Characterization and development of EST-SSR markers to study the genetic diversity and populations analysis of Jerusalem artichoke (Helianthus tuberosus L.)

Shipeng Yang,Qiwen Zhong,Jie Tian,Lihui Wang,Mengliang Zhao,Li Li,Xuemei Sun 한국유전학회 2018 Genes & Genomics Vol.40 No.10

In recent years, Jerusalem artichoke has received widespread attention as a novel source of sugar, biofuel, and animal feed. Currently, only few gDNA-SSRs derived from sunflower were verified in the Jerusalem artichoke; therefore, it is particularly important to develop SSR primer markers that belonged to Jerusalem artichoke resources. Using EST data to develop EST-SSR markers is simple and effective. In order to understand the general characteristics of SSR markers in Jerusalem artichoke EST sequences and accelerate the use of SSR markers in Jerusalem artichoke research. This study used 40,370 sequenced unigene fragments and MISA software to identify SSR loci. The 48 pairs of EST-SSR primers assessed for the identification of 45 varieties of Jerusalem artichoke. Cluster, genetic diversity parameters and AMOVA analysis was conducted using the genetic similarity coefficient, revealing genetic differences between 48 genetic material. A total of 1204 SSR loci were identified with 13 different types of repeats, distributed among 1020 EST sequences, of which trinucleotide repeats were the most common, accounting for 38.21% of the total SSR loci. Among the 44 repeat motifs, AG/CT, AAG/ CTT, and ATC/ATG motifs had the highest frequencies, accounting for 22.45, 14.71, and 7.84% of all motifs, respectively. From these sequences, 48 pairs of EST-SSR primers were designed, and 22 primer pairs for loci with high polymorphism were selected to analyze the genetic diversity of 45 Jerusalem artichoke germplasm sources. The results indicated that the variation range of the effective number of alleles for 22 primers ranged between 1.7502 and 4.5660. The Shannon’s information index ranged between 0.6200 and 1.6423. The variation range of PIC ranged between 0.3121 and 0.6662 with an average of 0.5184. Cluster analysis was conducted using the genetic similarity coefficient, revealing significant genetic differences between Asian and European genetic material. Cluster analysis revealed a relationship between the genotypes and geographic origins of the Jerusalem artichoke. The results of AMOVA as well as the genetic identity and genetic distance in the Jerusalem artichoke population showed that there presented certain genetic heterogeneity in Jerusalem artichoke genetic structure of 45 samples from seven different geographic populations. The Jerusalem artichoke EST-SSR marker system established in this study provides an effective molecular marker system for future research focused on Jerusalem artichoke genetic diversity and the breeding of new varieties.

Incomplete Cholesky Decomposition based Kernel Cross Modal Factor Analysis for Audiovisual Continuous Dimensional Emotion Recognition

( Xia Li ),( Guanming Lu ),( Jingjie Yan ),( Haibo Li ),( Zhengyan Zhang ),( Ning Sun ),( Shipeng Xie ) 한국인터넷정보학회 2019 KSII Transactions on Internet and Information Syst Vol.13 No.2

Recently, continuous dimensional emotion recognition from audiovisual clues has attracted increasing attention in both theory and in practice. The large amount of data involved in the recognition processing decreases the efficiency of most bimodal information fusion algorithms. A novel algorithm, namely the incomplete Cholesky decomposition based kernel cross factor analysis (ICDKCFA), is presented and employed for continuous dimensional audiovisual emotion recognition, in this paper. After the ICDKCFA feature transformation, two basic fusion strategies, namely feature-level fusion and decision-level fusion, are explored to combine the transformed visual and audio features for emotion recognition. Finally, extensive experiments are conducted to evaluate the ICDKCFA approach on the AVEC 2016 Multimodal Affect Recognition Sub-Challenge dataset. The experimental results show that the ICDKCFA method has a higher speed than the original kernel cross factor analysis with the comparable performance. Moreover, the ICDKCFA method achieves a better performance than other common information fusion methods, such as the Canonical correlation analysis, kernel canonical correlation analysis and cross-modal factor analysis based fusion methods.

