Molecular Cloning and Bioinformatic Analysis of SPATA4 Gene

Liu, Shang-Feng,Ai, Chao,Ge, Zhong-Qi,Liu, Hai-Luo,Liu, Bo-Wen,He, Shan,Wang, Zhao Korean Society for Biochemistry and Molecular Biol 2005 Journal of biochemistry and molecular biology Vol.38 No.6

Full-length cDNA sequences of four novel SPATA4 genes in chimpanzee, cow, chicken and ascidian were identified by bioinformatic analysis using mouse or human SPATA4 cDNA fragment as electronic probe. All these genes have 6 exons and have similar protein molecular weight and do not localize in sex chromosome. The mouse SPATA4 sequence is identified as significantly changed in cryptorchidism, which shares no significant homology with any known protein in swissprot databases except for the homologous genes in various vertebrates. Our searching results showed that all SPATA4 proteins have a putative conserved domain DUF1042. The percentages of putative SPATA4 protein sequence identity ranging from 30% to 99%. The high similarity was also found in 1 kb promoter regions of human, mouse and rat SPATA4 gene. The similarities of the sequences upstream of SPATA4 promoter also have a high proportion. The results of searching SymAtlas (http://symatlas.gnf.org/SymAtlas/) showed that human SPATA4 has a high expression in testis, especially in testis interstitial, leydig cell, seminiferous tubule and germ cell. Mouse SPATA4 was observed exclusively in adult mouse testis and almost no signal was detected in other tissues. The pI values of the protein are negative, ranging from 9.44 to 10.15. The subcellular location of the protein is usually in the nucleus. And the signal peptide possibilities for SPATA4 are always zero. Using the SNPs data in NCBI, we found 33 SNPs in human SPATA4 gene genomic DNA region, with the distribution of 29 SNPs in the introns. CpG island searching gives the data about CpG island, which shows that the regions of the CpG island have a high similarity with each other, though the length of the CpG island is different from each other.This research is a fundamental work in the fields of the bioinformational analysis, and also put forward a new way for the bioinformatic analysis of other genes.

Optimization Model of Reliable Data Storage in Cloud Environment Using Genetic Algorithm

Feng Liu,Haitao Wu,Xiaochun Lu,Xiyang Liu 보안공학연구지원센터 2014 International Journal of Grid and Distributed Comp Vol.7 No.6

Massive data storage is one of the great challenges for cloud computing service, and reliable storage of sensitive data directly affects quality of storage service. In this paper, based on analysis of data storage process in cloud environment, the cost of massive data storage is considered to be comprised of data storage price, data migration and communication; and the storage reliability consists of data transmission reliability and hardware dependability. A multi-objective optimization model for reliable massive storage is proposed, in which storage cost and reliability are the objectives. Then, a genetic algorithm for solving the model is designed. Finally, experimental results indicate that the proposed model is positive and effective.

Parallel Distributed Acceleration Based on MPI and OpenMP Technology

Feng Liu,Haitao Wu,Xiaochun Lu,Xiyang Liu 보안공학연구지원센터 2015 International Journal of Grid and Distributed Comp Vol.8 No.6

In order to speed up data processing in a signal monitoring and evaluation system, we need to use a parallel method. It is obvious that the traditional stand-alone store has no ability to satisfy the performance requirements, and the use of single core CPU is unable to content the severe requirement of speed. Consequently, multi-machine parallel acceleration technique based on MPI (cooperated with multi-core parallel acceleration technique based on OpenMP) can effectively solve all above problems. In this paper, a parallel distributed acceleration framework based on MPI and Open MP technology was given. Experimental tests were carried to verify our proposal. Finally, some suggestions to speed up the data processing was given.

Sputum Metabolomic Profiling Reveals Metabolic Pathways and Signatures Associated With Inflammatory Phenotypes in Patients With Asthma

Liu Ying,Zhang Xin,Zhang Li,Oliver Brian G,Wang Hong Guang,Liu Zhi Peng,Chen Zhi Hong,Wood Lisa,Hsu Alan Chen-Yu,Xie Min,McDonald Vanessa,Wan Hua Jing,Luo Feng Ming,Liu Dan,Li Wei Min,Wang Gang 대한천식알레르기학회 2022 Allergy, Asthma & Immunology Research Vol.14 No.4

