Genomic identification of microRNA promoters and their cis-acting elements in Populus

Yanwei Wang,Min Chen,Ming Wei,Zhanghui Dong,Hai Bao 한국유전학회 2016 Genes & Genomics Vol.38 No.4

MicroRNAs (miRNAs) are non-coding singlestranded RNAs of appropriately 21 nucleotides in length that negatively regulate post-transcriptional processes in plants and animals. In recent years, while an increasing number of miRNAs has been identified in various species, little is known regarding the specific transcriptional regulation of miRNAs in Populus. In this investigation, 368 miRNAs belonging to 37 miRNA families in Populus were analyzed to identify promoter regions and predict the distribution patterns of core promoter elements [TATA boxes and transcription start sites (TSSs)], as well as main cisacting elements through a bioinformatics approach. A total of 368 precursor miRNA (pre-miRNA) gene loci belonging to 213 unique miRNAs were detected. We identified 229 promoters and further predicted 121 TSSs and TATA boxes for 139 pre-miRNAs. The conserved motifs, base composition and the average free energy profiles in the neighboring regions of TSSs were further analyzed. In addition, 101 types of cis-acting elements, such as anaerobic induction elements, abscisic acid-response elements, and MYB binding sites, were predicted in the predicted promoter regions of the pre-miRNAs. The data obtained in our investigation may aid in the analysis of specific upstream sequences of pre-miRNAs for differential expression and further our understanding of the molecular biology of miRNAs in Populus.

Low-voltage blue light emission from n-ZnO/p-GaN heterojunction formed by RF magnetron sputtering method

Yanwei Shen,Xiang Chen,Xiaoqin Yan,Fang Yi,Zhiming Bai,Xin Zheng,Pei Lin,Yue Zhang 한국물리학회 2014 Current Applied Physics Vol.14 No.3

High quality n-ZnO/p-GaN heterojunction was fabricated by growing highly crystalline ZnO epitaxial films on commercial p-type GaN substrates via radio frequency (RF) magnetron sputtering. Low-voltage blue light emitting diode with a turn-on voltage of w2.5 V from the n-ZnO/p-GaN heterojunction was demonstrated. The diode gives a bright blue light emission located at w460 nm and a low threshold voltage of 2.7 V for emission. Based on the results of the photoluminescence (PL) and electroluminescence (EL) spectra, the origins of the EL emissions were studied in the light of energy band diagrams of ZnOeGaN heterojunction, and may attribute to the radiative recombination of the holes in p-GaN and the electrons injected from n-ZnO, which almost happened on the side of p-GaN layer. These results may have important implications for developing short wavelength optoelectronic devices.

A cosmic ray muons tomography system with triangular bar plastic scintillator detectors and improved 3d image reconstruction algorithm: A simulation study

Zhao Yanwei,Luo Xujia,Qin Kemian,Liu Guorui,Chen Daiyuan,Augusto R.S.,Zhang Weixiong,Luo Xiaogang,Liu Chunxian,Liu Juntao,Liu Zhiyi 한국원자력학회 2023 Nuclear Engineering and Technology Vol.55 No.2

Purpose: Muons are characterized by a strong penetrating ability and can travel through thousands of meters of rock, making them ideal to image large volumes and substances typically impenetrable to, for example, electrons and photons. The feasibility of 3D image reconstruction and material identification based on a cosmic ray muons tomography (MT) system with triangular bar plastic scintillator detectors has been verified in this paper. Our prototype shows potential application value and the authors wish to apply this prototype system to 3D imaging. In addition, an MT experiment with the same detector system is also in progress. Methods: A simulation based on GEANT4 was developed to study cosmic ray muons' physical processes and motion trails. The yield and transportation of optical photons scintillated in each triangular bar of the detector system were reproduced. An image reconstruction algorithm and correction method based on muon scattering, which differs from the conventional PoCA algorithm, has been developed based on simulation data and verified by experimental data. Results: According to the simulation result, the detector system’s position resolution is below 1 ~ mm in simulation and 2 mm in the experiment. A relatively legible 3D image of lead bricks in size of 20 cm 5 cm 10 cm used our inversion algorithm can be presented below 1 104 effective events, which takes 16 h of acquisition time experimentally. Conclusion: The proposed method is a potential candidate to monitor the cosmic ray MT accurately. Monte Carlo simulations have been performed to discuss the application of the detector and the simulation results have indicated that the detector can be used in cosmic ray MT. The cosmic ray MT experiment is currently underway. Furthermore, the proposal also has the potential to scan the earth, buildings, and other structures of interest including for instance computerized imaging in an archaeological framework.

