In silico identification and computational characterization of endogenous small interfering RNAs from diverse grapevine tissues and stages

Xudong Zhu,Songtao Jiu,Xiaopeng Li,Kekun Zhang,Mengqi Wang,Chen Wang,Jinggui Fang 한국유전학회 2018 Genes & Genomics Vol.40 No.8

Small interfering RNAs (siRNAs) are effectors of regulatory pathways underlying plant development, metabolism, and stress- and nutrient-signaling regulatory networks. The endogenous siRNAs are generally not conserved between plants; consequently, it is necessary and important to identify and characterize siRNAs from various plants. To address the nature and functions of siRNAs, and understand the biological roles of the huge siRNA population in grapevine (Vitis vinifera L.). The high-throughput sequencing technology was used to identify a large set of putative endogenous siRNAs from six grapevine tissues/organs. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed to classify the target genes of siRNA. In total, 520,519 candidate siRNAs were identified and their expression profiles exhibited typical temporal characters during grapevine development. In addition, we identified two grapevine trans-acting siRNA (TAS) gene homologs (VvTAS3 and VvTAS4) and the derived trans-acting siRNAs (tasiRNAs) that could target grapevine auxin response factor (ARF) and myeloblastosis (MYB) genes. Furthermore, the GO and KEGG analysis of target genes showed that most of them covered a broad range of functional categories, especially involving in disease-resistance process. The large-scale and completely genome-wide level identification and characterization of grapevine endogenous siRNAs from the diverse tissues by high throughput technology revealed the nature and functions of siRNAs in grapevine.

Triterpenoid saponins from Clinopodium chinense (Benth.) O. Kuntze and their biological activity

Yin-Di Zhu,Jing-Yi Hong,Feng-Da Bao,Na Xing,Ling-Tian Wang,Zhong-Hao Sun,Yun Luo,Hai Jiang,Xudong Xu,Nai-Liang Zhu,Hai-Feng Wu,Gui-Bo Sun,Jun-Shan Yang 대한약학회 2018 Archives of Pharmacal Research Vol.41 No.12

Four new ursane-type triterpenoid saponins, clinopoursaponins A–D (1–4), six new oleanane-type triterpenoid saponins, clinopodiside VII–XII (5–10), as well as eight known triterpene analogues (11–18), were isolated from the aerial parts of Clinopodium chinense (Benth.) O. Kuntze. The structures of the new compounds were determined based on extensive spectral analyses, including 1D (1H and 13C) and 2D NMR experiments (COSY, NOESY, HSQC, 2D TOCSY, HSQC-TOCSY and HMBC), HR-ESI-MS and chemical methods. Compounds 1–18 were evaluated for their protective effects against anoxia/reoxygenation-induced apoptosis in H9c2 cells and cytotoxicities against murine mammary carcinoma cell line 4T1. Compounds 8, 9 and 18 exhibited significant protective effects, while compound 1 exhibited cytotoxic activity with IC50 value of 7.4 μm compared to 7.6 μm for the positive control 10-hydroxycamptothecin.

Stress field interference of hydraulic fractures in layered formation

Zhu, Haiyan,Zhang, Xudong,Guo, Jianchun,Xu, Yaqin,Chen, Li,Yuan, Shuhang,Wang, Yonghui,Huang, Jingya Techno-Press 2015 Geomechanics & engineering Vol.9 No.5

Single treatment and staged treatments in vertical wells are widely applied in sandstone and mudstone thin interbedded (SMTI) reservoir to stimulate the reservoir. The keys and difficulties of stimulating this category of formations are to avoid hydraulic fracture propagating through the interface between shale and sand as well as control the fracture height. In this paper, the cohesive zone method was utilized to build the 3-dimensional fracture dynamic propagation model in shale and sand interbedded formation based on the cohesive damage element. Staged treatments and single treatment were simulated by single fracture propagation model and double fractures propagation model respectively. Study on the changes of fracture vicinity stress field during propagation is to compare and analyze the parameters which influence the interfacial induced stresses between two different fracturing methods. As a result, we can prejudge how difficult it is that the fracture propagates along its height direction. The induced stress increases as the pumping rate increasing and it changes as a parabolic function of the fluid viscosity. The optimized pump rate is $4.8m^3/min$ and fluid viscosity is $0.1Pa{\cdot}s$ to avoid the over extending of hydraulic fracture in height direction. The simulation outcomes were applied in the field to optimize the treatment parameters and the staged treatments was suggested to get a better production than single treatment.

