SNP Discovery from Transcriptome of Cashmere Goat Skin

Wang, Lele,Zhang, Yanjun,Zhao, Meng,Wang, Ruijun,Su, Rui,Li, Jinquan Asian Australasian Association of Animal Productio 2015 Animal Bioscience Vol.28 No.9

The goat Capra hircus is one of several economically important livestock in China. Advances in molecular genetics have led to the identification of several single nucleotide variation markers associated with genes affecting economic traits. Validation of single nucleotide variations in a whole-transcriptome sequencing is critical for understanding the information of molecular genetics. In this paper, we aim to develop a large amount of convinced single nucleotide polymorphisms (SNPs) for Cashmere goat through transcriptome sequencing. In this study, the transcriptomes of Cashmere goat skin at four stages were measured using RNA-sequencing and 90% to 92% unique-mapped-reads were obtained from total-mapped-reads. A total of 56,231 putative SNPs distributed among 10,057 genes were identified. The average minor allele frequency of total SNPs was 18%. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Our follow up biological validation revealed that 64% of SNPs were true SNPs. Our results show that RNA-sequencing is a fast and efficient method for identification of a large number of SNPs. This work provides significant genetic resources for further research on Cashmere goats, especially for the high density linkage map construction and genome-wide association studies.

Dysregulated lncRNA and mRNA may promote the progression of ischemic stroke via immune and inflammatory pathways: results from RNA sequencing and bioinformatics analysis

Wang Yingshuang,Feng Feifei,Zheng Pingping,Wang Lijuan,Wang Yanjun,Lv Yaogai,Shen Li,Li Kexin,Feng Tianyu,Chen Yang,Liu Zhigang,Yao Yan 한국유전학회 2022 Genes & Genomics Vol.44 No.1

Background: Long non-coding RNAs (lncRNAs) are widely involved in gene transcription regulation and which act as epigenetic modifiers in many diseases. Objective: To determine whether lncRNAs are involved in ischemic stroke (IS), we analyzed the expression profile of lncRNAs and mRNAs in IS. Methods: RNA sequencing was performed on the blood of three pairs of IS patients and healthy controls. Differential expression analysis was used to identify differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs). Based on the co-expression relationships between lncRNA and mRNA, a series of bioinformatics analysis including GO and KEGG enrichment analysis and PPI analysis, were conducted to predict the function of lncRNA. Results: RNA sequencing produced a total of 5 DElncRNAs and 144 DEmRNAs. Influenza A pathway and Herpes simplex infection pathway were the most significant pathways. EP300 and NFKB1 were the most important target proteins, and Human leucocyte antigen (HLA) family were the key genes in IS. Conclusions: Analysis of this study revealed that dysregulated lncRNAs in IS may lead to IS by affecting the immune and inflammation system.

SNP Discovery from Transcriptome of Cashmere Goat Skin

Lele Wang,Yanjun Zhang,Meng Zhao,Ruijun Wang,Rui Su,Jinquan Li 아세아·태평양축산학회 2015 Animal Bioscience Vol.28 No.9

The goat Capra hircus is one of several economically important livestock in China. Advances in molecular genetics have led to the identification of several single nucleotide variation markers associated with genes affecting economic traits. Validation of single nucleotide variations in a whole-transcriptome sequencing is critical for understanding the information of molecular genetics. In this paper, we aim to develop a large amount of convinced single nucleotide polymorphisms (SNPs) for Cashmere goat through transcriptome sequencing. In this study, the transcriptomes of Cashmere goat skin at four stages were measured using RNA-sequencing and 90% to 92% unique-mapped-reads were obtained from total-mapped-reads. A total of 56,231 putative SNPs distributed among 10,057 genes were identified. The average minor allele frequency of total SNPs was 18%. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Our follow up biological validation revealed that 64% of SNPs were true SNPs. Our results show that RNA-sequencing is a fast and efficient method for identification of a large number of SNPs. This work provides significant genetic resources for further research on Cashmere goats, especially for the high density linkage map construction and genome-wide association studies.

