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MicroRNA-202 (miR-202) controls female fecundity by regulating medaka oogenesis [article]

Stephanie Gay, Jerome Bugeon, Amine Bouchareb, Laure Henry, Jerome Montfort, Aurelie Le Cam, Julien Bobe, Violette Thermes
2018 bioRxiv   pre-print
Female gamete production relies on coordinated molecular and cellular processes that occur in the ovary throughout oogenesis. In fish, as in other vertebrates, these processes have been extensively studied both in terms of endocrine/paracrine regulation and protein expression and activity. The role of small non-coding RNAs in the regulation of animal reproduction remains however largely unknown and poorly investigated, despite a growing interest for the importance of miRNAs in a wide variety of
more » ... biological processes. Here, we analyzed the role of miR-202, a miRNA predominantly expressed in male and female gonads in several vertebrate species. We studied its expression in the medaka ovary and generated a mutant line (using CRISPR/Cas9 genome engineering) to determine its importance for reproductive success with special interest for egg production. Our results show that miR-202-5p is the biologically active form of the miRNA and that it is expressed in granulosa cells and in the unfertilized egg. The knock out (KO) of miR-202 resulted in a strong phenotype both in terms of number and quality of eggs produced. Mutant females exhibited either no egg production or produced a drastically reduced number of eggs that could not be fertilized, ultimately leading to no reproductive success. We quantified the size distribution of the oocytes in the ovary of KO females and performed a genome-wide transcriptomic analysis approach to identified dysregulated molecular pathways. Together, cellular and molecular analyses indicate that lack of miR-202 impairs the early steps of oogenesis/folliculogenesis and decreases the number of large (i.e. vitellogenic) follicles, ultimately leading to dramatically reduced female fecundity. This study sheds new light on the regulatory mechanisms that control the early steps of follicular development and provides the first in vivo functional evidence that an ovarian-predominant microRNA may have a major role in female reproduction.
doi:10.1101/287359 fatcat:44j47dxqhresbojp7lgqkybu7i

Gene expression profiling of trout muscle during flesh quality recovery following spawning

Yéléhi-Diane Ahongo, Aurélie Le Cam, Jérôme Montfort, Jérôme Bugeon, Florence Lefèvre, Pierre-Yves Rescan
2022 BMC Genomics  
Background Sexual maturation causes loss of fish muscle mass and deterioration of fillet quality attributes that prevent market success. We recently showed that fillet yield and flesh quality recover in female trout after spawning. To gain insight into the molecular mechanisms regulating flesh quality recovery, we used an Agilent-based microarray platform to conduct a large-scale time course analysis of gene expression in female trout white muscle from spawning to 33 weeks post-spawning.
more » ... In sharp contrast to the situation at spawning, muscle transcriptome of female trout at 33 weeks after spawning was highly similar to that of female trout of the same cohort that did not spawn, which is consistent with the post-spawning flesh quality recovery. Large-scale time course analysis of gene expression in trout muscle during flesh quality recovery following spawning led to the identification of approximately 3340 unique differentially expressed genes that segregated into four major clusters with distinct temporal expression profiles and functional categories. The first cluster contained approximately 1350 genes with high expression at spawning and downregulation after spawning and was enriched with genes linked to mitochondrial ATP synthesis, fatty acid catabolism and proteolysis. A second cluster of approximately 540 genes with transient upregulation 2 to 8 weeks after spawning was enriched with genes involved in transcription, RNA processing, translation, ribosome biogenesis and protein folding. A third cluster containing approximately 300 genes upregulated 4 to 13 weeks after spawning was enriched with genes encoding ribosomal subunits or regulating protein folding. Finally, a fourth cluster that contained approximately 940 genes with upregulation 8 to 24 weeks after spawning, was dominated by genes encoding myofibrillar proteins and extracellular matrix components and genes involved in glycolysis. Conclusion Overall, our study indicates that white muscle tissue restoration and flesh quality recovery after spawning are associated with transcriptional changes promoting anaerobic ATP production, muscle fibre hypertrophic growth and extracellular matrix remodelling. The generation of the first database of genes associated with post-spawning muscle recovery may provide insights into the molecular and cellular mechanisms controlling muscle yield and fillet quality in fish and provide a useful list of potential genetic markers for these traits.
doi:10.1186/s12864-021-08228-3 pmid:34983401 pmcid:PMC8725336 fatcat:unzotob53rg4ld3tcrehgvl7xq

