Functional signatures of ex-vivo dental caries onset.

Background: The etiology of dental caries remains poorly understood. With the advent of next-generation sequencing, a number of studies have focused on the microbial ecology of the disease. However, taxonomic associations with caries have not been consistent. Researchers have also pursued function-centric studies of the caries microbial communities aiming to identify consistently conserved functional pathways. A major question is whether changes in microbiome are a cause or a consequence of the disease. Thus, there is a critical need to define conserved functional signatures at the onset of dental caries. Methods: Since it is unethical to induce carious lesions clinically, we developed an innovative longitudinal ex-vivo model integrated with the advanced non-invasive multiphoton second harmonic generation bioimaging to spot the very early signs of dental caries, combined with 16S rRNA short amplicon sequencing and liquid chromatography-mass spectrometry-based targeted metabolomics. Findings: For the first time, we induced longitudinally monitored caries lesions validated with the scanning electron microscope. Consequently, we spotted the caries onset and, associated with it, distinguished five differentiating metabolites - Lactate, Pyruvate, Dihydroxyacetone phosphate, Glyceraldehyde 3-phosphate (upregulated) and Fumarate (downregulated). Those metabolites co-occurred with certain bacterial taxa; Streptococcus, Veillonella, Actinomyces, Porphyromonas, Fusobacterium, and Granulicatella, regardless of the abundance of other taxa. Interpretation: These findings are crucial for understanding the etiology and dynamics of dental caries, and devising targeted interventions to prevent disease progression.

Survey of metaproteomics software tools for functional microbiome analysis.

To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the NCBI non-redundant database revealed that the sensitivity and specificity of functional annotation varied between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated more accurate GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform.

Development and calibration of biochemical models for testing dental restorations.

Currently, resin composites are the most popular materials for dental restoration in clinical practice. Although the properties of such materials have been improved significantly, together with better clinical techniques used for their placement, early restoration failure still occurs too frequently. As clinical studies take years to complete, and new resin composites are being produced at ever increasing pace, laboratory assessment using accelerated but representative tests is necessary. The main types of failure in resin-composite restoration are tooth/restoration fracture and secondary caries, which are caused by a combination of mechanical and biochemical challenges. In this study, a biofilm model (S. mutans) and a chemical model (lactic-acid buffer) for producing artificial caries in bovine dentin are developed and calibrated against in situ data. Using a power law relationship between the demineralization depth and challenge duration, scale factors that convert the in vitro durations to the equivalent clinical durations are determined for different pH values for each model. The scale factors will allow the synchronization of biochemical and mechanical challenges in terms of their rates of action to potentially test resin-composite restoration in an accelerated but clinically representative manner. STATEMENT OF SIGNIFICANCE: Although the properties of resin composites for dental restoration have been improved significantly, early restoration failure still occurs too frequently. As clinical studies take years to complete, accelerated laboratory testing is necessary. Resin-composite restoration fail mainly through fracture and secondary caries, caused by a combination of mechanical and biochemical challenges. In this study, a biofilm and a chemical model for producing artificial caries in bovine dentin are calibrated against in situ data. Using a power law relationship between demineralization depth and challenge duration, scale factors are determined for different pH for each model. The scale factors will allow the synchronization of biochemical and mechanical challenges in testing resin-composite restoration in an accelerated but clinically representative manner.

metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes.

