Thymine DNA glycosylase mediates chromatin phase separation in a DNA methylation-dependent manner

Thymine DNA glycosylase (TDG) is an essential enzyme involved in numerous biological pathways, including DNA repair, DNA demethylation, and transcriptional activation. Despite these important functions, the mechanisms surrounding the actions and regulation of TDG are poorly understood. In this study, we demonstrate that TDG induces phase separation of DNA and nucleosome arrays under physiologically relevant conditions in vitro and show that the resulting chromatin droplets exhibited behaviors typical of phase-separated liquids, supporting a liquid-liquid phase separation model. We also provide evidence that TDG has the capacity to form phase-separated condensates in the cell nucleus. The ability of TDG to induce chromatin phase separation is dependent on its intrinsically disordered N- and C-terminal domains, which in isolation, promote the formation of chromatin-containing droplets having distinct physical properties, consistent with their unique mechanistic roles in the phase separation process. Interestingly, DNA methylation alters the phase behavior of the disordered domains of TDG and compromises formation of chromatin condensates by full-length TDG, indicating that DNA methylation regulates the assembly and coalescence of TDG-mediated condensates. Overall, our results shed new light on the formation and physical nature of TDG-mediated chromatin condensates, which have broad implications for the mechanism and regulation of TDG and its associated genomic processes.

Fluorescence lifetime image microscopy prediction with convolutional neural networks for cell detection and classification in tissues

Convolutional neural networks (CNNs) and other deep-learning models have proven to be transformative tools for the automated analysis of microscopy images, particularly in the domain of cellular and tissue imaging. These computer-vision models have primarily been applied with traditional microscopy imaging modalities (e.g. brightfield and fluorescence), likely due to the availability of large datasets in these regimes. However, more advanced microscopy imaging techniques could, potentially, allow for improved model performance in various computational histopathology tasks. In this work, we demonstrate that CNNs can achieve high accuracy in cell detection and classification without large amounts of data when applied to histology images acquired by fluorescence lifetime imaging microscopy (FLIM). This accuracy is higher than what would be achieved with regular single or dual-channel fluorescence images under the same settings, particularly for CNNs pretrained on publicly available fluorescent cell or general image datasets. Additionally, generated FLIM images could be predicted from just the fluorescence image data by using a dense U-Net CNN model trained on a subset of ground-truth FLIM images. These U-Net CNN generated FLIM images demonstrated high similarity to ground truth and improved accuracy in cell detection and classification over fluorescence alone when used as input to a variety of commonly used CNNs. This improved accuracy was maintained even when the FLIM images were generated by a U-Net CNN trained on only a few example FLIM images.

Design and development of multifunctional polyphosphoester-based nanoparticles for ultrahigh paclitaxel dual loading

Multifunctional polyphosphoester-based nanoparticles capable of loading paclitaxel (PTX) both chemically and physically were prepared, achieving an ultrahigh equivalent PTX aqueous concentration of 25.30 mg mL^-1. The dual-loaded nanoparticles were effective in killing cancer cells, which has the potential to minimize the amount of nanocarriers needed for clinical applications, due to their ultrahigh loading capacity.

Degradable polyphosphoester-based silver-loaded nanoparticles as therapeutics for bacterial lung infections

In this study, a new type of degradable polyphosphoester-based polymeric nanoparticle, capable of carrying silver cations via interactions with alkyne groups, has been developed as a potentially effective and safe treatment for lung infections. It was found that up to 15% (w/w) silver loading into the nanoparticles could be achieved, consuming most of the pendant alkyne groups along the backbone, as revealed by Raman spectroscopy. The well-defined Ag-loaded nanoparticles released silver in a controlled and sustained manner over 5 days, and displayed enhanced in vitro antibacterial activities against cystic fibrosis-associated pathogens and decreased cytotoxicity to human bronchial epithelial cells, in comparison to silver acetate.

