105 results on '"Sire JY"'
Search Results
2. Skin development in bony fish with particular emphasis on collagen deposition in the dermis of the zebrafish (Danio rerio)
- Author
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Leguellec, D., Morvan-Dubois, G., Sire, Jy, and Deleage, Gilbert
- Subjects
animal structures ,[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology - Abstract
The first part of this article is a review of the current status of knowledge of the fish skin, with particular attention to its development. In the second part we present original results obtained in zebrafish (Danio rerio), with particular emphasis on the deposition and organisation of the dermal collagenous stroma. Using a series of zebrafish specimens aged between 15 hours postfertilization (hpf) and 4.5 years old, we have combined Transmission Electron Microscopy (TEM) observations and in situ hybridisation using type I collagen a2 chain (Col1a2) probe. Collagen fibrils, with a diameter of 22 nm, appear first in an acellular subepidermal space at 24 hpf, are first all oriented in the same direction, and form the primary dermal stroma. Subsequently, three events occur. (1) From 5-7 days pf (dpf) onwards the collagen fibrils self-organise into several lamellae arranged in a plywood-like structure, starting in the upper layers and progressing throughout the entire thickness of the dermis. (2) At 20-26 dpf, fibroblasts of unknown origin progressively invade the acellular collagenous stroma, some of them accumulating below the epidermis. (3) Concomitant with the invasion of fibroblasts, the collagen fibrils increase progressively in diameter to reach 160 nm towards the end of the fish life. In situ hybridisation experiments reveal that, between 24 and 48 hpf, the collagen matrix is produced by the epidermis only. From 72 hpf to 20-26 dpf, both the basal epidermal cells and the dermal cells bordering the deep region of the dermis are involved in the production of collagen. When the fibroblasts invade the plywood-like structure, the epidermal cells progressively cease to synthesise collagen, which from this point is produced only by the fibroblasts. This suggests that the fibroblasts secrete a still unidentified signalling molecule that downregulates collagen production by the epidermis.The first part of this article is a review of the current status of knowledge of the fish skin, with particular attention to its development. In the second part we present original results obtained in zebrafish (Danio rerio), with particular emphasis on the deposition and organisation of the dermal collagenous stroma. Using a series of zebrafish specimens aged between 15 hours postfertilization (hpf) and 4.5 years old, we have combined Transmission Electron Microscopy (TEM) observations and in situ hybridisation using type I collagen a2 chain (Col1a2) probe. Collagen fibrils, with a diameter of 22 nm, appear first in an acellular subepidermal space at 24 hpf, are first all oriented in the same direction, and form the primary dermal stroma. Subsequently, three events occur. (1) From 5-7 days pf (dpf) onwards the collagen fibrils self-organise into several lamellae arranged in a plywood-like structure, starting in the upper layers and progressing throughout the entire thickness of the dermis. (2) At 20-26 dpf, fibroblasts of unknown origin progressively invade the acellular collagenous stroma, some of them accumulating below the epidermis. (3) Concomitant with the invasion of fibroblasts, the collagen fibrils increase progressively in diameter to reach 160 nm towards the end of the fish life. In situ hybridisation experiments reveal that, between 24 and 48 hpf, the collagen matrix is produced by the epidermis only. From 72 hpf to 20-26 dpf, both the basal epidermal cells and the dermal cells bordering the deep region of the dermis are involved in the production of collagen. When the fibroblasts invade the plywood-like structure, the epidermal cells progressively cease to synthesise collagen, which from this point is produced only by the fibroblasts. This suggests that the fibroblasts secrete a still unidentified signalling molecule that downregulates collagen production by the epidermis.
- Published
- 2004
3. Evolutionary story of mammalian-specific amelogenin exons 4, "4b", 8, and 9.
- Author
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Sire JY, Huang Y, Li W, Delgado S, Goldberg M, Denbesten PK, Sire, J-Y, Huang, Y, Li, W, Delgado, S, Goldberg, M, and Denbesten, P K
- Abstract
Amelogenin gene organization varies from 6 exons (1,2,3,5,6,7) in amphibians and sauropsids to 10 in rodents. The additional exons are exons 4, 8, 9, and "4b", the latter being as yet unidentified in AMELX transcripts. To learn more about the evolutionary origin of these exons, we used an in silico approach to find them in 39 tetrapod genomes. AMEL organization with 6 exons was the ancestral condition. Exon 4 was created in an ancestral therian (marsupials + placentals), then exon 9 in an ancestral placental, and finally exons "4b" and 8 in rodents, after divergence of the squirrel lineage. These exons were either inactivated in some lineages or remained functional: Exon 4 is functional from artiodactyls onward; exon 9 is known, to date, only in rodents, but could be coding in various mammals; and exon "4b" was probably coding in some rodents. We performed PCR of cDNA isolated from mouse and human tooth buds to identify the presence of these transcripts. A sequence analogous to exon "4b", and to exon 9, could not be amplified from the respective tooth cDNA, indicating that even though sequences similar to these exons are present, they are not transcribed in these species. [ABSTRACT FROM AUTHOR]
- Published
- 2012
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4. High-Resolution Histology for Craniofacial Studies on Zebrafish and Other Teleost Models.
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Huysseune A, Soenens M, Sire JY, and Witten PE
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- Animals, Bone and Bones, Epoxy Resins, Microscopy, Electron, Transmission, Staining and Labeling, Histological Techniques, Skull, Zebrafish genetics
- Abstract
In the era of molecular biology, identification of cells and even tissues mostly relies on the presence of fluorescent tags, or of "marker gene" expression. We list a number of caveats and present a protocol for embedding, sectioning, and staining semithin plastic sections. The method is neither new nor innovative, but is meant to revive skills that tend to get lost.This easy-to-use and inexpensive protocol (1) yields high-resolution images in transmitted and polarized light, (2) can be utilized simultaneously for transmission electron microscopy, and (3) is applicable to any type of material (wild type, morphants, mutants, transgenic, or pharmacologically treated animals as well as all of their controls), provided the sample size is kept under a limit. Thus, we hope to encourage researchers to use microanatomy and histology to complement molecular studies investigating, e.g., gene function., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
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- 2022
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5. Collagen Suprafibrillar Confinement Drives the Activity of Acidic Calcium-Binding Polymers on Apatite Mineralization.
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Silvent J, Robin M, Bussola Tovani C, Wang Y, Soncin F, Delgado S, Azaïs T, Sassoye C, Giraud-Guille MM, Sire JY, and Nassif N
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- Collagen, Extracellular Matrix Proteins, Polymers, Apatites, Calcium
- Abstract
Bone collagenous extracellular matrix provides a confined environment into which apatite crystals form. This biomineralization process is related to a cascade of events partly controlled by noncollagenous proteins. Although overlooked in bone models, concentration and physical environment influence their activities. Here, we show that collagen suprafibrillar confinement in bone comprising intra- and interfibrillar spaces drives the activity of biomimetic acidic calcium-binding polymers on apatite mineralization. The difference in mineralization between an entrapping dentin matrix protein-1 (DMP1) recombinant peptide (rpDMP1) and the synthetic polyaspartate validates the specificity of the 57-KD fragment of DMP1 in the regulation of mineralization, but strikingly without phosphorylation. We show that all the identified functions of rpDMP1 are dedicated to preclude pathological mineralization. Interestingly, transient apatite phases are only found using a high nonphysiological concentration of additives. The possibility to combine biomimetic concentration of both collagen and additives ensures specific chemical interactions and offers perspectives for understanding the role of bone components in mineralization.
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- 2021
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6. Evolution of dental tissue mineralization: an analysis of the jawed vertebrate SPARC and SPARC-L families.
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Enault S, Muñoz D, Simion P, Ventéo S, Sire JY, Marcellini S, and Debiais-Thibaud M
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- Animals, Collagen Type I genetics, Collagen Type I metabolism, Collagen Type II genetics, Collagen Type II metabolism, Dental Enamel metabolism, Gene Expression Regulation, Developmental, Osteonectin genetics, Phylogeny, Tooth embryology, Vertebrates genetics, Biological Evolution, Jaw anatomy & histology, Minerals metabolism, Osteonectin metabolism, Tooth metabolism, Vertebrates anatomy & histology
- Abstract
Background: The molecular bases explaining the diversity of dental tissue mineralization across gnathostomes are still poorly understood. Odontodes, such as teeth and body denticles, are serial structures that develop through deployment of a gene regulatory network shared between all gnathostomes. Dentin, the inner odontode mineralized tissue, is produced by odontoblasts and appears well-conserved through evolution. In contrast, the odontode hypermineralized external layer (enamel or enameloid) produced by ameloblasts of epithelial origin, shows extensive structural variations. As EMP (Enamel Matrix Protein) genes are as yet only found in osteichthyans where they play a major role in the mineralization of teeth and others skeletal organs, our understanding of the molecular mechanisms leading to the mineralized odontode matrices in chondrichthyans remains virtually unknown., Results: We undertook a phylogenetic analysis of the SPARC/SPARC-L gene family, from which the EMPs are supposed to have arisen, and examined the expression patterns of its members and of major fibrillar collagens in the spotted catshark Scyliorhinus canicula, the thornback ray Raja clavata, and the clawed frog Xenopus tropicalis. Our phylogenetic analyses reveal that the single chondrichthyan SPARC-L gene is co-orthologous to the osteichthyan SPARC-L1 and SPARC-L2 paralogues. In all three species, odontoblasts co-express SPARC and collagens. In contrast, ameloblasts do not strongly express collagen genes but exhibit strikingly similar SPARC-L and EMP expression patterns at their maturation stage, in the examined chondrichthyan and osteichthyan species, respectively., Conclusions: A well-conserved odontoblastic collagen/SPARC module across gnathostomes further confirms dentin homology. Members of the SPARC-L clade evolved faster than their SPARC paralogues, both in terms of protein sequence and gene duplication. We uncover an osteichthyan-specific duplication that produced SPARC-L1 (subsequently lost in pipidae frogs) and SPARC-L2 (independently lost in teleosts and tetrapods).Our results suggest the ameloblastic expression of the single chondrichthyan SPARC-L gene at the maturation stage reflects the ancestral gnathostome situation, and provide new evidence in favor of the homology of enamel and enameloids in all gnathostomes.
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- 2018
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7. Bony pseudoteeth of extinct pelagic birds (Aves, Odontopterygiformes) formed through a response of bone cells to tooth-specific epithelial signals under unique conditions.
- Author
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Louchart A, Buffrénil V, Bourdon E, Dumont M, Viriot L, and Sire JY
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- Animals, Birds anatomy & histology, Epithelium metabolism, Extinction, Biological, Jaw anatomy & histology, Jaw metabolism, Tooth, Biological Evolution, Birds physiology, Odontoblasts metabolism, Odontogenesis, Phylogeny, Signal Transduction
- Abstract
Modern birds (crown group birds, called Neornithes) are toothless; however, the extinct neornithine Odontopterygiformes possessed bone excrescences (pseudoteeth) which resembled teeth, distributed sequentially by size along jaws. The origin of pseudoteeth is enigmatic, but based on recent evidence, including microanatomical and histological analyses, we propose that conserved odontogenetic pathways most probably regulated the development of pseudodentition. The delayed pseudoteeth growth and epithelium keratinization allowed for the existence of a temporal window during which competent osteoblasts could respond to oral epithelial signaling, in place of the no longer present odontoblasts; thus, bony pseudoteeth developed instead of true teeth. Dynamic morphogenetic fields can explain the particular, sequential size distribution of pseudoteeth along the jaws of these birds. Hence, this appears as a new kind of deep homology, by which ancient odontogenetic developmental processes would have controlled the evolution of pseudodentition, structurally different from a true dentition, but morphologically and functionally similar.
