Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Position and course of the mandibular canal in skulls

Objective. The aim of this study was to examine and describe the topography of the mandibular canal (MC) in both vertical and occlusal dimensions. Study Design. Fifty-two adult skulls deposited in the University of Pittsburgh School of Dental Medicine skull collection were evaluated in this study. Cone-beam computerized tomographic scans of each skull were obtained. Results. The vertical course of MC was classified into 3 types: straight projection (12.2%), catenary-like configuration (51.1%), and progressive descent from posterior to anterior (36.7%). The evaluation of the buccolingual dimension showed that the mandibular canal was located either in contact with or close to the lingual cortical plate (μ2 mm) in the molar region of the majority of the cases. As it proceeds anteriorly it moves toward the buccal aspect of the mandible, where it finally emerges through the mental foramen. Three emerging patterns of mandibular canal were observed: sharp turn (53.2%), soft curved exit (28.8%), and straight path (17.4%). The examination of the vertical dimension showed that the canal was located almost 1 cm above the inferior border of the mandible and then ascended to reach the mental foramen, which is located 16 mm (range 13.4-20.3 mm) above the inferior border of the mandible. We found a strong correlation between height of the mandible and location of the mental foramen (r 0.64; P> .0001). Conclusions. The course of mandibular canal described in vertical and axial dimensions and variation in its path have been classified. In addition to variation in location of MC, it has different anatomic configurations which clinicians should be familiar with in any surgical procedures involving the posterior mandible. © 2012 Elsevier Inc. All rights reserved

Genetics and caries-prospects

Caries remains the most prevalent non-contagious infectious disease in humans. It is clear that the current approaches to decrease the prevalence of caries in human populations, including water fluoridation and school-based programs, are not enough to protect everyone. The scientific community has suggested the need for innovative work in a number of areas in cariology, encompassing disease etiology, epidemiology, definition, prevention, and treatment. We have pioneered the work on genetic studies to identify genes and genetic markers of diagnostic, prognostic, and therapeutic value. This paper summarizes a presentation that elaborated on these initial findings

Multi-Dimensional Prioritization of Dental Caries Candidate Genes and Its Enriched Dense Network Modules

A number of genetic studies have suggested numerous susceptibility genes for dental caries over the past decade with few definite conclusions. The rapid accumulation of relevant information, along with the complex architecture of the disease, provides a challenging but also unique opportunity to review and integrate the heterogeneous data for follow-up validation and exploration. In this study, we collected and curated candidate genes from four major categories: association studies, linkage scans, gene expression analyses, and literature mining. Candidate genes were prioritized according to the magnitude of evidence related to dental caries. We then searched for dense modules enriched with the prioritized candidate genes through their protein-protein interactions (PPIs). We identified 23 modules comprising of 53 genes. Functional analyses of these 53 genes revealed three major clusters: cytokine network relevant genes, matrix metalloproteinases (MMPs) family, and transforming growth factor-beta (TGF-β) family, all of which have been previously implicated to play important roles in tooth development and carious lesions. Through our extensive data collection and an integrative application of gene prioritization and PPI network analyses, we built a dental caries-specific sub-network for the first time. Our study provided insights into the molecular mechanisms underlying dental caries. The framework we proposed in this work can be applied to other complex diseases