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Chen, Dan

Publications and source records attributed to Chen, Dan.

12 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Discovery of Five SOS2 Fragment Hits with Binding Modes Determined by SOS2 X-Ray Cocrystallography

SOS1 and SOS2 are guanine nucleotide exchange factors that mediate RTK-stimulated RAS activation. Selective SOS1:KRAS PPI inhibitors are currently under clinical investigation, whereas there are no reports to date of SOS2:KRAS PPI inhibitors. SOS2 activity is implicated in MAPK rebound when divergent SOS1 mutant cell lines are treated with the SOS1 inhibitor BI-3406; therefore, SOS2:KRAS inhibitors are of therapeutic interest. In this report, we detail a fragment-based screening strategy to identify X-ray cocrystal structures of five diverse fragment hits bound to SOS2.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Tunicamycin-induced endoplasmic reticulum stress inhibits chemoresistance of FaDu hypopharyngeal carcinoma cells in 3D collagen I cultures and in vivo

Highlights: • 3D collagen I culture induces chemoresistance of FaDu hypopharyngeal carcinoma cells. • Tunicamycin-induced ER stress inhibits chemoresistance in collagen I cultures. • Tunicamycin-induced ER stress potentiates anticancer efficacy in vivo. • Tunicamycin-induced ER stress inhibits TGF-β1 and modifies integrin β1 glycosylation. The prognosis in patients with advanced head and neck squamous cell carcinoma (HNSCC) is widely affected by the resistance to chemotherapy. As a culture scaffold, collagen I was showed to promote CSC (cancer stem cell) properties of cancer cells which could be used as in vitro models to study the chemoresistance in HNSCC. Endoplasmic reticulum (ER) stress is a cellular stress condition which could affect tumor progression and promote the anti-tumor effects of certain drugs. However, the impact of ER stress on collagen I induced CSC properties and chemoresistance of HNSCC cells has not been addressed. In this study we investigated the effects of tunicamycin (TM) induced ER stress on the stemness and sensitivity to chemotherapeutic drugs of FaDu hypopharyngeal carcinoma cells in 3D (three-dimensional) collagen I cultures and mouse xenograft models. Our study revealed that Collagen I scaffold promoted CSC properties and increased G1 population of FaDu cells in 3D cultures, accompanied by maturation of integrin β1 and enhanced activated TGF-β1 concentration. Compared to 2D (two-dimensional) cultured cells, cells in 3D Collagen I scaffold exhibited significantly increased resistance to chemotherapeutic drugs of cisplatin and paclitaxel. Further analysis revealed that TM induced ER stress preferentially attenuated chemoresistance of FaDu cells in 3D collagen I, downregulated their CSC properties and TGF-β1 concentration and resulted in deglycosylation of integrin β1. TM was further evaluated in the mouse xenograft models and showed significant tumor growth inhibition in combination with paclitaxel than either TM or paclitaxel alone. Taken together, Our findings suggest that TM-induced ER stress potentiates anticancer efficacy of FaDu cells in 3D cultures and in vivo, and highlight implications for targeting chemotherapy-resistant cancer stem cells under ER stress conditions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

MicroRNA-92a -mediated endothelial to mesenchymal transition controls vein graft neointimal lesion formation

Highlights: • TGF-β triggers microRNA-92a mediated EndMT by targeting ITGA5 is key role in vein graft vascular remodeling. • Silencing of microRNA-92a-mediated endothelial to mesenchymal transition inhibits vein graft neointimal hyperplasia. • Local adeno-associated virus delivery gene therapy deregulation of microRNA-92a-mediated EndMT may represent promising therapeutic approach for vein grafts failure. Long-term failure of vein grafts due to neointimal hyperplasia remains an important problem in coronary artery bypass graft surgery. Endothelial to mesenchymal transition (EndMT) contributes to vein graft vascular remodeling. However, there is little study on microRNA-mediated EndMT contributions to neointimal formation in vein graft. We hypothesized that microRNA-92a (miR-92a) might play an important role in determining EndMT contributions to neointimal formation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

miR-448-3p controls intracranial aneurysm by regulating KLF5 expression

Highlights: • KLF5 was significantly upregulated and miR-448-3p was downregulated in the rat model of IA. • Klf5 was the direct target of miR-448-3p. • Overexpression of miR-448-3p inhibits IA development in the rat model. • Overexpression of miR-488-3p suppresses macrophage infiltration and activation in IA. microRNAs (miRNAs) control several processes known to be involved in progression of aneurysm. Here, intracranial aneurysms (IAs) were surgically induced in Sprague–Dawley rats, and we found that miR-448-3p was downregulated and KLF5 was upregulated in IA rats. We identified Klf5 as a direct target of miR-448-3p in smooth muscle cells (SMCs). In addition, aneurysms size and the lumen area of the aneurysms were smaller 4 weeks after IA induction in the miR-448-3p–treated group. miR-448-3p treatment protected the wall thickness ratio and suppressed macrophage infiltration after IA induction. IAs caused a significant increase in KLF5 expression and were alleviated by miR-448-3p. Moreover, the anti-inflammatory effect of miR-448-3p was verified in lipopolysaccharide -stimulated RAW 264.7 macrophage cells. The expression levels of KLF5, MMP2, and MMP9 levels were elevated by LPS, and were attenuated by miR-448-3p. These data suggest that miR-448-3p plays the inhibitory role in IA progression, indicating that miR-448-3p overexpression is crucial for preventing the development of IA through downregulation of macrophage-mediated inflammation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