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- 2018
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8. Identification of a new mineralized tissue in the notochord of reared Siberian sturgeon (Acipenser baerii).
- Author
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Leprévost A, Azaïs T, Trichet M, and Sire JY
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- Analysis of Variance, Animals, Imaging, Three-Dimensional, Magnetic Resonance Spectroscopy, Minerals metabolism, Notochord diagnostic imaging, Notochord ultrastructure, X-Ray Microtomography, Calcification, Physiologic physiology, Fishes physiology, Notochord physiology
- Abstract
In a study aiming to improve knowledge on the mineralization of the axial skeleton in reared Siberian sturgeon (Acipenser baerii Brandt, 1869), we discovered a new mineralized tissue within the notochord. To our knowledge, such a structure has never been reported in any vertebrate species with the exception of the pathological mineralization of the notochord remains in degenerative intervertebral disks of mammals. Here, we describe this enigmatic tissue using X-ray microtomography, histological analyses and solid state NMR-spectroscopy. We also performed a 1-year monitoring of the mineral content (MC) of the notochord in relation with seasonal variations of temperature. In all specimens studied from 2-year-old juveniles onwards, this mineralized structure was found within a particular region of the notochord called funiculus. This feature first appears in the abdominal region then extends posteriorly with ageing, while the notochord MC also increases. The mineral phase is mainly composed of amorphous calcium phosphate, a small amount of which changes into hydroxyapatite with ageing. The putative role of this structure is discussed as either a store of minerals available for the phosphocalcic metabolism, or a mechanical support in a species with a poorly mineralized axial skeleton. A pathological feature putatively related to rearing conditions is also discussed., (© 2017 Wiley Periodicals, Inc.)
- Published
- 2017
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9. Unravelling the ontogeny of a Devonian early gnathostome, the "acanthodian" Triazeugacanthus affinis (eastern Canada).
- Author
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Chevrinais M, Sire JY, and Cloutier R
- Abstract
The study of vertebrate ontogenies has the potential to inform us of shared developmental patterns and processes among organisms. However, fossilised ontogenies of early vertebrates are extremely rare during the Palaeozoic Era. A growth series of the Late Devonian "acanthodian" Triazeugacanthus affinis , from the Miguasha Fossil - Fish Lagerstätte , is identified as one of the best known early vertebrate fossilised ontogenies given the exceptional preservation, the large size range, and the abundance of specimens. Morphological, morphometric, histological and chemical data are gathered on a growth series of Triazeugacanthus ranging from 4 to 52 mm in total length. The developmental trajectory of this Devonian "acanthodian" is characteristic of fishes showing a direct development with alternating steps and thresholds. Larvae show no squamation but a progressive appearance of cartilaginous neurocranial and vertebral elements, and appendicular elements, whereas juveniles progress in terms of ossification and squamation. The presence of cartilaginous and bony tissues, discriminated on histological and chemical signatures, shows a progressive mineralisation of neurocranial and vertebral elements. Comparison among different body proportions for larvae, juveniles and adults suggest allometric growth in juveniles. Because of the phylogenetic position of "acanthodians", Triazeugacanthus ontogeny informs us about deep time developmental conditions in gnathostomes., Competing Interests: The authors declare there are no competing interests.
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- 2017
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10. Phylotranscriptomic consolidation of the jawed vertebrate timetree.
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Irisarri I, Baurain D, Brinkmann H, Delsuc F, Sire JY, Kupfer A, Petersen J, Jarek M, Meyer A, Vences M, and Philippe H
- Abstract
Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on "standards" for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes and some relationships remain controversial. We tested a novel bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and find this phylotranscriptomic approach successful and highly cost-effective. Increased sequencing effort up to ca. 10Gbp allows recovering more genes, but shallower sequencing (1.5Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large curated nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates., Competing Interests: Competing financial interests The authors declare no competing financial interests.
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- 2017
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11. Evolutionary Analysis Predicts Sensitive Positions of MMP20 and Validates Newly- and Previously-Identified MMP20 Mutations Causing Amelogenesis Imperfecta.
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Gasse B, Prasad M, Delgado S, Huckert M, Kawczynski M, Garret-Bernardin A, Lopez-Cazaux S, Bailleul-Forestier I, Manière MC, Stoetzel C, Bloch-Zupan A, and Sire JY
- Abstract
Amelogenesis imperfecta (AI) designates a group of genetic diseases characterized by a large range of enamel disorders causing important social and health problems. These defects can result from mutations in enamel matrix proteins or protease encoding genes. A range of mutations in the enamel cleavage enzyme matrix metalloproteinase-20 gene ( MMP20 ) produce enamel defects of varying severity. To address how various alterations produce a range of AI phenotypes, we performed a targeted analysis to find MMP20 mutations in French patients diagnosed with non-syndromic AI. Genomic DNA was isolated from saliva and MMP20 exons and exon-intron boundaries sequenced. We identified several homozygous or heterozygous mutations, putatively involved in the AI phenotypes. To validate missense mutations and predict sensitive positions in the MMP20 sequence, we evolutionarily compared 75 sequences extracted from the public databases using the Datamonkey webserver. These sequences were representative of mammalian lineages, covering more than 150 million years of evolution. This analysis allowed us to find 324 sensitive positions (out of the 483 MMP20 residues), pinpoint functionally important domains, and build an evolutionary chart of important conserved MMP20 regions. This is an efficient tool to identify new- and previously-identified mutations. We thus identified six functional MMP20 mutations in unrelated families, finding two novel mutated sites. The genotypes and phenotypes of these six mutations are described and compared. To date, 13 MMP20 mutations causing AI have been reported, making these genotypes and associated hypomature enamel phenotypes the most frequent in AI.
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- 2017
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12. From body scale ontogeny to species ontogeny: Histological and morphological assessment of the Late Devonian acanthodian Triazeugacanthus affinis from Miguasha, Canada.
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Chevrinais M, Sire JY, and Cloutier R
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- Animals, Canada, Epidermis anatomy & histology, Fishes classification, Fossils, Phylogeny, Spine anatomy & histology, Fishes anatomy & histology
- Abstract
Growth series of Palaeozoic fishes are rare because of the fragility of larval and juvenile specimens owing to their weak mineralisation and the scarcity of articulated specimens. This rarity makes it difficult to describe early vertebrate growth patterns and processes in extinct taxa. Indeed, only a few growth series of complete Palaeozoic fishes are available; however, they allow the growth of isolated elements to be described and individual growth from these isolated elements to be inferred. In addition, isolated and in situ scales are generally abundant and well-preserved, and bring information on (1) their morphology and structure relevant to phylogenetic relationships and (2) individual growth patterns and processes relative to species ontogeny. The Late Devonian acanthodian Triazeugacanthus affinis from the Miguasha Fossil-Lagerstätte preserves one of the best known fossilised ontogenies of early vertebrates because of the exceptional preservation, the large size range, and the abundance of complete specimens. Here, we present morphological, histological, and chemical data on scales from juvenile and adult specimens (scales not being formed in larvae). Histologically, Triazeugacanthus scales are composed of a basal layer of acellular bone housing Sharpey's fibers, a mid-layer of mesodentine, and a superficial layer of ganoine. Developmentally, scales grow first through concentric addition of mesodentine and bone around a central primordium and then through superposition of ganoine layers. Ontogenetically, scales form first in the region below the dorsal fin spine, then squamation spreads anteriorly and posteriorly, and on fin webs. Phylogenetically, Triazeugacanthus scales show similarities with acanthodians (e.g. "box-in-box" growth), chondrichthyans (e.g. squamation pattern), and actinopterygians (e.g. ganoine). Scale histology and growth are interpreted in the light of a new phylogenetic analysis of gnathostomes supporting acanthodians as stem chondrichthyans.
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- 2017
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13. Evolutionary Analysis of the Mammalian Tuftelin Sequence Reveals Features of Functional Importance.
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Delgado S, Deutsch D, and Sire JY
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- Amino Acid Sequence genetics, Animals, Base Sequence genetics, Biological Evolution, Conserved Sequence genetics, Evolution, Molecular, Humans, Mammals genetics, Molecular Sequence Data, Phylogeny, Sequence Alignment methods, Dental Enamel Proteins genetics
- Abstract
Tuftelin (TUFT1) is an acidic, phosphorylated glycoprotein, initially discovered in developing enamel matrix. TUFT1 is expressed in many mineralized and non-mineralized tissues. We performed an evolutionary analysis of 82 mammalian TUFT1 sequences to identify residues and motifs that were conserved during 220 million years (Ma) of evolution. We showed that 168 residues (out of the 390 residues composing the human TUFT1 sequence) are under purifying selection. Our analyses identified several, new, putatively functional domains and confirmed previously described functional domains, such as the TIP39 interaction domain, which correlates with nuclear localization of the TUFT1 protein, that was demonstrated in several tissues. We also identified several sites under positive selection, which could indicate evolutionary changes possibly related to the functional diversification of TUFT1 during evolution in some lineages. We discovered that TUFT1 and MYZAP (myocardial zonula adherens protein) share a common ancestor that was duplicated circa 500 million years ago. Taken together, these findings expand our knowledge of TUFT1 evolution and provide new information that will be useful for further investigation of TUFT1 functions.
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- 2017
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14. Vertebral Development and Ossification in the Siberian Sturgeon (Acipenser Baerii), with New Insights on Bone Histology and Ultrastructure of Vertebral Elements and Scutes.
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Leprévost A, AzaÏs T, Trichet M, and Sire JY
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- Animals, Cartilage anatomy & histology, Cartilage diagnostic imaging, Fishes, Spine anatomy & histology, Spine diagnostic imaging, X-Ray Microtomography, Cartilage growth & development, Osteogenesis physiology, Spine growth & development
- Abstract
In order to improve our knowledge on the vertebral development, structure and mineralization in Acipenseriformes, we undertook a study in a growth series of reared Siberian sturgeons (Acipenser baerii) using in toto clear and stain specimens, histological and ultrastructural observations, X-ray micro-tomography, and solid state NMR analyses. Scutes were also studied to compare the tissue structure and mineralization of endoskeletal and dermal skeletal elements. This study completes and clarifies previous investigations on vertebral development and architecture in sturgeons, and brings original data on the structure of (i) the perichondral bone that is progressively deposited around the vertebral elements during ontogeny, (ii) the typical cartilage composing these elements, and (iii) the scutes. In addition we provide data on the mineralization process, on the nature of the bone mineral phase, and on the growth dynamics of the vertebral elements. Anat Rec, 300:437-449, 2017. © 2016 Wiley Periodicals, Inc., (© 2016 Wiley Periodicals, Inc.)
