3D Histology visualizing hypoxia-induced upregulation of N-terminal cysteine using de novo fluorophore generation

Our research group developed a novel fluorescence staining strategy based on the DNFC targeting N-Cys in proteins. By treating biological samples with non-fluorogenic citrate and coupling reagents, we achieved strong cyan fluorescence, enabling effective visualization of N-Cys proteins in cells and tissues. The DNFC reaction occurs specifically on N-Cys residues, making it highly ideal for monitoring protein processing events, particularly within the Arg/N-degron pathway. Under hypoxic conditions, DNFC fluorescence is significantly enhanced, likely due to the increased presence of N-Cys-containing proteins. Using immunoassays and mass spectrometry, we identified Class 2 actin as a target protein under hypoxia, emphasizing the utility of 3D histopathology for analyzing actin's spatial distribution. Furthermore, we have identified a novel finding indicating a significant presence of RGS5 in red blood cells (RBCs), a discovery that has not been previously reported. Our fluorescence imaging studies, conducted across various cell types, animal tissues, and human clinical samples suggest that DNFC staining, when combined with tissue-clearing techniques, enables detailed 3D imaging of N-Cys proteins and may offer a means to assess molecular responses to hypoxia within tissues. This study highlights the potential of DNFC as a valuable tool for imaging and quantitative analysis of N-proteomes and providing a foundation for 3D histopathology in hypoxia-related disease research.

Three-dimensional imaging and analysis of pathological tissue samples with de novo generation of citrate-based fluorophores

Two-dimensional (2D) histopathology based on the observation of thin tissue slides is the current paradigm in diagnosis and prognosis. However, labeling strategies in conventional histopathology are limited in compatibility with 3D imaging combined with tissue clearing techniques. Here, we present a rapid and efficient volumetric imaging technique of pathological tissues called 3D tissue imaging through de novo formation of fluorophores, or 3DNFC, which is the integration of citrate-based fluorogenic reaction DNFC and tissue clearing techniques. 3DNFC markedly increases the fluorescence intensity of tissues by generating fluorophores on nonfluorescent amino-terminal cysteine and visualizes the 3D structure of the tissues to provide their anatomical morphology and volumetric information. Furthermore, the application of 3DNFC to pathological tissue achieves the 3D reconstruction for the unbiased analysis of diverse features of the disorders in their natural context. We suggest that 3DNFC is a promising volumetric imaging method for the prognosis and diagnosis of pathological tissues.

The role of molecular fluorophores in the photoluminescence of carbon dots derived from citric acid: current state-of-the-art and future perspectives

Carbon dots (CDs), an emerging class of nanomaterials, have attracted considerable attention due to their intriguing photophysical properties. Despite their indisputable potential of utilization in many fascinating areas of research and life, some fundamental aspects concerning their structure and the origin of their photoluminescence (PL) properties still await clarification. The mechanism of PL emission of CDs is associated with their structure, which is dependent on the carbonization process. At the initial stages of CD synthesis via a bottom-up approach, molecular fluorophores are considered to dominate the optical characteristics of the resulting nanomaterials. In this review, the recent progress in the use of molecular state theory for explanation of the structure-property relationship in CDs is summarized. This review focuses exclusively on the molecular fluorophores existing in nanomaterials prepared from citric acid (CA) as one of the most frequent carbon sources reported for the bottom-up synthesis of CDs. Consequently, the most relevant transformations of CA and the history of molecular fluorophores derived from it are described, followed by an in-depth discussion on their relevance in understanding the specific photophysical properties of blue-, green-, and red-emitting CDs. Finally, the challenging issues and future perspectives of molecular state PL mechanism exploration in CDs are highlighted.

A solvent-free and efficient synthesis of bicyclic 2-pyridone derivatives for endoplasmic reticulum imaging

A solvent-free method was developed for the synthesis of bicyclic 2-pyridone (DHIP) derivatives, which demonstrated excellent endoplasmic reticulum (ER) targeting and antibacterial activity after a slight structure regulation.

Characterization of in silico modeled synthetic protein enriched with branched-chain amino acids expressed in Pichia pastoris

We have designed earlier the 3-dimensional structure of protein enriched with 56% branched-chain amino acids (BCAA) based on an α-helical coiled-coil structure. The chemically synthesized DNA (BCAA51 gene) was expressed in Pichia pastoris and confirmed by SDS-PAGE and western blot analysis. In the present study, the purified recombinant protein was characterized using circular dichroism and data revealed that the secondary structure contained 53.5% α-helix, 3.2% β-strand, and 43.3% turns, which is in concurrence with the overall structure predicted by in silico modeling. The LC-ESI-MS/MS spectra revealed that three peptide masses showed similarity to peptides like EQLTK, LEIVIR, and ILDK, of the modeled BCAA51 protein with the sequence coverage of ~16% from N-terminal region. The N-terminal sequence of the first seven amino acid residues (EQLTKLE) was exactly matching with the in silico designed protein. In vitro digestibility of the protein using SGF and SIF showed the disappearance of ~11 kDa band and appearance of low molecular weight peptides, which indicated that the protein was easily digestible and non-allergenic, which is the overall objective of this study. Further in vivo digestibility and toxicology studies are required to conclusively utilize this protein as a supplement for the treatment of chronic liver diseases.