Microbiome research offers promising insights into the impact of microorganisms on biological systems. Metaproteomics, the study of microbial proteins at the community level, integrates genomic, transcriptomic, and proteomic data to determine the taxonomic and functional state of a microbiome. However, standard metaproteomics software is subject to several limitations, commonly supporting only spectral counts, emphasizing exploratory analysis rather than hypothesis testing and rarely offering the ability to analyze the interaction of function and taxonomy - that is, which taxa are responsible for different processes.Here we present metaQuantome, a novel, multifaceted software suite that analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information, emphasizing label-free intensity-based methods. For experiments with multiple experimental conditions, metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. We benchmark metaQuantome analysis against standard methods, using two previously published datasets: (1) an artificially assembled microbial community dataset (taxonomy benchmarking) and (2) a dataset with a range of recombinant human proteins spiked into an Escherichia coli background (functional benchmarking). Furthermore, we demonstrate the use of metaQuantome on a previously published human oral microbiome dataset.In both the taxonomic and functional benchmarking analyses, metaQuantome quantified taxonomic and functional terms more accurately than standard summarization-based methods. We use the oral microbiome dataset to demonstrate metaQuantome's ability to produce publication-quality figures and elucidate biological processes of the oral microbiome. metaQuantome enables advanced investigation of metaproteomic datasets, which should be broadly applicable to microbiome-related research. In the interest of accessible, flexible, and reproducible analysis, metaQuantome is open source and available on the command line and in Galaxy.

Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome.

The human cervical-vaginal area contains proteins derived from microorganisms that may prevent or predispose women to gynecological conditions. The liquid Pap test fixative is an unexplored resource for analysis of microbial communities and the microbe-host interaction. Previously, we showed that the residual cell-free fixative from discarded Pap tests of healthy women could be used for mass spectrometry (MS) based proteomic identification of cervical-vaginal proteins. In this study, we reprocessed these MS raw data files for metaproteomic analysis to characterize the microbial community composition and function of microbial proteins in the cervical-vaginal region. This was accomplished by developing a customized protein sequence database encompassing microbes likely present in the vagina. High-mass accuracy data were searched against the protein FASTA database using a two-step search method within the Galaxy for proteomics platform. Data was analyzed by MEGAN6 (MetaGenomeAnalyzer) for phylogenetic and functional characterization. We identified over 300 unique peptides from a variety of bacterial phyla and Candida. Peptides corresponding to proteins involved in carbohydrate metabolism, oxidation-reduction, and transport were identified. By identifying microbial peptides in Pap test supernatants it may be possible to acquire a functional signature of these microbes, as well as detect specific proteins associated with cervical health and disease.

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.

The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research. The Galaxy for proteomics platform (Galaxy-P) offers an open source, web-based bioinformatics platform for disseminating metaproteomics software and workflows. Within this platform, we have developed easily-accessible and documented metaproteomic software tools and workflows aimed at training researchers in their operation and disseminating the tools for more widespread use. The modular workflows encompass the core requirements of metaproteomic informatics: (a) database generation; (b) peptide spectral matching; (c) taxonomic analysis and (d) functional analysis. Much of the software available via the Galaxy-P platform was selected, packaged and deployed through an online metaproteomics "Contribution Fest" undertaken by a unique consortium of expert software developers and users from the metaproteomics research community, who have co-authored this manuscript. These resources are documented on GitHub and freely available through the Galaxy Toolshed, as well as a publicly accessible metaproteomics gateway Galaxy instance. These documented workflows are well suited for the training of novice metaproteomics researchers, through online resources such as the Galaxy Training Network, as well as hands-on training workshops. Here, we describe the metaproteomics tools available within these Galaxy-based resources, as well as the process by which they were selected and implemented in our community-based work. We hope this description will increase access to and utilization of metaproteomics tools, as well as offer a framework for continued community-based development and dissemination of cutting edge metaproteomics software.

Interfacial degradation of adhesive composite restorations mediated by oral biofilms and mechanical challenge in an extracted tooth model of secondary caries.