Combined effect of carbonation and chloride ingress in concrete

Zhu, Xingji,Zi, Goangseup,Cao, Zhifeng,Cheng, Xudong Elsevier 2016 Construction and Building Materials Vol.110 No.-

<P><B>Abstract</B></P> <P>The combined effect of carbonation and chloride ingress in concrete is studied in this paper. Based on the change of the pore structure and the chemical equilibrium, a comprehensive model is proposed for this problem. A coupled simulation of the transports of carbon dioxide, chloride ions, heat and moisture is carried out. Several sets of experimental data were compared with the prediction by the numerical model developed in this paper, for its verification. Parametric study shows that the differences between the combined mechanism and the independent mechanisms are significant in many aspects.</P> <P><B>Highlights</B></P> <P> <UL> <LI> A comprehensive model for the combined carbonation and chloride ingress in concrete is developed. </LI> <LI> The effect of CSH is directly considered for the estimation of the degree of carbonation. </LI> <LI> The changes of the pore structure and the binding capacity are considered for the combined action. </LI> <LI> The corrosion initiation can be accelerated significantly by the combined mechanism. </LI> </UL> </P>

Microstructure and Texture Evolution of Rolled Plate for Cu–15Cr In-Situ Composite

XuDong Wu,LvQi Zhu,RuiRui Liu,HaiTao Zhou 대한금속·재료학회 2021 METALS AND MATERIALS International Vol.27 No.11

The microstructure and texture of different rolling processes in situ Cu–15Cr sheets are studied. The results show that thesecond phase Cr in the material gradually become broken, flattened, merged and homogenized from dendritic state to orientedthin lath. Meanwhile, the texture in distributed copper matrix grains finally forms Brass {110}<112>, Goss {001}<110>and Copper {112}<111> textures along with Cr phase texture of randomly distributed α-fiber (<110> fiber) and γ-fiber(<111> fiber) texture. Based on VPSC (visco-plastic self-consistent model), the texture of cold rolled Cu–15Cr compositeis simulated, and the simulation result indicates that obvious twinning effect in the copper matrix appears with a feature ofa special texture evolution law of Goss.

Mechanical Behavior and Damage Evolution for Concrete Subjected to Multiple Impact Loading

Xudong Chen,Lingyu Xu,Qiao Zhu 대한토목학회 2017 KSCE JOURNAL OF CIVIL ENGINEERING Vol.21 No.6

In order to explore the dynamic mechanical properties and damage evolution for concrete under the repeated impact loading, the large-diameter (74 mm) Split Hopkinson Pressure Bar (SHPB) was used to conduct the dynamic compression test. The damage was calculated by the Weibull statistical damage model, and the stress-strain curves of concrete were analyzed to study the repeated impact loading effects on the damage of concrete. Meanwhile, the fracture process of the concrete was simulated with the finite element software (LS-DYNA) and Johnson Holmquist Concrete (*MAT_JOHNSON_HOLMQUIST_CONCRETE) constitutive model. The results showed that the dynamic elastic modulus and the peak stress of the specimens decreased with the increased number of repeated impacts, while the peak strain increased. The damage of concrete increased with the increased strain, and the damage increased sharply after the “inflection point”. In addition, the results obtained by finite element simulation agree with the experimental results.

Mechanical properties of pervious concrete with recycled aggregate

Xiangyi Zhu,Xudong Chen,Nan Shen,Huaxuan Tian,Xiangqian Fan,Jun Lu 사단법인 한국계산역학회 2018 Computers and Concrete, An International Journal Vol.21 No.6

In order to research the influence of different recycled aggregate contents on the mechanical properties of pervious concrete, the experimental study and numerical simulation analysis of the mechanical properties of pervious concrete with five kinds of recycled aggregates contents (0%, 25%, 50%, 75% and 100%) are carried out in this paper. The experimental test were first performed on concrete specimens of different sizes in order to determine the influence of recycled aggregate on the compressive strength and splitting tensile strength, direct tension strength and bending strength. Then, the development of the internal cracks of pervious concrete under different working conditions is studied more intuitively by PFC3D. The experimental results show that the concrete compressive strength, tensile strength and bending strength decrease with the increase of the recycled aggregate contents. This trend of reduction is not only related to the brittleness of recycled aggregate concrete, but also to the weak viscosity of recycled aggregate and cement paste. It is found that the fracture surface of pervious concrete with recycled aggregate is smoother than that of natural aggregate pervious concrete by PFC3D, which means that the bridging effect is weakened in the stress transfer between the left and right sides of the crack. Through the analysis of the development of the internal cracks, the recycled aggregate concrete generated more cracks than the natural aggregate concrete, which means that the recycled aggregate concrete is easier to form a coalescence fracture surface and eventually break.

