Genome-wide identification and resistance expression analysis of the NBS gene family in Triticum urartu

Jing Liu,Linyi Qiao,Xiaojun Zhang,Xin Li,Haixian Zhan,Huijuan Guo,Jun Zheng,Zhijian Chang 한국유전학회 2017 Genes & Genomics Vol.39 No.6

As the largest class of resistant genes, the nucleotide binding site (NBS) has been studied extensively at a genome-wide level in rice, sorghum, maize, barley and hexaploid wheat. However, no such comprehensive analysis has been conducted of the NBS gene family in Triticum urartu, the donor of the A genome to the common wheat. Using a bioinformatics method, 463 NBS genes were isolated from the whole genome of T. urartu, of which 461 had location information. The expansion pattern and evolution of the 461 NBS candidate proteins were analyzed, and 118 of them were duplicated. By calculating the lengths of the copies, it was inferred that the NBS resistance gene family of T. urartu has experienced at least two duplication events. Expression analysis based on RNA-seq data found that 6 genes were differentially expressed among Tu38, Tu138 and Tu158 in response to Blumeria graminis f.sp.tritici (Bgt). Following Bgt infection, the expression levels of these genes were up-regulated. These results provide critical references for further identification and analysis of NBS family genes with important functions.

A Methodology for Task placement and Scheduling Based on Virtual Machines

( Xiaojun Chen ),( Jing Zhang ),( Junhuai Li ) 한국인터넷정보학회 2011 KSII Transactions on Internet and Information Syst Vol.5 No.9

Task placement and scheduling are traditionally studied in following aspects: resource utilization, application throughput, application execution latency and starvation, and recently, the studies are more on application scalability and application performance. A methodology for task placement and scheduling centered on tasks based on virtual machines is studied in this paper to improve the performances of systems and dynamic adaptability in applications development and deployment oriented parallel computing. For parallel applications with no real-time constraints, we describe a thought of feature model and make a formal description for four layers of task placement and scheduling. To place the tasks to different layers of virtual computing systems, we take the performances of four layers as the goal function in the model of task placement and scheduling. Furthermore, we take the personal preference, the application scalability for a designer in his (her) development and deployment, as the constraint of this model. The workflow of task placement and scheduling based on virtual machines has been discussed. Then, an algorithm TPVM is designed to work out the optimal scheme of the model, and an algorithm TEVM completes the execution of tasks in four layers. The experiments have been performed to validate the effectiveness of time estimated method and the feasibility and rationality of algorithms. It is seen from the experiments that our algorithms are better than other four algorithms in performance. The results show that the methodology presented in this paper has guiding significance to improve the efficiency of virtual computing systems.

Instantaneous frequency extraction in time-varying structures using a maximum gradient method

Jing-liang Liu,Xiaojun Wei,Ren-Hui Qiu,Jin-Yang Zheng,Yan-Jie Zhu,Irwanda Laory 국제구조공학회 2018 Smart Structures and Systems, An International Jou Vol.22 No.3

A method is proposed for the identification of instantaneous frequencies (IFs) in time-varying structures. The proposed method combines a maximum gradient algorithm and a smoothing operation. The maximum gradient algorithm is designed to extract the wavelet ridges of response signals. The smoothing operation, based on a polynomial curve fitting algorithm and a threshold method, is employed to reduce the effects of random noises. To verify the effectiveness and accuracy of the proposed method, a numerical example of a signal with two frequency modulated components is investigated and an experimental test on a steel cable with time-varying tensions is also conducted. The results demonstrate that the proposed method can extract IFs from the noisy multi-component signals and practical response signals successfully. In addition, the proposed method can provide a better IF identification results than the standard synchrosqueezing wavelet transform.

AMPK alleviates high uric acid-induced Na+-K+-ATPase signaling impairment and cell injury in renal tubules

Jing Xiao,Sibo Zhu,Haochen Guan,Haochen Guan,Fengqin Li,Xiaoli Zhang,Hui Guo,Xiaojun Wang,Zhibin Ye 생화학분자생물학회 2019 Experimental and molecular medicine Vol.51 No.-