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- 2017
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15. Comparative expression of the four enamel matrix protein genes, amelogenin, ameloblastin, enamelin and amelotin during amelogenesis in the lizard Anolis carolinensis.
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Gasse B and Sire JY
- Abstract
Background: In a recent study, we have demonstrated that amelotin (AMTN) gene structure and its expression during amelogenesis have changed during tetrapod evolution. Indeed, this gene is expressed throughout enamel matrix deposition and maturation in non-mammalian tetrapods, while in mammals its expression is restricted to the transition and maturation stages of amelogenesis. Previous studies of amelogenin (AMEL) gene expression in a lizard and a salamander have shown similar expression pattern to that in mammals, but to our knowledge there are no data regarding ameloblastin (AMBN) and enamelin (ENAM) expression in non-mammalian tetrapods. The present study aims to look at, and compare, the structure and expression of four enamel matrix protein genes, AMEL, AMBN, ENAM and AMTN during amelogenesis in the lizard Anolis carolinensis., Results: We provide the full-length cDNA sequence of A. carolinensis AMEL and AMBN, and show for the first time the expression of ENAM and AMBN in a non-mammalian species. During amelogenesis in A. carolinensis, AMEL, AMBN and ENAM expression in ameloblasts is similar to that described in mammals. It is noteworthy that AMEL and AMBN expression is also found in odontoblasts., Conclusions: Our findings indicate that AMTN is the only enamel matrix protein gene that is differentially expressed in ameloblasts between mammals and sauropsids. Changes in AMTN structure and expression could be the key to explain the structural differences between mammalian and reptilian enamel, i.e. prismatic versus non-prismatic.
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- 2015
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16. Evolutionary analysis of selective constraints identifies ameloblastin (AMBN) as a potential candidate for amelogenesis imperfecta.
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Delsuc F, Gasse B, and Sire JY
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- Amelogenesis Imperfecta metabolism, Amino Acid Sequence, Animals, Conserved Sequence, Dental Enamel metabolism, Dental Enamel Proteins chemistry, Dental Enamel Proteins metabolism, Evolution, Molecular, Humans, Mammals metabolism, Molecular Sequence Data, Mutation, Phylogeny, Protein Biosynthesis, Protein Sorting Signals, Sequence Alignment, Amelogenesis Imperfecta genetics, Dental Enamel Proteins genetics, Mammals genetics
- Abstract
Background: Ameloblastin (AMBN) is a phosphorylated, proline/glutamine-rich protein secreted during enamel formation. Previous studies have revealed that this enamel matrix protein was present early in vertebrate evolution and certainly plays important roles during enamel formation although its precise functions remain unclear. We performed evolutionary analyses of AMBN in order to (i) identify residues and motifs important for the protein function, (ii) predict mutations responsible for genetic diseases, and (iii) understand its molecular evolution in mammals., Results: In silico searches retrieved 56 complete sequences in public databases that were aligned and analyzed computationally. We showed that AMBN is globally evolving under moderate purifying selection in mammals and contains a strong phylogenetic signal. In addition, our analyses revealed codons evolving under significant positive selection. Evidence for positive selection acting on AMBN was observed in catarrhine primates and the aye-aye. We also found that (i) an additional translation initiation site was recruited in the ancestral placental AMBN, (ii) a short exon was duplicated several times in various species including catarrhine primates, and (iii) several polyadenylation sites are present., Conclusions: AMBN possesses many positions, which have been subjected to strong selective pressure for 200 million years. These positions correspond to several cleavage sites and hydroxylated, O-glycosylated, and phosphorylated residues. We predict that these conserved positions would be potentially responsible for enamel disorder if substituted. Some motifs that were previously identified as potentially important functionally were confirmed, and we found two, highly conserved, new motifs, the function of which should be tested in the near future. This study illustrates the power of evolutionary analyses for characterizing the functional constraints acting on proteins with yet uncharacterized structure.
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- 2015
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17. Amelotin Gene Structure and Expression during Enamel Formation in the Opossum Monodelphis domestica.
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Gasse B, Liu X, Corre E, and Sire JY
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- Amino Acid Sequence, Animals, Animals, Newborn, Dental Enamel Proteins chemistry, Dental Enamel Proteins genetics, Dental Enamel Proteins metabolism, Molecular Sequence Data, Monodelphis growth & development, RNA, Messenger genetics, RNA, Messenger metabolism, Sequence Alignment, Amelogenesis genetics, Dental Enamel growth & development, Dental Enamel metabolism, Gene Expression Regulation, Developmental, Monodelphis genetics
- Abstract
Amelotin (AMTN) is an ameloblast-secreted protein that belongs to the secretory calcium-binding phosphoprotein family, which also includes the enamel matrix proteins amelogenin, ameloblastin and enamelin. Although AMTN is supposed to play an important role in enamel formation, data were long limited to the rodents, in which it is expressed during the maturation stage. Recent comparative studies in sauropsids and amphibians revealed that (i) AMTN was expressed earlier, i.e. as soon as ameloblasts are depositing the enamel matrix, and (ii) AMTN structure was different, a change which mostly resulted from an intraexonic splicing in the large exon 8 of an ancestral mammal. The present study was performed to know whether the differences in AMTN structure and expression in rodents compared to non-mammalian tetrapods dated back to an early ancestral mammal or were acquired later in mammalian evolution. We sequenced, assembled and screened the jaw transcriptome of a neonate opossum Monodelphis domestica, a marsupial. We found two AMTN transcripts. Variant 1, representing 70.8% of AMTN transcripts, displayed the structure known in rodents, whereas variant 2 (29.2%) exhibited the nonmammalian tetrapod structure. Then, we studied AMTN expression during amelogenesis in a neonate specimen. We obtained similar data as those reported in rodents. These findings indicate that more than 180 million years ago, before the divergence of marsupials and placentals, changes occurred in AMTN function and structure. The spatiotemporal expression was delayed to the maturation stage of amelogenesis and the intraexonic splicing gave rise to isoform 1, encoded by variant 1 and lacking the RGD motif. The ancestral isoform 2, housing the RGD, was initially conserved, as demonstrated here in a marsupial, then secondarily lost in the placental lineages. These findings bring new elements towards our understanding of the non-prismatic to prismatic enamel transition that occurred at the onset of mammals.
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- 2015
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18. Amelotin: an enamel matrix protein that experienced distinct evolutionary histories in amphibians, sauropsids and mammals.
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Gasse B, Chiari Y, Silvent J, Davit-Béal T, and Sire JY
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- Amelogenesis, Animals, Base Sequence, Dental Enamel metabolism, Mammals genetics, Molecular Sequence Data, RNA Splicing, Sequence Alignment, Vertebrates classification, Dental Enamel Proteins genetics, Dental Enamel Proteins metabolism, Evolution, Molecular, Vertebrates genetics
- Abstract
Background: Amelotin (AMTN) is an ameloblast-secreted protein that belongs to the secretory calcium-binding phosphoprotein (SCPP) family, which originated in early vertebrates. In rodents, AMTN is expressed during the maturation stage of amelogenesis only. This expression pattern strongly differs from the spatiotemporal expression of other ameloblast-secreted SCPPs, such as the enamel matrix proteins (EMPs). Furthermore, AMTN was characterized in rodents only. In this study, we applied various approaches, including in silico screening of databases, PCRs and transcriptome sequencing to characterize AMTN sequences in sauropsids and amphibians, and compared them to available mammalian and coelacanth sequences., Results: We showed that (i) AMTN is tooth (enamel) specific and underwent pseudogenization in toothless turtles and birds, and (ii) the AMTN structure changed during tetrapod evolution. To infer AMTN function, we studied spatiotemporal expression of AMTN during amelogenesis in a salamander and a lizard, and compared the results with available expression data from mouse. We found that AMTN is expressed throughout amelogenesis in non-mammalian tetrapods, in contrast to its expression limited to enamel maturation in rodents., Conclusions: Taken together our findings suggest that AMTN was primarily an EMP. Its functions were conserved in amphibians and sauropsids while a change occurred early in the mammalian lineage, modifying its expression pattern during amelogenesis and its gene structure. These changes likely led to a partial loss of AMTN function and could have a link with the emergence of prismatic enamel in mammals.
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- 2015
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19. The revival of a so-called rotten fish: the ontogeny of the Devonian acanthodian Triazeugacanthus.
- Author
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Chevrinais M, Cloutier R, and Sire JY
- Subjects
- Animals, Bone Development, Bone and Bones anatomy & histology, Fishes anatomy & histology, Fishes classification, Fishes growth & development, Fossils
- Abstract
Since its original description as a chordate, the Late Devonian Scaumenella mesacanthi has been interpreted alternately as a prochordate, a larval ostracoderm and an immature acanthodian. For the past 30 years, these minute specimens were generally considered as decayed acanthodians, most of them belonging to Triazeugacanthus affinis. Among the abundant material of 'Scaumenella', we identified a size series of 188 specimens of Triazeugacanthus based on otolith characteristics. Despite taphonomic alteration, we describe proportional growth and progressive appearance of skeletal elements through size increase. Three ontogenetic stages are identified based on squamation extent, ossification completion and allometric growth. We demonstrate that what has been interpreted previously as various degrees of decomposition corresponds to ontogenetic changes., (© 2015 The Author(s) Published by the Royal Society. All rights reserved.)
- Published
- 2015
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20. Molecular evolution of the tissue-nonspecific alkaline phosphatase allows prediction and validation of missense mutations responsible for hypophosphatasia.
- Author
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Silvent J, Gasse B, Mornet E, and Sire JY
- Subjects
- Alkaline Phosphatase chemistry, Alkaline Phosphatase classification, Amino Acid Sequence, Amino Acid Substitution, Animals, Base Sequence, DNA Primers, Humans, Molecular Sequence Data, Phylogeny, Protein Processing, Post-Translational, Alkaline Phosphatase genetics, Evolution, Molecular, Hypophosphatasia genetics, Mutation, Missense
- Abstract
ALPL encodes the tissue nonspecific alkaline phosphatase (TNSALP), which removes phosphate groups from various substrates. Its function is essential for bone and tooth mineralization. In humans, ALPL mutations lead to hypophosphatasia, a genetic disorder characterized by defective bone and/or tooth mineralization. To date, 275 ALPL mutations have been reported to cause hypophosphatasia, of which 204 were simple missense mutations. Molecular evolutionary analysis has proved to be an efficient method to highlight residues important for the protein function and to predict or validate sensitive positions for genetic disease. Here we analyzed 58 mammalian TNSALP to identify amino acids unchanged, or only substituted by residues sharing similar properties, through 220 millions years of mammalian evolution. We found 469 sensitive positions of the 524 residues of human TNSALP, which indicates a highly constrained protein. Any substitution occurring at one of these positions is predicted to lead to hypophosphatasia. We tested the 204 missense mutations resulting in hypophosphatasia against our predictive chart, and validated 99% of them. Most sensitive positions were located in functionally important regions of TNSALP (active site, homodimeric interface, crown domain, calcium site, …). However, some important positions are located in regions, the structure and/or biological function of which are still unknown. Our chart of sensitive positions in human TNSALP (i) enables to validate or invalidate at low cost any ALPL mutation, which would be suspected to be responsible for hypophosphatasia, by contrast with time consuming and expensive functional tests, and (ii) displays higher predictive power than in silico models of prediction., (© 2014 by The American Society for Biochemistry and Molecular Biology, Inc.)