VisEgg: A robust phenotyping tool to assess rainbow trout egg features and viability [article]

Emilie Cardona, Emilien Segret, Jerome Bugeon, Julien Bobe
2020 bioRxiv   pre-print
Assessing female fish reproductive success requires a thorough evaluation of egg characteristics, including egg number, size and variability as well as egg developmental potential through the monitoring of embryo survival after fertilization. While embryonic success relies, at least in part, on paternal contribution, some parameters are strictly related to egg characteristics, one of the main ones being the viability of the egg when released into the water at spawning. It is however not
more » ... ily possible, at least in salmonid fish that lay non-transparent eggs, to separate the different causes of egg/embryo failure. In this context, our aim was i) to develop a simple and rapid system to capture images of rainbow trout eggs combined with computerized processing of these images to perform a fully automatic individual characterization of egg features including number and size ii) to estimate unfertilized egg viability through the monitoring of the percentage of eggs that will not survive to water hydration. To evaluate the VisEgg system, unfertilized eggs (approximatively 400 eggs per batch) originating from 105 different females were hydrated in water. After 24h, a picture of the eggs was obtained using a dedicated shooting system consisting of a light source and a digital single-lens reflex (SLR) camera. An image processing algorithm was developed to allow the automatic detection and separation of the eggs and to perform automatic measurements of egg number and individual egg size. The presence of white egg was used as an indirect measure of egg integrity, the whitening being the result of water entry into the egg through the vitelline membrane. These white eggs were therefore considered as non-viable, as a result of their lack of physical integrity. Fertilization assays were performed in parallel using a subsample of the same egg batch. Embryonic development was monitored and hatching rate was calculated. A significant correlation between white egg percentage after hydration and hatching rate was observed (Spearman coefficient =-0.557, p<0.001), in consistency with the fact that non-viable egg will not allow successful embryonic development. In contrast, the percentage of eggs that do not successfully hatched includes egg/embryo failures of different nature including egg viability, their capacity to be fertilized and to develop into an embryo. Using VisEgg, we were able to quantify the lack of viability of the eggs separately from the different other events that may occur during fertilization and incubation. VisEgg is a convenient and reliable tool to obtain individuals measures on trout eggs. It can be used to assess not only egg size and egg number but also unfertilized egg viability before fertilization.
doi:10.1101/2020.04.21.052472 fatcat:kpok3q5vynaw5oi266xns2xw6q

MiR-202 controls female fecundity by regulating medaka oogenesis

Stéphanie Gay, Jérôme Bugeon, Amine Bouchareb, Laure Henry, Clara Delahaye, Fabrice Legeai, Jérôme Montfort, Aurélie Le Cam, Anne Siegel, Julien Bobe, Violette Thermes, Manfred Schartl
2018 PLoS Genetics  
(PDF) Methodology: Stéphanie Gay, Jérôme Bugeon, Amine Bouchareb, Clara Delahaye, Fabrice Legeai, Julien Bobe, Violette Thermes.  ... 
doi:10.1371/journal.pgen.1007593 pmid:30199527 pmcid:PMC6147661 fatcat:g5kikkftsvdjvilltvc4d4tju4

Naa15 knockdown enhances c2c12 myoblast fusion and induces defects in zebrafish myotome morphogenesis [article]

Olivier Monestier, Aurelie Landemaine, Jerome Bugeon, Pierre-Yves Rescan, Jean-Charles Gabillard
2018 bioRxiv   pre-print
The comprehension of muscle tissue formation and regeneration is essential to develop therapeutic approaches against muscle diseases or loss in muscle mass and strength during ageing or cancer. One of the critical steps in muscle formation is the fusion of muscle cells to form or regenerate muscle fibres. To identify new genes controlling myoblast fusion, we undertook an siRNA screen in c2c12 myoblasts and found that N-alpha-acetyltransferase 15 (Naa15) knockdown enhanced c2c12 myoblast fusion
more » ... uggesting that Naa15 negatively regulated myogenic cell fusion. We identified two Naa15 orthologous genes in zebrafish genome: naa15a and naa15b. These two orthologs are both expressed in myogenic domain of the somite. Knockdown of zebrafish naa15a and naa15b genes induced a U shaped segmentation of the myotome and alteration of myotome boundaries resulting in the formation of abnormally long myofibres spanning adjacent somites. Taken together these results show that Naa15 regulates myotome formation and myogenesis in fish.
doi:10.1101/306563 fatcat:uslgq3ve5fcbnb2254v3asgnki

