De novo assembly, gene annotation, and molecular marker development using Illumina paired-end transcriptome sequencing in the clam Saxidomus purpuratus

Hongjun Li,Min Liu,Sheng Ye,Feng Yang 한국유전학회 2017 Genes & Genomics Vol.39 No.6

The clam Saxidomus purpuratus is an important economic marine bivalve species in China. In this study, we performed a de novo transcriptome sequencing of S. purpuratus gill tissues to generate a transcriptome dataset by performing Illumina paired-end sequencing on the HiSeq 2500 platform. A total of 10,488,024 raw reads were produced. After removing the inferior sequences, adaptor sequences, and rRNAs, 68,080,636 high-quality reads were obtained, from which 5,115,494 assembled contigs were produced. These contigs were assembled into 120,479 transcripts and 66,388 unigenes with mean lengths of 674.96 and 562.70 bp, respectively. All unigene sequences were compared against the NCBI databases, and 26,781 unigenes were annotated. Both the gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that several functional genes were involved in the stress response, immune system, and oxidation reduction process. Meanwhile, 414 simple sequence repeats (SSRs) were identified in the S. purpuratus transcriptome. SSR validation via PCR confirmed that 26 primer pairs had expected products, and 13 primers proved to be polymorphism among 30 individuals. The S. purpuratus transcriptome advances the underlying molecular understanding of this economic shellfish and provides a basis for further exploring S. purpuratus genomics resources.

Hybrid Full Frequency Precoding for Integrated Remote Wireless Sensor and Multibeam Satellite Networks

( Hongjun Li ),( Feihong Dong ),( Xiangwu Gong ),( Changliang Deng ),( Luliang Jia ),( Jingchao Wang ) 한국인터넷정보학회 2016 KSII Transactions on Internet and Information Syst Vol.10 No.6

This paper investigates an efficient transmission scheme for the remote wireless sensors to receive information which is rarely discussed in the integrated remote wireless sensor and multibeam satellite networks (IWSMSNs). The networks can be employed to exchange sensing information for emergency scenario, ocean scenario, and so on, which are isolated from available terrestrial networks. As the efficient transmission link is important to the IWSMSNs, we propose a hybrid full frequency (HFF) precoding by taking advantage of frequency reuse and multiple-input multiple-output (MIMO) precoding. Considering energy efficiency and sinks fairness are crucial to transmission link, thus the HFF precoding problems are formulated as transmit power minimization (TPM) and max-min fair (MMF) received signal to interference plus noise ratio (SINR) problems, which can be transformed to indefinite quadratic optimization programs. Then this paper presents a semi-definite programming (SDP) algorithm to solve the problems for the IWSMSNs. The promising potential of HFF for the real IWSMSNs is demonstrated through simulations.

王守仁與鄭齊斗"良知"思想的相同性與特殊性探究

이홍군 ( Hongjun Li ) 한국동서철학회 2015 동서철학연구 Vol.77 No.-

陽明學은 조선에 전래된 이래, 정제두 등 학자들에 의해 계승, 발전 되어왔다. "良知"는 왕수인 심학체계의 최고범주이다. "양지"에 대한 이해와 해석에 있어서 왕수인과 정제두는 기본적으로 상동하다. 양자 모두 "양지"를 "마음의 본체", "행위의 강령", "밝혀야 할 대상"으로 이해하였다. 그러나 양자가 처한 시대배경과 정치상황의 차이로 인해 "양지"에 대한 해석에 있어서 약간의 차이성 즉 특수성을 보인다. 정제두는 왕수인의 "양지" 범주를 축소시켜, "양지와 우주"의 관계로부터 "양지와 사람"의 관계 차원에 치중하여 인간의 가치와 인간의 주체적 의식 활동을 강조하였다. 정제두는 왕수인에 비해 도덕적 이성, 人性本善의 측면에 치중하여 "양지"를 해석하였다. 정제두는 또한 "生氣", "生理", "生道"등 범주를 가지고 왕수인의 기본명제를 해석하는데, 이는 정제두의 "活理"를 추구하는 생태철학적 사유이며, 또한 정제두의 대왕수인의 특수성이라고 하겠다. "양지"정신은 현대사회가 안고 있는 문제를 해결하는 良藥이다. 그것은 다름 아니라 도덕이상주의, 인문정신, 和而不同정신, 力行實踐정신이라 하겠다. 이러한 "양지"정신에 대한 학문적 추구는 강력한 생명력과 실천의미를 가지고 있는 살아있는 문화에 대한 추구라 하겠다. 이에 우리는 "양지"정신을 더욱 깊이 발굴하고 발전시켜야 할 것이다. intuitive knowledge is the highest category of Wang Shouren``s mental outlook system. After Yangming Doctrine was transferred to North Korea, it was inherited and developed by Zheng Qidou and other scholars. On the understanding and interpretation of the ``intuitive knowledge``, Wang Shouren and Zheng Qidou are basically the same, both regard intuitive knowledge as the substance of the heart, the outline of behavior , the object of Ming. However, there are some differences between Wang Shouren and Zheng Qidou``s interpretation of the ``intuitive knowledge``, which due to the different background and political situation of the times. Zheng Qidou relatively narrowed Wang Shouren``s ``category of intuitive knowledge, from ``conscience and the universe`` level to the ``conscience and the human`` level, which pays more attention to the meaning of human and subject``s Conscious Activity.Compared with Wang Shouren , Zheng Qidou chose to focus more on the perspective of moral reason and good human nature to interpret ``intuitive knowledge`` . In addition, Zheng Qidou also used the concept of "live spirit," "live reason", "live Tao" and other conceptions to elaborate the basic proposition of Yangming Doctrine.This is not only the distinguishing feature of Zheng Qidou relative to Wang Shouren and other Yangming Doctrine, but also the Philosophical characteristics which Zheng Qidou put much emphasis on. Theory of Wang Shouren``s intuitive knowledge`` includes the spirit of moral idealism, humanism, harmony but not sameness and practice. ``Conscience`` spirit is of practical significance to the modern social problems acting as an antidote against the disease. In a word, Yangming Doctrine was not dead, but has strong vitality and practical significance of the living culture, we should explore and carry them forward.