- Published
- 2014
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21. Ameloblasts express type I collagen during amelogenesis.
- Author
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Assaraf-Weill N, Gasse B, Silvent J, Bardet C, Sire JY, and Davit-Béal T
- Subjects
- Ameloblasts cytology, Amelogenin analysis, Animals, Cell Differentiation physiology, Collagen Type I, alpha 1 Chain, Dental Enamel cytology, Dental Enamel metabolism, Dentinogenesis physiology, Enamel Organ anatomy & histology, Metamorphosis, Biological physiology, Microscopy, Electron, Transmission, Models, Animal, Odontoblasts cytology, Odontoblasts metabolism, Odontogenesis physiology, Pleurodeles, Tooth Germ anatomy & histology, Ameloblasts metabolism, Amelogenesis physiology, Collagen Type I analysis
- Abstract
Enamel and enameloid, the highly mineralized tooth-covering tissues in living vertebrates, are different in their matrix composition. Enamel, a unique product of ameloblasts, principally contains enamel matrix proteins (EMPs), while enameloid possesses collagen fibrils and probably receives contributions from both odontoblasts and ameloblasts. Here we focused on type I collagen (COL1A1) and amelogenin (AMEL) gene expression during enameloid and enamel formation throughout ontogeny in the caudate amphibian, Pleurodeles waltl. In this model, pre-metamorphic teeth possess enameloid and enamel, while post-metamorphic teeth possess enamel only. In first-generation teeth, qPCR and in situ hybridization (ISH) on sections revealed that ameloblasts weakly expressed AMEL during late-stage enameloid formation, while expression strongly increased during enamel deposition. Using ISH, we identified COL1A1 transcripts in ameloblasts and odontoblasts during enameloid formation. COL1A1 expression in ameloblasts gradually decreased and was no longer detected after metamorphosis. The transition from enameloid-rich to enamel-rich teeth could be related to a switch in ameloblast activity from COL1A1 to AMEL synthesis. P. waltl therefore appears to be an appropriate animal model for the study of the processes involved during enameloid-to-enamel transition, especially because similar events probably occurred in various lineages during vertebrate evolution.
- Published
- 2014
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22. Dental caries and enamelin haplotype.
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Chaussain C, Bouazza N, Gasse B, Laffont AG, Opsahl Vital S, Davit-Béal T, Moulis E, Chabadel O, Hennequin M, Courson F, Droz D, Vaysse F, Laboux O, Tassery H, Carel JC, Alcais A, Treluyer JM, Beldjord C, and Sire JY
- Subjects
- Amino Acid Substitution genetics, Arginine genetics, Child, DMF Index, Dental Caries Susceptibility genetics, Exons genetics, Extracellular Matrix Proteins, Female, Gene Frequency genetics, Genetic Predisposition to Disease genetics, Genetic Variation genetics, Glutamine genetics, Humans, Introns genetics, Isoleucine genetics, Linkage Disequilibrium genetics, Male, Mutation, Missense genetics, Polymorphism, Single Nucleotide genetics, Threonine genetics, Young Adult, Dental Caries genetics, Haplotypes genetics, Proteins genetics
- Abstract
In the literature, the enamelin gene ENAM has been repeatedly designated as a possible candidate for caries susceptibility. Here, we checked whether ENAM variants could increase caries susceptibility. To this aim, we sequenced coding exons and exon-intron boundaries of ENAM in 250 children with a severe caries phenotype and in 149 caries-free patients from 9 French hospital groups. In total, 23 single-nucleotide polymorphisms (SNPs) were found, but none appeared to be responsible for a direct change of ENAM function. Six SNPs had a high minor allele frequency (MAF) and 6 others were identified for the first time. Statistical and evolutionary analyses showed that none of these SNPs was associated with caries susceptibility or caries protection when studied separately and challenged with environmental factors. However, haplotype interaction analysis showed that the presence, in a same variant, of 2 exonic SNPs (rs7671281 and rs3796704; MAF 0.12 and 0.10, respectively), both changing an amino acid in the protein region encoded by exon 10 (p.I648T and p.R763Q, respectively), increased caries susceptibility 2.66-fold independent of the environmental risk factors. These findings support ENAM as a gene candidate for caries susceptibility in the studied population.
- Published
- 2014
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23. Structure and growth pattern of pseudoteeth in Pelagornis mauretanicus (Aves, Odontopterygiformes, Pelagornithidae).
- Author
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Louchart A, Sire JY, Mourer-Chauviré C, Geraads D, Viriot L, and de Buffrénil V
- Subjects
- Animals, Birds classification, Jaw anatomy & histology, Phylogeny, Birds anatomy & histology, Birds growth & development, Bone and Bones anatomy & histology
- Abstract
The extinct Odontopterygiformes are the sole birds known to possess strong and sharp bony pseudoteeth, the shape and location of which are closely mimetic of real teeth. The structure of the pseudoteeth is investigated here in a late Pliocene/early Pleistocene species, Pelagornis mauretanicus, using X-ray microtomography and thin sections. The results are interpreted with regard to the pseudotooth mode of growth, and have implications concerning aspects of Pelagornis ecology. The larger pseudoteeth are hollow and approximately cone-shaped, and the smaller ones are rostro-caudally constricted. The walls of pseudoteeth are composed of bone tissue of the fibro-lamellar type, which is intensively remodeled by Haversian substitution. The jaw bones display the same structure as the pseudoteeth, but their vascular canals are oriented parallel to the long axis of the bones, whereas they are perpendicular to this direction in the pseudoteeth. There is no hiatus or evidence of a fusion between the pseudoteeth and the jaw bones. Two possible models for pseudotooth growth are derived from the histological data. The most plausible model is that pseudotooth growth began after the completion of jaw bone growth, as a simple local protraction of periosteal osteogenic activity. Pseudotooth development thus occurred relatively late during ontogeny. The highly vascularized structure and the relative abundance of parallel-fibered bone tissue in the pseudoteeth suggest poor mechanical capabilities. The pseudoteeth were most likely covered and protected by the hardened, keratinized rhamphotheca in the adult during life. The late development of the pseudoteeth would involve a similarly late and/or partial hardening of the rhamphotheca, as displayed by extant Anseriformes, Apterygiformes and some Charadriiformes. This would add support to the hypothesis of a close phylogenetic relationship between Odontopterygiformes and Anseriformes. The late maturation of the Pelagornis feeding apparatus, and hence the delayed capability for efficient prey catching, suggests that Pelagornis was altricial.
- Published
- 2013
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24. Digit loss in archosaur evolution and the interplay between selection and constraints.
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de Bakker MA, Fowler DA, den Oude K, Dondorp EM, Navas MC, Horbanczuk JO, Sire JY, Szczerbińska D, and Richardson MK
- Subjects
- Animals, Dromaiidae anatomy & histology, Dromaiidae embryology, Extremities embryology, Forelimb anatomy & histology, Forelimb embryology, Gene Expression Regulation, Developmental, Hedgehog Proteins metabolism, Hindlimb anatomy & histology, Hindlimb embryology, Homeodomain Proteins metabolism, Molecular Sequence Data, Phenotype, Phylogeny, Wings, Animal anatomy & histology, Wings, Animal embryology, Alligators and Crocodiles anatomy & histology, Alligators and Crocodiles embryology, Biological Evolution, Birds anatomy & histology, Birds embryology, Extremities anatomy & histology, Selection, Genetic
- Abstract
Evolution involves interplay between natural selection and developmental constraints. This is seen, for example, when digits are lost from the limbs during evolution. Extant archosaurs (crocodiles and birds) show several instances of digit loss under different selective regimes, and show limbs with one, two, three, four or the ancestral number of five digits. The 'lost' digits sometimes persist for millions of years as developmental vestiges. Here we examine digit loss in the Nile crocodile and five birds, using markers of three successive stages of digit development. In two independent lineages under different selection, wing digit I and all its markers disappear. In contrast, hindlimb digit V persists in all species sampled, both as cartilage, and as Sox9- expressing precartilage domains, 250 million years after the adult digit disappeared. There is therefore a mismatch between evolution of the embryonic and adult phenotypes. All limbs, regardless of digit number, showed similar expression of sonic hedgehog (Shh). Even in the one-fingered emu wing, expression of posterior genes Hoxd11 and Hoxd12 was conserved, whereas expression of anterior genes Gli3 and Alx4 was not. We suggest that the persistence of digit V in the embryo may reflect constraints, particularly the conserved posterior gene networks associated with the zone of polarizing activity (ZPA). The more rapid and complete disappearance of digit I may reflect its ZPA-independent specification, and hence, weaker developmental constraints. Interacting with these constraints are selection pressures for limb functions such as flying and perching. This model may help to explain the diverse patterns of digit loss in tetrapods. Our study may also help to understand how selection on adults leads to changes in development.
- Published
- 2013
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25. Homozygous and compound heterozygous MMP20 mutations in amelogenesis imperfecta.
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Gasse B, Karayigit E, Mathieu E, Jung S, Garret A, Huckert M, Morkmued S, Schneider C, Vidal L, Hemmerlé J, Sire JY, and Bloch-Zupan A
- Subjects
- Amelogenesis Imperfecta genetics, Apatites analysis, Base Sequence genetics, Calcium analysis, Child, Preschool, Codon, Nonsense genetics, Crystallography, Cytosine, Dental Enamel ultrastructure, Electron Probe Microanalysis, Exons genetics, Female, Genes, Recessive genetics, Humans, Magnesium analysis, Microscopy, Electron, Scanning, Minerals analysis, Mutation, Missense genetics, Sequence Deletion genetics, Thymine, Amelogenesis Imperfecta enzymology, Heterozygote, Homozygote, Matrix Metalloproteinase 20 genetics, Mutation genetics
- Abstract
In this article, we focus on hypomaturation autosomal-recessive-type amelogenesis imperfecta (type IIA2) and describe 2 new causal Matrix metalloproteinase 20 (MMP20) mutations validated in two unrelated families: a missense mutation p.T130I at the expected homozygous state, and a compound heterozygous mutation having the same mutation combined with a nucleotide deletion, leading to a premature stop codon (p.N120fz*2). We characterized the enamel structure of the latter case using scanning electron microscopy analysis and microanalysis (Energy-dispersive X-ray Spectroscopy, EDX) and confirmed the hypomaturation-type amelogenesis imperfecta as identified in the clinical diagnosis. The mineralized content was slightly decreased, with magnesium substituting for calcium in the crystal structure. The anomalies affected enamel with minimal inter-rod enamel present and apatite crystals perpendicular to the enamel prisms, suggesting a possible new role for MMP20 in enamel formation.
- Published
- 2013
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26. Conservation of amelogenin gene expression during tetrapod evolution.
