Optimizing qPCR for the Quantification of Periodontal Pathogens in a Complex Plaque Biofilm

Quantitative PCR (qPCR) has recently been used to quantify microorganisms in complex communities, including dental plaque biofilms. However, there is variability in the qPCR protocols being used. This study was designed to evaluate the validity of two of these variables with the intent of developing a more standardized qPCR protocol. The two variables evaluated were (1) the use of DNA content versus actual cell counts to estimate bacterial numbers in mixed plaque samples and (2) the effectiveness of three different universal primers versus species specific primers in amplifying specific target pathogens in these samples. Results lead to the development of a standardized protocol that was shown to be highly reproducible as demonstrated by low coefficients of variation. The results also confirmed that this standardized qPCR protocol can be used as a sensitive method for quantifying specific bacterial species in human plaque samples

The Alaska Arctic Vegetation Archive (AVA-AK)

The Alaska Arctic Vegetation Archive (AVA-AK, GIVD-ID: NA-US-014) is a free, publically available database archive of vegetation-plot data from the Arctic tundra region of northern Alaska. The archive currently contains 24 datasets with 3,026 non-overlapping plots. Of these, 74% have geolocation data with 25-m or better precision. Species cover data and header data are stored in a Turboveg database. A standardized Pan Arctic Species List provides a consistent nomenclature for vascular plants, bryophytes, and lichens in the archive. A web-based online Alaska Arctic Geoecological Atlas (AGA-AK) allows viewing and downloading the species data in a variety of formats, and provides access to a wide variety of ancillary data. We conducted a preliminary cluster analysis of the first 16 datasets (1,613 plots) to examine how the spectrum of derived clusters is related to the suite of datasets, habitat types, and environmental gradients. We present the contents of the archive, assess its strengths and weaknesses, and provide three supplementary files that include the data dictionary, a list of habitat types, an overview of the datasets, and details of the cluster analysis

Immunodominant antigens in periodontal disease: a real or illusive concept?

The humoral arm of the immune system provides protection from many medically significant pathogens. The antigenic epitopes of the pathogens which induce these responses, and the subsequent characteristics of the host response, have been extensively documented in the medical literature, and in many cases have resulted in the development and implementation of effective vaccines or diagnostic tests. There is a substantial body of literature on the humoral immune response in periodontal disease, which is targeted at micro-organisms present within periodontal pockets. However, the significance and specificity of the immune response in periodontal disease have proved difficult to elucidate, due to the large number of potential pathogens in the plaque biofilm and the apparent commensal nature of many of these opportunistic pathogens. This review addresses our current knowledge of the approaches and strategies which have been used to elucidate and examine the concept of immunodominant antigens in medical infections and, more recently, periodontal disease. An identification/understanding of the immunodominant antigens would be informative with respect to: (i) the relative importance of the implicated pathogens, (ii) new approaches to immunological diagnosis, (iii) specific bacterial virulence determinants, (iv) natural protective responses, and (v) the selection of potential vaccine candidate antigens. We conclude that immunodominance of antigens in periodontal disease may be relevant to our understanding of periodontal disease pathogenesis, but due to the complexity and diversity of the 'pathogenic microbial ecology', it is currently an enigmatic topic requiring a multidisciplinary approach linking clinical, microbiological, and immunological investigations. We also conclude, after assessing the literature available on the topic of immunodominance, that it is a term that, if used, must be clearly defined and understood, since it is often used loosely, leading to a general misinterpretation by readers of oral and medical literature

Apoptotic Genes are Differentially Expressed in Aged Gingival Tissue

Cellular and molecular changes of the periodontium associated with a higher prevalence of oral diseases (e.g., chronic periodontitis) in aged populations have received little attention. Since impaired apoptosis during aging appears to be related to chronic inflammatory disorders, we hypothesized that the expression of genes associated with apoptotic processes are altered in aged healthy and periodontitis-affected gingival tissue. Ontology analysis of 88 genes related to apoptotic pathways was performed in gingival biopsies of healthy and periodontitis sites from young, adult, and aged non-human primates (Macaca mulatta), using the GeneChip® Rhesus Macaque Genome Array. Lower expression of anti-apoptotic and higher expression of pro-apoptotic genes were associated with healthy gingival tissue from young compared with aged animals. Few differences in gene expression were observed in healthy gingival tissue between adult and aged animals. Comparison between healthy and periodontitis gingival tissues showed that the up- or down-regulated apoptotic genes in diseased gingival tissue are different in adults compared with aged animals. These results suggest that apoptotic events normally occurring in gingival tissues could be reduced in aging,and unique aspects of apoptotic pathways are potentially involved in the pathophysiology of perio-dontal disease in adult vs. aged gingival tissues