Skin Lesion Image Segmentation Based on Adversarial Networks

( Ning Wang ),( Yanjun Peng ),( Yuanhong Wang ),( Meiling Wang ) 한국인터넷정보학회 2018 KSII Transactions on Internet and Information Syst Vol.12 No.6

Traditional methods based active contours or region merging are powerless in processing images with blurring border or hair occlusion. In this paper, a structure based convolutional neural networks is proposed to solve segmentation of skin lesion image. The structure mainly consists of two networks which are segmentation net and discrimination net. The segmentation net is designed based U-net that used to generate the mask of lesion, while the discrimination net is designed with only convolutional layers that used to determine whether input image is from ground truth labels or generated images. Images were obtained from “Skin Lesion Analysis Toward Melanoma Detection” challenge which was hosted by ISBI 2016 conference. We achieved segmentation average accuracy of 0.97, dice coefficient of 0.94 and Jaccard index of 0.89 which outperform the other existed state-of-the-art segmentation networks, including winner of ISBI 2016 challenge for skin melanoma segmentation.

Based on charge-transfer interaction organic light-response materials: From sphere-like nanoparticles to fibers

Lushan Wang,Tao Wang,Yanxin Jin,Peng Chen,Yanjun Gong,Yingyuan Zhao,Li Yu 한국물리학회 2015 Current Applied Physics Vol.15 No.8

We employed a potent and versatile ionic self-assembly (ISA) to prepare stimuli-responsive supramolecular materials using charged surfactants, N-dodecyl-4-(1-methylpip-erazine)-1,8-naphthalimide iodine [C12ndi]I and oppositely charged small molecule, 4-(phenylazo)benzoic acid sodium (PBAS). By transmission electron microscopy, nanospheres could be observed to transform into nanofibers upon irradiated with UV light (365 nm) for 1 h. The UVevis absorption spectra and fluorescence spectra of the fibers indicate that charge-transfer interaction is regarded as the driving force for the formation of fibers. Density functional theory (DFT) calculations prove that the pep stacking and electrostatic interactions between [C12ndi]I and PBAS contributes significantly to the resulting aggregates. The supramolecular fibers have the potential applications in some fields, e.g. drug delivery and electro-optical devices.

Expression of fox-related genes in the skin follicles of Inner Mongolia cashmere goat

Wenjing Han,Xiaoyan Li,Lele Wang,Honghao Wang,Kun Yang,Zhixin Wang,Ruijun Wang,Rui Su,Zhihong Liu,Yanhong Zhao,Yanjun Zhang,Jinquan Li 아세아·태평양축산학회 2018 Animal Bioscience Vol.31 No.3

Objective: This study investigated the expression of genes in cashmere goats at different periods of their fetal development. Methods: Bioinformatics analysis was used to evaluate data obtained by transcriptome sequencing of fetus skin samples collected from Inner Mongolia cashmere goats on days 45, 55, and 65 of fetal age. Results: We found that FoxN1, FoxE1, and FoxI3 genes of the Fox gene family were probably involved in the growth and development of the follicle and the formation of hair, which is consistent with previous findings. Real-time quantitative polymerase chain reaction detecting system and Western blot analysis were employed to study the relative differentially expressed genes FoxN1, FoxE1, and FoxI3 in the body skin of cashmere goat fetuses and adult individuals. Conclusion: This study provided new fundamental information for further investigation of the genes related to follicle development and exploration of their roles in hair follicle initiation, growth, and development.

Atomic insights into regulation of graphene sheets vertically attached to the FeF3·0.33H2O (002) surface by cation doping

Yanjun Pan,Yang Li,Jinda Luo,Xianyou Wang,Zhenhua Yang 한국물리학회 2019 Current Applied Physics Vol.19 No.10

Tightly and vertically attached graphene nanosheets (GNS) on the surface of FeF3·0.33H2O is extremely desirable to substantially accelerate electron transport, promoting rate capability of FeF3·0.33H2O. Based on present experiment and calculated surface energies, firstly, it has confirmed that F-terminated FeF3·0.33H2O (002) surface (FeF3·0.33H2O (002)-F) is more stable than FeF-terminated FeF3·0.33H2O (002) surface (FeF3·0.33H2O (002)- FeF) when μF varies from −1.92 eV to −0.30 eV. Then, by analysis of the interfacial structure and adsorption energies, it was proposed that GNS is incline to stand vertically on the FeF3·0.33H2O (002) surface via C–F bond. However, structural stability of FeF3·0.33H2O/GNS heterostructure is gradually weakened with increasing the number of GNS layers. Therefore, we further reported the important role of optimal doping element (Hf) in strengthening the vertical adsorption behavior of GNS on FeF3·0.33H2O (002) surface via thorough doping element search. And it turns out interfacial structure with hexa-coordinate polyhedron consists of Hf, F and O atoms is formed by strong hybridization of atomic orbits, which induces the interaction between FeF3·0.33H2O (002) surface and GNS to be profoundly strengthened.