Identification and comparative profiling of microRNAs in wild-type Xanthoceras sorbifolia and its double flower mutant

Yan Ao,Yanwei Wang,Lei Chen,Tao Wang,Haiyan Yu,Zhixiang Zhang 한국유전학회 2012 Genes & Genomics Vol.34 No.5

MicroRNAs are small, non-coding RNAs that regulate gene expression post-transcriptionally and have crucial roles in plant biological and metabolic processes. To date, there has been no report concerning miRNAs in Xanthoceras sorbifolia, one of the most important woody energy plants for biofuel production. To study the roles of miRNAs during floral organ differentiation and development in X. sorbifolia, two small RNA libraries were constructed from the flower buds of simple flowers (wild-type) and double flowers (mutant). Each library was sequenced individually and generated over 33 million raw reads in total. Forty-three conserved miRNAs belonging to 30families and 10 novel miRNAs were identified. The expressions of a selected group of conserved and novel miRNAs were validated by qRT-PCR. Target gene prediction identified 230 target genes for most of the conserved and novel miRNAs. Fifteen miRNAs were demonstrated to be differentially ex-pressed between wild-type and mutant. This is the first study to identify conserved and novel miRNAs and profile their expression changes during floral organ differentiation and development in X. sorbifolia.

Component Prototyping for the China Spallation Neutron Source Project

Jie Wei,Yanwei Chen,Yunlong Chi,Changdong Deng,Haiyi Dong,Shinian Fu,Wei He,Kaixi Huang,Wen Kang,Jian Li,Huafu Ouyang,Huamin Qu,Caitu Shi,Hong Sun,Jingyu Tang,Juzhou Tao,Sheng Wang,Zhongxiong Xu,Xueju 한국물리학회 2009 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.54 No.5

The China Spallation Neutron Source (CSNS) complex consists of an H- linear accelerator, a rapid cycling synchrotron accelerating the beam to 1.6 GeV, a solid tungsten target station and instruments for spallation neutron applications. The facility operates at a 25-Hz repetition rate with an initial design beam power of 120 kW and is upgradeable to 500 kW. The primary challenge is to build a robust and reliable user-friendly facility with upgrade potential at a fraction of the \world standard" cost. Success of the project relies on the results of prototyping research & development (R&D) of key technical systems and components. This paper discusses the prototyping experiences of the past two and a half years. The China Spallation Neutron Source (CSNS) complex consists of an H- linear accelerator, a rapid cycling synchrotron accelerating the beam to 1.6 GeV, a solid tungsten target station and instruments for spallation neutron applications. The facility operates at a 25-Hz repetition rate with an initial design beam power of 120 kW and is upgradeable to 500 kW. The primary challenge is to build a robust and reliable user-friendly facility with upgrade potential at a fraction of the \world standard" cost. Success of the project relies on the results of prototyping research & development (R&D) of key technical systems and components. This paper discusses the prototyping experiences of the past two and a half years.

Transcriptome-wide identification of miRNA targets and a TAS3- homologous gene in Populus by degradome sequencing

Hai Bao,Min Chen,Hui Chen,Liang Du,Yanwei Wang 한국유전학회 2019 Genes & Genomics Vol.41 No.7

Background Degradome sequencing has been applied to identify miRNA-directed mRNA cleavage and understand the biological function of miRNAs and their target genes in plants defense to stress. miRNAs involved in the response to cold stress have been identified in Populus, however, there are few reports about the validated targets of miRNAs in Populus under cold stress. Objectives The primary objective of this investigation was to globally identify and validate the targets of the miRNAs and regulatory components in Populus under cold stress. Methods Populus plantlets grown in vitro were treated with cold (4 °C for 8 h) and total RNA was extracted using Trizol reagent. Approximately 200 μg total RNA was used for the construction of the degradome library, and degradome sequencing was conducted on an Illumina HiSeq 2000. The sequences were mapped to Populus genome using SOAP 2.0 and then were collected for degradome analysis. Additionally, trans-acting siRNA sequences from transacting siRNA gene 3 sequences and mature miRNAs cleaved from precursor miRNAs of Populus were analyzed. 5′ RNA ligase-mediated-RACE (5′-RACE) were further conducted. Results 80 genes were experimentally determined to be the target of 51 unique miRNAs, including three down-regulated miRNAs (pto-miR156k, pto-miR169i-m, and pto-miR394a-5p/b-5p) and two up-regulated miRNAs (pto-miR167a-d and pto-miR167f/g). The specificity and diversity of cleavage sites of miRNA targets were validated through 5′-RACE experiment and the results were similar with that of degradome sequencing, further supporting the empirical cleavage of miRNAs on targets in vivo in Populus. Interestingly, the TAS-homologous gene pto-TAS3 (EF146176.1) was identified and 11 potential ta-siRNAs [D1(+)–D11(+)] and their possible biogenesis sites within the pto-TAS3 transcript sequence were predicted in Populus. In addition, the biosynthesis of miRNA from precursor miRNA (pre-miRNA) was also validated through the detection of a total of 17 pre-miRNAs. Conclusion Our investigation expands the application of degradome sequencing for evaluating miRNA regulatory elements and evidence of the miRNA synthesis process, and provides empirical evidence of bona fide cleavage of target genes by miRNAs in Populus, which might be used for the research of miRNA-mediated regulation mechanism and molecular improvement of resistance to cold stress.