New positive feedback mechanism between boundary layer meteorology and secondary aerosol formation during severe haze events

Severe haze events during which particulate matter (PM) increases quickly from tens to hundreds of microgram per cubic meter in 1-2 days frequently occur in China. Although it has been known that PM is influenced by complex interplays among emissions, meteorology, and physical and chemical processes, specific mechanisms remain elusive. In this paper, a new positive feedback mechanism between planetary boundary layer (PBL), relative humidity (RH), and secondary PM (SPM) formation is proposed based on a comprehensive field experiment and model simulation. The decreased PBL associated with increased PM increases RH by weakening the vertical transport of water vapor; the increased RH in turn enhances the SPM formation through heterogeneous aqueous reactions, which further enhances PM, weakens solar radiation, and decreases PBL height. This positive feedback, together with the PM-Radiation-PBL feedback, constitutes a key mechanism that links PM, radiation, PBL properties (e.g. PBL height and RH), and SPM formation, This mechanism is self-amplifying, leading to faster PM production, accumulation, and more severe haze pollution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Simulations of Sulfate-Nitrate-Ammonium (SNA) aerosols during the extreme haze events over Northern China in 2014

Extreme haze events have occurred frequently over China in recent years. Although many studies have investigated the formation mechanisms associated with PM2.5 for heavily polluted regions in China based on observational data, adequately predicting peak PM2.5 concentrations is still challenging for regional air quality models. In this study, we evaluate the performance of one configuration of the Weather Research and Forecasting model coupled with chemistry (WRF-Chem) and use the model to investigate the sensitivity of heterogeneous reactions on simulated peak sulfate, nitrate, and ammonium concentrations in the vicinity of Beijing during four extreme haze episodes in October 2014 over the North China Plain. The highest observed PM2.5 concentration of 469 μg m-3 occurred in Beijing. Comparisons with observations show that the model reproduced the temporal variability in PM2.5 with the highest PM2.5 values on polluted days (defined as days in which observed PM2.5 is greater than 75 μg m-3), but predictions of sulfate, nitrate, and ammonium were too low on days with the highest observed concentrations. Observational data indicate that the sulfur/nitric oxidation rates are strongly correlated with relative humidity during periods of peak PM2.5; however, the model failed to reproduce the highest PM2.5 concentrations due to missing heterogeneous reactions. As the parameterizations of those reactions is not well established yet, estimates of SO2-to-H2SO4 and NO2/NO3-to-HNO3 reaction rates that depend on relative humidity were applied which improved the simulation of sulfate, nitrate, and ammonium enhancement on polluted days in terms of both concentrations and partitioning among those species. Sensitivity simulations showed that the extremely high heterogeneous reaction rates and also higher emission rates than those reported in the emission inventory

Chen, Dan↗
DOE OSTI2016

Genome-wide survey of Aux/IAA gene family members in potato (Solanum tuberosum): Identification, expression analysis, and evaluation of their roles in tuber development

The Auxin/indole-3-acetic acid (Aux/IAA) genes encode short-lived nuclear proteins that are known to be involved in the primary cellular responses to auxin. To date, systematic analysis of the Aux/IAA genes in potato (Solanum tuberosum) has not been conducted. In this study, a total of 26 potato Aux/IAA genes were identified (designated from StIAA1 to StIAA26), and the distribution of four conserved domains shared by the StIAAs were analyzed based on multiple sequence alignment and a motif-based sequence analysis. A phylogenetic analysis of the Aux/IAA gene families of potato and Arabidopsis was also conducted. In order to assess the roles of StIAA genes in tuber development, the results of RNA-seq studies were reformatted to analyze the expression patterns of StIAA genes, and then verified by quantitative real-time PCR. A large number of StIAA genes (12 genes) were highly expressed in stolon organs and in during the tuber initiation and expansion developmental stages, and most of these genes were responsive to indoleacetic acid treatment. Our results suggested that StIAA genes were involved in the process of tuber development and provided insights into functional roles of potato Aux/IAA genes. - Highlights: • A systematic analysis of the potato AUX/IAA gene family were performed. • StIAA genes were related to auxin perception and signal transduction. • Candidate StIAA genes likely related to tuber initiation and expansion were screened.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

MiR-145, a microRNA targeting ADAM17, inhibits the invasion and migration of nasopharyngeal carcinoma cells