Synthesis, characterization, and in vivo efficacy of shell cross-linked nanoparticle formulations carrying silver antimicrobials as aerosolized therapeutics

The use of nebulizable, nanoparticle-based antimicrobial delivery systems can improve efficacy and reduce toxicity for treatment of multi-drug-resistant bacteria in the chronically infected lungs of cystic fibrosis patients. Nanoparticle vehicles are particularly useful for applying broad-spectrum silver-based antimicrobials, for instance, to improve the residence time of small-molecule silver carbene complexes (SCCs) within the lung. Therefore, we have synthesized multifunctional, shell cross-linked knedel-like polymeric nanoparticles (SCK NPs) and capitalized on the ability to independently load the shell and core with silver-based antimicrobial agents. We formulated three silver-loaded variants of SCK NPs: shell-loaded with silver cations, core-loaded with SCC10, and combined loading of shell silver cations and core SCC10. All three formulations provided a sustained delivery of silver over the course of at least 2-4 days. The two SCK NP formulations with SCC10 loaded in the core each exhibited excellent antimicrobial activity and efficacy in vivo in a mouse model of Pseudomonas aeruginosa pneumonia. SCK NPs with shell silver cation-load only, while efficacious in vitro, failed to demonstrate efficacy in vivo. However, a single dose of core SCC10-loaded SCK NPs (0.74 ± 0.16 mg Ag) provided a 28% survival advantage over sham treatment, and administration of two doses (0.88 mg Ag) improved survival to 60%. In contrast, a total of 14.5 mg of Ag(+) delivered over 5 doses at 12 h intervals was necessary to achieve a 60% survival advantage with a free-drug (SCC1) formulation. Thus, SCK NPs show promise for clinical impact by greatly reducing antimicrobial dosage and dosing frequency, which could minimize toxicity and improve patient adherence.

In vivo gene delivery with L-tyrosine polyphosphate nanoparticles

The concept of gene therapy is promising; however, the perceived risks and side effects associated with this technology have severely dampened the researchers' enthusiasm. Thus, the development of a nonviral gene vector without immunological effects and with high transfection efficiency is necessary. Currently, most nonviral vectors have failed to achieve the in vivo transfection efficiencies of viral vectors due to their toxicity, rapid clearance, and/or inappropriate release rates. Although our previous studies have successfully demonstrated the controlled-release of plasmid DNA (pDNA) polyplexes encapsulated into nanoparticles formulated with l-tyrosine polyphosphate (LTP-pDNA nanoparticles), the in vivo transfection capabilities and immunogenicity of this delivery system have yet to be examined. Thus, we evaluate LTP-pDNA nanoparticles in an in vivo setting via injection into rodent uterine tissue. Our results demonstrate through X-gal staining and immunohistochemistry of uterine tissue that transfection has successfully occurred after a nine-day incubation. In contrast, the results for the control nanoparticles show results similar to those of shams. Furthermore, reverse transcriptase polymerase chain reaction (RT-PCR) from the injected tissues confirms the transfection in vivo. To examine the immunogenicity, the l-tyrosine polyphosphate (LTP) nanoparticles have been evaluated in a mouse model. No significant differences in the activation of the innate immune system are observed. These data provide the first report for the potential use of controlled-release nanoparticles formulated from an amino acid based polymer as an in vivo nonviral vector for gene therapy.

Aerosolized antimicrobial agents based on degradable dextran nanoparticles loaded with silver carbene complexes

Degradable acetalated dextran (Ac-DEX) nanoparticles were prepared and loaded with a hydrophobic silver carbene complex (SCC) by a single-emulsion process. The resulting particles were characterized for morphology and size distribution using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and dynamic light scattering (DLS). The average particle size and particle size distribution were found to be a function of the ratio of the organic phase to the surfactant containing aqueous phase with a 1:5 volume ratio of Ac-DEX CH(2)Cl(2) (organic):PBS (aqueous) being optimal for the formulation of nanoparticles with an average size of 100 ± 40 nm and a low polydispersity. The SCC loading was found to increase with an increase in the SCC quantity in the initial feed used during particle formulation up to 30% (w/w); however, the encapsulation efficiency was observed to be the best at a feed ratio of 20% (w/w). In vitro efficacy testing of the SCC loaded Ac-DEX nanoparticles demonstrated their activity against both Gram-negative and Gram-positive bacteria; the nanoparticles inhibited the growth of every bacterial species tested. As expected, a higher concentration of drug was required to inhibit bacterial growth when the drug was encapsulated within the nanoparticle formulations compared with the free drug illustrating the desired depot release. Compared with free drug, the Ac-DEX nanoparticles were much more readily suspended in an aqueous phase and subsequently aerosolized, thus providing an effective method of pulmonary drug delivery.