Elevated TRAF4 expression impaired LPS-induced autophagy in mesenchymal stem cells from ankylosing spondylitis patients

Jinteng Li,Peng Wang,Zhongyu Xie,Rui Yang,Yuxi Li,Xiaohua Wu,Hongjun Su,Wen Deng,Shan Wang,Zhenhua Liu,Shuizhong Cen,Yi Ouyang,Yanfeng Wu,Huiyong Shen 생화학분자생물학회 2017 Experimental and molecular medicine Vol.49 No.-

Ankylosing spondylitis (AS) is a type of autoimmune disease that predominantly affects the spine and sacroiliac joints. However, the pathogenesis of AS remains unclear. Some evidence indicates that infection with bacteria, especially Gram-negative bacteria, may have an important role in the onset and progression of AS. Recently, many studies have demonstrated that mesenchymal stem cells (MSCs) dysfunction may contribute to the pathogenesis of many rheumatic diseases. We previously demonstrated that MSCs from AS patients exhibited markedly enhanced osteogenic differentiation capacity in vitro under non-inflammatory conditions. However, the properties of MSCs from AS patients in an inflammatory environment have never been explored. Lipopolysaccharide (LPS), a proinflammatory substance derived from the outer membrane of Gram-negative bacteria, can alter the status and function of MSCs. However, whether MSCs from AS patients exhibit abnormal responses to LPS stimulation has not been reported. Autophagy is a lysosome-mediated catabolic process that participates in many physiological and pathological processes. The link between autophagy and AS remains largely unknown. The level of autophagy in ASMSCs after LPS stimulation remains to be addressed. In this study, we demonstrated that although the basal level of autophagy did not differ between MSCs from healthy donors (HDMSCs) and ASMSCs, LPS-induced autophagy was weaker in ASMSCs than in HDMSCs. Specifically, increased TRAF4 expression in ASMSCs impaired LPS-induced autophagy, potentially by inhibiting the phosphorylation of Beclin-1. These data may provide further insight into ASMSC dysfunction and the precise mechanism underlying the pathogenesis of AS.

Predicting the Weed Control Efficacy of Photosynthesis Inhibitors by PPM Method

HONGJUN ZHANG,HAILAN CUI,JIMING YE,XUE LIU,XIANGJUN LI,CORNE KEMPENAAR,SHOUHUI WEI,HANWEN NI 韓國雜草學會 2009 Weed&Turfgrass Science Vol.29 No.3

The experiment was conducted in a greenhouse in Beijing, China, to determine whether weed control efficacy could be predicted based on Plant Photosynthesis Meter (PPM) values measured shortly after the application of photosynthesis inhibitors. The decrease of PPM values of the weed leaves treated with the mixture of atrazine and bentazone could be measured 1 day after treatment (DAT). The decreased extents depended on weed susceptibility and application dosage. There was significant correlation between the PPM values of the treated leaves 1 to 3 DAT and the biomass reduction 14 DAT. The experimental findings indicated that PPM values measured in early days after treatment could give reasonable prediction on weed control. The herbicide usually provided 90% control by weed biomass when PPM value was about 20 and relatively poor control when PPM value over 20.

