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Wang, Dong

Publications and source records attributed to Wang, Dong.

11 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Molecular model of TFIIH recruitment to the transcription-coupled repair machinery

Transcription-coupled repair (TCR) is a vital nucleotide excision repair sub-pathway that removes DNA lesions from actively transcribed DNA strands. Binding of CSB to lesion-stalled RNA Polymerase II (Pol II) initiates TCR by triggering the recruitment of downstream repair factors. Yet it remains unknown how transcription factor IIH (TFIIH) is recruited to the intact TCR complex. Combining existing structural data with AlphaFold predictions, we build an integrative model of the initial TFIIH-bound TCR complex. We show how TFIIH can be first recruited in an open repair-inhibited conformation, which requires subsequent CAK module removal and conformational closure to process damaged DNA. In our model, CSB, CSA, UVSSA, elongation factor 1 (ELOF1), and specific Pol II and UVSSA-bound ubiquitin moieties come together to provide interaction interfaces needed for TFIIH recruitment. STK19 acts as a linchpin of the assembly, orienting the incoming TFIIH and bridging Pol II to core TCR factors and DNA. Molecular simulations of the TCR-associated CRL4CSA ubiquitin ligase complex unveil the interplay of segmental DDB1 flexibility, continuous Cullin4A flexibility, and the key role of ELOF1 for Pol II ubiquitination that enables TCR. Collectively, these findings elucidate the coordinated assembly of repair proteins in early TCR.

Paul, Tanmoy↗
DOE OSTI2024

Exciton engineering of 2D Ruddlesden–Popper perovskites by synergistically tuning the intra and interlayer structures

Designing two-dimensional halide perovskites for high-performance optoelectronic applications requires deep understanding of the structure-property relationship that governs their excitonic behaviors. However, a design framework that considers both intra and interlayer structures modified by the A-site and spacer cations, respectively, has not been developed. Here, we use pressure to synergistically tune the intra and interlayer structures and uncover the structural modulations that result in improved optoelectronic performance. Under applied pressure, (BA) 2 (GA)Pb 2 I 7 exhibits a 72-fold boost of photoluminescence and 10-fold increase of photoconductivity. Based on the observed structural change, we introduce a structural descriptor χ that describes both the intra and interlayer characteristics and establish a general quantitative relationship between χ and photoluminescence quantum yield: smaller χ correlates with minimized trapped excitons and more efficient emission from free excitons. Building on this principle, we design a perovskite (CMA) 2 (FA)Pb 2 I 7 that exhibits a small χ and an impressive photoluminescence quantum yield of 59.3%.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Predicting oncology drug-induced cardiotoxicity with donor-specific iPSC-CMs—a proof-of-concept study with doxorubicin

Abstract Many oncology drugs have been found to induce cardiotoxicity in a subset of patients, which significantly limits their clinical use and impedes the benefit of lifesaving anticancer treatments. Human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) carry donor-specific genetic information and have been proposed for exploring the interindividual difference in oncology drug-induced cardiotoxicity. Herein, we evaluated the inter- and intraindividual variability of iPSC-CM-related assays and presented a proof of concept to prospectively predict doxorubicin (DOX)-induced cardiotoxicity (DIC) using donor-specific iPSC-CMs. Our findings demonstrated that donor-specific iPSC-CMs exhibited greater line-to-line variability than the intraindividual variability in impedance cytotoxicity and transcriptome assays. The variable and dose-dependent cytotoxic responses of iPSC-CMs resembled those observed in clinical practice and largely replicated the reported mechanisms. By categorizing iPSC-CMs into resistant and sensitive cell lines based on their time- and concentration-related phenotypic responses to DOX, we found that the sensitivity of donor-specific iPSC-CMs to DOX may predict in vivo DIC risk. Furthermore, we identified a differentially expressed gene, DND microRNA-mediated repression inhibitor 1 (DND1), between the DOX-resistant and DOX-sensitive iPSC-CMs. Our results support the utilization of donor-specific iPSC-CMs in assessing interindividual differences in DIC. Further studies will encompass a large panel of donor-specific iPSC-CMs to identify potential novel molecular and genetic biomarkers for predicting DOX and other oncology drug-induced cardiotoxicity.