Characteristics and metabolism of different adipose tissues in fish

Claudine Weil, Florence Lefèvre, Jerôme Bugeon
2012 Reviews in Fish Biology and Fisheries  
Table 3 ) 3 , whereas only an 18% increase was observed for the adipocyte diameter(Bugeon et al., unpublished results; Comment citer ce document : Weil, C., Lefèvre, F., Bugeon, J. (2013).  ...  ., Bugeon, J. (2013). Characteristics and metabolism of different adipose tissues in fish. Reviews in Fish Biology and Fisheries, 23, 157-173.  ... 
doi:10.1007/s11160-012-9288-0 fatcat:hpefcq3u3jazbdjwcqm2kvwoua

VisEgg: a robust phenotyping tool to assess rainbow trout egg features and viability

Emilie Cardona, Jerome Bugeon, Emilien Segret, Julien Bobe
2020 Fish Physiology & Biochemistry  
Assessing female fish reproductive success requires a thorough evaluation of egg characteristics, including egg number, size, and variability as well as egg developmental potential through the monitoring of embryo survival after fertilization. While embryonic success relies, at least in part, on paternal contribution, some parameters are strictly related to egg characteristics, one of the main ones being the viability of the egg when released into the water at spawning. It is however not
more » ... rily possible, at least in salmonid fish that lay nontransparent eggs, to separate the different causes of egg/embryo failure. In this context, our aim was (i) to develop a simple and rapid system to capture images of rainbow trout eggs combined with computerized processing of these images to perform a fully automatic individual characterization of egg features including number and size (ii) to estimate unfertilized egg viability through the monitoring of the percentage of eggs that will not survive to water hydration. To evaluate the VisEgg system, unfertilized eggs (approximatively 400 eggs per batch) originating from 105 different females were hydrated in water. After 24 h, a picture of the eggs was obtained using a dedicated shooting system consisting of a light source and a digital single-lens reflex (SLR) camera. An image processing algorithm was developed to allow the automatic detection and separation of the eggs and to perform automatic measurements of egg number and individual egg size. The presence of white egg was used as an indirect measure of egg integrity, the "whitening" being the result of water entry into the egg through the vitelline membrane. These white eggs were therefore considered nonviable, as a result of their lack of physical integrity. Fertilization assays were performed in parallel using a subsample of the same egg batch. Embryonic development was monitored and hatching rate was calculated. A significant correlation between white egg percentage after hydration and hatching rate was observed (Spearman coefficient = -0.557, p < 0.001), in consistency with the fact that nonviable egg will not allow successful embryonic development. In contrast, the percentage of eggs that do not successfully hatch includes egg/embryo failures of different nature including reduced egg viability. Using the VisEgg, we were able to quantify the lack of viability of the eggs separately from the different other events that may occur during fertilization and incubation. the VisEgg is a convenient and reliable tool to obtain individual measures on trout eggs. It can be used to assess not only egg size and egg number but also unfertilized egg viability before fertilization.
doi:10.1007/s10695-020-00844-2 pmid:32607663 fatcat:3v7cw5ashzfgrfxp3nttpiritq

How Muscle Structure and Composition Influence Meat and Flesh Quality

Anne Listrat, Bénédicte Lebret, Isabelle Louveau, Thierry Astruc, Muriel Bonnet, Louis Lefaucheur, Brigitte Picard, Jérôme Bugeon
2016 The Scientific World Journal  
Skeletal muscle consists of several tissues, such as muscle fibers and connective and adipose tissues. This review aims to describe the features of these various muscle components and their relationships with the technological, nutritional, and sensory properties of meat/flesh from different livestock and fish species. Thus, the contractile and metabolic types, size and number of muscle fibers, the content, composition and distribution of the connective tissue, and the content and lipid
more » ... ion of intramuscular fat play a role in the determination of meat/flesh appearance, color, tenderness, juiciness, flavor, and technological value. Interestingly, the biochemical and structural characteristics of muscle fibers, intramuscular connective tissue, and intramuscular fat appear to play independent role, which suggests that the properties of these various muscle components can be independently modulated by genetics or environmental factors to achieve production efficiency and improve meat/flesh quality.
doi:10.1155/2016/3182746 pmid:27022618 pmcid:PMC4789028 fatcat:6dkdjglqrfazneqy2ft7iei42i

