The SysteMHC Atlas project.

Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility complex (MHC) molecules. The broad clinical relevance of MHC-associated peptides, e.g. in precision medicine, provides a strong rationale for the large-scale generation of immunopeptidomic datasets and recent developments in MS-based peptide analysis technologies now support the generation of the required data. Importantly, the availability of diverse immunopeptidomic datasets has resulted in an increasing need to standardize, store and exchange this type of data to enable better collaborations among researchers, to advance the field more efficiently and to establish quality measures required for the meaningful comparison of datasets. Here we present the SysteMHC Atlas (https://systemhcatlas.org), a public database that aims at collecting, organizing, sharing, visualizing and exploring immunopeptidomic data generated by MS. The Atlas includes raw mass spectrometer output files collected from several laboratories around the globe, a catalog of context-specific datasets of MHC class I and class II peptides, standardized MHC allele-specific peptide spectral libraries consisting of consensus spectra calculated from repeat measurements of the same peptide sequence, and links to other proteomics and immunology databases. The SysteMHC Atlas project was created and will be further expanded using a uniform and open computational pipeline that controls the quality of peptide identifications and peptide annotations. Thus, the SysteMHC Atlas disseminates quality controlled immunopeptidomic information to the public domain and serves as a community resource toward the generation of a high-quality comprehensive map of the human immunopeptidome and the support of consistent measurement of immunopeptidomic sample cohorts.

Effect of low-intensity pulsed ultrasound on orthodontically induced root resorption in beagle dogs.

We investigated the effect of low-intensity pulsed ultrasound (LIPUS) on orthodontically induced inflammatory root resorption in vivo. Ten beagle dogs were treated with an orthodontic appliance to move the mandibular fourth premolars bodily. The orthodontic movement was carried out for 4 wk with a continuous force of 1 N/side; using a split-mouth model, LIPUS was applied daily for 20 min. Fourth premolar and surrounding periodontal tissue were evaluated with micro-computed tomography and hematoxylin and eosin and tartrate-resistant acid phosphatase staining. We calculated the number, volume and distribution of root resorption lacunae and their percentage relative to total root volume, orthodontic tooth movement and periodontal ligament space. There was no significant difference in orthodontic tooth movement between the two sides. LIPUS significantly reduced the number of orthodontically induced inflammatory root resorption initiation areas by 71%, reduced their total volume by 68% and reduced their volume relative to the affected root total volume by 70%. LIPUS induced the formation of a precementum layer, thicker cementum and reparative cellular cementum.

Short-term effect of low-intensity pulsed ultrasound on an ex-vivo 3-d tooth culture.

We investigated the short-term effect of LIPUS on human dentin-pulp complex in vitro. We collected sixty-three premolars from patients who needed the extraction. The premolars were sectioned transversely into 600-µm-thick slices, and then divided into five groups according to LIPUS application time (control, 5, 10, 15 and 20 min). LIPUS transducer produced an incident intensity of 30 mW/cm(2). After 24 h, tissue was harvested for histomorphometrical analysis and RT-PCR (Genes of interest: Collagen I, DMP1, DSPP, TGF ß1, RANKL and OPG). Histomorphometric analysis showed no significant difference among the five groups in the odontoblast count and predentin thickness. RT-PCR demonstrated no expression of TGF ß1, low amounts of DSPP, a twofold increase in collagen I expression in the 5- and 10-minute LIPUS groups and a threefold increase in DMP1 expression in the 10-minute LIPUS group. LIPUS application was stimulatory to the dentin-pulp complex in vitro and increased the expression of collagen I and DMP1.

Long term effect of low intensity pulsed ultrasound on a human tooth slice organ culture.

OBJECTIVE: Investigate the effect of therapeutic Low Intensity Pulsed Ultrasound (LIPUS) on human dentine-pulp complex in an in vitro model. DESIGN: 92 premolars were extracted from 23 adolescent orthodontic patients. The premolars were sectioned transversely into 600 µm thick slices. The slices were divided into two main groups according to how often the LIPUS was applied (single or daily application), and then subdivided into five subgroups each (5, 10, 15 and 20 min and one control group). The tooth slices were cultured at (37 °C/5% CO(2)) in a humidified incubator where medium was changed every 48 h. LIPUS was applied using a 3.9 cm(2) transducer that produces an incident intensity of 30 mW/cm(2). After five days, tissue was harvested for histomorphometrical analysis and real time PCR to investigate expression of genes of interest (Collagen I, DMP1, DSPP, TGF-ß1, RANKL and OPG). RESULTS: Histomorphometric analyses revealed that odontoblast cell count was higher in the single application groups (5, 10 and 15 min, respectively) than in the control and other treatment groups. Predentin thickness was higher in the single application group (10, 5 and 15 min) respectively than in the daily application group and the control groups, however they were not significantly different from each other. Real time PCR demonstrated no statistically significant difference between the groups in the expression of Collagen I, DMP1, TGF-ß1, DSPP, RANKL and OPG. CONCLUSION: Reproducible responses from cultured dentine-pulp complex were observed in groups with single application of LIPUS for 5, 10 and 15 min.