One of the mechanisms in hyperuricemia (HUA)-induced renal tubular injury is the impairment of Na+-K+-ATPase (NKA) signaling, which further triggers inflammation, autophagy, and mitochondrial dysfunction and leads to cell injury. Here, we used RNA sequencing to screen the most likely regulators of NKA signaling and found that the liver kinase B1(LKB1)/adenosine monophosphate (AMP)-activated protein kinase (AMPK)/ mammalian target of rapamycin (mTOR) pathway was the most abundantly enriched pathway in HUA. AMPK is a key regulator of cell energy metabolism; hence, we examined the effect of AMPK on HUA-induced dysregulation of NKA signaling and cell injury. We first detected AMPK activation in high uric acid (UA)-stimulated proximal tubular epithelial cells (PTECs). We further found that sustained treatment with the AMPK activator 5-aminoimidazole-4-carboxamide 1-β-d-ribofuranoside (AICAR), but not the AMPK inhibitor Compound C, significantly alleviated UA-induced reductions in NKA activity and NKA α1 subunit expression on the cell membrane by reducing NKA degradation in lysosomes; sustained AICAR treatment also significantly alleviated activation of the NKA downstream molecules Src and interleukin-1β (IL-1β) in PTECs. AICAR further alleviated high UA-induced apoptosis, autophagy, and mitochondrial dysfunction. Although AMPK activation by metformin did not reduce serum UA levels in hyperuricemic rats, it significantly alleviated HUAinduced renal tubular injury and NKA signaling impairment in vivo with effects similar to those of febuxostat. Our study suggests that AMPK activation may temporarily compensate for HUA-induced renal injury. Sustained AMPK activation could reduce lysosomal NKA degradation and maintain NKA function, thus alleviating NKA downstream inflammation and protecting tubular cells from high UA-induced renal tubular injury.

Molecular dynamics study of H4TTP crystal morphology

Chen Jing,Li Jun,Li Yongxiang,Liu Qiao'e,Zhang Xuan,Ruan Jian,Wang Xiaojun,Liu Wendong,Kim Chan Kyung 대한화학회 2022 Bulletin of the Korean Chemical Society Vol.43 No.7

To understand the role of dimethyl sulfoxide (DMSO) on the crystal growth morphology of 2,3,5,6-tetra(1H-tetrazol-5-yl)pyrazine (H4TTP), the vacuum morphology of H4TTP crystal was predicted by the Bravais–Friedel–Donnay–Harker (BFDH) and the attachment energy (AE) models. The growth morphology of H4TTP in DMSO solvent was predicted using a modified AE model. The results show that the main growth surfaces of H4TTP in vacuum are (1 0 0), (0 0 2), (0 1 1), and (1 1 0) surfaces. Among them, (1 0 0) surface is the most important growth surface. (0 0 2) surface is the roughest crystal surface, while (1 1 0) surface is the flattest. (1 1 0) surface grows rapidly, and (1 0 0) surface has the greatest morphological importance. The analysis of radial distribution function shows that (1 0 0) surface has the strongest hydrogen bonding interactions in the interface between H4TTP and DMSO solvent.

Instantaneous frequency extraction in time-varying structures using a maximum gradient method

Liu, Jing-liang,Wei, Xiaojun,Qiu, Ren-Hui,Zheng, Jin-Yang,Zhu, Yan-Jie,Laory, Irwanda Techno-Press 2018 Smart Structures and Systems, An International Jou Vol.22 No.3

A method is proposed for the identification of instantaneous frequencies (IFs) in time-varying structures. The proposed method combines a maximum gradient algorithm and a smoothing operation. The maximum gradient algorithm is designed to extract the wavelet ridges of response signals. The smoothing operation, based on a polynomial curve fitting algorithm and a threshold method, is employed to reduce the effects of random noises. To verify the effectiveness and accuracy of the proposed method, a numerical example of a signal with two frequency modulated components is investigated and an experimental test on a steel cable with time-varying tensions is also conducted. The results demonstrate that the proposed method can extract IFs from the noisy multi-component signals and practical response signals successfully. In addition, the proposed method can provide a better IF identification results than the standard synchrosqueezing wavelet transform.

A New Fuzzy Key Generation Method Based on PHY-Layer Fingerprints in Mobile Cognitive Radio Networks

( Ning Gao ),( Xiaojun Jing ),( Songlin Sun ),( Junsheng Mu ),( Xiang Lu ) 한국인터넷정보학회 2016 KSII Transactions on Internet and Information Syst Vol.10 No.7

Classical key generation is complicated to update and key distribution generally requires fixed infrastructures. In order to eliminate these restrictions researchers have focused much attention on physical-layer (PHY-layer) based key generation methods. In this paper, we present a PHY-layer fingerprints based fuzzy key generation scheme, which works to prevent primary user emulation (PUE) attacks and spectrum sensing data falsification (SSDF) attacks, with multi-node collaborative defense strategies. We also propose two algorithms, the EA algorithm and the TA algorithm, to defend against eavesdropping attacks and tampering attacks in mobile cognitive radio networks (CRNs). We give security analyses of these algorithms in both the spatial and temporal domains, and prove the upper bound of the entropy loss in theory. We present a simulation result based on a MIMO-OFDM communication system which shows that the channel response characteristics received by legitimates tend to be consistent and phase characteristics are much more robust for key generation in mobile CRNs. In addition, NIST statistical tests show that the generated key in our proposed approach is secure and reliable.

