Identification and expression analysis of WRKY transcription factor genes in response to fungal pathogen and hormone treatments in apple (Malus domestica)

Shuai Lui,Changguo Luo,Longming Zhu,Renhe Sha,Shenchun Qu,Binhua Ca,Sanhong Wang 한국식물학회 2017 Journal of Plant Biology Vol.60 No.2

The WRKY family, a large family of transcription factors (TFs) found in higher plants, plays central roles in many aspects of biological processes and adaption to environment. However, little information is available on this family in apple (Malus domestica). In the present study, a total of 119 candidate WRKY genes in apple genome were identified and classified into three main groups (Group I–III) based on the structure of the conserved domains. Each group or subgroup showed similar exon–intron structures and motif compositions. The evolution analysis showed that 44 MdWRKY genes clustered into 20 intensive regions (<100 kb) and 78 MdWRKY formed 85 pairs of collinear relationships, suggesting that both tandem and segmental duplications played an important role in the evolution and diversification of the WRKY gene family in apple. Furthermore, the expression of the MdWRKY genes in apple leaves in response to biotic stress (Alternaria alternate) and hormone treatments [salicylic acid (SA), methyl jasmonate (MeJA) and ethephon] was examined by using RNA-seq and qRT-PCR. The results showed that 63 MdWRKY genes had differential expression in their transcript abundance in response to Alternaria alternata apple pathotype infection. Moreover, most pathogen responsive MdWRKY genes were also changed significantly when apple leaves were treated by SA, MeJA or ethephon plant growth regulations, suggesting an interaction between SA, JA and ethylene (Eth) hormone signaling under biotic stress. This work may provide the basis for future studies of the genetic modification of WRKY genes for pathogen resistance in apple.

qPALS: Quality-Aware Synchrony Protocol for Distributed Real-Time Systems

( Woochul Kang ),( Lui Sha ) 한국인터넷정보학회 2014 KSII Transactions on Internet and Information Syst Vol.8 No.10

Synchronous computing models provided by real-time synchrony protocols, such as TTA [1] and PALS [2], greatly simplify the design, implementation, and verification of real-time distributed systems. However, their application to real systems has been limited since their assumptions on underlying systems are hard to satisfy. In particular, most previous real-time synchrony protocols hypothesize the existence of underlying fault tolerant real-time networks. This, however, might not be true in most soft real-time applications. In this paper, we propose a practical approach to a synchrony protocol, called Quality-Aware PALS (qPALS), which provides the benefits of a synchronous computing model in environments where no fault-tolerant real-time network is available. qPALS supports two flexible global synchronization protocols: one tailored for the performance and the other for the correctness of synchronization. Hence, applications can make a negotiation flexibly between performance and correctness. In qPALS, the Quality-of-Service (QoS) on synchronization and consistency is specified in a probabilistic manner, and the specified QoS is supported under dynamic and unpredictable network environments via a control-theoretic approach. Our simulation results show that qPALS supports highly reliable synchronization for critical events while still supporting the efficiency and performance even when the underlying network is not stable.

Design of a crossbar VOQ real-time switch with clock-driven scheduling for a guaranteed delay bound

Kang, Kyungtae,Park, Kyung-Joon,Sha, Lui,Wang, Qixin Springer-Verlag 2013 Real-time systems Vol.49 No.1

Worst Case Analysis of Packet Delay in Avionics Systems for Environmental Monitoring

Kyungtae Kang,Min-Young Nam,Lui Sha IEEE 2015 IEEE systems journal Vol.9 No.4

<P>Early analysis of timing is essential in the design of reliable avionics systems. We consider an environmental monitoring system that allows the surroundings of an aircraft to be observed continuously in real time. We analyze timing aspects of the partitions within the sensor and monitoring nodes, and of the intermediate switches that connect them. We use the application-specific I/O integration support tool (ASIIST) to evaluate the worst case delay in the peripheral component interconnect buses of the end nodes. We describe a novel switching algorithm that guarantees a bounded delay for any feasible traffic through each switch, and then derive the worst case delay incurred in a switched network that contains switches operating with the proposed algorithm. By composing these delays, we are able to determine the end-to-end delay over the internal buses and network comprising the entire system, and show how it can be bounded by using our switching algorithm. Our worst case end-to-end delay analysis contributes to more reliable and better verified environmental monitoring services over packet-switched networks in avionics systems. We expect that our work will help reduce the cost of designing and implementing environmental monitoring avionics systems, by making it easier to identify unsatisfactory designs at an early stage.</P>

Guaranteeing the End-to-End Latency of an IMA System with an Increasing Workload

Min-Young Nam,Jaemyoun Lee,Kyung-Joon Park,Lui Sha,Kyungtae Kang IEEE 2014 IEEE Transactions on Computers Vol.63 No.6

<P>New features are often added incrementally to avionics systems to minimize the need for redesign and recertification. However, it then becomes necessary to check that the timing constraints of existing as well as new applications are met. We facilitate these checks by introducing a new data switch that bounds the latency of end-to-end communications across a network. This switch runs a clock-driven switching algorithm that is throughput-optimal with a bounded worst-case delay for all feasible traffic. We propose associated heuristics that determine whether the timing constraints of an integrated modular avionics (IMA) system network that uses this switch are met, even if new features have caused traffic to increase, and then search for alternative network configurations if necessary. Virtual integration is used to make a combined analysis of the worst-case delay in the network and the local buses of individual computing modules. This analysis considers the shared network topology, local hardware architectures, and specified IMA configurations. Our approach can be used by a system architect as an effective method for quickly determining which possible system architectures should be pursued to meet timing constraints, and it allows the cascading effects of changes to be tracked and managed. We demonstrate how these heuristics work through an example in which changes are made to an environmental monitoring facility within an avionics system that uses our switch.</P>

Medical-Grade Quality of Service for Real-Time Mobile Healthcare

Kyungtae Kang,Qixin Wang,Junbeom Hur,Kyung-Joon Park,Lui Sha IEEE 2015 Computer Vol.48 No.2

<P>A wireless electrocardiogram case study suggests that current CDMA2000 cellular technology has considerable potential in medical telemetry. Modifications to the network protocol stack ensure the highest data integrity and lowest service delay.</P>

A Medical-Grade Wireless Architecture for Remote Electrocardiography

Kyungtae Kang,Kyung-Joon Park,Jae-Jin Song,Chang-Hwan Yoon,Lui Sha IEEE 2011 IEEE transactions on information technology in bio Vol.15 No.2

<P>In telecardiology, electrocardiogram (ECG) signals from a patient are acquired by sensors and transmitted in real time to medical personnel across a wireless network. The use of IEEE 802.11 wireless LANs (WLANs), which are already deployed in many hospitals, can provide ubiquitous connectivity and thus allow cardiology patients greater mobility. However, engineering issues, including the error-prone nature of wireless channels and the unpredictable delay and jitter due to the nondeterministic nature of access to the wireless medium, need to be addressed before telecardiology can be safely realized. We propose a medical-grade WLAN architecture for remote ECG monitoring, which employs the point-coordination function (PCF) for medium access control and Reed-Solomon coding for error control. Realistic simulations with uncompressed two-lead ECG data from the MIT-BIH arrhythmia database demonstrate reliable wireless ECG monitoring; the reliability of ECG transmission exceeds 99.99% with the initial buffering delay of only 2.4 s.</P>