-scale than cytoplasmic degradation, and nuclear lifetime has only a minor contribution to the total RNA lifetime. However, a subset of metabolic genes remain in the nucleus for more than one hour (up to four hours), which accounts for the long phase delay between the peak times of transcription and of cytoplasmic accumulation. Furthermore, nuclear export contributes to the modulation and generation of rhythmic profiles of ~10% of the cycling nuclear mRNA. This study provides a comprehensive estimation of the nuclear and cytoplasmic life times in the liver and contributes to a better understanding of the dynamic regulation of the transcriptome during the feeding-fasting cycle.

EPFL2021

Circadian dynamics of RNA localisation in the mammalian liver

Clémence Yumie Syloun Hurni

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EPFL2021