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Dong, Yan

Publications and source records attributed to Dong, Yan.

10 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Widespread transposon co-option in the Caenorhabditis germline regulatory network

The movement of selfish DNA elements can lead to widespread genomic alterations with potential to create novel functions. We show that transposon expansions in Caenorhabditis nematodes led to extensive rewiring of germline transcriptional regulation. We find that about one-third of Caenorhabditis elegans germline-specific promoters have been co-opted from two related miniature inverted repeat transposable elements (TEs), CERP2 and CELE2. These promoters are regulated by HIM-17, a THAP domain–containing transcription factor related to a transposase. Expansion of CERP2 occurred before radiation of the Caenorhabditis genus, as did fixation of mutations in HIM-17 through positive selection, whereas CELE2 expanded only in C. elegans. Through comparative analyses in Caenorhabditis briggsae, we find not only evolutionary conservation of most CERP2 co-opted promoters but also a substantial fraction that are species-specific. Our work reveals the emergence and evolutionary conservation of a novel transcriptional network driven by TE co-option with a major impact on regulatory evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Association Between Changes in Timing of Spring Onset and Asthma Hospitalization in Maryland

The proposed association between climate change and increased burden of allergic diseases are based on three different thematic observational studies that have linked (i) increased CO 2 concentration with higher pollen production, (ii) warmer air/surface temperatures with early spring onset and longer pollen season, and (iii) higher pollen exposure with increased risk of asthma hospitalizations. Yet empirical evidence collectively linking climate change with pollen season and asthma exacerbation is still lacking. Using satellite observations, in situ pollen monitoring data, and hospitalization records (2001-2012), here we show that changes in the timing of spring onset resulting from ongoing climate variability and change is directly related to a longer tree pollen season and increased risk of asthma hospitalization. More specifically, we observed that very early start of season (SOS) to be associated with 10% increase in risk of asthma hospitalization (Incident Rate Ratio (IRR): 1.10, 95% Confidence Interval (CI): 1.02- 1.20) while late onset of SOS to be associated with 3% increase in risk of asthma hospitalization in Maryland (IRR: 1.03, 95% CI: 0.97-1.11), however the risk in the latter case was not statistically significant. Our results serve as a wake-up call to public health and medical communities regarding the need to anticipate and adapt to the ongoing changes in the timing and severity of the spring allergy season.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Atom Probe Tomography Interlaboratory Study on Clustering Analysis in Experimental Data Using the Maximum Separation Distance Approach

We summarize the findings from an interlaboratory study conducted between ten international research groups and investigate the use of the commonly used maximum separation distance and local concentration thresholding methods for solute clustering quantification. The study objectives are: to bring clarity to the range of applicability of the methods; identify existing and/or needed modifications; and interpretation of past published data. Participants collected experimental data from a proton-irradiated 304 stainless steel and analyzed Cu-rich and Ni–Si rich clusters. The datasets were also analyzed by one researcher to clarify variability originating from different operators. The Cu distribution fulfills the ideal requirements of the maximum separation method (MSM), namely a dilute matrix Cu concentration and concentrated Cu clusters. This enabled a relatively tight distribution of the cluster number density among the participants. By contrast, the group analysis of the Ni–Si rich clusters by the MSM was complicated by a high Ni matrix concentration and by the presence of Si-decorated dislocations, leading to larger variability among researchers. While local concentration filtering could, in principle, tighten the results, the cluster identification step inevitably maintained a high scatter. Recommendations regarding reporting, selection of analysis method, and expected variability when interpreting published data are discussed.

APT, Round Robin Studies, atom probe tomography, c↗
DOE OSTI2018

Monitoring autophagic flux using p62/SQSTM1 based luciferase reporters in glioma cells

