Biology subjects

Oh, N.

Publications and source records attributed to Oh, N..

4 recordsLinked to original sources

bioRxiv2026

Minimal diadenylate cyclases have been co-opted to detect phage immune evasion

Many bacterial immune defenses transmit recognition of phage infection via the generation of diverse cyclic nucleotide second messengers. Phage have evolved to subvert this kind of immunity by sequestering, degrading, or inhibiting synthesis of these signaling molecules. Consequently, bacteria have evolved counter-mechanisms to detect disruption of cyclic nucleotide signaling and induce another layer of immune protection. Here we detail our discovery of the PanDA defense system (Panoptes-like DisA), an antiphage defense which detects sequestration of 3'3'-c-di-AMP by phage sponge proteins. PanDA consists of two proteins, PanS and PanE, which are both necessary for defense. PanS contains a minimal diadenylate cyclase (DAC) domain that constitutively generates the cyclic dinucleotide 3'3'-c-di-AMP which binds to and represses a toxic effector, the 2TM-{beta} family protein PanE. When a cell is infected by a phage encoding the sponge protein Acb4 (anti-CBASS protein 4), PanE is activated and induces membrane permeability. This work represents the first confirmed use of 3'3'-c-di-AMP as an immune second messenger in bacteria, facilitated by the exaptation of a DAC domain which has thus far only been best understood for its non-immune signaling roles.

microbiology↗

bioRxiv2022

Enhanced intramyocardial vascular cell delivery promotes post-myocardial infarction healing by polarizing pro-regenerative neutrophils

The success of vascular progenitor cell transplantation to treat myocardial infarction (MI) is primarily limited by the low engraftment of delivered cells due to a washout effect during myocardium contraction. A clinically applicable biomaterial to improve cell retention is arguably needed to enable optimization of intramyocardial cell delivery. Here, we developed a novel therapeutic cell delivery method for MI treatment based on a photocrosslinkable gelatin methacryloyl (GelMA) hydrogel. A combination of human vascular progenitor cells (endothelial progenitors and mesenchymal stem cells) with the capacity to form functional vasculatures after transplantation, were injected with a rapid in-situ photopolymerization approach into the infarcted zone of mouse hearts. Our approach significantly improved acute cell retention and achieved a long-term beneficial post-MI cardiac healing, including stabilizing cardiac functions, preserving viable myocardium, and preventing cardiac fibrosis. Furthermore, the engrafted vascular cells polarized recruited bone marrow-derived neutrophils toward a non-inflammatory phenotype via TGF{beta} signaling, establishing a pro-regenerative microenvironment. Depletion of neutrophils canceled the therapeutic benefits produced by cell delivery in the ischemic hearts, indicating that the non-inflammatory, pro-regenerative neutrophils were indispensable mediators of cardiac remodeling. In summary, our novel GelMA hydrogel-based intramyocardial vascular cell delivery approach has the potential to improve the treatment of acute MI.

bioengineering↗

bioRxiv2018

TGFam-Finder: An optimal solution for target-gene family annotation in eukaryotic genomes

Whole genome annotation errors that omit essential protein-coding genes hinder further research. We developed Target Gene Family Finder (TGFam-Finder), an optimal tool for structural annotation of protein-coding genes containing target domain(s) of interest in eukaryotic genomes. Large-scale re-annotation of 100 publicly available eukaryotic genomes led to the discovery of essential genes that were missed in previous annotations. An average of 117 (346%) and 148 (45%) additional FAR1 and NLR genes were newly identified in 50 plant genomes. Furthermore, 117 (47%) additional C2H2 zinc finger genes were detected in 50 animal genomes including human and mouse. Accuracy of the newly annotated genes was validated by RT-PCR and cDNA sequencing in human, mouse and rice. In the human genome, 26 newly annotated genes were identical with known functional genes. TGFam-Finder along with the new gene models provide an optimized platform for unbiased functional and comparative genomics and comprehensive evolutionary study in eukaryotes.

bioinformatics↗

bioRxiv2016

Label-free high-resolution 3-D imaging of gold nanoparticles inside live cells using optical diffraction tomography

Delivery of gold nanoparticles (GNPs) into live cells has high potentials, ranging from molecular-specific imaging, photodiagnostics, to photothermal therapy. However, studying the long-term dynamics of cells with GNPs using conventional fluorescence techniques suffers from phototoxicity and photobleaching. Here, we present a method for 3-D imaging of GNPs inside live cells exploiting refractive index (RI) as imaging contrast. Employing optical diffraction tomography, 3-D RI tomograms of live cells with GNPs are precisely measured for an extended period with sub-micrometer resolution. The locations and contents of GNPs in live cells are precisely addressed and quantified due to their distinctly high RI values, which was validated by confocal fluorescence imaging of fluorescent dye conjugated GNPs. In addition, we perform quantitative imaging analysis including the segmentations of GNPs in the cytosol, the volume distributions of aggregated GNPs, and the temporal evolution of GNPs contents in HeLa and 4T1 cells.\n\nAbbreviations

biophysics↗