Transcript Profiling of Toll-Like Receptor mRNAs in Selected Tissues of Mink (Neovison vison)

( Mingwei Tong ),( Li Yi ),( Yuening Cheng ),( Miao Zhang ),( Zhigang Cao ),( Jianke Wang ),( Hang Zhao ),( Peng Lin ),( Yong Yang ),( Shipeng Cheng ) 한국미생물 · 생명공학회 2016 Journal of microbiology and biotechnology Vol.26 No.12

Toll-like receptors (TLRs) can recognize conserved molecular patterns and initiate a wide range of innate and adaptive immune responses against invading infectious agents. The aim of this study was to assess the transcript profile of mink TLRs (mTLRs) in mink peripheral blood mononuclear cells (PBMCs) and a range of tissues, and to explore the potential role of mTLRs in the antiviral immune response process. The results indicated that the mTLR partial nucleotide sequences had a high degree of nucleotide identity with ferret sequences (95-98%). Phylogenetic analysis showed that mammalian TLRs grouped into five TLR families, with a closer relationship of the mTLRs with those of ferret than the other mammalian sequences. Moreover, all the mTLRs were ubiquitously expressed in lymphoid organs (spleen and lymph nodes) and PBMCs. Interestingly, the mTLR expression patterns in lung, uterus, and heart showed quite a lot of similarity. Another remarkable observation was the wide expression of mTLR1-3 mRNAs in all tissues. Among the analyzed tissues, skeletal muscle was revealed to being the lowest repertoire of mTLR expression. Additionally, mink PBMCs exposed to the canine distemper virus revealed significant upregulation of mTLR2, mTLR4, mTLR7, and mTLR8 mRNAs, indicating that mTLRs have a role in innate immunity in the mink. Collectively, our results are the first to establish the basic expression patterns of mTLRs and the relationship between mTLRs and a virus, which will contribute to better understanding of the evolution and the functions of mTLRs in the innate immune system in minks.

The Mechanism for the Quasi-Back-Attack Phenomenon of Gas Jets Submerged in Water

Tang Yunlong,Li Shipeng 한국항공우주학회 2019 International Journal of Aeronautical and Space Sc Vol.20 No.1

Over-expanded and under-expanded gas jets submerged in water have been studied through numerical simulation and experiments. Comparisons between numerical and experimental results are made to validate the conclusion that the ‘quasi-back-attack’ phenomenon in high-unexpanded conditions is caused by the obstruction of the shock waves acted on back-attacked gas. As a consequence, back-attacked gas cannot reach the wall of the motor. A detailed analysis of the results reveals the underlying mechanism of the structure of the gas jet under different operating conditions. Meanwhile, the characterization of the motor’s thrust indicates that the oscillation amplitude of thrust drops sharply after the occurrence of quasi-back-attack phenomenon, which is beneficial to the stability of the motor.

A rapid prediction method for the stiffness and the machining accuracy evaluation of a parallel kinematic mechanism

Mengrui Shi,Hao Li,Shipeng Li,Xuda Qin,Haitao Liu 대한기계학회 2023 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.37 No.11

This paper innovatively proposes a rapid prediction method for the stiffness the parallel kinematic mechanism (PKM) considering the geometric characteristics of the limb and the external loads with structural mechanics method. And the hybrid PKM named TriMule is taken as an example to demonstrate the correctness of the method by milling experiments of titanium alloy. In the slot milling, the deviation between the simulation of this method and experimental results of dimensional accuracy was only 0.21 %, and in the helical milling, the deviation was only 21 %. On this basis, the average stiffness index is proposed to evaluate the machining dimensional accuracy of the PKM, which is maintain at a high level around 10 5 -10 7 . The method proposed in this paper can predict the machining capacity of the PKM and the approximate machining deviation in working space, and provide a basis for the subsequent optimization of the cutting process parameters and working space.