Purpose: The molecular links between metabolism and inflammation that drive different inflammatory phenotypes in asthma are poorly understood. We aimed to identify the metabolic signatures and underlying molecular pathways of different inflammatory asthma phenotypes. Methods: In the discovery set (n = 119), untargeted ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) was applied to characterize the induced sputum metabolic profiles of asthmatic patients with different inflammatory phenotypes using orthogonal partial least-squares discriminant analysis (OPLS-DA), and pathway topology enrichment analysis. In the validation set (n = 114), differential metabolites were selected to perform targeted quantification. Correlations between targeted metabolites and clinical indices in asthmatic patients were analyzed. Logistic and negative binomial regression models were established to assess the association between metabolites and severe asthma exacerbations. Results: Seventy-seven differential metabolites were identified in the discovery set. Pathway topology analysis uncovered that histidine metabolism, glycerophospholipid metabolism, nicotinate and nicotinamide metabolism, linoleic acid metabolism as well as phenylalanine, tyrosine and tryptophan biosynthesis were involved in the pathogenesis of different asthma phenotypes. In the validation set, 24 targeted quantification metabolites were significantly expressed between asthma inflammatory phenotypes. Finally, adenosine 5′-monophosphate (adjusted relative risk [adj RR] = 1.000; 95% confidence interval [CI] = 1.000–1.000; P = 0.050), allantoin (adj RR = 1.000; 95% CI = 1.000–1.000; P = 0.043) and nicotinamide (adj RR = 1.001; 95% CI = 1.000–1.002; P = 0.021) were demonstrated to predict severe asthma exacerbation rates. Conclusions: Different inflammatory asthma phenotypes have specific metabolic profiles in induced sputum. The potential metabolic signatures may identify therapeutic targets in different inflammatory asthma phenotypes.

ATP6V0d2 Suppresses Alveoli Macrophage Alternative Polarization and Allergic Asthma via Degradation of PU.1

Liu Na,Feng Yuchen,Liu Huicheng,Wu Wenliang,Liang Yuxia,Li Pingfei,Wei Zhengping,Wu Min,Tang Zhao-Hui,Han Junyan,Cheng Xiang,Liu Zheng,Laurence Arian,Li Huabin,Zhen Guohua,Yang Xiang-Ping 대한천식알레르기학회 2021 Allergy, Asthma & Immunology Research Vol.13 No.3

Purpose Macrophages are important regulators of environmental allergen-induced airway inflammation and asthma. ATP6V0d2 is a subunit of vacuolar ATPase highly expressed in macrophages. However, the functions of ATP6V0d2 in the regulation of pathogenesis of allergic asthma remain unclear. The aim of this study is to determine the function and related molecular mechanisms of macrophage protein ATP6V0d2 in allergic asthma. Methods We compared the disease severity between female C57BL/6 wild-type and ATP6V0d2−/− mice in an ovalbumin (OVA)-induced asthma model. We also investigated the association of expression of ATP6V0d2, PU.1 and CCL17 with disease severity among asthmatic patients. Results The expression of ATP6V0d2 in sputum cells of asthmatic patients and in the lungs of OVA-challenged mice was enhanced compared to healthy subjects and their counterparts, respectively. However, ATP6V0d2-deficient mice exaggerated inflammatory cell infiltration as well as enhanced alternative activated macrophage (AAM) polarization and mucus production in an OVA-induced asthma model. Furthermore, we found that Atp6v0d2 promoted lysosomal degradation of Pu.1, which induced AAM polarization and Ccl17 production. Among asthma patients, ATP6V0d2 expression was inversely associated with disease severity, whereas PU.1 and CCL17 expression was positively associated with disease severity. Conclusions Our results identify macrophage Atp6v0d2, as an induced feedback inhibitor of asthma disease severity by promoting Pu.1 lysosomal degradation, which may in turn leads to reduced AAM polarization and Ccl17 production.

Temperature-dependent development of Lista haraldusalis (Walker) (Lepidoptera: Pyralidae) on Platycarya strobilacea

Jian-Feng Liu,Man Liu,Mao-Fa Yang,Dimitris C. Kontodimas,Xiao-Fei Yu,Qi-Xian Lian 한국응용곤충학회 2014 Journal of Asia-Pacific Entomology Vol.17 No.4

The effect of constant temperatures on development and survival of Lista haraldusalis (Walker) (Lepidoptera:Pyralidae), a newly reported insect species used to produce insect tea in Guizhou province (China), was studiedin laboratory conditions at seven temperatures (19 °C, 22 °C, 25 °C, 28 °C, 31 °C, 34 °C, and 37 °C) on Platycaryastrobilacea. Increasing the temperature from 19 °C to 31 °C led to a significant decrease in the developmentaltime from egg to adult emergence, and then the total developmental time increased at 34 °C. Egg incubationwas the stage where L. haraldusalis experienced the highest mortality at all temperatures. The survival ofL. haraldusalis was significantly higher at 25 °C and 28 °C, whereas none of the eggs hatched at 37 °C. Commonand Ikemoto linear models were used to describe the relationship between the temperature and the developmentalrate for each immature stage of L. haraldusalis. The estimated values of the lower temperature thresholdand thermal constant of the total immature stages using Common and Ikemoto linear models were 11.34 °C and11.20 °C, and 939.85 and 950.41 degree-days, respectively. Seven nonlinear models were used to fit the experimentaldata to estimate the developmental rate of L. haraldusalis. Based on the biological significance for modelevaluation, Ikemoto linear, Logan-6, and SSI were the best models that fitted each immature stage ofL. haraldusalis and they were used to estimate the temperature thresholds. These thermal requirements and temperaturethresholds are crucial for facilitating the development of factory-based mass rearing of L. haraldusalis.