- Author
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Assaraf-Weill N, Gasse B, Al-Hashimi N, Delgado S, Sire JY, and Davit-Béal T
- Subjects
- Ameloblasts cytology, Ameloblasts metabolism, Amelogenesis genetics, Amelogenin metabolism, Amino Acid Sequence, Amphibians genetics, Animals, Conserved Sequence genetics, Dental Enamel metabolism, Dental Enamel ultrastructure, In Situ Hybridization, Lizards genetics, Mammals genetics, Phylogeny, Sequence Alignment, Amelogenin genetics, Dental Enamel chemistry, Evolution, Molecular, Gene Expression
- Abstract
Well studied in mammals, amelogenesis is less known at the molecular level in reptiles and amphibians. In the course of extensive studies of enamel matrix protein (EMP) evolution in tetrapods, we look for correlation between changes in protein sequences and temporospatial protein gene expression during amelogenesis, using an evo-devo approach. Our target is the major EMP, amelogenin (AMEL) that plays a crucial role in enamel structure. We focused here our attention to an amphibian, the salamander Pleurodeles waltl. RNAs were extracted from the lower jaws of a juvenile P. waltl and the complete AMEL sequence was obtained using PCR and RACE PCR. The alignment of P. waltl AMEL with other tetrapodan (frogs, reptiles and mammals) sequences revealed residue conservation in the N- and C-terminal regions, and a highly variable central region. Using sense and anti-sense probes synthetized from the P. waltl AMEL sequence, we performed in situ hybridization on sections during amelogenesis in larvae, juveniles, and adults. We demonstrated that (i) AMEL expression was always found to be restricted to ameloblasts, (ii) the expression pattern was conserved through ontogeny, even in larvae where enameloid is present in addition to enamel, and (iii) the processes are similar to those described in lizards and mammals. These findings indicate that high variations in the central region of AMEL have not modified its temporospatial expression during amelogenesis for 360 million years of tetrapod evolution., (Copyright © 2013 Wiley Periodicals, Inc.)
- Published
- 2013
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27. Common SNPs of AmelogeninX (AMELX) and dental caries susceptibility.
- Author
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Gasse B, Grabar S, Lafont AG, Quinquis L, Opsahl Vital S, Davit-Béal T, Moulis E, Chabadel O, Hennequin M, Courson F, Droz D, Vaysse F, Laboux O, Tassery H, Al-Hashimi N, Boillot A, Carel JC, Treluyer JM, Jeanpierre M, Beldjord C, Sire JY, and Chaussain C
- Subjects
- Adolescent, Adult, Child, Child, Preschool, DMF Index, Dental Plaque Index, Female, Genetic Predisposition to Disease, Humans, Male, Polymorphism, Single Nucleotide, Young Adult, Amelogenin genetics, Dental Caries genetics, Dental Caries Susceptibility genetics
- Abstract
Genetic approaches have shown that several genes could modify caries susceptibility; AmelogeninX (AMELX) has been repeatedly designated. Here, we hypothesized that AMELX mutations resulting in discrete changes of enamel microstructure may be found in children with a severe caries phenotype. In parallel, possible AMELX mutations that could explain resistance to caries may be found in caries-free patients. In this study, coding exons of AMELX and exon-intron boundaries were sequenced in 399 individuals with extensive caries (250) or caries-free (149) individuals from nine French hospital groups. No mutation responsible for a direct change of amelogenin function was identified. Seven single-nucleotide polymorphisms (SNPs) were found, 3 presenting a high allele frequency, and 1 being detected for the first time. Three SNPs were located in coding regions, 2 of them being non-synonymous. Both evolutionary and statistical analyses showed that none of these SNPs was associated with caries susceptibility, suggesting that AMELX is not a gene candidate in our studied population.
- Published
- 2013
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28. The dentin matrix acidic phosphoprotein 1 (DMP1) in the light of mammalian evolution.
- Author
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Silvent J, Sire JY, and Delgado S
- Subjects
- Amino Acid Motifs, Animals, Binding Sites, Cattle, Conserved Sequence, Dentin metabolism, Exons, Extracellular Matrix Proteins metabolism, Humans, Mice, Mutation, Oligopeptides genetics, Oligopeptides metabolism, Osteogenesis, Phosphoproteins metabolism, Phylogeny, Protein Processing, Post-Translational, Rats, Selection, Genetic, Sequence Alignment, Sialoglycoproteins genetics, Sialoglycoproteins metabolism, Swine, Evolution, Molecular, Extracellular Matrix Proteins genetics, Phosphoproteins genetics
- Abstract
Dentin matrix acidic phosphoprotein 1 (DMP1) is an acidic, highly phosphorylated, noncollagenous protein secreted during dentin and bone formation. Previous functional studies of DMP1 have revealed various motifs playing a role in either mineralization or cell differentiation. We performed an evolutionary analysis of DMP1 to identify residues and motifs that were conserved during 220 millions years (Ma) of mammalian evolution, and hence have an important function. In silico search provided us with 41 sequences that were aligned and analyzed using the Hyphy program. We showed that DMP1 contains 55 positions that were kept unchanged for 220 Ma. We also defined in a more precise manner some motifs that were already known (i.e., cleavage sites, RGD motif, ASARM peptide, glycosaminoglycan chain attachment site, nuclear localization signal sites, and dentin sialophosphoprotein-binding site), and we found five, highly conserved, new functional motifs. In the near future, functional studies could be performed to understand the role played by them.
- Published
- 2013
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29. Collagen osteoid-like model allows kinetic gene expression studies of non-collagenous proteins in relation with mineral development to understand bone biomineralization.
- Author
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Silvent J, Nassif N, Helary C, Azaïs T, Sire JY, and Guille MM
- Subjects
- Animals, Apatites metabolism, Bone Matrix metabolism, Bone Matrix ultrastructure, Bone and Bones ultrastructure, Cells, Cultured, Humans, Kinetics, Male, Middle Aged, Osteoblasts cytology, Osteoblasts metabolism, Osteoblasts ultrastructure, Rats, Bone and Bones metabolism, Calcification, Physiologic genetics, Collagen metabolism, Gene Expression Regulation, Minerals metabolism, Models, Biological
- Abstract
Among persisting questions on bone calcification, a major one is the link between protein expression and mineral deposition. A cell culture system is here proposed opening new integrative studies on biomineralization, improving our knowledge on the role played by non-collagenous proteins in bone. This experimental in vitro model consisted in human primary osteoblasts cultured for 60 days at the surface of a 3D collagen scaffold mimicking an osteoid matrix. Various techniques were used to analyze the results at the cellular and molecular level (adhesion and viability tests, histology and electron microscopy, RT- and qPCR) and to characterize the mineral phase (histological staining, EDX, ATG, SAED and RMN). On long term cultures human bone cells seeded on the osteoid-like matrix displayed a clear osteoblast phenotype as revealed by the osteoblast-like morphology, expression of specific protein such as alkaline phosphatase and expression of eight genes classically considered as osteoblast markers, including BGLAP, COL1A1, and BMP2. Von Kossa and alizarine red allowed us to identify divalent calcium ions at the surface of the matrix, EDX revealed the correct Ca/P ratio, and SAED showed the apatite crystal diffraction pattern. In addition RMN led to the conclusion that contaminant phases were absent and that the hydration state of the mineral was similar to fresh bone. A temporal correlation was established between quantified gene expression of DMP1 and IBSP, and the presence of hydroxyapatite, confirming the contribution of these proteins to the mineralization process. In parallel a difference was observed in the expression pattern of SPP1 and BGLAP, which questioned their attributed role in the literature. The present model opens new experimental possibilities to study spatio-temporal relations between bone cells, dense collagen scaffolds, NCPs and hydroxyapatite mineral deposition. It also emphasizes the importance of high collagen density environment in bone cell physiology.
- Published
- 2013
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30. Evolutionary analysis suggests that AMTN is enamel-specific and a candidate for AI.
- Author
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Gasse B, Silvent J, and Sire JY
- Subjects
- Amelogenesis Imperfecta metabolism, Amino Acid Sequence, Amino Acid Substitution, Animals, Armadillos genetics, Conserved Sequence, Dental Enamel Proteins chemistry, Evolution, Molecular, Humans, Mammals genetics, Mice, Phosphorylation genetics, Protein Sorting Signals, Rats, Sloths genetics, Amelogenesis Imperfecta genetics, Dental Enamel chemistry, Dental Enamel Proteins genetics
- Abstract
Molecular evolutionary analysis is an efficient method to predict and/or validate amino acid substitutions that could lead to a genetic disease and to highlight residues and motifs that could play an important role in the protein structure and/or function. We have applied such analysis to amelotin (AMTN), a recently identified enamel protein in the rat, mouse, and humans. An in silico search for AMTN provided 42 new mammalian sequences that were added to the 3 published sequences with which we performed the analysis using a dataset representative of all lineages (circa 220 million years of evolution), including 2 enamel-less species, sloth and armadillo. During evolution, of the 209 residues of human AMTN, 17 were unchanged and 34 had conserved their chemical properties. Substituting these important residues could lead to amelogenesis imperfecta (AI). Also, AMTN possesses a well-conserved signal peptide, 2 conserved motifs whose function is certainly important but unknown, and a putative phosphorylation site (SXE). In addition, the sequences of the 2 enamel-less species display mutations revealing that AMTN underwent pseudogenization, which suggests that AMTN is an enamel-specific protein.
- Published
- 2012
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31. Identification of two carbonic anhydrases in the mantle of the European Abalone Haliotis tuberculata (Gastropoda, Haliotidae): phylogenetic implications.
- Author
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LE Roy N, Marie B, Gaume B, Guichard N, Delgado S, Zanella-Cléon I, Becchi M, Auzoux-Bordenave S, Sire JY, and Marin F
- Subjects
- Animals, Base Sequence, Calcification, Physiologic genetics, Cloning, Molecular, DNA Primers genetics, DNA, Complementary genetics, Electrophoresis, Polyacrylamide Gel, Gastropoda genetics, Likelihood Functions, Models, Genetic, Molecular Sequence Data, Polymerase Chain Reaction, Proteomics, Real-Time Polymerase Chain Reaction, Sequence Analysis, DNA, Species Specificity, Animal Shells enzymology, Calcification, Physiologic physiology, Carbonic Anhydrases genetics, Gastropoda enzymology, Models, Biological, Phylogeny
- Abstract
Carbonic anhydrases (CAs) represent a diversified family of metalloenzymes that reversibly catalyze the hydration of carbon dioxide. They are involved in a wide range of functions, among which is the formation of CaCO(3) skeletons in metazoans. In the shell-forming mantle tissues of mollusks, the location of the CA catalytic activity is elusive and gives birth to contradicting views. In the present paper, using the European abalone Haliotis tuberculata, a key model gastropod in biomineralization studies, we identified and characterized two CAs (htCA1 and htCA2) that are specific of the shell-forming mantle tissue. We analyzed them in a phylogenetic context. Combining various approaches, including proteomics, activity tests, and in silico analyses, we showed that htCA1 is secreted but is not incorporated in the organic matrix of the abalone shell and that htCA2 is transmembrane. Together with previous studies dealing with molluskan CAs, our findings suggest two possible modes of action for shell mineralization: the first mode applies to, for example, the bivalves Unio pictorum and Pinctada fucata, and involves a true CA activity in their shell matrix; the second mode corresponds to, for example, the European abalone, and does not include CA activity in the shell matrix. Our work provides new insight on the diversity of the extracellular macromolecular tools used for shell biomineralization study in mollusks., (© 2012 WILEY PERIODICALS, INC.)
