3D mouse pose from single-view video and a new dataset

We present a method to infer the 3D pose of mice, including the limbs and feet, from monocular videos. Many human clinical conditions and their corresponding animal models result in abnormal motion, and accurately measuring 3D motion at scale offers insights into health. The 3D poses improve classification of health-related attributes over 2D representations. The inferred poses are accurate enough to estimate stride length even when the feet are mostly occluded. This method could be applied as part of a continuous monitoring system to non-invasively measure animal health, as demonstrated by its use in successfully classifying animals based on age and genotype. We introduce the Mouse Pose Analysis Dataset, the first large scale video dataset of lab mice in their home cage with ground truth keypoint and behavior labels. The dataset also contains high resolution mouse CT scans, which we use to build the shape models for 3D pose reconstruction.

An immune-based tool platform for in vivo cell clearance

Immunological targeting of pathological cells has been successful in oncology and is expanding to other pathobiological contexts. Here, we present a flexible platform that allows labeling cells of interest with the surface-expressed model antigen ovalbumin (OVA), which can be eliminated via either antigen-specific T cells or newly developed OVA antibodies. We demonstrate that hepatocytes can be effectively targeted by either modality. In contrast, pro-fibrotic fibroblasts associated with pulmonary fibrosis are only eliminated by T cells in initial experiments, which reduced collagen deposition in a fibrosis model. This new experimental platform will facilitate development of immune-based approaches to clear potential pathological cell types in vivo.

Diverse partial reprogramming strategies restore youthful gene expression and transiently suppress cell identity

Partial pluripotent reprogramming can reverse features of aging in mammalian cells, but the impact on somatic identity and the necessity of individual reprogramming factors remain unknown. Here, we used single-cell genomics to map the identity trajectory induced by partial reprogramming in multiple murine cell types and dissected the influence of each factor by screening all Yamanaka Factor subsets with pooled single-cell screens. We found that partial reprogramming restored youthful expression in adipogenic and mesenchymal stem cells but also temporarily suppressed somatic identity programs. Our pooled screens revealed that many subsets of the Yamanaka Factors both restore youthful expression and suppress somatic identity, but these effects were not tightly entangled. We also found that a multipotent reprogramming strategy inspired by amphibian regeneration restored youthful expression in myogenic cells. Our results suggest that various sets of reprogramming factors can restore youthful expression with varying degrees of somatic identity suppression. A record of this paper's Transparent Peer Review process is included in the supplemental information.