Spectrum Usage Forecasting Model for Cognitive Radio Networks

( Wei Yang ),( Xiaojun Jing ),( Hai Huang ) 한국인터넷정보학회 2018 KSII Transactions on Internet and Information Syst Vol.12 No.4

Spectrum reuse has attracted much concern of researchers and scientists, however, the dynamic spectrum access is challenging, since an individual secondary user usually just has limited sensing abilities. One key insight is that spectrum usage forecasting among secondary users, this inspiration enables users to obtain more informed spectrum opportunities. Therefore, spectrum usage forecasting is vital to cognitive radio networks (CRNs). With this insight, a spectrum usage forecasting model for the occurrence of primary users prediction is derived in this paper. The proposed model is based on auto regressive enhanced primary user emergence reasoning (AR-PUER), which combines linear prediction and primary user emergence reasoning. Historical samples are selected to train the spectrum usage forecasting model in order to capture the current distinction pattern of primary users. The proposed scheme does not require the knowledge of signal or of noise power. To verify the performance of proposed spectrum usage forecasting model, we apply it to the data during the past two months, and then compare it with some other sensing techniques. The simulation results demonstrate that the spectrum usage forecasting model is effective and generates the most accurate prediction of primary users occasion in several cases.

An Efficient Markov Chain Based Channel Model for 6G Enabled Massive Internet of Things

( Wei Yang ),( Xiaojun Jing ),( Hai Huang ),( Chunsheng Zhu ),( Qiaojie Jiang ),( Dongliang Xie ) 한국인터넷정보학회 2021 KSII Transactions on Internet and Information Syst Vol.15 No.11

Accelerated by the Internet of Things (IoT), the need for further technical innovations and developments within wireless communications beyond the fifth generation (B5G) networks is up-and-coming in the past few years. High altitude platform station (HAPS) communication is expected to achieve such high levels that, with high data transfer rates and low latency, millions of devices and applications can work seamlessly. The HAPS has emerged as an indispensable component of next-generations of wireless networks, which will therefore play an important role in promoting massive IoT interconnectivity with 6G. The performance of communication and key technology mainly depend on the characteristic of channel, thus we propose an efficient Markov chain based channel model, then analyze the HAPS communication system's uplink capability and swing effect through experiments. According to the simulation results, the efficacy of the proposed scheme is proven to meet the requirements of ubiquitous connectivity in future IoT enabled by 6G.

A Novel Xylanase from Streptomyces sp. FA1: Purification, Characterization, Identification, and Heterologous Expression

Jie He,Lingqia Su,Xiaojun Sun,Jiajia Fu,Jian Chen,Jing Wu 한국생물공학회 2014 Biotechnology and Bioprocess Engineering Vol.19 No.1

A xylanase (XynA) was purified from the culturemedium of Streptomyces sp. FA1, which was previouslyisolated from a bamboo retting system. XynA had amolecular mass of 43 kDa, displayed maximal activity atpH 5.5, retained 41% of its maximal activity at pH 11.0,and was stable over a wide pH range (3.0 ~ 11.0). PurifiedXynA was subjected to peptide mass fingerprinting, whichled to the cloning of the xynA gene. The xynA gene, whichencodes a mature protein of 436 amino acids, washeterologously expressed in E. coli BL21(DE3). The activityin the culture medium could reach 213.5 U/mL, which was11.2-fold higher than that produced by Streptomyces sp. FA1. BLAST searching revealed that full-length XynAshares less than 90% identity with most of its homologues,whereas amino acids 48-436 of the enzyme share 97%identity with an open reading frame encoding a putativefull-length mature xylanase from Streptomyces tendae. Thetruncated xynA gene, xynA48-436, was cloned and expressedin E. coli, however, no xylanase activity could be detectedin the culture medium. Based on these results, it is suggestedthat XynA is a new member of glycoside hydrolasesfamily10 with exceptional catalytic efficiency at alkalinepH.