- Published
- 2012
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32. Effect of an experimental oil spill on vertebral bone tissue quality in European sea bass (Dicentrarchus labrax L.).
- Author
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Danion M, Deschamps MH, Thomas-Guyon H, Bado-Nilles A, Le Floch S, Quentel C, and Sire JY
- Subjects
- Animals, Biomarkers analysis, Bone Density drug effects, Calcification, Physiologic drug effects, Seawater, Spine abnormalities, Toxicity Tests, Acute, Bass abnormalities, Petroleum Pollution adverse effects, Polycyclic Aromatic Hydrocarbons adverse effects, Spine drug effects
- Abstract
In order to identify biomarkers of oil pollution in fish we tested the effects of an experimental Light Cycle Oil (LCO) exposure on vertebral bone of sea bass, Dicentrarchus labrax L. A total of 60 adult fish were acclimated for fifteen days, then twenty were collected as controls (Day 0) while 40 were exposed to a soluble fraction of LCO (1136 ng L(-1) of ten Polycyclic Aromatic Hydrocarbons, PAHs) for seven days. Twenty of them were sampled at the end of the exposure period and the twenty last after a recovery period of fourteen days in clean seawater. Vertebral abnormalities were counted and bone mineralization, total bone area and bone density profiles were established for several post-cranial and caudal vertebrae. In sea bass, seven days of LCO exposure did not affect the frequency and severity of the vertebral abnormalities. No significant differences were observed in bone density and bone repartition (parameters of bone area profiles) between unexposed (Day 0), exposed (D7) and decontaminated (D21) fish. In contrast, bone mineralization of the vertebrae decreased in contaminated sea bass, but in a reversible way, which confirms a previous study in trout showing that this parameter is an early stress indicator. Our results suggest that vertebral bone mineralization could be used as a biomarker of PAH pollution in sea bass. It would be interesting to check this new biomarker in other teleost species exposed to various xenobiotics., (Crown Copyright © 2011. Published by Elsevier Inc. All rights reserved.)
- Published
- 2011
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33. The evolution of milk casein genes from tooth genes before the origin of mammals.
- Author
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Kawasaki K, Lafont AG, and Sire JY
- Subjects
- Amyloid, Animals, Carrier Proteins genetics, Computational Biology, Dental Enamel, Exons genetics, Gene Duplication, Genome, Humans, Intracellular Signaling Peptides and Proteins, Micelles, Models, Genetic, Neoplasm Proteins, Phylogeny, Calcium-Binding Proteins genetics, Caseins genetics, Evolution, Molecular, Phosphoproteins genetics, Tooth
- Abstract
Caseins are among cardinal proteins that evolved in the lineage leading to mammals. In milk, caseins and calcium phosphate (CaP) form a huge complex called casein micelle. By forming the micelle, milk maintains high CaP concentrations, which help altricial mammalian neonates to grow bone and teeth. Two types of caseins are known. Ca-sensitive caseins (α(s)- and β-caseins) bind Ca but precipitate at high Ca concentrations, whereas Ca-insensitive casein (κ-casein) does not usually interact with Ca but instead stabilizes the micelle. Thus, it is thought that these two types of caseins are both necessary for stable micelle formation. Both types of caseins show high substitution rates, which make it difficult to elucidate the evolution of caseins. Yet, recent studies have revealed that all casein genes belong to the secretory calcium-binding phosphoprotein (SCPP) gene family that arose by gene duplication. In the present study, we investigated exon-intron structures and phylogenetic distributions of casein and other SCPP genes, particularly the odontogenic ameloblast-associated (ODAM) gene, the SCPP-Pro-Gln-rich 1 (SCPPPQ1) gene, and the follicular dendritic cell secreted peptide (FDCSP) gene. The results suggest that contemporary Ca-sensitive casein genes arose from a putative common ancestor, which we refer to as CSN1/2. The six putative exons comprising CSN1/2 are all found in SCPPPQ1, although ODAM also shares four of these exons. By contrast, the five exons of the Ca-insensitive casein gene are all reminiscent of FDCSP. The phylogenetic distribution of these genes suggests that both SCPPPQ1 and FDCSP arose from ODAM. We thus argue that all casein genes evolved from ODAM via two different pathways; Ca-sensitive casein genes likely originated directly from SCPPPQ1, whereas the Ca-insensitive casein genes directly differentiated from FDCSP. Further, expression of ODAM, SCPPPQ1, and FDCSP was detected in dental tissues, supporting the idea that both types of caseins evolved as Ca-binding proteins. Based on these findings, we propose two alternative hypotheses for micelle formation in primitive milk. The conserved biochemical characteristics in caseins and their immediate ancestors also suggest that many slight genetic modifications have created modern caseins, proteins vital to the sustained success of mammals.
- Published
- 2011
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34. Coupling proteomics and transcriptomics for the identification of novel and variant forms of mollusk shell proteins: a study with P. margaritifera.
- Author
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Berland S, Marie A, Duplat D, Milet C, Sire JY, and Bédouet L
- Subjects
- Amino Acid Sequence, Animals, Databases, Genetic, Kinesins chemistry, Molecular Sequence Data, Mollusca, Proteins genetics, Sequence Alignment, Gene Expression Profiling, Proteins chemistry, Proteomics
- Abstract
Shell matrix proteins from Pinctada margaritifera were characterized by combining proteomics analysis of shell organic extracts and transcript sequences, both obtained from the shell-forming cell by using the suppression subtractive hybridization method (SSH) and from an expressed sequence tag (EST) database available from Pinctada maxima mantle tissue. Some of the identified proteins were homologues to proteins reported in other mollusk shells, namely lysine-rich matrix proteins (KRMPs), shematrins and molluscan prismatic and nacreous layer 88 kDa (MPN88). Sequence comparison within and among Pinctada species pointed to intra- and interspecies variations relevant to polymorphism and to evolutionary distance, respectively. In addition, a novel shell matrix protein, linkine was identified. BLAST analysis of the peptide sequences obtained from the shell of P. margaritifera against the EST database revealed the presence of additional proteins: two proteins similar to the Pif97 protein that was identified in the shell of P. fucata, a chitinase-like protein previously identified in Crassostrea gigas, two chitin-binding proteins, and two incomplete sequences of proteins unknown so far in mollusk shells. Combining proteomics and transcriptomics analysis we demonstrate that all these proteins, including linkine, are addressed to the shell. Retrieval of motif-forming sequences, such as chitin-binding, with functional annotation from several peptides nested in the shell could indicate protein involvement in shell patterning., (Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2011
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35. [Reappraisal of the role of pTα for pre-TCR signaling: lessons from non mammalian vertebrates].
- Author
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Smelty P, Marchal C, Jaffredo T, Sire JY, and Fellah JS
- Subjects
- Animals, Birds genetics, Birds immunology, CD3 Complex chemistry, Gene Order, Gene Rearrangement, T-Lymphocyte, Humans, Lizards genetics, Lizards immunology, Mammals genetics, Mammals immunology, Membrane Glycoproteins chemistry, Membrane Glycoproteins genetics, Mice, Protein Conformation, Protein Structure, Tertiary, Receptors, Antigen, T-Cell, alpha-beta chemistry, Receptors, Antigen, T-Cell, alpha-beta genetics, Signal Transduction physiology, Vertebrates genetics, Membrane Glycoproteins immunology, Receptors, Antigen, T-Cell, alpha-beta immunology, T-Lymphocyte Subsets immunology, Vertebrates immunology
- Published
- 2011
- Full Text
- View/download PDF
36. OC-116, the chicken ortholog of mammalian MEPE found in eggshell, is also expressed in bone cells.
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Bardet C, Vincent C, Lajarille MC, Jaffredo T, and Sire JY
- Subjects
- Animals, Bone and Bones cytology, Calcification, Physiologic, Chick Embryo, Chickens metabolism, Extracellular Matrix Proteins metabolism, Mandible metabolism, Osteogenesis, Tibia metabolism, Bone and Bones metabolism, Egg Proteins metabolism, Gene Expression Regulation
- Abstract
In chicken, ovocleidin 116 (OC-116) is found in the eggshell matrix and its encoding gene, OC-116, is expressed in uterine cells. In mammals, its orthologue MEPE encodes the matrix extracellular phosphoglycoprotein (MEPE), which has been shown to be involved in bone mineralization. Using RT-PCR and in situ hybridization on sections, we have checked whether OC-116 was also expressed in osteoblasts and osteocytes during bone development and mineralization in chicken embryos. We monitored OC-116 expression in the tibia and mandible of a growth series of chicken embryos from E3 to E19. Transcripts were identified in the osteoblasts as early as E5 in the tibia and E7 in the mandible, before matrix mineralization, then from these stages onwards in both the osteoblasts lining the mineralized bone matrix and the osteocytes. Therefore, early in chicken ontogeny and as soon as osteogenesis begins, OC-116 is involved. Its function, which remains still unknown, is maintained during further bone growth and mineralization, and later in adult, in which it is recruited for eggshell formation. We hypothesize that the ancestral OC-116/MEPE in a stem amniote was involved in these two functions and that the loss of eggshell in the mammalian lineage has probably favored the recruitment of some MEPE domains toward new functions in osteogenesis and mineralization, and in phosphatemia regulation., (© 2010 Wiley-Liss, Inc.)
- Published
- 2010
- Full Text
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37. Identification of the pre-T-cell receptor alpha chain in nonmammalian vertebrates challenges the structure-function of the molecule.
- Author
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Smelty P, Marchal C, Renard R, Sinzelle L, Pollet N, Dunon D, Jaffredo T, Sire JY, and Fellah JS
- Subjects
- Amino Acid Sequence, Animals, Anura immunology, Birds immunology, Fishes immunology, Gene Expression Regulation, Humans, Mammals immunology, Mice, Molecular Sequence Data, RNA, Messenger genetics, RNA, Messenger metabolism, Receptors, Antigen, T-Cell, alpha-beta genetics, Reptiles immunology, Sequence Alignment, Structure-Activity Relationship, Vertebrates genetics, Receptors, Antigen, T-Cell, alpha-beta chemistry, Receptors, Antigen, T-Cell, alpha-beta immunology, Vertebrates immunology
- Abstract
In humans and mice, the early development of αβ T cells is controlled by the pre-T-cell receptor α chain (pTα) that is covalently associated with the T-cell receptor β (TCRβ) chain to form the pre-T-cell receptor (pre-TCR) at the thymocyte surface. Pre-TCR functions in a ligand-independent manner through self-oligomerization mediated by pTα. Using in silico and gene synteny-based approaches, we identified the pTα gene (PTCRA) in four sauropsid (three birds and one reptile) genomes. We also identified 25 mammalian PTCRA sequences now covering all mammalian lineages. Gene synteny around PTCRA is remarkably conserved in mammals but differences upstream of PTCRA in sauropsids suggest chromosomal rearrangements. PTCRA organization is highly similar in sauropsids and mammals. However, comparative analyses of the pTα functional domains indicate that sauropsids, monotremes, marsupials, and lagomorphs display a short pTα cytoplasmic tail and lack most residues shown to be critical for human and murine pre-TCR self-oligomerization. Chicken PTCRA transcripts similar to those in mammals were detected in immature double-negative and double-positive thymocytes. These findings give clues about the evolution of this key molecule in amniotes and suggest that the ancestral function of pTα was exclusively to enable expression of the TCRβ chain at the thymocyte surface and to allow binding of pre-TCR to the CD3 complex. Together, our data provide arguments for revisiting the current model of pTα signaling.