Highlights: • A luciferase based autophagic flux detection system, Luc2p-p62 vs. Luc2p-p62ΔU, was developed. • This system can be used to detect TMZ-induced autophagic flux changes in U87MG cells. • This system can assay the effect of autophagy modulators in different types of tumor cells. Autophagy is a highly dynamic process characterized with the term of autophagic flux. In the present study, we developed a quantifiable luciferase reporter system to measure the capacity as well as the dynamics of autophagic flux. Briefly, a luciferase variant of Luc2p was fused with p62/SQSTM1 or its UBA domain deletion mutant (p62ΔU) and transfected into cells. The expressed Luc2p-p62 fusion protein was primarily degraded via autophagy, while Luc2p-p62ΔU was employed as a normalization control due to its resistance to autophagic degradation. The luciferase activity of the lysates from two parallel populations of glioma cells expressing either Luc2p-p62 or Luc2p-p62ΔU was determined and the ratio of Luc2p-p62ΔU/Luc2p-p62 was used to assay the autophagic flux. By this approach, the induction of autophagy was manifested as an increased Luc2p-p62ΔU/Luc2p-p62 ratio, which could be neutralized by autophagy inhibitors or knockdown of ATG5. The performance of our autophagic flux detection system was comparable to a recently reported GFP-LC3-RFP-LC3ΔG probe. We tested the system in TMZ treated glioma cells, and found that coadministration of chloroquine to attenuate cellular autophagic flux significantly improved the TMZ efficacy by triggering more early apoptosis. Collectively, our luciferase-based autophagic flux assay may serve as a useful alternative yet sensitive method for autophagic flux detection in tumor cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Thermostability and photostability of Sr{sub 3}SiO{sub 5}:Eu{sup 2+} phosphors for white LED applications

Sr{sub 3}SiO{sub 5}:Eu{sup 2+} phosphors were synthesized by solid-state reactions, and their photoluminescence (PL) stability under the impact of heat or light was studied. The thermal degradation in air was observed for the Sr{sub 3}SiO{sub 5}:Eu{sup 2+} phosphor, furthermore, this drop in emission intensity could be accelerated by simultaneously illuminating the phosphor with a high-power blue LED during the heating process. This enhanced thermal degradation phenomenon in the blue light can be ascribed to the photo-assisted thermal oxidation of Eu{sup 2+} ions. A reversible decrease in emission intensity at room temperature was observed on illuminating the Sr{sub 3}SiO{sub 5}:Eu{sup 2+} phosphor alone by the blue light, which could be related to trapping centers in the phosphor. The existence of traps is also responsible for the anomalous increase of emission intensity with increasing temperature from 30 to 100 °C. Considering the influences of Ba{sup 2+} doping on temperature-dependent PL properties of the Sr{sub 3}SiO{sub 5}:Eu{sup 2+} phosphor, the thermal quenching origin may be ascribed to the thermally assisted photoionization process. - Graphical abstract: The photo-induced reversible decrease in emission intensity and the anomalous emission enhancement with increasing temperature are related to trapping centers in the phosphor. - Highlights: • The photo-assisted thermal degradation was observed for the Sr{sub 3}SiO{sub 5}:Eu{sup 2+} phosphor. • The phosphor showed a reversible intensity decrease under the blue light irradiation. • An anomalous emission enhancement with increasing temperature was found. • Ba{sup 2+} substitution could suppress the thermal quenching of Sr{sub 3}SiO{sub 5}:Eu{sup 2+}. • Mechanisms for photostability and thermostability were discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

A novel bHLH transcription factor PebHLH35 from Populus euphratica confers drought tolerance through regulating stomatal development, photosynthesis and growth in Arabidopsis

Highlights: • PebHLH35 is firstly cloned from Populus euphratica and characterized its functions. • PebHLH35 is important for earlier seedling establishment and vegetative growth. • PebHLH35 enhances tolerance to drought by regulating growth. • PebHLH35 enhances tolerance to drought by regulating stomatal development. • PebHLH35 enhances tolerance to drought by regulating photosynthesis and transpiration. - Abstract: Plant basic helix-loop-helix (bHLH) transcription factors (TFs) are involved in a variety of physiological processes including the regulation of plant responses to various abiotic stresses. However, few drought-responsive bHLH family members in Populus have been reported. In this study, a novel bHLH gene (PebHLH35) was cloned from Populus euphratica. Expression analysis in P. euphratica revealed that PebHLH35 was induced by drought and abscisic acid. Subcellular localization studies using a PebHLH35-GFP fusion showed that the protein was localized to the nucleus. Ectopic overexpression of PebHLH35 in Arabidopsis resulted in a longer primary root, more leaves, and a greater leaf area under well-watered conditions compared with vector control plants. Notably, PebHLH35 overexpression lines showed enhanced tolerance to water-deficit stress. This finding was supported by anatomical and physiological analyses, which revealed a reduced stomatal density, stomatal aperture, transpiration rate, and water loss, and a higher chlorophyll content and photosynthetic rate. Our results suggest that PebHLH35 functions as a positive regulator of drought stress responses by regulating stomatal density, stomatal aperture, photosynthesis and growth.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Lysophosphatidic acid receptor-5 negatively regulates cellular responses in mouse fibroblast 3T3 cells