Characteristics and formation mode of salt-bearing series in typical rift valley basin, eastern China

Yanjun Zhao,Chenglin Liu,Hua Zhang,Licheng Wang,Baokun Liu,Fenglin Lv 한국지질과학협의회 2015 Geosciences Journal Vol.19 No.1

The Shulu Sag is a typical rift valley basin in easternChina, where the formation mechanism of Cenozoic salt-bearingseries has been poorly understood. In this paper, petrologic analysis,X-ray powder Diffraction (XRD) analysis and the analysis ofhalite ion concentrations of the first member of the Shahejie Formationfrom two drilling cores were conducted to interpret theformation mechanism of these salt-bearing series in Shulu Sag. Theresults indicated that the salt-bearing series is mainly composed of calcilutiteor mudstone at top and bottom, and anhydrite-bearing haliteand thin interbeds of salt-bearing calcilutite and dark grey shale inthe middle part. These thin interbeds with porphyritic or petalshapedglauberite crystals or some thinner dark grey shale interbedsseparated halites into several members with the average thicknessof only 9~12 cm in the two drilling holes. This typical rhythmicpattern due to frequent alternation of concentration was evidencedby the variation of chemical composition and hydrogen isotopes ofhalite fluid inclusions. The presence of large number of primaryfluid inclusions within chevron crystals and vertically orientedbottom-growth crystals showed that the halite were precipitated inshallow water (<60 cm). These features are direct evidence for thisfrequent alternation of dissolution and concentration of brines andterrigenous detrital-chemical shallow-water sedimentary model ofthese small rift-valley basins in eastern China.

Methylation of methyltrichlorosilane with methyl chloride over active metals and activated carbon

Yanjun Liu,Yiqian Jiang,Weiguang Chen,Yutang Shen,Yonghai Feng,Lingqin Shen,Aili Wang,Tingshun Jiang,Zhanao Wu 한국화학공학회 2011 Korean Journal of Chemical Engineering Vol.28 No.12

Gas phase methylation of methyltrichlorosilane with methyl chloride to high-valued dimethyldichlorosilane was carried out by using metallic aluminum as a chlorine acceptor in the co-presence of activated carbon, tin, and zinc. The addition of activated carbon in metallic aluminum significantly enhanced the methylation of methyltrichlorosilane,and dimethyldichlorosilane was dominantly produced. Activated carbon played a catalyst role in the methylation reaction. When active metals, such as tin and zinc, were added in the mixture of aluminum and activated carbon,the active metals and activated carbon synergistically catalyzed the methylation of methyltrichlorosilane with methyl chloride toward the formation of dimethyldichlorosilane.

Multi‑objective parameter optimization of multi‑shaft ring‑plate magnetic gear

Yanjun Ge,Dongning Liu,Junyue Yang,Daming Wang 전력전자학회 2023 JOURNAL OF POWER ELECTRONICS Vol.23 No.3

Parameter setting and optimization are key steps to improving the transmission performance of eccentric permanent magnetgear. Studying this step makes it possible to analyze the transmission relationship between the design parameters, and improve both the operation stability and the carrying capacity of eccentric permanent magnet gear. Taking multi-shaft ring-plate magnet gear (MRMG) as the research object, this paper analyzes the influence of actual structural parameters on torque performance through the comprehensive sensitivity method, and selects the parameters with the greatest influence as the main optimization parameters. Then using the BSO algorithm and the BP neural network, a prediction model of MRMG electromagnetic torque and torque density is established, the relationship between each of the parameters is analyzed, and the optimization parameter points are determined. By comparison with finite element simulations and experiments, the built model and its measured results and FEM analysis are shown to have good accuracy (error < 6%). Moreover, the model can quickly and accurately obtain optimization parameters, and greatly improve the transmission performance of the structure (the maximum torque increases by 15%, and the torque density increases by 36%).