OBJECTIVE: To study the combined effect of simulated occlusal loading and plaque-derived biofilm on the interfacial integrity of dental composite restorations, and to explore whether the effects are modulated by the incorporation of sucrose. METHODS: MOD-class-II restorations were prepared in third molars. Half of the specimens (n=27) were subjected to 200,000 cycles of mechanical loading using an artificial oral environment (ART). Then, both groups of specimens (fatigued and non-fatigued) were divided into three subgroups for testing in CDC-reactors under the following conditions: no biofilm (Control), biofilm with no sucrose (BNS) and biofilm pulsed with sucrose (BWS). BNS and BWS reactors were incubated with a multispecies inoculum from a single plaque donor whereas the control reactor was not. The BWS reactor was pulsed with sucrose five times a day. The biofilm challenges were repeated sequentially for 12 weeks. pH was recorded for each run. Specimens were examined for demineralization with micro-CT and load capacity by fast fracture test. RESULTS: Demineralization next to the restorations was only detectable in BWS teeth. Fracture loads were significantly reduced by the concomitant presence of biofilm and sucrose, regardless of whether cyclic mechanical loading was applied. Cyclic loading reduced fracture loads under all reactor conditions, but the reduction was not statistically significant. CONCLUSIONS: Sucrose pulsing was required to induce biofilm-mediated degradation of the adhesive interface. We have presented a comprehensive and clinically relevant model to study the effects of mechanical loading and microbial challenge on the interfacial integrity of dental restorations.

Dentin-composite bond strength measurement using the Brazilian disk test.

OBJECTIVES: This study presents a variant of the Brazilian disk test (BDT) for assessing the bond strength between composite resins and dentin. METHODS: Dentin-composite disks (ϕ 5mm×2mm) were prepared using either Z100 or Z250 (3M ESPE) in combination with one of three adhesives, Adper Easy Bond (EB), Adper Scotchbond Multi-Purpose (MP) and Adper Single Bond (SB), and tested under diametral compression. Acoustic emission (AE) and digital image correlation (DIC) were used to monitor debonding of the composite from the dentin ring. A finite element (FE) model was created to calculate the bond strengths using the failure loads. Fracture modes were examined by scanning electron microscopy (SEM). RESULTS: Most specimens fractured along the dentin-resin composite interface. DIC and AE confirmed interfacial debonding immediately before fracture of the dentin ring. Results showed that the mean bond strength with EB (14.9±1.9MPa) was significantly higher than with MP (13.2±2.4MPa) or SB (12.9±3.0MPa) (p<0.05); no significant difference was found between MP and SB (p>0.05). Z100 (14.5±2.3MPa) showed higher bond strength than Z250 (12.7±2.5MPa) (p<0.05). Majority of specimens (91.3%) showed an adhesive failure mode. EB failed mostly at the dentin-adhesive interface, whereas MP at the composite-adhesive interface; specimens with SB failed at the composite-adhesive interface and cohesively in the adhesive. CONCLUSIONS: The BDT variant showed to be a suitable alternative for measuring the bond strength between dentin and composite, with zero premature failure, reduced variability in the measurements, and consistent failure at the dentin-composite interface. CLINICAL SIGNIFICANCE: The new test could help to predict the clinical performance of adhesive systems more effectively and consistently by reducing the coefficient of variation in the measured bond strength.

Antimicrobial Agents Used in the Treatment of Peri-Implantitis Alter the Physicochemistry and Cytocompatibility of Titanium Surfaces.

BACKGROUND: Chemotherapeutic agents (ChAs) are considered an integral part of current treatment protocols for the decontamination of titanium implants with peri-implantitis, based on their antimicrobial effect. Despite the proven antimicrobial effect of ChAs on titanium-bound biofilms, previous studies have elucidated an unexpected disassociation between bacterial reduction and biologically acceptable treatment outcomes. In this study, the authors hypothesize that ChAs residues alter titanium physicochemistry and thus compromise cellular response to decontaminated surfaces. METHODS: Grit-blasted acid-etched titanium disks were contaminated with multispecies microcosm biofilms grown from in vivo peri-implant plaque samples. To simulate implant decontamination, the contaminated disks were burnished with 0.12% chlorhexidine, 20% citric acid, 24% EDTA/1.5% NaOCl, or sterile saline and assessed surface physicochemical properties. Sterile untreated surfaces were the controls. The biologic effects of decontamination were assessed via cell proliferation and differentiation assays. RESULTS: Bacterial counts after decontamination confirmed that the ChAs were antimicrobial. X-ray photoelectron spectroscopy invariably detected elemental contaminants associated with each ChA molecule or salt that significantly altered wettability compared with controls. Notably, all surfaces with ChA residues showed some cytotoxic effect compared with controls (P <0.05). Increased cell counts were consistently found in the saline-treated group compared with chlorhexidine (P = 0.03). Interestingly, no association was found between antimicrobial effect and cell counts (P >0.05). CONCLUSIONS: ChA-specific residues left on the titanium surfaces altered titanium physical properties and adversely affected the osteoblastic response irrespective of their observed antimicrobial effect. Chlorhexidine may compromise the biocompatibility of titanium surfaces, and its use is not recommended to detoxify implants. Sterile saline, citric acid, and NaOCl-EDTA may be proposed for use in the treatment of peri-implantitis. Contrary to previous studies that recommended the selection of ChAs for the decontamination of titanium implants according to their antimicrobial effects, the present study demonstrated that the restoration of the biocompatibility of contaminated titanium surfaces is also contingent on the preservation of titanium material properties.

Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.

BACKGROUND: The etiology of dental caries is multifactorial, but frequent consumption of free sugars, notably sucrose, appears to be a major factor driving the supragingival microbiota in the direction of dysbiosis. Recent 16S rRNA-based studies indicated that caries-associated communities were less diverse than healthy supragingival plaque but still displayed considerable taxonomic diversity between individuals. Metagenomic studies likewise have found that healthy oral sites from different people were broadly similar with respect to gene function, even though there was an extensive individual variation in their taxonomic profiles. That pattern may also extend to dysbiotic communities. In that case, shifts in community-wide protein relative abundance might provide better biomarkers of dysbiosis that can be achieved through taxonomy alone. RESULTS: In this study, we used a paired oral microcosm biofilm model of dental caries to investigate differences in community composition and protein relative abundance in the presence and absence of sucrose. This approach provided large quantities of protein, which facilitated deep metaproteomic analysis. Community composition was evaluated using 16S rRNA sequencing and metaproteomic approaches. Although taxonomic diversity was reduced by sucrose pulsing, considerable inter-subject variation in community composition remained. By contrast, functional analysis using the SEED ontology found that sucrose induced changes in protein relative abundance patterns for pathways involving glycolysis, lactate production, aciduricity, and ammonia/glutamate metabolism that were conserved across taxonomically diverse dysbiotic oral microcosm biofilm communities. CONCLUSIONS: Our findings support the concept of using function-based changes in protein relative abundance as indicators of dysbiosis. Our microcosm model cannot replicate all aspects of the oral environment, but the deep level of metaproteomic analysis it allows makes it suitable for discovering which proteins are most consistently abundant during dysbiosis. It then may be possible to define biomarkers that could be used to detect at-risk tooth surfaces before the development of overt carious lesions.

Metaproteomic analysis using the Galaxy framework.

Metaproteomics characterizes proteins expressed by microorganism communities (microbiome) present in environmental samples or a host organism (e.g. human), revealing insights into the molecular functions conferred by these communities. Compared to conventional proteomics, metaproteomics presents unique data analysis challenges, including the use of large protein databases derived from hundreds or thousands of organisms, as well as numerous processing steps to ensure high data quality. These challenges limit the use of metaproteomics for many researchers. In response, we have developed an accessible and flexible metaproteomics workflow within the Galaxy bioinformatics framework. Via analysis of human oral tissue exudate samples, we have established a modular Galaxy-based workflow that automates a reduction method for searching large sequence databases, enabling comprehensive identification of host proteins (human) as well as "meta-proteins" from the nonhost organisms. Downstream, automated processing steps enable basic local alignment search tool analysis and evaluation/visualization of peptide sequence match quality, maximizing confidence in results. Outputted results are compatible with tools for taxonomic and functional characterization (e.g. Unipept, MEGAN5). Galaxy also allows for the sharing of complete workflows with others, promoting reproducibility and also providing a template for further modification and enhancement. Our results provide a blueprint for establishing Galaxy as a solution for metaproteomic data analysis. All MS data have been deposited in the ProteomeXchange with identifier PXD001655 (http://proteomecentral.proteomexchange.org/dataset/PXD001655).

