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.

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.

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.

Affinity Propagation Algorithm Based on Locality Preserving Projections and Particle Swarm Optimization

Lele Liu,Zhiping Zhou,Jiefeng Wang 보안공학연구지원센터 2016 International Journal of Hybrid Information Techno Vol.9 No.6

Affinity propagation algorithm is a new powerful and effective clustering method. One of the major problems in clustering is the determination of the optimal number of clusters. In this paper, the particle swarm optimization algorithm is utilized to cope with this problem by using the parameter p as each particle and Silhouette index as the fitness, which can search for the optimal value of p and determine the optimal number of clusters automatically. Moreover, the problem of information overlap is the main drawback of affinity propagation algorithm in dealing with complex structure or high dimensional data for clustering. Hence the enhanced Locality preserving projections method is proposed to integrate with affinity propagation algorithm to reduce the dimension of the data as a processing step. As the result of experiment shows, the proposed method can simultaneously obtain the optimal number of clusters accurately and improve the clustering accuracy by eliminating the redundant information of the data without losing the internal nonlinear structure.

Design & Research of Legal Affairs Information Service Platform Based on UIMA and Semantics

Wang Chen,Zhang Jia,Qin Lele 보안공학연구지원센터 2016 International Journal of Future Generation Communi Vol.9 No.3

The law is the most powerful weapon to safeguard national stability and ensure flourishing of all causes as well as an instrument to protect the rights and interests of the masses, therefore, the just and accurate use of legal provisions is of crucial importance. With the increase of informatization level of the legal industry itself, more and more services in legal affairs are provided in information-based forms, and there is a large number of unstructured information in such business data. It’s a problem the legal industry needs to tackle in information management to rapidly acquire valuable content from the massive unstructured data and make use of such content. Based on analysis of problems arising in existing laws and regulations informatization system, this paper comes up with solution of a legal affairs information service platform based on cloud computing, UIMA, semantics, big data and Chinese word segmentation. This paper also proposes the four-layer technical framework solution on the basis of the design of integration and management method of unstructured data of heterology and isomerism, analyzing and processing method of unstructured data, semantics based unstructured information retrieval method and construction and maintenance method of ontology library. It also provides detailed introduction to the realization of the combination of big data and cloud computing and its application in this information platform by virtue of designing UFS - a distributed file system, MapReduce - a batch processing technology and BigTable - a distributed database. Data acquisition and expanded data analysis can be conducted by making use of the expandable UIMA framework and the sequential indexing of data content and analysis results can be materialized by means of applying Lucene indexing technology. With regard to information retrieval, the concept of ontology is introduced on the basis of traditional search model and a new search model based on domain ontology is proposed. IKAnalyzer 3.x is proposed to facilitate Chinese word segmentation. By taking advantage of such information service platform, legal affairs enterprises can effectively integrate structured and unstructured information resources and implement the storage, analysis, retrieval and decision-making applications of business data content.

Depositional and diagenetic controls on the reservoir quality of Upper Triassic Chang-7 tight oil sandstones, southwestern Ordos basin, China

Ai Wang,Dakang Zhong,Haihua Zhu,Lele Guo,Zhuopei Li,Yangjinfeng Jiang,Xueqi Yang,Rui Xie,Xiaowei Zheng 한국지질과학협의회 2019 Geosciences Journal Vol.23 No.3

The seventh oil layer of the Upper Triassic Yanchang Formation (Chang-7) tight oil sandstone reservoirs is a major exploration target. A significant amount of hydrocarbons has been discovered in these reservoirs in the southwestern Ordos basin in China. The Chang-7 tight sandstones are characterised as tight with low porosity, low permeability, and strong heterogeneity. This study investigates the sedimentary facies, diagenesis, and their impact on the reservoir quality of the Chang-7 tight oil sandstones. The sandstones were deposited in a deltaic-lacustrine depositional system. Three major depositional facies are identified consisting of delta front fed by braided rivers and meandering rivers, and slump turbidite fans. The depositional environment exerts a key control on reservoir quality. The distinct low-energy sedimentary environment produced fine to very fine-grained sandstones with high matrix and mica contents, characterised by low initial porosity and permeability. Diagenesis mainly comprised mechanical compaction and cementation by quartz, carbonate minerals and various clay minerals. The reservoir properties of the Chang-7 sandstones are generally poor, with porosity of 1.4–20.7% (average porosity 8.6%) and permeability of 0.001–116.7 mD (average 0.2 mD), which are attributed to significant compaction and cementation. Mechanical compaction was more important than cementation for reducing porosity, whereas secondary dissolution porosity was significant for the Chang-7 tight oil sandstones due to closer proximity to the underlying Chang-73 source rocks.