Proteomic Analysis of Shigella Virulence Effectors Secreted under Different Conditions

( Xingming Liu ),( Lilan Lu ),( Xinrui Liu ),( Xiankai Liu ),( Chao Pan ),( Erling Feng ),( Dongshu Wang ),( Chang Niu ),( Li Zhu ),( Hengliang Wang ) 한국미생물 · 생명공학회 2017 Journal of microbiology and biotechnology Vol.27 No.1

A series of novel effector molecules secreted by the type three secretion system (T3SS) of Shigella spp. have been reported in recent years. In this study, a proteomic approach was applied to study T3SS effectors systematically. First, proteins secreted by the S. flexneri wildtype strain after Congo Red induction were separated and identified using two-dimensional electrophoresis to display the relative abundance of all kinds of early effectors for the first time. Then, a gene deletion mutant of known virulence repressor (OspD1) and a gene overexpressed mutant of two known virulence activators (MxiE and IpgC) were constructed and analyzed to discover potential late effectors. Furthermore, the supernatant proteins of gene deletion mutants of two known translocators (IpaB and IpaD), which would constantly secrete effectors, were also analyzed. Among all of the secreted proteins identified in our study, IpaH1.4, IpaH_5, and IpaH_7 have not been reported before. These proteomics data of the secreted effectors will be valuable to understand the pathogenesis of S. flexneri.

Cloning and Functional Characterization of Putative Escherichia coli ABC Multidrug Efflux Transporter YddA

( Zhenyue Feng ),( Defu Liu ),( Ziwen Liu ),( Yimin Liang ),( Yanhong Wang ),( Qingpeng Liu ),( Zhenhua Liu ),( Zhongjing Zang ),( Yudong Cui ) 한국미생물 · 생명공학회 2020 Journal of microbiology and biotechnology Vol.30 No.7

A putative multidrug efflux gene, yddA, was cloned from the Escherichia coli K-12 strain. A drugsensitive strain of E. coli missing the main multidrug efflux pump AcrB was constructed as a host and the yddA gene was knocked out in wild-type (WT) and drug-sensitive E. coliΔacrB to study the yddA function. Sensitivity to different substrates of WT E.coli, E. coliΔyddA, E. coliΔacrB and E. coliΔacrBΔyddA strains was compared with minimal inhibitory concentration (MIC) assays and fluorescence tests. MIC assay and fluorescence test results showed that YddA protein was a multidrug efflux pump that exported multiple substrates. Three inhibitors, ortho-vanadate, carbonyl cyanide m-chlorophenylhydrazone (CCCP), and reserpine, were used in fluorescence tests. Ortho-vanadate and reserpine significantly inhibited the efflux and increased accumulation of ethidium bromide and norfloxacin, while CCCP had no significant effect on YddA-regulated efflux. The results indicated that YddA relies on energy released from ATP hydrolysis to transfer the substrates and YddA is an ABC-type multidrug exporter. Functional study of unknown ATP-binding cassette (ABC) superfamily transporters in the model organism E. coli is conducive to discovering new multidrug resistance-reversal targets and providing references for studying other ABC proteins of unknown function.

Volatile Chemical and Carotenoid Profiles in Watermelons [Citrullus vulgaris (Thunb.) Schrad (Cucurbitaceae)] with Different Flesh Colors

Cuihua Liu,Hongyan Zhang,Zhaoyi Dai,Xi Liu,Yue Liu,Xiuxin Deng,Feng Chen,Juan Xu 한국식품과학회 2012 Food Science and Biotechnology Vol.21 No.2

Twelve watermelon [Citrullus vulgaris (Thunb.)Schrad (Cucurbitaceae)] cultivars with different flesh colors were analyzed by HPLC, GC-FID, and GC-MS for their differences in carotenoid, soluble sugar, organic acid,and flavor. Results showed that all-trans violaxanthin, 9-cis-violaxanthin, and luteoxanthin were the main carotenoid esters in watermelons with yellow flesh. However,watermelons with red flesh were rich in all-trans lycopene and their cis-isomers. High concentrations of β-carotene and pro-lycopenes were found in watermelon with orangeyellow flesh. Large variations in the sucrose concentration were observed among the different watermelons. Sucrose and/or fructose were the dominant sugars, while citric acid and malic acid were the main organic acids in watermelon flesh. Limonene was detected in the watermelon flesh of all investigated genotypes. Interestingly, partial correlation analysis of the chemical concentrations revealed 2 significant (p<0.01) positive correlations between β-ionone and β-carotene, and between (E)-geranyl acetone and prolycopenes

Molecular Cloning and Bioinformatic Analysis of SPATA4 Gene

Shang Feng Liu,Chao Ai,Zhong Qi Ge,Hai Luo Liu,Bo Wen Liu,Shan He,Zhao Wang 한국생활환경학회 2005 BMB Reports Vol.38 No.6