Fatigue failure of dentin-composite disks subjected to cyclic diametral compression.

OBJECTIVE: Our aim was to establish the relationship between cyclic loading and fatigue life of the dentin-composite interface using the newly developed disk in diametral compression tests. The results were then used to estimate the fatigue life of restored teeth under occlusal loading. METHODS: Disk specimens (5mm dia.×2mm thick) were prepared using bovine incisors and restored with either a methacrylate-based composite Z100™ with Adper Single Bond Plus (Z100) or silorane-based composite Filtek™ LS with LS System adhesive (LS). The dentin-composite disks were tested under cyclic diametral compression to determine the number of cycles to failure (Nf) at three load levels (n=3 per group). Finite element analysis (FEA) was used to calculate the interfacial stresses (σ) within the specimen, to establish the σ vs. Nf curves, and those within a restored tooth under normal chewing forces (15N maximum). These were then used to estimate the lifetime of the restored tooth for the two restorative systems. RESULTS: The disks restored with LS had a higher fatigue resistance than those restored with Z100. The maximum interfacial stress in the restored tooth determined by FEA was ∼0.5MPa. Based on the estimate of 300,000 cycles of chewing per year, the predicted lifetime under occlusal loading for teeth restored with LS and Z100 was 33 and 10 years, respectively. SIGNIFICANCE: The disk in cyclic diametral compression has been used successfully to provide fatigue data which allows the lifetime of composite-restored teeth under occlusal loading to be predicted using numerical simulation.

The use of micro-CT with image segmentation to quantify leakage in dental restorations.

OBJECTIVE: To develop a method for quantifying leakage in composite resin restorations after curing, using non-destructive X-ray micro-computed tomography (micro-CT) and image segmentation. METHODS: Class-I cavity preparations were made in 20 human third molars, which were divided into 2 groups. Group I was restored with Z100 and Group II with Filtek LS. Micro-CT scans were taken for both groups before and after they were submerged in silver nitrate solution (AgNO3 50%) to reveal any interfacial gap and leakage at the tooth restoration interface. Image segmentation was carried out by first performing image correlation to align the before- and after-treatment images and then by image subtraction to isolate the silver nitrate penetrant for precise volume calculation. Two-tailed Student's t-test was used to analyze the results, with the level of significance set at p<0.05. RESULTS: All samples from Group I showed silver nitrate penetration with a mean volume of 1.3 ± 0.7mm(3). In Group II, only 2 out of the 10 restorations displayed infiltration along the interface, giving a mean volume of 0.3 ± 0.3mm(3). The difference between the two groups was statistically significant (p<0.05). The infiltration showed non-uniform patterns within the interface. SIGNIFICANCE: We have developed a method to quantify the volume of leakage using non-destructive micro-CT, silver nitrate infiltration and image segmentation. Our results confirmed that substantial leakage could occur in composite restorations that have imperfections in the adhesive layer or interfacial debonding through polymerization shrinkage. For the restorative systems investigated in this study, this occurred mostly at the interface between the adhesive system and the tooth structure.

Clinical cross-polarization optical coherence tomography assessment of subsurface enamel below dental resin composite restorations.

A newly designed intraoral swept source cross-polarization optical coherence tomography (CP-OCT) imaging system was used to examine the integrity of the subsurface enamel below resin composite restorations placed in primary teeth. CP-OCT analysis was performed using images obtained from resin composite restoration in 62 ([Formula: see text]) pediatric subjects. Clinical examination was performed by a single examiner prior to CP-OCT imaging and analysis. CP-OCT images are presented using a unique combined intensity image, where a false color scale is overlaid on the grayscale intensity image. There was a clear difference in the distribution of the mean-backscattered intensity (mR) between restorations recently placed and those possessing frank cavitation (Student's t-test, [Formula: see text]). For mR above 15.49 dB, the sensitivity was 80% and specificity 86%. The Youden index J was 0.8 above 12.3 dB where sensitivity was 100% and specificity was 80%. CP-OCT imaging may be used to confirm the subsurface marginal integrity below resin composite restorations but with careful consideration of limitations of the imaging modality. CP-OCT imaging may be a useful adjunct to clinical visual investigation to confirm that a composite margin has a sound and well-adapted interface.

