We introduce novel profile-based string kernels for use with support vector machines (SVMs) for the problems of protein classification and remote homology detection. These kernels use probabilistic profiles, such as those produced by the PSI-BLAST algorithm, to define position-dependent mutation neighborhoods along protein sequences for inexact matching of k-length subsequences ("k-mers") in the data. By use of an efficient data structure, the kernels are fast to compute once the profiles have been obtained. For example, the time needed to run PSI-BLAST in order to build the pro- files is significantly longer than both the kernel computation time and the SVM training time. We present remote homology detection experiments based on the SCOP database where we show that profile-based string kernels used with SVM classifiers strongly outperform all recently presented supervised SVM methods. We also show how we can use the learned SVM classifier to extract "discriminative sequence motifs" -- short regions of the original profile that contribute almost all the weight of the SVM classification score -- and show that these discriminative motifs correspond to meaningful structural features in the protein data. The use of PSI-BLAST profiles can be seen as a semi-supervised learning technique, since PSI-BLAST leverages unlabeled data from a large sequence database to build more informative profiles. Recently presented "cluster kernels" give general semi-supervised methods for improving SVM protein classification performance. We show that our profile kernel results are comparable to cluster kernels while providing much better scalability to large datasets.

Wnt–β-catenin signaling plays a key role in orthodontic tooth movement (OTM), a common clinical practice for malocclusion correction. However, its targeted periodontal ligament (PDL) progenitor cells remain largely unclear. In this study, we first showed a synchronized increase in Wnt–β-catenin levels and Axin2⁺ PDL progenitor cell numbers during OTM using immunostaining of β-catenin in wild-type mice and X-gal staining in the Axin2-LacZ knock-in line. Next, we demonstrated time-dependent increases in Axin2⁺ PDL progenitors and their progeny cell numbers within PDL and alveolar bones during OTM using a one-time tamoxifen-induced Axin2 tracing line ( Axin2^CreERT2/+; R26R^tdTomato/+). Coimmunostaining images displayed both early and late bone markers (such as RUNX2 and DMP1) in the Axin2^Lin PDL cells. Conversely, ablation of Axin2⁺ PDL cells via one-time tamoxifen-induced diphtheria toxin subunit A (DTA) led to a drastic decrease in osteogenic activity (as reflected by alkaline phosphatase) in PDL and alveolar bone. There was also a decrease in new bone mass and a significant reduction in the mineral apposition rate on both the control side (to a moderate degree) and the OTM side (to a severe degree). Thus, we conclude that the Axin2⁺ PDL cells (the Wnt-targeted key cells) are highly sensitive to orthodontic tension force and play a critical role in OTM-induced PDL expansion and alveolar bone formation. Future drug development targeting the Axin2⁺ PDL progenitor cells may accelerate alveolar bone formation during orthodontic treatment.

The vertebrate musculoskeletal system is known to be formed by mesenchymal stem cells condensing into tissue elements, which then differentiate into cartilage, bone, tendon/ligament, and muscle cells. These lineage-committed cells mature into end-stage differentiated cells, like hypertrophic chondrocytes and osteocytes, which are expected to expire and to be replaced by newly differentiated cells arising from the same lineage pathway. However, there is emerging evidence of the role of cell transdifferentiation in bone development and disease. Although the concept of cell transdifferentiation is not new, a breakthrough in cell lineage tracing allowed scientists to trace cell fates in vivo. Using this powerful tool, new theories have been established: (1) hypertrophic chondrocytes can transdifferentiate into bone cells during endochondral bone formation, fracture repair, and some bone diseases, and (2) tendon cells, beyond their conventional role in joint movement, directly participate in normal bone and cartilage formation, and ectopic ossification. The goal of this review is to obtain a better understanding of the key roles of cell transdifferentiation in skeletal development and diseases. We will first review the transdifferentiation of chondrocytes to bone cells during endochondral bone formation. Specifically, we will include the history of the debate on the fate of chondrocytes during bone formation, the key findings obtained in recent years on the critical factors and molecules that regulate this cell fate change, and the role of chondrocyte transdifferentiation in skeletal trauma and diseases. In addition, we will also summarize the latest discoveries on the novel roles of tendon cells and adipocytes on skeletal formation and diseases.

Objective: To characterize the effects of parathyroid hormone (PTH) and alendronate (Alend) on the osteochondral tissue of temporomandibular joint (TMJ). Materials and Methods: Ninety-six male and female transgenic reporter mice, 4 to 5 weeks old were divided into 6 groups: (1) Control group: Saline was injected daily for 14 days; (2) PTH: PTH was injected daily for 14 days; (3) Alend: Alend was injected every alternate days for 14 days; (4) Combined PTH and Alend: PTH was injected daily and Alend injected every alternate days for 14 days; (5) PTH then Alend: PTH was injected daily for 14 days followed by Alend injections in alternate days for 14 days; and (6) PTH wait Alend: PTH was injected daily for 14 days. There was a waiting period of 1 week before administration of Alend in alternate days for 14 days. Mice were injected with 5-ethnyl-2′-deoxyuridine (EdU), 48 and 24 hours prior to euthanization. Results: There was significant increase in bone volume and decrease in osteoclastic activity in groups in which Alend was administered after PTH in both gender. There was significant increase in cartilage thickness with PTH or Alend alone in females, whereas in males, PTH alone led to increase in cartilage thickness. Chondrocyte apoptosis was significantly decreased with PTH or Alend alone in both male and female. Matrix metallopeptidase 13, and aggreganase-2 (ADAMTS5) expression were significantly decreased with PTH and Alend alone in both gender. Conclusion: PTH and Alend administration causes anabolic effects in the osteochondral tissue of TMJ.