Analytical prediction for depth of subsurface damage in silicon wafer due to self-rotating grinding process

Lixiang Zhang,Pei Chen,Tong An,Yanwei Dai,Fei Qin 한국물리학회 2019 Current Applied Physics Vol.19 No.4

Subsurface damage (SSD) induced by silicon wafer grinding process is an unavoidable problem in semiconductor manufacturing. Although experimental attempts have been made on investigation of the influential factors on the SSD depth, however, few theoretical studies have been conducted to obtain SSD depth through grinding parameters. To fill the gap, an analytical model is developed to predict the SSD depth in silicon wafer due to selfrotating grinding process, which can reveal the relationship among SSD depth and the grinding parameters, the size of the abrasive grains and the radial distance from the wafer center. The establishment of the proposed model is based on scratch theory and fracture mechanics of isotropic brittle materials, and we further consider the effects of elastic recovery, cleavage plane and crystalline orientation on SSD formation. To validate the applicability of the proposed predictive model, grinding experiments with varied grinding parameters are performed and the depths of SSD along the<110>and<100>crystal directions are also measured and analyzed. The results given by the proposed model present reasonable accuracy of less than 20% deviation with experimental results. Effects of grinding parameters, wafer radial distance, crystalline orientation, and abrasive grain size on SSD depth are discussed in detail.

Modulation of contact resistance between metal and graphene by controlling the graphene edge, contact area, and point defects: An <i>ab initio</i> study

Ma, Bo,Gong, Cheng,Wen, Yanwei,Chen, Rong,Cho, Kyeongjae,Shan, Bin American Institute of Physics 2014 Journal of Applied Physics Vol.115 No.18

Comparison of junction temperature variations of IGBT modules under DC and PWM power cycling test conditions

An, Tong,Tian, Yanzhong,Qin, Fei,Dai, Yanwei,Gong, Yanpeng,Chen, Pei The Korean Institute of Power Electronics 2022 JOURNAL OF POWER ELECTRONICS Vol.22 No.9

This paper presents an experimental investigation and a finite element (FE) analysis study on the thermal and mechanical behaviors of insulated-gate bipolar transistor (IGBT) power modules under various operating conditions. The power cycling test conditions are provided by two test benches, a direct current (DC) test bench and a pulse width modulation (PWM) test bench. Infrared (IR) camera acquisition methods are suggested as an approach for transient temperature measurements to estimate the effects of operating conditions and switching frequency on the thermal performance of an IGBT module. An electrical-thermal-mechanical FE model of an IGBT module is employed to determine the stress in the interconnections of an IGBT module induced by junction temperature fluctuations. Results indicate that the operating conditions significantly impact the maximum junction temperature, the junction temperature increase rate, and the junction temperature distribution of an IGBT chip and the thermally induced stress in the interconnections. The switching frequency strongly impacts the junction temperature of an IGBT chip, and the maximum junction temperature increases when the switching frequency increases due to the increasing switching loss. Furthermore, the junction temperature variation induced by the instantaneous switching loss is estimated by the proposed IR camera measurement method.

ZnO nanowire array ultraviolet photodetectors with self-powered properties

Zhiming Bai,Xiaoqin Yan,Xiang Chen,Hanshuo Liu,Yanwei Shen,Yue Zhang 한국물리학회 2013 Current Applied Physics Vol.13 No.1

A ZnO nanowire (NW) array ultraviolet photodetector (PD) with Pt Schottky contacts has been fabricated on a glass substrate. Under UV light illumination, this PD showed a high photo-to-dark current ratio of 892 at 30 V bias. Interestingly, it was also found that this PD had a high sensitivity of 475 without external bias. This phenomenon could be explained by the asymmetric Schottky barrier height (SBH) at the two ends causing different separation efficiency of photogenerated electronehole pairs, which resulted in the formation of photocurrent. It is anticipated to have potential applications in self-powered UV detection field.