Influence of dental resin material composition on cross-polarization-optical coherence tomography imaging.

The purpose of this study was to investigate cross-polarization-optical coherence tomography (CP-OCT) signal attenuation through different resin material compositions. Four distinct composite systems were used: Filtek supreme ultra (FSU) (3M ESPE), IPS empress direct (EMD) (Ivoclar Vivadent), estelite sigma quick (SQK) (Tokuyama Dental), and Z100 (3M ESPE). Cross-sectional images of different composite-demineralized phantoms (n=108) were collected using a 1310-nm intraoral cross-polarization swept source OCT (CP-OCT) imaging system. %T quantified the CP-OCT signal attenuation. Scanning electron microscopy, transmission electron microscopy, and energy-dispersive x-ray spectrometer chemical analysis was utilized to determine how different matrix/filler compositions affected attenuation of the near infrared (NIR) signal. CP-OCT imaging of dental resin composites showed enormous variation in signal attenuation. For each of our composite systems, there was not a consistent attenuation difference in the NIR signal for A to D shades. The four composites had similar measured backscattering values but attenuated the overall signal to different degrees. When comparing the A2 shades between the four different composite systems, the order of highest to lowest of %T was EMD>Z100, FSU>SQK (ANOVA, Tukey, p<0.0001). As a result, we demonstrate the importance of understanding how the constituents of composite materials affect CP-OCT signal attenuation.

Imaging in vivo secondary caries and ex vivo dental biofilms using cross-polarization optical coherence tomography.

OBJECTIVE: Conventional diagnostic methods frequently detect only late stage enamel demineralization under composite resin restorations. The objective of this study is to examine the subsurface tooth-composite interface and to assess for the presence of secondary caries in pediatric patients using a novel Optical Coherence Tomography System with an intraoral probe. METHODS: A newly designed intraoral cross polarization swept source optical coherence tomography (CP-OCT) imaging system was used to examine the integrity of the enamel-composite interfaces in vivo. Twenty-two pediatric subjects were recruited with either recently placed or long standing composite restorations in their primary teeth. To better understand how bacterial biofilms cause demineralization at the interface, we also used the intraoral CP-OCT system to assess ex vivo bacterial biofilm growth on dental composites. RESULTS: As a positive control, cavitated secondary carious interfaces showed a 18.2dB increase (p<0.001), or over 1-2 orders of magnitude higher, scattering than interfaces associated with recently placed composite restorations. Several long standing composite restorations, which appeared clinically sound, had a marked increase in scattering than recently placed restorations. This suggests the ability of CP-OCT to assess interfacial degradation such as early secondary caries prior to cavitation. CP-OCT was also able to image ex vivo biofilms on dental composites and assess their thickness. SIGNIFICANCE: This paper shows that CP-OCT imaging using a beam splitter based design can examine the subsurface interface of dental composites in human subjects. Furthermore, the probe dimensions and acquisition speed of the CP-OCT system allowed for analysis of caries development in children.

Deep metaproteomic analysis of human salivary supernatant.

