ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.

ANISEED 2015: a digital framework for the comparative developmental biology of ascidians

Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalis embryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalis genome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.

Oct-3/4 dose dependently regulates specification of embryonic stem cells toward a cardiac lineage and early heart development

The transcriptional mechanisms underlying lineage specification and differentiation of embryonic stem (ES) cells remain elusive. Oct-3/4 (POU5f1) is one of the earliest transcription factors expressed in the embryo. Both the pluripotency and the fate of ES cells depend upon a tight control of Oct-3/4 expression. We report that transgene- or TGFbeta-induced increase in Oct-3/4 mRNA and protein levels in undifferentiated ES cells and at early stages of differentiation triggers expression of mesodermal and cardiac specific genes through Smad2/4. cDNA antisense- and siRNA-mediated inhibition of upregulation of Oct-3/4 in ES cells prevent their specification toward the mesoderm and their differentiation into cardiomyocytes. Similarly, Oct-3/4 siRNA injected in the inner cell mass of blastocysts impairs cardiogenesis in early embryos. Thus, quantitative Oct-3/4 expression is regulated by a morphogen, pointing to a pivotal and physiological function of the POU factor in mesodermal and cardiac commitments of ES cells and of the epiblast.

Degradation of hydroxylapatite, fluorapatite, and fluorhydroxyapatite coatings of dental implants in dogs

Calcium phosphate coatings on dental implants enhance integration of the material. Resorption of the ceramic coatings has raised some concern about the behavior of the bone-implant interfaces after the coating disappearance. Substitution of the OH- ions by fluoride in the hydroxylapatite (HA) lattice makes the calcium phosphate more stable. We investigated the degradation rate of dental implants with 50- and 100-microm coatings of HA, fluorapatite (FA), or fluorhydroxylapatite (FHA). The implants were inserted in dog jaws and retrieved for histological analysis after 3, 6, and 12 months. The thickness of the calcium phosphate coatings was evaluated using an image analysis device. A relative resorption index and its standard deviation were studied. HA and FA coatings (even at 100-microm thickness) were almost totally degraded within the implantation period. In contrast, the FHA coatings did not show significant degradation during the same period. The standard deviation showed that the resorption process for FHA with thicknesses of 50 or 100 microm was the same. Such a difference was not observed between the 50- and 100-microm thick coatings of FA and HA. In conclusion, the FHA coatings showed good integration in the bone tissue and lasted much longer than classic calcium phosphate coatings.

[Polynuclear neutrophils and periodontal diseases]

Periodontal diseases are bacteria associated diseases. The host response to these bacteria is critical. Non specific defense mechanisms are mainly mediated by the polymorphonuclear neutrophil which out numbers the others crevicular leucocytes. This paper reviews the beneficial and possible detrimental aspect of the neutrophil functions.

Physicochemical characterization of deposits associated with HA ceramics implanted in nonosseous sites

Pellets of well-characterized microporous hydroxyapatite (HA) ceramic were implanted in hamsters in two nonosseous sites: (1) in the fatty tissue of the gingival crease, far from bony tissue and (2) in intraperitoneal sites. The implants in site 1 were placed directly in contact with tissues, cells, and extracellular fluids while the implants in site 2 were placed in special chambers made of plexiglass cylinders covered in both ends with millipore filters, preventing contact with tissues and cells, but not with extracellular fluids. The hamsters were sacrificed and the implants recovered after 8, 16, 30, 150, and 365 days. The pellets were characterized using x-ray diffraction, infrared absorption, thermogravimetry, scanning and transmission electron microscopy, and calcium and phosphate analyses before and after implantation. Physicochemical analyses of HA ceramic implants before and after implantation demonstrated the formation of new material which was significantly different from the HA ceramic in terms of the following: (a) morphology (size of shape) of crystals; (b) intimate association of the inorganic phase of the new material with an organic phase similar to inorganic/organic association in bone; (c) the inorganic phase of the new material is a CO3-apatite, similar to that of bone, while the HA in ceramic is CO3-free; (d) electron diffraction of apatite of new material is similar to that of bone apatite. This study also demonstrated that the new material associated with the HA ceramics implanted in two different nonosseous sites were identical in spite of the differences in their microenvironment (cellular and acellular).

[Ultrastructural study of bone formation after bioapatite implantation in man]

Synthetic hydroxyapatite crystals (Bioapatite) were implanted in a vestibular longitudinal groove made in the alveolar bone, the periodontal membrane and the superficial root dentine of 2 human canines in the absence of periodontal disease. The healing process was followed in scanning as well as in transmission electron microscopy. At 6 months, the aggregate of synthetic hydroxyapatite crystals was surrounded by a fibrous connective tissue, devoid of inflammatory cells. Small apatite crystals, similar to the neighbouring bone crystals, were deposited between the Bioapatite crystals in the central area of the aggregates. These small crystals filled the intercrystalline spaces from the center to the periphery. The mineralization extended then directly in the collagen matrix (osteoid tissue) surrounding the synthetic apatite aggregates. Bone tissue was thus formed around the apatite implants. At 1 year, the thickness of the bone tissue formed around the synthetic hydroxyapatite aggregates was increased. It consisted of bone with a well-oriented collagen matrix, with osteocyte lacunae, osteocytes and interosteocytic canaliculi, with normal ultrastructure.

[Histological study of the biocompatibility of hydroxyapatite crystals in periodontal surgery]

The purpose of this investigation was to analyse, after 6 years of clinical trials, the findings obtained from biopsies of infrabony defects in man treated by grafts of hydroxyapatite. Filled extraction sockets in miniature swine treated in a similar manner with apatite were also studied. Light microscope analysis showed bone neoformation around and in the neighbourhood of grafted apatite fragments with the presence of osteocytes, osteoblasts and a normal peripheral connective tissue without inflammatory reaction. These results demonstrate the biocompatibility of the implanted apatites accompanied by a normal fibrogenesis and a seeming osteogenesis.

Influence of 3-methoxy 5,7,3',4'-tetrahydroxyflavan (ME) on experimental periodontitis in the golden hamster

Experimental periodontal disease was induced in golden hamsters by feeding the animals with a Keyes 2 000 diet. The aim of the present study was to investigate the effect of 3-methoxy 5,7,3',4'-tetrahydroxyflavan (ME), a flavanoid derivative, on periodontally induced changes by this diet which was fed ad libitum to half of the animals for 2 months prior to the start of drug therapy. The animals were then divided into 4 groups: A) control animals on normal diet; B) ME-treated (200 mg/kg 3 times a week i.p.) animals on normal diet; C) animals on Keyes 2 000 diet; D) ME-treated (200 mg/kg 3 times a week i.p.) animals on Keyes 2 000 diet. ME inhibited the diminution of bone volume as measured morphometrically. The growth of dental plaque as evaluated by a sensitive index (PII) appeared to be retarded by ME. The average PII in the ME-treated animals reached after 2 months of diet remained unchanged during the drug therapy period (4 months); whereas it was significantly increased in the group C hamsters. The biochemical data further suggest that the resorption process of the alveolar bone was decreased by ME.