Toxicology↗
DOE OSTI2023

Anomalous Charge Transfer from Organic Ligands to Metal Halides in Zero‐Dimensional [(C 6 H 5 ) 4 P] 2 SbCl 5 Enabled by Pressure‐Induced Lone Pair‐π Interaction

Abstract Low‐dimensional (low‐D) organic metal halide hybrids (OMHHs) have emerged as fascinating candidates for optoelectronics due to their integrated properties from both organic and inorganic components. However, for most of low‐D OMHHs, especially the zero‐D (0D) compounds, the inferior electronic coupling between organic ligands and inorganic metal halides prevents efficient charge transfer at the hybrid interfaces and thus limits their further tunability of optical and electronic properties. Here, using pressure to regulate the interfacial interactions, efficient charge transfer from organic ligands to metal halides is achieved, which leads to a near‐unity photoluminescence quantum yield (PLQY) at around 6.0 GPa in a 0D OMHH, [(C 6 H 5 ) 4 P] 2 SbCl 5 . In situ experimental characterizations and theoretical simulations reveal that the pressure‐induced electronic coupling between the lone‐pair electrons of Sb 3+ and the π electrons of benzene ring (lp‐π interaction) serves as an unexpected “bridge” for the charge transfer. Our work opens a versatile strategy for the new materials design by manipulating the lp‐π interactions in organic–inorganic hybrid systems.

Luo, Hui↗
DOE OSTI2023

Anomalous Charge Transfer from Organic Ligands to Metal Halides in Zero-Dimensional [(C 6 H 5 ) 4 P] 2 SbCl 5 Enabled by Pressure-Induced Lone Pair-π Interaction

Low-dimensional (low-D) organic metal halide hybrids (OMHHs) have emerged as fascinating candidates for optoelectronics due to their integrated properties from both organic and inorganic components. However, for most of low-D OMHHs, especially the zero-D (0D) compounds, the inferior electronic coupling between organic ligands and inorganic metal halides prevents efficient charge transfer at the hybrid interfaces and thus limits their further tunability of optical and electronic properties. Here, using pressure to regulate the interfacial interactions, efficient charge transfer from organic ligands to metal halides is achieved, which leads to a near-unity photoluminescence quantum yield (PLQY) at around 6.0 GPa in a 0D OMHH, [(C 6 H 5 ) 4 P] 2 SbCl 5 . In situ experimental characterizations and theoretical simulations reveal that the pressure-induced electronic coupling between the lone-pair electrons of Sb 3+ and the π electrons of benzene ring (lp-π interaction) serves as an unexpected “bridge” for the charge transfer. Further, our work opens a versatile strategy for the new materials design by manipulating the lp-π interactions in organic–inorganic hybrid systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Ballistic Ejection of Microdroplets from Overpacked Interfacial Assemblies

Spontaneous emulsification, resulting from the assembly and accumulation of surfactants at liquid–liquid interfaces, is an interfacial instability where microdroplets are generated and diffusively spread from the interface until complete emulsification. Here, it is shown that an external magnetic field can modulate the assembly of paramagnetic nanoparticle surfactants (NPSs) at liquid–liquid interfaces to trigger an oversaturation in the areal density of the NPSs at the interface, as evidenced by a marked reduction in the interfacial tension, γ, and corroborated with a magnetostatic continuum theory. Despite the significant reduction in γ, the presence of the magnetic field does not cause stable interfaces to become unstable. Upon rapid removal of the field, however, an explosive ejection of a plume of microdroplets from the surface occurs, a dynamical interfacial instability which is termed explosive emulsification. Further, this explosive event rapidly reduces the areal density of the NPSs to its pre-field level, stabilizing the interface. The ability to externally suppress or trigger the explosive emulsification and controlled generation of tens of thousands of microdroplets, uncovers an efficient energy storage and release process, that has potential applications for controlled and directed delivery of chemicals and remotely controlled soft microrobots, taking advantage of the ferromagnetic nature of the microdroplets.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase

Bacteriophage T7 RNA polymerase (T7 RNAP) is widely used for synthesizing RNA molecules with synthetic modifications and unnatural base pairs (UBPs) for a variety of biotechnical and therapeutic applications. However, the molecular basis of transcription recognition of UBPs by T7 RNAP remains poorly understood. Here we focused on a representative UBP, 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and pyrrole 2-carbaldehyde (Pa), and investigated how the hydrophobic Ds–Pa pair is recognized by T7 RNAP. Our kinetic assays revealed that T7 RNAP selectively recognizes the Ds or Pa base in the templates and preferentially incorporates their cognate unnatural base nucleotide substrate (PaTP or DsTP) over natural NTPs. Our structural studies reveal that T7 RNAP recognizes the unnatural substrates at the pre-insertion state in a distinct manner compared to natural substrates. These results provide mechanistic insights into transcription recognition of UBP by T7 RNAP and provide valuable information for designing the next generation of UBPs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Protective Effect of Phloretin against Hydrogen Peroxide-Induced Oxidative Damage by Enhancing Autophagic Flux in DF-1 Cells

Phloretin (PHL) is a dihydrochalcone flavonoid isolated from the peel and root bark of apples, strawberries, and other plants with antioxidative characteristic. In this study, we aimed to investigate the protective effect and the potential mechanism of PHL on hydrogen peroxide (H2O2)-induced oxidative damage in DF-1 cells. The results showed that PHL exhibited no cytotoxic effect on DF-1 cells at concentration below 20 μM. PHL markedly increased H2O2-reduced cell viability, decreased H2O2-induced apoptosis, as evidenced by reduced apoptosis rate, the upregulation of gene and protein level of Bcl-2, and the downregulation of gene and protein level of Bax and Cleaved caspase3. In addition, PHL reduced H2O2-induced reactive oxygen species (ROS) production and restored antioxidant enzymes activities as well as mitochondrial membrane potential in a dose-dependent manner. Moreover, PHL prior to H2O2 further increased LC3-II level, promoted p62 turnover and improved lysosomal function. Importantly, autophagy inhibitor chloroquine (CQ) reversed the protective effect of PHL, and increased H2O2-induced apoptosis. Furthermore, PHL inhibited the phosphorylation levels of ERK, p38, and JNK. Collectively, these results indicate that PHL could attenuate H2O2-induced oxidative injury and apoptosis by maintaining lysosomal function and promoting autophagic flux, and MAPKs pathway may be involved in this process. Our study provides evidence that PHL could as a new strategy to against oxidative damage in poultry industry.

Song, Dan↗
DOE OSTI2022

A Multi-Branch Decoder Network Approach to Adaptive Temporal Data Selection and Reconstruction for Big Scientific Simulation Data

A key challenge in scientific simulation is that the simulation outputs often require intensive I/O and storage space to store the results for effective post hoc analysis. This article focuses on a quality-aware adaptive temporal data selection and reconstruction problem where the goal is to adaptively select simulation data samples at certain key timesteps in situ and reconstruct the discarded samples with quality assurance during post hoc analysis. This problem is motivated by the limitation of current solutions that a significant amount of simulation data samples are either discarded or aggregated during the sampling process, leading to inaccurate modeling of the simulated phenomena. Two unique challenges exist: 1) the sampling decisions have to be made in situ and adapted to the dynamics of the complex scientific simulation data; 2) the reconstruction error must be strictly bounded to meet the application requirement. To address the above challenges, we develop DeepSample , an error-controlled convolutional neural network framework, that jointly integrates a set of coherent multi-branch deep decoders to effectively reconstruct the simulation data with rigorous quality assurance. The results on two real-world scientific simulation applications show that DeepSample significantly outperforms other state-of-the-art methods on both sampling efficiency and reconstructed simulation data quality.

Zhang, Yang↗