Highlights: • LPA{sub 5} inhibits the cell growth and motile activities of 3T3 cells. • LPA{sub 5} suppresses the cell motile activities stimulated by hydrogen peroxide in 3T3 cells. • Enhancement of LPA{sub 5} on the cell motile activities inhibited by LPA{sub 1} in 3T3 cells. • The expression and activation of Mmp-9 were inhibited by LPA{sub 5} in 3T3 cells. • LPA signaling via LPA{sub 5} acts as a negative regulator of cellular responses in 3T3 cells. - Abstract: Lysophosphatidic acid (LPA) signaling via G protein-coupled LPA receptors (LPA{sub 1}–LPA{sub 6}) mediates a variety of biological functions, including cell migration. Recently, we have reported that LPA{sub 1} inhibited the cell motile activities of mouse fibroblast 3T3 cells. In the present study, to evaluate a role of LPA{sub 5} in cellular responses, Lpar5 knockdown (3T3-L5) cells were generated from 3T3 cells. In cell proliferation assays, LPA markedly stimulated the cell proliferation activities of 3T3-L5 cells, compared with control cells. In cell motility assays with Cell Culture Inserts, the cell motile activities of 3T3-L5 cells were significantly higher than those of control cells. The activity levels of matrix metalloproteinases (MMPs) were measured by gelatin zymography. 3T3-L5 cells stimulated the activation of Mmp-2, correlating with the expression levels of Mmp-2 gene. Moreover, to assess the co-effects of LPA{sub 1} and LPA{sub 5} on cell motile activities, Lpar5 knockdown (3T3a1-L5) cells were also established from Lpar1 over-expressing (3T3a1) cells. 3T3a1-L5 cells increased the cell motile activities of 3T3a1 cells, while the cell motile activities of 3T3a1 cells were significantly lower than those of control cells. These results suggest that LPA{sub 5} may act as a negative regulator of cellular responses in mouse fibroblast 3T3 cells, similar to the case for LPA{sub 1}.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2011

Coherent population transfer and quantum entanglement generation involving a Rydberg state by stimulated Raman adiabatic passage

We study a dilute sample of cold atoms to achieve efficient population transfer from a ground state to a Rydberg state. This sample is approximately divided into many independent microspheres containing only two atoms. Each pair of atoms in a microsphere may become quantum correlated via the dipole-dipole interaction characterized by a van der Waals potential. Our numerical results show that, by modulating detunings of a pump pulse and a Stokes pulse applied in the counterintuitive order, we can drive the dilute sample either into the blockade regime or into the antiblockade regime. In the blockade regime, only one atom is allowed to be coherently transferred into the Rydberg state in a microsphere, which then results in a maximal entangled state. In the antiblockade regime, however, both atoms in a microsphere can be efficiently excited into the Rydberg state, which is not accompanied by quantum entanglement. A second maximal entangled state may also be generated if we work between the blockade regime and the antiblockade regime. Note that the existence of a quasidark state is essential for exciting both atoms in a microsphere into the Rydberg state when the van der Waals potential is nonzero.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

Electromagnetically induced transparency in a five-level {Lambda} system dominated by two-photon resonant transitions

We study the steady optical response of a five-level atomic system in the parametric region where resonant two-photon transitions are much stronger than far-detuned single-photon transitions. We find that the concurrent absorption of two weak probe fields can be well suppressed in a narrow spectral region to attain electromagnetically induced transparency (EIT) via quantum destructive interference between different two-photon transition pathways. To gain a deeper insight into relevant physics, we adiabatically reduce this five-level system with trivial single-photon transitions into a three-level system with vanishing single-photon transitions by deriving an effective Hamiltonian. The two systems have almost the same two-photon absorption spectra exhibiting typical EIT features but are a little different in fine details. This means that most characteristics of two-photon quantum destructive interference are reserved after the adiabatic elimination approximation. In addition, we verify by numerical calculations that the two-photon EIT spectra are insensitive to the dipole-dipole interaction of cold Rydberg atoms when the uppermost level has a high principle quantum number.

74 ATOMIC AND MOLECULAR PHYSICS↗