The human salivary proteome is extremely complex, including proteins from salivary glands, serum, and oral microbes. Much has been learned about the host component, but little is known about the microbial component. Here we report a metaproteomic analysis of salivary supernatant pooled from six healthy subjects. For deep interrogation of the salivary proteome, we combined protein dynamic range compression (DRC), multidimensional peptide fractionation, and high-mass accuracy MS/MS with a novel two-step peptide identification method using a database of human proteins plus those translated from oral microbe genomes. Peptides were identified from 124 microbial species as well as uncultured phylotypes such as TM7. Streptococcus, Rothia, Actinomyces, Prevotella, Neisseria, Veilonella, Lactobacillus, Selenomonas, Pseudomonas, Staphylococcus, and Campylobacter were abundant among the 65 genera from 12 phyla represented. Taxonomic diversity in our study was broadly consistent with metagenomic studies of saliva. Proteins mapped to 20 KEGG pathways, with carbohydrate metabolism, amino acid metabolism, energy metabolism, translation, membrane transport, and signal transduction most represented. The communities sampled appear to be actively engaged in glycolysis and protein synthesis. This first deep metaproteomic catalog from human salivary supernatant provides a baseline for future studies of shifts in microbial diversity and protein activities potentially associated with oral disease.

A novel dentin bond strength measurement technique using a composite disk in diametral compression.

New methods are needed that can predict the clinical failure of dental restorations that primarily rely on dentin bonding. Existing methods have shortcomings, e.g. severe deviation in the actual stress distribution from theory and a large standard deviation in the measured bond strength. We introduce here a novel test specimen by examining an endodontic model for dentin bonding. Specifically, we evaluated the feasibility of using the modified Brazilian disk test to measure the post-dentin interfacial bond strength. Four groups of resin composite disks which contained a slice of dentin with or without an intracanal post in the center were tested under diametral compression until fracture. Advanced nondestructive examination and imaging techniques in the form of acoustic emission (AE) and digital image correlation (DIC) were used innovatively to capture the fracture process in real time. DIC showed strain concentration first appearing at one of the lateral sides of the post-dentin interface. The appearance of the interfacial strain concentration also coincided with the first AE signal detected. Utilizing both the experimental data and finite-element analysis, the bond/tensile strengths were calculated to be: 11.2 MPa (fiber posts), 12.9 MPa (metal posts), 8.9 MPa (direct resin fillings) and 82.6 MPa for dentin. We have thus established the feasibility of using the composite disk in diametral compression to measure the bond strength between intracanal posts and dentin. The new method has the advantages of simpler specimen preparation, no premature failure, more consistent failure mode and smaller variations in the calculated bond strength.

Persistence of extracrevicular bacterial reservoirs after treatment of aggressive periodontitis.

BACKGROUND: The purpose of this study was to test the hypothesis that periodontal pathogens associated with aggressive periodontitis persist in extracrevicular locations following scaling and root planing, systemic antibiotics, and antimicrobial rinses. METHODS: Eighteen patients with aggressive periodontitis received a clinical examination during which samples of subgingival plaque and buccal epithelial cells were obtained. Treatment consisted of full-mouth root planing, systemic antibiotics, and chlorhexidine rinses. Clinical measurements and sampling were repeated at 3 and 6 months. Quantitative polymerase chain reaction determined the number of Aggregatibacter actinomycetemcomitans (previously Actinobacillus actinomycetemcomitans), Prevotella intermedia, Porphyromonas gingivalis, Tannerella forsythia (previously T. forsythensis), and Treponema denticola in the plaque. Fluorescence in situ hybridization and confocal microscopy determined the extent of intracellular invasion in epithelial cells. RESULTS: Clinical measurements improved significantly following treatment. All bacterial species except P. gingivalis were significantly reduced in plaque between baseline and 3 months. However, all species showed a trend to repopulate between 3 and 6 months. This increase was statistically significant for log T. denticola counts. All species were detected intracellularly. The percentage of cells infected intracellularly was not affected by therapy. CONCLUSIONS: The 6-month increasing trend in the levels of plaque bacteria suggests that subgingival recolonization was occurring. Because the presence of these species within epithelial cells was not altered after treatment, it is plausible that recolonization may occur from the oral mucosa. Systemic antibiotics and topical chlorhexidine did not reduce the percentage of invaded epithelial cells. These data support the hypothesis that extracrevicular reservoirs of bacteria exist, which might contribute to recurrent or refractory disease in some patients.