Synthesis, Crystal Structure and Fungicidal Activities of New Type Oxazolidinone-Based Strobilurin Analogues

Li, Yuhao,Liu, Rui,Yan, Zhangwei,Zhang, Xiangning,Zhu, Hongjun Korean Chemical Society 2010 Bulletin of the Korean Chemical Society Vol.31 No.11

A series of oxazolidinone-based strobilurin analogues were efficiently synthesized by the reaction of 3-(2-bromomethylphenyl) oxazolidin-2-one with 1-substituted phenyl-2H-pyrazolin-3-one. Their structures were confirmed and characterized by $^1H$-NMR, $^{13}C$-NMR, elemental analysis, and mass spectroscopy. In addition, the crystal structure of the target compound 3-(2-((1-phenyl-2H-pyrazol-3-yloxy)methyl)phenyl) oxazolidin-2-one was determined by single crystal X-ray diffraction. The bioassay results of these compounds indicated that some of the oxazolidin-2-one derivatives containing N-substituted phenyl 2H-pyrazol ring exhibited potential in vivo fungicidal activities against M. grisea at the dosage of $1\;g\;L^{-1}$.

Al nanocluster arrays onSi(111)−7×7surfaces: Formation process and interactions among clusters

Li, Run-Wei,Liu, Hongjun,Owen, J. H. G.,Wakayama, Y.,Miki, K.,Yeom, H. W. American Physical Society 2007 Physical review. B, Condensed matter and materials Vol.76 No.7

Protein Kinase C Mediates the Corticosterone-induced Sensitization of Dorsal Root Ganglion Neurons Innervating the Rat Stomach

( Meng Li ),( Lu Xue ),( Hong-yan Zhu ),( Hongjun Wang ),( Xue Xu ),( Ping-an Zhang ),( Geping Wu ),( Guang-yin Xu ) 대한소화기기능성질환·운동학회 2017 Journal of Neurogastroenterology and Motility (JNM Vol.23 No.3

Background/Aims Gastric hypersensitivity contributes to abdominal pain in patients with functional dyspepsia. Recent studies showed that hormones induced by stress are correlated with visceral hypersensitivity. However, the precise mechanisms underlying gastric hypersensitivity remain largely unknown. The aim of the present study was designed to investigate the roles of corticosterone (CORT) on excitability of dorsal root ganglion (DRG) neurons innervating the stomach. Methods DRG neurons innervating the stomach were labeled by DiI injection into the stomach wall. Patch clamp recordings were employed to examine neural excitability and voltage-gated sodium channel currents. Electromyograph technique was used to determine the responses of neck muscles to gastric distension. Results Incubation of acutely isolated DRG neurons with CORT significantly depolarized action potential threshold and enhanced the number of action potentials induced by current stimulation of the neuron. Under voltage-clamp mode, incubation of CORT enhanced voltage-gated sodium current density of the recorded neurons. Pre-incubation of GF109203X, an inhibitor of protein kinase C, blocked the CORT-induced hyperexcitability and potentiation of sodium currents. However, pre-incubation of H-89, an inhibitor of protein kinase A, did not alter the sodium current density. More importantly, intraperitoneal injection of CORT produced gastric hypersensitivity of healthy rats, which was blocked by pre-administration of GF109203X but not H-89. Conclusions Our data strongly suggest that CORT rapidly enhanced neuronal excitability and sodium channel functions, which is most likely mediated by protein kinase C but not protein kinase A signaling pathway in DRG neurons innervating the stomach, thus underlying the gastric hypersensitivity induced by CORT injection. (J Neurogastroenterol Motil 2017;23:464-476)

Adaptive Pinning Synchronization of Complex Networks with Partial Delay and Noise Coupling

Wang Li,Yue Qiao,Jiaming Wu,Hongjun Shi,Yongzheng Sun 제어·로봇·시스템학회 2023 International Journal of Control, Automation, and Vol.21 No.1

In this paper, we investigate the adaptive pinning synchronization of complex networks with partial delay and noise coupling. First, more realistic complex networks with partial delay and noise perturbation are established. Combining the advantages of the adaptive control method and pinning control technology, a novel coupling is designed to realize the synchronization. Several sufficient criteria for almost sure outer synchronization are developed based on the LaSalle invariance principle for stochastic differential equations. Finally, numerical simulations are performed to verify the effectiveness of the proposed synchronization scheme.

Synthesis, Crystal Structure and Fungicidal Activities of New Type Oxazolidinone-Based Strobilurin Analogues

Yuhao Li,Rui Liu,Zhangwei Yan,Xiangning Zhang,Hongjun Zhu 대한화학회 2010 Bulletin of the Korean Chemical Society Vol.31 No.11

A series of oxazolidinone-based strobilurin analogues were efficiently synthesized by the reaction of 3-(2-bromomethylphenyl)oxazolidin-2-one with 1-substituted phenyl-2H-pyrazolin-3-one. Their structures were confirmed and characterized by 1H-NMR, 13C-NMR, elemental analysis, and mass spectroscopy. In addition, the crystal structure of the target compound 3-(2-((1-phenyl-2H-pyrazol-3-yloxy)methyl)phenyl) oxazolidin-2-one was determined by single crystal X-ray diffraction. The bioassay results of these compounds indicated that some of the oxazolidin-2-one derivatives containing N-substituted phenyl 2H-pyrazol ring exhibited potential in vivo fungicidal activities against M. grisea at the dosage of 1 g L‒1.