Analysis of oligosaccharides from Panax ginseng by using solid-phase permethylation method combined with ultra-high-performance liquid chromatography-Q-Orbitrap/mass spectrometry

Li, Lele,Ma, Li,Guo, Yunlong,Liu, Wenlong,Wang, Yang,Liu, Shuying The Korean Society of Ginseng 2020 Journal of Ginseng Research Vol.44 No.6

Background: The reports about valuable oligosaccharides in ginseng are quite limited. There is an urgent need to develop a practical procedure to detect and analyze ginseng oligosaccharides. Methods: The oligosaccharide extracts from ginseng were permethylated by solid-phase methylation method and then were analyzed by ultra-high-performance liquid chromatography-Q-Orbitrap/MS. The sequence, linkage, and configuration information of oligosaccharides were determined by using accurate m/z value and tandem mass information. Several standard references were used to further confirm the identification. The oligosaccharide composition in white ginseng and red ginseng was compared using a multivariate statistical analysis method. Results: The nonreducing oligosaccharide erlose among 12 oligosaccharides identified was reported for the first time in ginseng. In the comparison of the oligosaccharide extracts from white ginseng and red ginseng, a clear separation was observed in the partial least squares-discriminate analysis score plot, indicating the sugar differences in these two kinds of ginseng samples. The glycans with variable importance in the projection value large than 1.0 were considered to contribute most to the classification. The contents of oligosaccharides in red ginseng were lower than those in white ginseng, and the contents of maltose, maltotriose, maltotetraose, maltopentaose, maltohexaose, maltoheptaose, maltooctaose, maltononaose, sucrose, and erlose decreased significantly (p < 0.05) in red ginseng. Conclusion: A solid-phase methylation method combined with liquid chromatography-tandem mass spectrometry was successfully applied to analyze the oligosaccharides in ginseng extracts, which provides the possibility for holistic evaluation of ginseng oligosaccharides. The comparison of oligosaccharide composition of white ginseng and red ginseng could help understand the differences in pharmacological activities between these two kinds of ginseng samples from the perspective of glycans.

Diagentic features of illite in Upper Triassic Chang-7 tight oil sandstones, Ordos Basin

Ai Wang,Dakang Zhong,Haihua Zhu,Lele Guo,Yangjinfeng Jiang,Xueqi Yang,Rui Xie 한국지질과학협의회 2019 Geosciences Journal Vol.23 No.2

The Upper Triassic Chang-7 tight oil sandstones are the main tight clastic reservoirs in the Ordos Basin, central China. Illite is one of the most important cements affecting porosity and permeability of the tight oil sandstones, and this study focuses on different types of illitization and its relative formation time. The Chang-7 tight sandstones are mainly fine-grained lithic arkose and feldspar lithic sandstones, rich in mica and illite (hydrous mica). They are formed in distal delta front to semi-deep and deep lake facies, mainly deposited in a low energy environment. Porosity and permeability are very low (average porosity 8.58% and permeability 0.20 mD). The illite has many morphological characteristics and is multiphase, incorporating six types of illitization: hydrous mica, mica, and smectite illitization at the eodiagenetic stage, and kaolinite and K-feldspar illitization, and neoformation illite particles, at the mesodiagenetic stage. These different types of illitization are mainly controlled by sedimentary environment and provenance. Quartz overgrowth and diagenetic illites appear to be locally mutually exclusive, competing for detrital grain surfaces, but neoformation illite particles appear to form on the quartz overgrowth. The systematic study of Upper Triassic Chang-7 tight oil sandstones carried out here, enhances our understanding of illitization and the diagenetic model of the Ordos Basin, and contributes to reducing the exploration risk of continental tight sandstone reservoirs.

Effect of cooking methods on bioaccessibility of Zn, Se, Cd, Cu in sea cucumber (Apostichopus japonicus)

Chune Liu,Lele Wu,Ying Xue,Feng Liu,Shan Sun,Liming Wang 한국식품과학회 2018 Food Science and Biotechnology Vol.27 No.3

In this study, the total concentration and bioaccessibility of four metals (Zn, Se, Cd, Cu) in sea cucumbers (Apostichopus japonicus) before and after cooking were measured. The concentration of Zn, Se, Cd, and Cu were 22.24 ± 0.75, 0.75 ± 0.06, 0.32 ± 0.07, and 1.88 ± 0.09 mg/kg in raw cucumber, respectively. The contents of Zn, Se, and Cu in high-pressured samples were significantly higher than that in the raw sea cumber (p\0.01). The levels of Cd were all decreased after three thermal treatments. The intake of Zn and Cu increased in sea cucumber cooked by all thermal processes. While the bioaccessibility of Se and Cd decreased after cooking. A significant correlation was observed between the concentration and bioaccessibility of minerals. These data provide useful information for dietary risk assessments of minerals in sea cucumbers.

Effect of cooking methods on bioaccessibility of Zn, Se, Cd, Cu in sea cucumber (Apostichopus japonicus)

Liu, Chune,Wu, Lele,Xue, Ying,Liu, Feng,Sun, Shan,Wang, Liming 한국식품과학회 2018 Food Science and Biotechnology Vol.27 No.3

In this study, the total concentration and bioaccessibility of four metals (Zn, Se, Cd, Cu) in sea cucumbers (Apostichopus japonicus) before and after cooking were measured. The concentration of Zn, Se, Cd, and Cu were $22.24{\pm}0.75$, $0.75{\pm}0.06$, $0.32{\pm}0.07$, and $1.88{\pm}0.09mg/kg$ in raw cucumber, respectively. The contents of Zn, Se, and Cu in high-pressured samples were significantly higher than that in the raw sea cumber (p < 0.01). The levels of Cd were all decreased after three thermal treatments. The intake of Zn and Cu increased in sea cucumber cooked by all thermal processes. While the bioaccessibility of Se and Cd decreased after cooking. A significant correlation was observed between the concentration and bioaccessibility of minerals. These data provide useful information for dietary risk assessments of minerals in sea cucumbers.