- Published
- 2010
- Full Text
- View/download PDF
38. The enamelin genes in lizard, crocodile, and frog and the pseudogene in the chicken provide new insights on enamelin evolution in tetrapods.
- Author
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Al-Hashimi N, Lafont AG, Delgado S, Kawasaki K, and Sire JY
- Subjects
- Animals, Dental Enamel Proteins classification, Molecular Sequence Data, Polymerase Chain Reaction, Alligators and Crocodiles genetics, Anura genetics, Chickens genetics, Dental Enamel Proteins genetics, Evolution, Molecular, Lizards genetics, Pseudogenes genetics
- Abstract
Enamelin (ENAM) has been shown to be a crucial protein for enamel formation and mineralization. Previous molecular analyses have indicated a probable origin early in vertebrate evolution, which is supported by the presence of enamel/enameloid tissues in early vertebrates. In contrast to these hypotheses, ENAM was only characterized in mammals. Our aims were to 1) look for ENAM in representatives of nonmammalian tetrapods, 2) search for a pseudogene in the chicken genome, and 3) see whether the new sequences could bring new information on ENAM evolution. Using in silico approach and polymerase chain reaction, we obtained and characterized the messenger RNA sequences of ENAM in a frog, a lizard, and a crocodile; the genomic DNA sequences of ENAM in a frog and a lizard; and the putative sequence of chicken ENAM pseudogene. The comparison with mammalian ENAM sequences has revealed 1) the presence of an additional coding exon, named exon 8b, in sauropsids and marsupials, 2) a simpler 5'-untranslated region in nonmammalian ENAMs, 3) many sequence variations in the large exons while there are a few conserved regions in small exons, and 4) 25 amino acids that have been conserved during 350 million years of tetrapod evolution and hence of crucial biological importance. The chicken pseudogene was identified in a region that was not expected when considering the gene synteny in mammals. Together with the location of lizard ENAM in a homologous region, this result indicates that enamel genes were probably translocated in an ancestor of the sauropsid lineage. This study supports the origin of ENAM earlier in vertebrate evolution, confirms that tooth loss in modern birds led to the invalidation of enamel genes, and adds information on the important role played by, for example, the phosphorylated serines and the glycosylated asparagines for correct ENAM functions.
- Published
- 2010
- Full Text
- View/download PDF
39. Prenatal development of Crocodylus niloticus niloticus Laurenti, 1768.
- Author
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Peterka M, Sire JY, Hovorakova M, Prochazka J, Fougeirol L, Peterkova R, and Viriot L
- Subjects
- Alligators and Crocodiles anatomy & histology, Alligators and Crocodiles embryology, Animals, Body Weight, Head anatomy & histology, Alligators and Crocodiles genetics
- Abstract
Prenatal development in crocodilians represents a very interesting model for comparative studies. As the speed of prenatal development of crocodilians varies depending on incubation conditions, the staging of embryos and fetuses is a very important prerequisite for data correlation. To establish a background for future developmental studies on Crocodylus niloticus, we characterized its prenatal development in a collection comprising 169 animals during embryonic/incubation days 9-70. The characteristics included external morphology, head morphometry, and wet body weight determined before fixation. We documented the external morphology of prenatal Nile crocodiles in a large collection of photographs and described landmarks during the morphogenesis of the head, face and limbs. In the development of the facial processes (medial nasal, lateral nasal, maxillary), three phases could be distinguished: union, separation, reunion. At the free jaw margin, a regular series of prominences was present. The outer aspect of a prominence gave rise to a labial scale, the inner aspect to a tooth. In contrast to mammals (humans and mice), the hindlimbs of C. niloticus developed faster than the forelimbs. We also determined changes in basic measures of the head and of the wet body weight. Both morphological and morphometric characteristics showed an apparent inter-individual variability among animals of the same age. This variability decreased among animals of a similar body weight (irrespective of their age). Body weight can be considered as the most representative and complex parameter for crocodile staging reflecting the overall growth of a whole embryo/fetus.
- Published
- 2010
- Full Text
- View/download PDF
40. The histological structure of glyptosaurine osteoderms (Squamata: Anguidae), and the problem of osteoderm development in squamates.
- Author
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Buffrénil Vd, Sire JY, and Rage JC
- Subjects
- Adaptation, Physiological physiology, Animals, Biological Evolution, Bone Development physiology, Bone Remodeling physiology, Bone and Bones physiology, Dermis anatomy & histology, Dermis growth & development, Epidermis anatomy & histology, Epidermis growth & development, Fossils, Integumentary System growth & development, Lizards growth & development, Osteogenesis physiology, Paleontology methods, Phylogeny, Skin growth & development, Bone and Bones anatomy & histology, Calcification, Physiologic physiology, Integumentary System anatomy & histology, Lizards anatomy & histology, Skin anatomy & histology
- Abstract
Glyptosaurinae, a fossil clade of anguid lizards, possess robust osteoderms, with granular ornamentation. In this study, the structural and histological features of these osteoderms were described in order to reconstruct their developmental pattern and further document the degree of homology that could exist between vertebrate integumentary skeletons. Glyptosaurine osteoderms have a diploe architecture and display an unusually complex structure that includes four tissue types: a core of woven-fibered bone intensely remodeled; a peripheral formation of the same tissue containing dense bundles of long Sharpey fibers; a thick basal layer of lamellar bone; and a superficial layer of a non-osseous material that belongs to the category of hypermineralized tissues such as ganoine, or enameloid and enamel tissues. The growth pattern of glyptosaurine osteoderms involved appositional processes due to osteoblast activity. In early growth stages, osseous metaplasia might have also been involved, but this possibility is not substantiated by histological observations. The superficial layer of the osteoderms must have resulted from epidermal contribution, a conclusion that would support previous hypotheses on the role of epidermal-dermal interactions in the formation of squamate osteoderms.
- Published
- 2010
- Full Text
- View/download PDF
41. MEPE evolution in mammals reveals regions and residues of prime functional importance.
- Author
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Bardet C, Delgado S, and Sire JY
- Subjects
- Amino Acid Motifs, Amino Acid Sequence, Amino Acid Substitution, Animals, Cats, Cattle, Dogs, Exons genetics, Extracellular Matrix Proteins metabolism, Female, Glycoproteins metabolism, Guinea Pigs, Humans, Mice, Molecular Sequence Data, Phosphoproteins metabolism, Pregnancy, Rabbits, Rats, Selection, Genetic, Sequence Alignment, Evolution, Molecular, Extracellular Matrix Proteins chemistry, Extracellular Matrix Proteins genetics, Glycoproteins chemistry, Glycoproteins genetics, Phosphoproteins chemistry, Phosphoproteins genetics, Placenta metabolism
- Abstract
In mammals, the matrix extracellular phosphoglycoprotein (MEPE) is known to activate osteogenesis and mineralization via a particular region called dentonin, and to inhibit mineralization via its ASARM (acidic serine-aspartate rich MEPE-associated motif) peptide that also plays a role in phosphatemia regulation. In order to understand MEPE evolution in mammals, and particularly that of its functional regions, we conducted an evolutionary analysis based on the study of selective pressures. Using 37 mammalian sequences we: (1) confirmed the presence of an additional coding exon in most placentals; (2) highlighted several conserved residues and regions that could have important functions; (3) found that dentonin function was recruited in a placental ancestor; and (4) revealed that ASARM function was present earlier, pushing the recruitment of MEPE deep into amniote origins. Our data indicate that MEPE was involved in various functions (bone and eggshell mineralization) prior to acquiring those currently known in placental mammals.
- Published
- 2010
- Full Text
- View/download PDF
42. Evolutionary analysis of mammalian enamelin, the largest enamel protein, supports a crucial role for the 32-kDa peptide and reveals selective adaptation in rodents and primates.
- Author
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Al-Hashimi N, Sire JY, and Delgado S
- Subjects
- Amino Acid Sequence, Animals, Dental Enamel metabolism, Dental Enamel Proteins chemistry, Gene Expression Regulation, Humans, Molecular Sequence Data, Mutation, Peptides genetics, Peptides metabolism, Protein Sorting Signals, Tooth metabolism, Amelogenesis Imperfecta genetics, Dental Enamel Proteins genetics, Dental Enamel Proteins metabolism, Evolution, Molecular, Primates genetics, Rodentia genetics, Selection, Genetic
- Abstract
Enamelin (ENAM) plays an important role in the mineralization of the forming enamel matrix. We have performed an evolutionary analysis of mammalian ENAM to identify highly conserved residues or regions that could have important function (selective pressure), to predict mutations that could be associated with amelogenesis imperfecta in humans, and to identify possible adaptive evolution of ENAM during 200 million years ago of mammalian evolution. In order to fulfil these objectives, we obtained 36-ENAM sequences that are representative of the mammalian lineages. Our results show a remarkably high conservation pattern in the region of the 32-kDa fragment of ENAM, especially its phosphorylation, glycosylation, and proteolytic sites. In primates and rodents we also identified several sites under positive selection, which could indicate recent evolutionary changes in ENAM function. Furthermore, the analysis of the unusual signal peptide provided new insights on the possible regulation of ENAM secretion, a hypothesis that should be tested in the near future. Taken together, these findings improve our understanding of ENAM evolution and provide new information that would be useful for further investigation of ENAM function as well as for the validation of mutations leading to amelogenesis imperfecta.
- Published
- 2009
- Full Text
- View/download PDF
43. Origin and evolution of the integumentary skeleton in non-tetrapod vertebrates.
- Author
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Sire JY, Donoghue PC, and Vickaryous MK
- Subjects
- Animals, Bone and Bones anatomy & histology, Calcification, Physiologic genetics, Extremities anatomy & histology, Fossils, Phylogeny, Vertebrates anatomy & histology, Vertebrates genetics, Biological Evolution, Integumentary System anatomy & histology, Odontogenesis genetics, Osteogenesis genetics, Vertebrates classification
- Abstract
Most non-tetrapod vertebrates develop mineralized extra-oral elements within the integument. Known collectively as the integumentary skeleton, these elements represent the structurally diverse skin-bound contribution to the dermal skeleton. In this review we begin by summarizing what is known about the histological diversity of the four main groups of integumentary skeletal tissues: hypermineralized (capping) tissues; dentine; plywood-like tissues; and bone. For most modern taxa, the integumentary skeleton has undergone widespread reduction and modification often rendering the homology and relationships of these elements confused and uncertain. Fundamentally, however, all integumentary skeletal elements are derived (alone or in combination) from only two types of cell condensations: odontogenic and osteogenic condensations. We review the origin and diversification of the integumentary skeleton in aquatic non-tetrapods (including stem gnathostomes), focusing on tissues derived from odontogenic (hypermineralized tissues, dentines and elasmodine) and osteogenic (bone tissues) cell condensations. The novelty of our new scenario of integumentary skeletal evolution resides in the demonstration that elasmodine, the main component of elasmoid scales, is odontogenic in origin. Based on available data we propose that elasmodine is a form of lamellar dentine. Given its widespread distribution in non-tetrapod lineages we further propose that elasmodine is a very ancient tissue in vertebrates and predict that it will be found in ancestral rhombic scales and cosmoid scales.
