Cross-Sample Validation Provides Enhanced Proteome Coverage in Rat Vocal Fold Mucosa

The vocal fold mucosa is a biomechanically unique tissue comprised of a densely cellular epithelium, superficial to an extracellular matrix (ECM)-rich lamina propria. Such ECM-rich tissues are challenging to analyze using proteomic assays, primarily due to extensive crosslinking and glycosylation of the majority of high Mr ECM proteins. In this study, we implemented an LC-MS/MS-based strategy to characterize the rat vocal fold mucosa proteome. Our sample preparation protocol successfully solubilized both proteins and certain high Mr glycoconjugates and resulted in the identification of hundreds of mucosal proteins. A straightforward approach to the treatment of protein identifications attributed to single peptide hits allowed the retention of potentially important low abundance identifications (validated by a cross-sample match and de novo interpretation of relevant spectra) while still eliminating potentially spurious identifications (global single peptide hits with no cross-sample match). The resulting vocal fold mucosa proteome was characterized by a wide range of cellular and extracellular proteins spanning 12 functional categories

Bioinformatics and molecular modeling in glycobiology

The field of glycobiology is concerned with the study of the structure, properties, and biological functions of the family of biomolecules called carbohydrates. Bioinformatics for glycobiology is a particularly challenging field, because carbohydrates exhibit a high structural diversity and their chains are often branched. Significant improvements in experimental analytical methods over recent years have led to a tremendous increase in the amount of carbohydrate structure data generated. Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology. In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and data mining, and tools to support experimental glycan analysis are presented. Finally, the field of structural glycoinformatics and molecular modeling of carbohydrates, glycoproteins, and protein–carbohydrate interaction are reviewed

Glycol methacrylate: An alternative method for embedding subcutaneous implants

The aim of this investigation was to study the use of glycol methacrylate (GMA) as an embedding material for rat subcutaneous tissue, which received implants of tubes with endodontic sealer. After fixation, the specimens were dehydrated in a growing alcohol series up to 95%, immersed in infiltration GMA solution and then in embedding solution. The blocks were cut into 3.0 mum sections and stained with hematoxylin-eosin. The quality of cell definition and staining allowed a quantitative analysis of the cells infiltrated in the end of the tubes. It was also possible to identify each type of inflammatory cell. Moreover, it was possible to distinguish clearly chronic from acute inflammatory cells. The GMA technique is easy to execute and reproducible, and provides a better definition of tissue cells, thus permitting definition of the degree of the inflammatory process. Therefore, it is an excellent alternative for the evaluation of the biocompatibility of endodontic sealers.27426626

Evaluation of the biocompatibility of root canal sealers using subcutaneous implants

The purpose of this study was to evaluate in vivo the biocompatibility of Endomethasone, Pulp Canal Sealer EWT and AH-Plus root canal sealers after implantation in rat connective tissue. Twenty-four Wistar-Furth rats were used. Polyethylene tubes were filled with the sealers and implanted into specific dorsal subdermal tissue sites of the rats. Implants were removed after 3, 7 and 30 days, fixed and processed for glycol methacrylate-embedding technique to be examined microscopically. On the 3rd day, there was a mild inflammatory reaction to Pulp Canal Sealer EWT implants, but a severe response to the other sealers with presence of acute inflammatory cells. On the 7th day, tissue organization was more evident with attenuation of the inflammatory reaction, especially for the AH-Plus implants. On the 30th day, connective tissue with few inflammatory cells was observed in contact with all sealer implants. In this time interval, the tissue in contact with Pulp Canal Sealer EWT implants was more organized, while the tissue close to Endomethasone and AH-Plus implants showed a mild persistent inflammatory reaction and had similar results to each other. In conclusion, the sealers had a similar pattern of irritation, which was more severe in the beginning and milder with time, in such a way that all sealers showed a persistent mild reaction. Pulp Canal Sealer EWT yielded better tissue organization than Endomethasone and AH-Plus, which, in turn, showed similar results to each other.15318619