The recent advances in high-throughput omics technologies have enabled researchers to explore the intricacies of the human microbiome. On the clinical front, the gut microbial community has been the focus of many biomarker-discovery studies. While the recent deluge of high-throughput data in microbiome research has been vastly informative and groundbreaking, we have yet to capture the full potential of omics-based approaches. Realizing the promise of multi-omics data will require integration of disparate omics data, as well as a biologically relevant, mechanistic framework – or metabolic model – on which to overlay these data. Also, a new paradigm for metabolic model evaluation is necessary. Herein, we outline the need for multi-omics data integration, as well as the accompanying challenges. Furthermore, we present a framework for characterizing the ecology of the gut microbiome based on metabolic network modeling.

Periodontal ligament contains periodontal ligament stem cells that maintain tissue homeostasis. Targeting hPDLSCs (human periodontal ligament cells) is a promising strategy for repair and regeneration of bone tissue destroyed by periodontal diseases. However, the mechanisms by which PDLSCs differentiate into osteoblasts to form a mineralized matrix is unclear. In this study, we demonstrate for the first time the molecular events that contribute to osteogenic differentiation of PDLSCs. Dentin matrix protein 1 (DMP1) and its receptor, Glucose regulated protein-78 (GRP78), are localized in the progenitor cells of the PDL. Our overall goal is to demonstrate the formation of DMP1-GRP78 complex at the plasma membrane and subsequent protein trafficking and nuclear localization to promote osteogenic differentiation. To study the internalization and routing of the complex, we mimic an in vivo differentiation scenario by stimulating cells with DMP1 and culturing them in the presence of osteogenic differentiation conditions. We first demonstrate the translocation of the ER chaperone protein GRP78 to the plasma membrane during the differentiation process. Total internal reflection microscopy imaging demonstrates the formation and internalization of the receptor- ligand (GRP78-DMP1) complex. Confocal microscopy results show the internalization of the GRP78-DMP1 complex specifically through the caveolin pathway and trafficked through the cell with various endocytic markers such as Rab5 and 7 GTPases to early and late endosomes respectively. DMP1 is ultimately transported to the nucleus where it functions to promote osteogenic differentiation as demonstrated by quantitative Real-Time PCR. This observation is the first report that suggests DMP1 and GRP78 can interact at the plasma membrane, then packaged in vesicles and ultimately DMP1 is routed to the nucleus where it aids in osteogenic differentiation of PDLSCs. Characterizing the osteogenic potential of PDLSCs would favor the development of therapeutic strategies for reconstruction of mineralized tissues destroyed by periodontal diseases.

Background: Human kidney stones form via repeated events of mineral precipitation, partial dissolution and reprecipitation, which are directly analogous to similar processes in other natural and man-made environments where resident microbiomes strongly influence biomineralization. High-resolution microscopy and high-fidelity metagenomic (microscopy-to-omics) analyses, applicable to all forms of biomineralization, have been applied to assemble definitive evidence of in vivo microbiome entombment during urolithiasis. Methods: Stone fragments were collected from a randomly chosen cohort of 20 patients using standard percutaneous nephrolithotomy (PCNL). Fourier transform infrared (FTIR) spectroscopy indicated that 18 of these patients were calcium oxalate (CaOx) stone formers, while one patient each formed brushite and struvite stones. This apportionment is consistent with global stone mineralogy distributions. Stone fragments from 7 of these 20 patients (5 CaOx, 1 brushite and 1 struvite) were thin sectioned and analyzed using brightfield (BF), polarization (POL), confocal, superresolution autofluorescence (SRAF) and Raman techniques. DNA from remaining fragments, grouped according to each of the 20 patients, were analyzed with amplicon sequencing of 16S rRNA gene sequences (V1-V3, V3-V5) and internal transcribed spacer (ITS1, ITS2) regions. Results: Bulk entombed DNA was sequenced from stone fragments in 11 of the 18 CaOx patients, as well as the brushite and struvite patients. These analyses confirmed the presence of an entombed low-diversity community of bacteria and fungi, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Aspergillus niger. Bacterial cells ~1  µm in diameter were also optically observed to be entombed and well-preserved in amorphous hydroxyapatite spherules and fans of needle-like crystals of brushite and struvite. Conclusions: These results indicate a microbiome is entombed during in vivo CaOx stone formation. Similar processes are implied for brushite and struvite stones. This evidence lays the groundwork for future in vitro and in vivo experimentation to determine how the microbiome may actively and/or passively influence kidney stone biomineralization.

The advances in microscopy techniques enable the detection of intracellular molecular processes to be visualized and analyzed for periodontal ligament stem cells (PDLSCs). Confocal laser scanning microscopy (CLSM) and total internal reflection fluorescence microscopy (TIRFM) are two well-studied microscopy techniques that allow an increase in the resolution and contrast of the micrographs and the capability to pinpoint events at the plasma membrane, respectively. Confocal microscopy achieves its increased resolution and contrast through a spatial pinhole that hits the plane of the image. TIRF microscopy uses the principle of incident angles and the refractive index of the substances to study the events occurring at 100–200 nm range of the cover glass with minimal background interference. Here we describe two methods for intramolecular signaling visualization upon stimulation with a ligand in normal growth conditions and mineralization-induced conditions in periodontal ligament stem cells (PDLSCs). These methods are important for visualizing the signaling events within PDLSCs at a molecular level and thereby understand the mechanisms by which these cells could be manipulated for tissue engineering and regeneration.

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