Prediction of tissue-of-origin of early stage cancers using serum miRNomes.

Background: Noninvasive detection of early stage cancers with accurate prediction of tumor tissue-of-origin could improve patient prognosis. Because miRNA profiles differ between organs, circulating miRNomics represent a promising method for early detection of cancers, but this has not been shown conclusively.

Methods: A serum miRNA profile (miRNomes)-based classifier was evaluated for its ability to discriminate cancer types using advanced machine learning.

Machine learning-based exceptional response prediction of nivolumab monotherapy with circulating microRNAs in non-small cell lung cancer.

Immune checkpoint inhibitors (ICIs) have significantly improved the survival of advanced non-small cell lung cancer (NSCLC). Detecting NSCLC patients with exceptional response to ICIs is necessary to improve the treatment. This case control study profiled circulating microRNA expressions of 213 NSCLC patients treated with nivolumab monotherapy to identify patients with exceptional response.

Derivation of simple rules for complex flow vector fields on the lower part of the human face for robot face design.

It is quite difficult for android robots to replicate the numerous and various types of human facial expressions owing to limitations in terms of space, mechanisms, and materials. This situation could be improved with greater knowledge regarding these expressions and their deformation rules, i.e.

Identification of a function-specific mutation of clathrin heavy chain (CHC) required for p53 transactivation.

The p53 pathway is activated in response to various cellular stresses to protect cells from malignant transformation. We have previously shown that clathrin heavy chain (CHC), which is a cytosolic protein regulating endocytosis, is present in nuclei and binds to p53 to promote p53-mediated transcription. However, details of the binding interface between p53 and CHC remain unclear.

FAK nuclear export signal sequences.

Ubiquitously expressed focal adhesion kinase (FAK), a critical component in transducing signals from sites of cell contacts with extracellular matrix, was named after its typical localization in focal adhesions. A nuclear localization of FAK has been also reported and its scaffolding role in nucleus and requirement for p53 ubiquitination were only recently described. Whereas FAK nuclear localization signal (NLS) was found in F2 lobe of FERM domain, nuclear export signal (NES) sequences have not been yet determined.

Novel binding sites on clathrin and adaptors regulate distinct aspects of coat assembly.

Clathrin-coated vesicles (CCVs) sort proteins at the plasma membrane, endosomes and trans Golgi network for multiple membrane traffic pathways. Clathrin recruitment to membranes and its self-assembly into a polyhedral coat depends on adaptor molecules, which interact with membrane-associated vesicle cargo. To determine how adaptors induce clathrin recruitment and assembly, we mapped novel interaction sites between these coat components.

Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion.

A variety of experimental evidence suggests that rapid, long-range propagation of conformational changes through the core of proteins plays a vital role in allosteric communication. Here, we describe a non-equilibrium molecular dynamics simulation method, anisotropic thermal diffusion (ATD), which allowed us to observe a dominant intramolecular signaling pathway in PSD-95, a member of the PDZ domain protein family. The observed pathway is in good accordance with a pathway previously inferred using a multiple sequence analysis of 276 PDZ domain proteins.

The 0.83 A resolution crystal structure of alpha-lytic protease reveals the detailed structure of the active site and identifies a source of conformational strain.

The crystal structure of the extracellular bacterial serine protease alpha-lytic protease (alphaLP) has been solved at 0.83 A resolution at pH 8. This ultra-high resolution structure allows accurate analysis of structural elements not possible with previous structures.

Clathrin light and heavy chain interface: alpha-helix binding superhelix loops via critical tryptophans.

Clathrin light chain subunits (LCa and LCb) contribute to regulation of coated vesicle formation to sort proteins during receptor-mediated endocytosis and organelle biogenesis. LC binding to clathrin heavy chain (HC) was characterized by genetic and structural approaches. The core interactions were mapped to HC residues 1267-1522 (out of 1675) and LCb residues 90-157 (out of 228), using yeast two-hybrid assays.