It's widely appreciated that liquid–liquid phase separation (LLPS) underlies the formation of membraneless organelles, which function to concentrate proteins and nucleic acids. In the past few decades, major efforts have been devoted to identify the phase separation associated proteins and elucidate their functions. To better utilize the knowledge dispersed in published literature, we developed PhaSepDB (http://db.phasep.pro/), a manually curated database of phase separation associated proteins. Currently, PhaSepDB includes 2914 non-redundant proteins localized in different organelles curated from published literature and database. PhaSepDB provides protein summary, publication reference and sequence features of phase separation associated proteins. The sequence features which reflect the LLPS behavior are also available for other human protein candidates. The online database provides a convenient interface for the research community to easily browse, search and download phase separation associated proteins. As a centralized resource, we believe PhaSepDB will facilitate the future study of phase separation.

Spatial metabolomics can reveal intercellular heterogeneity and tissue organization. To achieve highest spatial resolution, we reported a novel Spatial single nuclEar metAboloMics (SEAM) method, a scalable platform combining high resolution imaging mass spectrometry (IMS) and a series of computational algorithms, that can display multiscale/multicolor tissue tomography together with identification and clustering of single nuclei by their in situ metabolic fingerprints. We firstly applied SEAM to a range of wild type mouse tissues, then delineate a consistent pattern of metabolic zonation in mouse liver. We further studied spatial metabolome in human fibrotic liver. Intriguingly, we discovered novel subpopulations of hepatocytes with special metabolic features associated with their proximity to fibrotic niche, which was further validated by spatial transcriptomics with Geo-seq. These demonstrations highlight how SEAM may be used to explore the spatial metabolome and tissue anatomy at single cell level, hence leading to a deeper understanding of the tissue metabolic organization.

The genome exists as an organized, three-dimensional (3D) dynamic architecture, and each cell type has a unique 3D genome organization that determines its cell identity. An unresolved question is how cell type-specific 3D genome structures are established during development. Here, we analyzed 3D genome structures in muscle cells from mice lacking the muscle lineage transcription factor (TF), MyoD, versus wild-type mice. We show that MyoD functions as a “genome organizer” that specifies 3D genome architecture unique to muscle cell development, and that H3K27ac is insufficient for the establishment of MyoD-induced chromatin loops in muscle cells. Moreover, we present evidence that other cell lineage-specific TFs might also exert functional roles in orchestrating lineage-specific 3D genome organization during development.

In the present paper, we will characterize the boundedness of the generalized fractional integral operators I ρ and the generalized fractional maximal operators M ρ on Orlicz spaces, respectively. Moreover, we will give a characterization for the Spanne-type boundedness and the Adams-type boundedness of the operators M ρ and I ρ on generalized Orlicz-Morrey spaces, respectively. Also we give criteria for the weak versions of the Spanne-type boundedness and the Adams-type boundedness of the operators M ρ and I ρ on generalized Orlicz-Morrey spaces.

Phase separation is an important mechanism that mediates the compartmentalization of proteins in cells. Proteins that can undergo phase separation in cells share certain typical sequence features, like intrinsically disordered regions (IDRs) and multiple modular domains. Sequence-based analysis tools are commonly used in the screening of these proteins. However, current phase separation predictors are mostly designed for IDR-containing proteins, thus inevitably overlook the phase-separating proteins with relatively low IDR content. Features other than amino acid sequence could provide crucial information for identifying possible phase-separating proteins: protein–protein interaction (PPI) networks show multivalent interactions that underlie phase separation process; post-translational modifications (PTMs) are crucial in the regulation of phase separation behavior; spherical structures revealed in immunofluorescence (IF) images indicate condensed droplets formed by phase-separating proteins, distinguishing these proteins from non-phase-separating proteins. Here, we summarize the sequence-based tools for predicting phase-separating proteins and highlight the importance of incorporating PPIs, PTMs, and IF images into phase separation prediction in future studies.