FLESH QUALITY IN LARGE RAINBOW TROUT WITH HIGH OR LOW FILLET YIELD

JEROME BUGEON, FLORENCE LEFEVRE, MIREILLE CARDINAL, AYHAN UYANIK, ARMEL DAVENEL, PIERRICK HAFFRAY
2010 Journal of Muscle Foods  
cellularity could influence flesh texture, as an inverse relationship was obtained between muscle fibre diameter and mechanical resistance of the raw flesh and sensory firmness of the smoked flesh (Bugeon  ...  The determinism of the mechanical resistance of raw flesh is rather complex and depends on collagen cross-link content like pyridinoline (Li et al. 2005) , muscle fibre size (Bugeon et al. 2003) , pH  ... 
doi:10.1111/j.1745-4573.2010.00214.x fatcat:qvjqeygvkfgmhp6mer3djuml6e

Selection for muscle fat content and triploidy affect flesh quality in pan-size rainbow trout, Oncorhynchus mykiss

Florence Lefevre, Mireille Cardinal, Jérôme Bugeon, Laurent Labbe, Françoise Medale, Edwige Quillet
2015 Aquaculture  
., 2008) , brown trout (Bugeon et al., 2003) , and smoked fillets from Atlantic salmon (Johnston et al., 2000) .  ...  This result can be related to the larger muscle fibers of triploid fish, as previously discussed (Bugeon et al., 2003; Johnston et al., 2000; Lefevre et al., 2008) .  ... 
doi:10.1016/j.aquaculture.2015.06.029 fatcat:rvd47lxl45gu7nuubceiw32qp4

C-Eci: A Cubic-Eci Combined Clearing Method For 3D Follicular Content Analysis In The Fish Ovary [article]

Manon Lesage, Manon Thomas, Jerome Bugeon, Adele Branthonne, Stephanie Gay, Emilie Cardona, Julien Bobe, Violette Thermes
2020 biorxiv/medrxiv   pre-print
Deciphering mechanisms of oocyte development in female fishes still remains challenging and a comprehensive overview of this process at the level of the organ is still needed. The recent development optical tissue clearing methods have tremendously boosted the 3D imaging of large size biological samples that are naturally opaque. However, no attempt of clearing on fish ovary that accumulates extremely high concentration of lipids within oocytes has been reported to date. To face with this
more » ... n-specific challenge, we combined two existing clearing methods, the non-toxic solvent-based Eci method for efficient clearing and the CUBIC method to enhance lipid removal and reduce non-specific staining. The methyl green fluorescent dye was used to stain nuclei and delineate follicles. Using this procedure (named C-Eci), ovaries of both medaka and trout could be imaged in 3D and all follicles analyzed. To our knowledge this is the first procedure elaborated for clearing and imaging fish ovary in 3D. The C-Eci methods thus provides an interesting tool for getting precise quantitative data on follicular content in fish ovary and promises to be useful for further morphological studies.
doi:10.1101/2020.03.05.978189 fatcat:qqaoycjdo5g3hjffzi2gmbqy4e

Selection for stress responsiveness and slaughter stress affect flesh quality in pan-size rainbow trout, Oncorhynchus mykiss

Florence Lefevre, Isabelle Cos, Tom G. Pottinger, Jérôme Bugeon
2016 Aquaculture  
.; Bugeon, Jérôme. 2016. Selection for stress responsiveness and slaughter stress affect flesh quality in pan-size rainbow trout, Oncorhynchus mykiss.  ...  A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT (2) , BUGEON Jérôme (1) , Statement of Relevance Stress in fish is a permanent  ...  Quillet, E., Bugeon, J., Le Guillou, S., Davenel, A., Collewet, G., Labbe, L., Medale, F., 2007.  ... 
doi:10.1016/j.aquaculture.2016.07.039 fatcat:nz4rqxxw25hctogckehqz5fni4