- Published
- 2009
- Full Text
- View/download PDF
44. The integumentary skeleton of tetrapods: origin, evolution, and development.
- Author
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Vickaryous MK and Sire JY
- Subjects
- Animals, Biological Evolution, Bone and Bones physiology, Calcification, Physiologic genetics, Dermis anatomy & histology, Extremities anatomy & histology, Fossils, Integumentary System physiology, Phylogeny, Vertebrates classification, Vertebrates genetics, Bone and Bones anatomy & histology, Integumentary System anatomy & histology, Odontogenesis genetics, Osteogenesis genetics, Vertebrates anatomy & histology
- Abstract
Although often overlooked, the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes but most details of their evolution and development remain confused and uncertain. Herein we re-evaluate the tetrapod integumentary skeleton by integrating comparative developmental and tissue structure data. Three types of tetrapod integumentary elements are recognized: (1) osteoderms, common to representatives of most major taxonomic lineages; (2) dermal scales, unique to gymnophionans; and (3) the lamina calcarea, an enigmatic tissue found only in some anurans. As presently understood, all are derivatives of the ancestral cosmoid scale and all originate from scleroblastic neural crest cells. Osteoderms are plesiomorphic for tetrapods but demonstrate considerable lineage-specific variability in size, shape, and tissue structure and composition. While metaplastic ossification often plays a role in osteoderm development, it is not the exclusive mode of skeletogenesis. All osteoderms share a common origin within the dermis (at or adjacent to the stratum superficiale) and are composed primarily (but not exclusively) of osseous tissue. These data support the notion that all osteoderms are derivatives of a neural crest-derived osteogenic cell population (with possible matrix contributions from the overlying epidermis) and share a deep homology associated with the skeletogenic competence of the dermis. Gymnophionan dermal scales are structurally similar to the elasmoid scales of most teleosts and are not comparable with osteoderms. Whereas details of development are lacking, it is hypothesized that dermal scales are derivatives of an odontogenic neural crest cell population and that skeletogenesis is comparable with the formation of elasmoid scales. Little is known about the lamina calcarea. It is proposed that this tissue layer is also odontogenic in origin, but clearly further study is necessary. Although not homologous as organs, all elements of the integumentary skeleton share a basic and essential relationship with the integument, connecting them with the ancestral rhombic scale.
- Published
- 2009
- Full Text
- View/download PDF
45. Evolutionary and developmental origins of the vertebrate dentition.
- Author
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Huysseune A, Sire JY, and Witten PE
- Subjects
- Animals, Biological Evolution, Odontogenesis physiology, Phylogeny, Tooth growth & development, Tooth physiology, Vertebrates genetics, Dentition, Odontogenesis genetics, Tooth anatomy & histology, Vertebrates anatomy & histology
- Abstract
According to the classical theory, teeth derive from odontodes that invaded the oral cavity in conjunction with the origin of jaws (the 'outside in' theory). A recent alternative hypothesis suggests that teeth evolved prior to the origin of jaws as endodermal derivatives (the 'inside out' hypothesis). We compare the two theories in the light of current data and propose a third scenario, a revised 'outside in' hypothesis. We suggest that teeth may have arisen before the origin of jaws, as a result of competent, odontode-forming ectoderm invading the oropharyngeal cavity through the mouth as well as through the gill slits, interacting with neural crest-derived mesenchyme. This hypothesis revives the homology between skin denticles (odontodes) and teeth. Our hypothesis is based on (1) the assumption that endoderm alone, together with neural crest, cannot form teeth; (2) the observation that pharyngeal teeth are present only in species known to possess gill slits, and disappear from the pharyngeal region in early tetrapods concomitant with the closure of gill slits, and (3) the observation that the dental lamina (sensu Reif, 1982) is not a prerequisite for teeth to form. We next discuss the progress that has been made to understand the spatially restricted loss of teeth from certain arches, and the many questions that remain regarding the ontogenetic loss of teeth in specific taxa. The recent advances that have been made in our knowledge on the molecular control of tooth formation in non-mammalians (mostly in some teleost model species) will undoubtedly contribute to answering these questions in the coming years.
- Published
- 2009
- Full Text
- View/download PDF
46. 'The integument story: origins, evolution and current knowledge'.
- Author
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Vickaryous M and Sire JY
- Subjects
- Animals, Humans, Biological Evolution, Integumentary System
- Published
- 2009
- Full Text
- View/download PDF
47. Loss of teeth and enamel in tetrapods: fossil record, genetic data and morphological adaptations.
- Author
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Davit-Béal T, Tucker AS, and Sire JY
- Subjects
- Animals, Dental Enamel physiology, Extremities, Fossils, Humans, Phylogeny, Tooth physiology, Vertebrates classification, Vertebrates genetics, Biological Evolution, Dental Enamel anatomy & histology, Tooth anatomy & histology, Vertebrates anatomy & histology
- Abstract
Since their recruitment in the oral cavity, approximately 450 million years ago, teeth have been subjected to strong selective constraints due to the crucial role that they play in species survival. It is therefore quite surprising that the ability to develop functional teeth has subsequently been lost several times, independently, in various lineages. In this review, we concentrate our attention on tetrapods, the only vertebrate lineage in which several clades lack functional teeth from birth to adulthood. Indeed, in other lineages, teeth can be absent in adults but be functionally present in larvae and juveniles, can be absent in the oral cavity but exist in the pharyngeal region, or can develop on the upper jaw but be absent on the lower jaw. Here, we analyse the current data on toothless (edentate) tetrapod taxa, including information available on enamel-less species. Firstly, we provide an analysis of the dispersed and fragmentary morphological data published on the various living taxa concerned (and their extinct relatives) with the aim of tracing the origin of tooth or enamel loss, i.e. toads in Lissamphibia, turtles and birds in Sauropsida, and baleen whales, pangolins, anteaters, sloths, armadillos and aardvark in Mammalia. Secondly, we present current hypotheses on the genetic basis of tooth loss in the chicken and thirdly, we try to answer the question of how these taxa have survived tooth loss given the crucial importance of this tool. The loss of teeth (or only enamel) in all of these taxa was not lethal because it was always preceded in evolution by the pre-adaptation of a secondary tool (beak, baleens, elongated adhesive tongues or hypselodonty) useful for improving efficiency in food uptake. The positive selection of such secondary tools would have led to relaxed functional constraints on teeth and would have later compensated for the loss of teeth. These hypotheses raise numerous questions that will hopefully be answered in the near future.
- Published
- 2009
- Full Text
- View/download PDF
48. Changes in vertebral structure during growth of reared rainbow trout, Oncorhynchus mykiss (Walbaum): a new approach using modelling of vertebral bone profiles.
- Author
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Deschamps MH, Girondot M, Labbé L, and Sire JY
- Subjects
- Animals, Fisheries, Temperature, Time Factors, Models, Biological, Oncorhynchus mykiss anatomy & histology, Oncorhynchus mykiss growth & development, Spine anatomy & histology, Spine growth & development
- Abstract
Severe bone resorption of the vertebral body in reared rainbow trout was thought to be a dysfunction in mineral balance induced by increased growth rate in unfavourable rearing conditions. To verify this assumption, we sampled market-sized trout (c. 250 g) from 20 fish farms with different rearing conditions. Growth rate was also studied by sampling trout reared in three different water temperatures from fry to market-size. Transverse sections of vertebrae were microradiographed, then digitized. Total bone area (Tt-B.Ar.) and bone profiles were obtained using BONE PROFILER 3.23 software and a mathematical model was developed to statistically compare bone profiles using 12 parameters in four vertebra regions. Tt-B.Ar. and bone profiles were found to vary with rearing conditions and growing temperatures, indicating obvious influences of these factors on bone remodelling. However, vertebral resorption was found to be a general phenomenon. In trout from 190 to 235 mm in length, vertebrae underwent important remodelling resulting in large resorption of the middle area, while the transition and peripheral areas showed an increase in bone deposition. Changes in vertebra architecture seem to be a good compromise between the need to mobilize stored minerals during growth while maintaining vertebral biomechanical properties.
- Published
- 2009
- Full Text
- View/download PDF
49. Hen's teeth with enamel cap: from dream to impossibility.
- Author
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Sire JY, Delgado SC, and Girondot M
- Subjects
- Amino Acid Sequence, Animals, Base Sequence, Biological Evolution, Chickens classification, Chickens physiology, Dental Enamel chemistry, Dental Enamel Proteins chemistry, Dental Enamel Proteins metabolism, Female, Genome, Molecular Sequence Data, Phylogeny, Sequence Alignment, Tooth chemistry, Chickens genetics, Dental Enamel metabolism, Dental Enamel Proteins genetics, Evolution, Molecular, Tooth physiology
- Abstract
Background: The ability to form teeth was lost in an ancestor of all modern birds, approximately 100-80 million years ago. However, experiments in chicken have revealed that the oral epithelium can respond to inductive signals from mouse mesenchyme, leading to reactivation of the odontogenic pathway. Recently, tooth germs similar to crocodile rudimentary teeth were found in a chicken mutant. These "chicken teeth" did not develop further, but the question remains whether functional teeth with enamel cap would have been obtained if the experiments had been carried out over a longer time period or if the chicken mutants had survived. The next odontogenetic step would have been tooth differentiation, involving deposition of dental proteins., Results: Using bioinformatics, we assessed the fate of the four dental proteins thought to be specific to enamel (amelogenin, AMEL; ameloblastin, AMBN; enamelin, ENAM) and to dentin (dentin sialophosphoprotein, DSPP) in the chicken genome. Conservation of gene synteny in amniotes allowed definition of target DNA regions in which we searched for sequence similarity. We found the full-length chicken AMEL and the only N-terminal region of DSPP, and both are invalidated genes. AMBN and ENAM disappeared after chromosomal rearrangements occurred in the candidate region in a bird ancestor., Conclusion: These findings not only imply that functional teeth with enamel covering, as present in ancestral Aves, will never be obtained in birds, but they also indicate that these four protein genes were dental specific, at least in the last toothed ancestor of modern birds, a specificity which has been questioned in recent years.
- Published
- 2008
- Full Text
- View/download PDF
50. Amelogenin, the major protein of tooth enamel: a new phylogenetic marker for ordinal mammal relationships.
- Author
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Delgado S, Vidal N, Veron G, and Sire JY
- Subjects
- Animals, Genetic Markers, Humans, Sequence Analysis, DNA, Amelogenin genetics, Dental Enamel metabolism, Mammals genetics, Phylogeny
- Published
- 2008
- Full Text
- View/download PDF
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