Analysis of notch depth and loading rate effects on crack growth in concrete by FE and DIC

Xiangyi Zhu,Xudong Chen,Jun Lu,Xiangqian Fan 사단법인 한국계산역학회 2019 Computers and Concrete, An International Journal Vol.24 No.6

In this paper, the fracture characteristics of concrete specimens with different notch depths under three-point flexural loads are studied by finite element and fracture mechanics methods. Firstly, the concrete beams (the size is 700×100×150 mm) with different notch depths (a=30 mm, 45 mm, 60 mm and 75 mm respectively) are tested to study the influence of notch depths on the mechanical properties of concrete. Subsequently, the concrete beams with notch depth of 60 mm are loaded at different loading rates to study the influence of loading rates on the fracture characteristics, and digital image correlation (DIC) is used to monitor the strain nephogram at different loading rates. The test results show that the flexural characteristics of the beams are influenced by notch depths, and the bearing capacity and ductility of the concrete decrease with the increase of notch depths. Moreover, the peak load of concrete beam gradually increases with the increase of loading rate. Then, the fracture energy of the beams is accurately calculated by tail-modeling method and the bilinear softening constitutive model of fracture behavior is determined by using the modified fracture energy. Finally, the bilinear softening constitutive function is embedded into the finite element (FE) model for numerical simulation. Through the comparison of the test results and finite element analysis, the bilinear softening model determined by the tail-modeling method can be used to predict the fracture behavior of concrete beams under different notch depths and loading rates.

CCCTC-Binding Factor Controls Its Own Nuclear Transport via Regulating the Expression of Importin 13

Rong Wang,Xudong Zhu,Jingjing Shen,Peitang Huang 한국분자세포생물학회 2013 Molecules and cells Vol.35 No.5

CCCTC-binding factor (CTCF), a multivalent zinc-finger protein, is involved in different aspects of regulation including promoter activation or repression, gene silencing, chromatin insulation, gene imprinting, X-chromosome inactivation, cell growth or differentiation and tumor genesis. However, the molecular mechanisms of CTCF nuclear import remains unclear. In this study, we showed that the expression of CTCF influenced the intracellular distribution of itself, which might go through transport receptor -import 13 (IPO13). We further confirmed that there is a CTCF target site in ipo13 -774~-573 bp promoter region and CTCF regulates the expression of IPO13. Besides, GST pull-down and Co-IP experiments demonstrated that CTCF interacts with IPO13. Immunofluorescence staining showed that IPO13 influenced intracellular distribution of CTCF. In all, we conclude that CTCF regulates the expression of IPO13, which, in turn, mediates the nuclear import of CTCF.

Rapid Identification of the Layer Number of Large-Area Graphene on Copper

Qi, Zhikai,Zhu, Xudong,Jin, Hongchang,Zhang, Tiezhu,Kong, Xianghua,Ruoff, Rodney S.,Qiao, Zhenhua,Ji, Hengxing American Chemical Society 2018 Chemistry of materials Vol.30 No.6

<P>Chemical vapor deposition (CVD) on Cu foils emerged as an important method for preparing high-quality and large-area graphene films for practical applications. However, to date it remains challenging to rapidly identify the structural features, especially the layer numbers, of CVD-graphene directly on Cu substrate. Herein, we report an O<SUB>2</SUB>-plasma-assisted approach for identifying the coverage, wrinkles, domain size, and layer number of large-area graphene films on Cu foils by optical microscopy. The wrinkles and grain boundaries of five-layer graphene can be observed with a grayscale increment of ∼23.4% per one graphene layer after O<SUB>2</SUB>-plasma treatment for only 15 s, which allows for checking graphene on Cu foils with a sample size of 17 cm × 20 cm in a few minutes. The Raman spectroscopy and X-ray photoelectron spectroscopy presents a strong layer number dependence of both the plasma induced graphene defects and Cu oxides, which, as indicated by molecular dynamic simulation, is responsible for the improved image contrast as a result of the interaction between O-ions and graphene with different layer numbers. We expect that this O<SUB>2</SUB>-plasma-assisted method would be applied to meter-scale samples if atmospheric-pressure plasma is used and therefore will be beneficial for the fast evaluation of CVD-graphene in both laboratory and industry.</P> [FIG OMISSION]</BR>