A Bayesian Network Approach to Launch Vehicle Software Failure Prediction

Tinggui Yan,Xiaoqian Chen,Shipeng Li,Li Ma,Jian Bai,Zhifang Yang 보안공학연구지원센터 2016 International Journal of Multimedia and Ubiquitous Vol.11 No.11

Launch Vehicle software has played an important role in Launch Vehicle system. However, the reliability assessment of Launch Vehicle software is still a hard problem due to the complexity of Launch Vehicle software. Failure prediction can be an effective approach of Launch Vehicle reliability evaluation, whereas failure prediction of software has not yet been fully explored. In this paper, a Markov Bayesian Network model for Launch Vehicle software failure prediction (MBNG) is proposed. In MBNG, unique features of Launch Vehicle software is considered as an important part in the modeling process, which improves the effectiveness of this novel model. Experiments are conducted to verify the effectiveness of MBNG model and compare its performance with classic models.

Enhanced photon shielding efficiency of a flexible and lightweight rare earth/polymer composite: A Monte Carlo simulation study

Wang Ying,Wang Guangke,Hu Tao,Wen Shipeng,Hu Shui,Liu Li 한국원자력학회 2020 Nuclear Engineering and Technology Vol.52 No.7

Photons with the energy of 60 keV are regularly used for some kinds of bone density examination devices, like the single photon absorptiometry (SPA). This article reports a flexible and lightweight rare earth/polymer composite for enhancing shielding efficiency against photon radiation with the energy of 60 keV. Lead oxide (PbO) and several rare earth element oxides (La2O3, Ce2O3, Nd2O3) were dispersed into natural rubber (NR) and the photon radiation shielding performance of the composites were assessed using monte carlo simulation method. For 60 keV photons, the shielding efficiency of rare earthbased composites were found to be much higher than that of the traditional lead-based composite, which has bad absorbing ability for photons with energies between 40 keV and 88 keV. In comparison with the lead oxide based composite, Nd2O3-NR composite with the same protection standard (the lead equivalent is 0.25 mmPb, 0.35 mmPb and 0.5 mmPb, respectively), can reduce the thickness by 35.29%, 37.5% and 38.24%, and reduce the weight by 38.91%, 40.99% and 41.69%, respectively. Thus, a flexible, lightweight and lead-free rare earth/NR composite could be designed, offering efficient photon radiation protection for the users of the single photon absorptiometry (SPA) with certain energy of 60 keV

Analysis of the DNA Methylation of Maize (Zea mays L.) in Response to Cold Stress Based on Methylation-sensitive Amplified Polymorphisms

Xiaohui Shan,Xiaoyu Wang,Guang Yang,Ying-Wu Lan,Shengzhong Su,Shipeng Li,Hongkui Liu,Yaping Yuan 한국식물학회 2013 Journal of Plant Biology Vol.56 No.1

DNA methylation plays a vital role in tuning geneexpression in response to environmental stimuli. Here,methylation-sensitive amplified polymorphisms (MSAP)were used to assess the effect of cold stress on the extent andpatterns of DNA methylation in maize seedlings. Overall,cold-induced genome-wide DNA methylation polymorphismsaccounted for 32.6 to 34.8% of the total bands at the differenttreatment time-points. It was demonstrated that the extentand pattern of DNA methylation was induced by cold stressthrough the cold treatment process and that thedemethylation of fully methylated fragments was the maincontributor of the DNA methylation alterations. The sequencesof 28 differentially amplified fragments relevant to stresswere successfully obtained. Under the cold stress, demethylationwas detected in most fragments. BLAST results indicate thatthe homologues of these fragments are involved in manyprocesses, including hormone regulation, cold response,photosynthesis, and transposon activation. The expressionanalysis demonstrated an increase in the transcription of fivedemethylated genes. Despite the fact that DNA methylationchanges and cold acclimation are not directly associated, ourresults may indicate that the specific demethylation of genesis an active and rapid epigenetic response to cold in maizeduring the seedling stage, further elucidating the mechanismof maize adaptation to cold stress.