Histological, transcriptomic and in vitro analysis reveal an intrinsic activated state of myogenic precursors in hyperplasic muscle of trout [article]

Sabrina Jagot, Nathalie Sabin, Aurelie Le Cam, Jerome Bugeon, Pierre-Yves Rescan, Jean-Charles Gabillard
2018 bioRxiv   pre-print
The dramatic increase in myotomal muscle mass in post-hatching fish is related to their ability to lastingly produce new muscle fibres, a process termed hyperplasia. The molecular and cellular mechanisms underlying fish muscle hyperplasia largely remain unknown. In this study, we aimed to characterize intrinsic properties of myogenic cells originating from fish hyperplasic muscle. For this purpose, we compared in situ proliferation, in vitro cell behavior and transcriptomic profile of myogenic
more » ... recursors originating from hyperplasic muscle of juvenile trout (JT) and from non-hyperplasic muscle of fasted juvenile trout (FJT) and adult trout (AT). For the first time, we showed that myogenic precursors proliferate in hyperplasic muscle from JT as shown by in vivo BrdU labeling. This proliferative rate was very low in AT and FJT muscle. Transcriptiomic analysis revealed that myogenic cells from FJT and AT displayed close expression profiles with only 64 differentially expressed genes (BH corrected p-val < 0.001). In contrast, 2623 differentially expressed genes were found between myogenic cells from JT and from both FJT and AT. Functional categories related to translation, mitochondrial activity, cell cycle, and myogenic differentiation were inferred from genes up regulated in JT compared to AT and FJT myogenic cells. Conversely, Notch signaling pathway, that signs cell quiescence, was inferred from genes down regulated in JT compared to FJT and AT. In line with our transcriptomic data, in vitro JT myogenic precursors displayed higher proliferation and differentiation capacities than FJT and AT myogenic precursors. The transcriptomic analysis and examination of cell behavior converge to support the view that myogenic cells extracted from hyperplastic muscle of juvenile trout are intrinsically more potent to form myofibres than myogenic cells extracted from non-hyperplasic muscle. The generation of gene expression profiles in myogenic cell extracted from muscle of juvenile trout may yield insights into the molecular and cellular mechanisms controlling hyperplasia and provides a useful list of potential molecular markers of hyperplasia.
doi:10.1101/332585 fatcat:n3gn6i6nvvelpjt4nfc2zh7phq

ATOL: The Multi-species Livestock Trait Ontology [chapter]

Wiktoria Golik, Olivier Dameron, Jérôme Bugeon, Alice Fatet, Isabelle Hue, Catherine Hurtaud, Matthieu Reichstadt, Marie-Christine Salaün, Jean Vernet, Léa Joret, Frédéric Papazian, Claire Nédellec (+1 others)
2012 Communications in Computer and Information Science  
This paper presents the multi-species Animal Trait Ontology for Livestock (ATOL) and the methodology used for its design. ATOL has been designed as a reference source for indexing phenotype databases and scientific papers. It covers five major topics related to animal productions: growth and meat quality, animal nutrition, milk production, reproduction and welfare. It is composed of species-independent concepts subsuming species-specific ones so that cross-species and species-specific reasoning
more » ... can be performed consistently. In order to ensure a large consensus, three complementary approaches have successively been applied to its design: reuse of existing ontologies, integration of production-specific livestock traits by a large team of domain experts and curators and terminology analysis of scientific papers. It resulted in a detailed taxonomy of 1,654 traits that is available at
doi:10.1007/978-3-642-35233-1_28 fatcat:vloi43ivjff47aslnd2udwtwz4

Naa15 knockdown enhances c2c12 myoblast fusion and induces defects in zebrafish myotome morphogenesis

Olivier Monestier, Aurélie Landemaine, Jérôme Bugeon, Pierre-Yves Rescan, Jean-Charles Gabillard
2019 Comparative Biochemistry and Physiology - Part B: Biochemistry & Molecular Biology  
doi:10.1016/j.cbpb.2018.11.005 fatcat:7he747ft4vaglomuvwisr5e46a
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