MiR-145 is downregulated and functions as a tumor suppressor in many malignancies. In this study, the biological function, molecular mechanism, and direct target genes of miR-145 in nasopharyngeal carcinoma (NPC) cells were investigated. Cell survival was detected by cell viability assay, and cell cycle was determined through flow cytometry. Invasion and migration of NPC cells were examined using cell invasion and wound healing assays, respectively. A disintegrin and metalloproteinase 17 (ADAM17) was verified as the target of miR-145 through luciferase reporter assay, qRT-PCR, and Western blot analysis. In NPC cell lines, miR-145 expression was significantly downregulated and ADAM17 protein expression was upregulated. ADAM17 was downregulated at the post-transcriptional level by miR-145 via the binding site of ADAM17-3′UTR. Transfection with miR-145 mimic suppressed cell growth and induced cell cycle arrest in the G0/G1 phase by upregulating key G0/G1 phase regulators, namely, p53 and p21. MiR-145 also inhibited cellular migration and invasion through targeting ADAM17 involving the regulation of EGFR and E-cadherin. Knockdown of ADAM17 elicited similar effects to that of miR-145 on NPC cells. This study reveals that miR-145 suppressed the invasion and migration of NPC cells by targeting ADAM17. Thus, miR-145 could be a therapeutic target for NPC. - Highlights: • MiR-145 inhibits proliferation, invasion, and migration in NPC cells. • Knockdown of ADAM17 inhibits invasion and migration in NPC cells. • MiR-145 inhibits invasion and migration in NPC cells by targeting ADAM17.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Ultra-high-performance core–shell structured Ru@Pt/C catalyst prepared by a facile pulse electrochemical deposition method

Core–shell structured catalysts, made by placing either a monolayer or a thin layer of a noble metal on relatively cheap core-metal nanoparticles, are fascinating and promising fuel cell catalysts due to their high utilization of noble metals. Here, we report our development of a core–shell structured catalyst, Ru@Pt/C, generated by a novel and facile pulse electrochemical deposition (PED) approach. We demonstrate that compared with a commercial Pt/C catalyst, this novel catalyst achieves over four times higher mass activity towards the anodic oxidation of methanol, and 3.6 times higher mass activity towards the cathodic reduction of oxygen. Importantly, we find that the intrinsic activity of Pt in this Ru@Pt/C catalyst is doubled due to the formation of the core–shell structure. The catalyst also shows superior stability: even after 2000 scans, it still retains up to 90% of the peak current. As a result, our findings demonstrate that this novel PED approach is a promising method for preparing high-performance core–shell catalysts for fuel cell applications.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2014

Global Chemical Composition of Ambient Fine Particulate Matter for Exposure Assessment

Epidemiologic and health impact studies are inhibited by the paucity of global, long-term measurements of the chemical composition of fine particulate matter. We inferred PM 2.5 chemical composition at 0.1° × 0.1° spatial resolution for 2004–2008 by combining aerosol optical depth retrieved from the MODIS and MISR satellite instruments, with coincident profile and composition information from the GEOS-Chem global chemical transport model. Evaluation of the satellite-model PM 2.5 composition data set with North American in situ measurements indicated significant spatial agreement for secondary inorganic aerosol, particulate organic mass, black carbon, mineral dust, and sea salt. We found that global population-weighted PM 2.5 concentrations were dominated by particulate organic mass (11.9 ± 7.3 μg/m 3 ), secondary inorganic aerosol (11.1 ± 5.0 μg/m 3 ), and mineral dust (11.1 ± 7.9 μg/m 3 ). Secondary inorganic PM 2.5 concentrations exceeded 30 μg/m 3 over East China. Sensitivity simulations suggested that population-weighted ambient PM 2.5 from biofuel burning (11 μg/m 3 ) could be almost as large as from fossil fuel combustion sources (17 μg/m 3 ). In conclusion, these estimates offer information about global population exposure to the chemical components and sources of PM 2.5 .

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2013

A survey on resource allocation in high performance distributed computing systems

An efficient resource allocation is a fundamental requirement in high performance computing (HPC) systems. Many projects are dedicated to large-scale distributed computing systems that have designed and developed resource allocation mechanisms with a variety of architectures and services. In our study, through analysis, a comprehensive survey for describing resource allocation in various HPCs is reported. The aim of the work is to aggregate under a joint framework, the existing solutions for HPC to provide a thorough analysis and characteristics of the resource management and allocation strategies. Resource allocation mechanisms and strategies play a vital role towards the performance improvement of all the HPCs classifications. Therefore, a comprehensive discussion of widely used resource allocation strategies deployed in HPC environment is required, which is one of the motivations of this survey. Moreover, we have classified the HPC systems into three broad categories, namely: (a) cluster, (b) grid, and (c) cloud systems and define the characteristics of each class by extracting sets of common attributes. All of the aforementioned systems are cataloged into pure software and hybrid/hardware solutions. The system classification is used to identify approaches followed by the implementation of existing resource allocation strategies that are widely presented in the literature.

97 MATHEMATICS AND COMPUTING↗