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Journal Article 7

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2023 1

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2016 1

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Sporisorium reilianum 1

Adaptive evolution 1

Branch parameter errors 1

Decoy PD-1 1

Dynamic state estimation 1

Epitope-oriented 1

Genomic mutations 1

Gut microbiota 1

Kalman filter 1

Lipase 1

Mammalian cell library 1

Measurement errors 1

Molecular dynamics simulation 1

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Genomic Mutations within the Host Microbiome: Adaptive Evolution or Purifying Selection Review

Jiachao Zhang,Rob Knight,

Engineering 2023, Volume 20, Issue 1,   Pages 96-102 doi: 10.1016/j.eng.2021.11.018

Abstract:

Next-generation sequencing technology has transformed our ability to assess the taxonomic composition functions of host-associated microbiota and microbiomes. More human microbiome research projects—particularly those that explore genomic mutations within the microbiome—will be launched in the next decade. This review focuses on the coevolution of microbes within a microbiome, which shapes strain-level diversity both within and between host species. We also explore the correlation between microbial genomic mutations and common metabolic diseases, and the adaptive evolution of pathogens and probiotics during invasion and colonization. Finally, we discuss advances in methods and algorithms for annotating and analyzing microbial genomic mutations.

Keywords： Gut microbiota     Genomic mutations     Adaptive evolution     Purifying selection     Single-nucleotide variants    

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A multi-functional dynamic state estimator for error validation: measurement and parameter errors and sudden load changes Article

Mehdi AHMADI JIRDEHI,Reza HEMMATI,Vahid ABBASI,Hedayat SABOORI

Frontiers of Information Technology & Electronic Engineering 2016, Volume 17, Issue 11,   Pages 1218-1227 doi: 10.1631/FITEE.1500301

Abstract: We propose a new and efficient algorithm to detect, identify, and correct measurement errors and branch parameter errors of power systems. A dynamic state estimation algorithm is used based on the Kalman filter theory. The proposed algorithm also successfully detects and identifies sudden load changes in power systems. The method uses three normalized vectors to process errors at each sampling time: normalized measurement residual, normalized Lagrange multiplier, and normalized innovation vector. An IEEE 14-bus test system was used to verify and demonstrate the effectiveness of the proposed method. Numerical results are presented and discussed to show the accuracy of the method.

Keywords： Dynamic state estimation     Kalman filter     Measurement errors     Branch parameter errors     Sudden load changes    

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Bio-inspired cryptosystem on the reciprocal domain: DNA strands mutate to secure health data Research Articles

S. Aashiq Banu, Rengarajan Amirtharajan,aashiqbanu@sastra.ac.in,amir@ece.sastra.edu

Frontiers of Information Technology & Electronic Engineering 2021, Volume 22, Issue 7,   Pages 940-956 doi: 10.1631/FITEE.2000071

Abstract: Healthcare and telemedicine industries are relying on technology that is connected to the Internet. Digital health data are more prone to cyber attacks because of the treasure trove of personal data they possess. This necessitates protection of digital medical images and their secure transmission. In this paper, an encryption technique based on mutated with Lorenz and Lü is employed to generate high pseudo-random key streams. The proposed chaos- cryptic system operates on the integer wavelet transform (IWT) domain and a bio-inspired , unit for enhancing the confusion and diffusion phase in an approximation coefficient. Finally, an XOR operation is performed with a quantised chaotic set from the developed combined attractors. The algorithm attains an average entropy of 7.9973, near-zero correlation with an NPCR of 99.642%, a UACI of 33.438%, and a keyspace of 10. Further, the experimental analyses and NIST statistical test suite have been designed such that the proposed technique has the potency to withstand any statistical, differential, and brute force attacks.

Keywords： 医学图像加密；DNA；混沌吸引子；交叉；突变；电子医疗    

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Rational Design, Over-expression and Characterization of a Novel Staphylokinase with Lower Tendency of Polymerization

Song Gang,Yu Min,Mo Wei,Song Houyan

Strategic Study of CAE 2000, Volume 2, Issue 11,   Pages 68-72

Abstract:

Staphylokinase has strong tendency to polymerize, which may hamper its clinical use. On the basis of crystal structure of staphylokinase, the dimer structure was modeled by software GRAMM V1.03 with high-resolution generic docking parameters. Two kinds of binding interfaces were generated, mainly linked by hydrophobic interaction and hydrogen bonds. The computer model of staphylokinase dimer provides a template for the design of improved staphylokinase without tendency to form polymer. A novel variant of staphylokinase (RGD-Sak) was designed based on the model. RGD-Sak gene was constructed by substitution mutagenesis of Lys-109 and Phe-111 with Arg-109 and Asp 111 respectively, confirmed by nucleotide sequencing. The mutant cDNA was ligated with prokaryotic expression vector pLY-4 and transformed into E. Coli JF1125. After temperature induction, over 50% expression level of RGD-Sak was achieved. RGD-Sak was isolated and purified by washing and solubilization of inclusion body, renaturation and ion exchange chromatography. The final product displayed a single band with a corresponding molecular weight of 15.5 kD in non-reducing SDS-PAGE with 95% of purity and 5×104 HU/mg of specific activity. The KM、Kcat value for the activation of plasminogen with RGD-Sak was 12.40 μmol L-1 、0.81 s-1, respectively. RGD-Sak show lower tendency to polymerize after incubated with 0.9% NaCl. This study provided the basis for further reconstruction of Sak by protein engineering.

Keywords： staphylokinase     dimer     molecular docking     molecular design     site-directed mutagenesis    

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Firefly algorithm with division of roles for complex optimal scheduling Research Articles

Jia Zhao, Wenping Chen, Renbin Xiao, Jun Ye,zhaojia925@163.com,chen_9731@163.com,rbxiao@hust.edu.cn,yejun68@sina.com

Frontiers of Information Technology & Electronic Engineering 2021, Volume 22, Issue 10,   Pages 1311-1333 doi: 10.1631/FITEE.2000691

Abstract: A single strategy used in the cannot effectively solve the complex problem. Thus, we propose the FA with (DRFA). Herein, fireflies are divided into leaders, developers, and followers, while a learning strategy is assigned to each role: the leader chooses the greedy ; the developer chooses two leaders randomly and uses the strategy for local development; the follower randomly selects two excellent particles for global exploration. To improve the efficiency of the fixed step size used in FA, a stepped variable step size strategy is proposed to meet different requirements of the algorithm for the step size at different stages. Role division can balance the development and exploration ability of the algorithm. The use of multiple strategies can greatly improve the versatility of the algorithm for complex optimization problems. The optimal performance of the proposed algorithm has been verified by three sets of test functions and a simulation of of cascade reservoirs.

Keywords： 萤火虫算法；角色分工；柯西突变；精英邻域搜索；优化调度    

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Efficient Activity Enhancement of a Lipase from Sporisorium reilianum for the Synthesis of a Moxifloxacin Chiral Intermediate via Rational Design Article

Xue Cai, Jiang-Wei Shen, Yu Qiang, Jing Hua, Zhang-Qi Ma, Zhi-Qiang Liu, Yu-Guo Zheng

Engineering 2022, Volume 19, Issue 12,   Pages 207-216 doi: 10.1016/j.eng.2022.03.020

Abstract:

Lipase-catalyzed stereoselective resolution of cis-(±)-dimethyl 1-acetylpiperidine-2,3-dicarboxylate (cis-(±)-1) is an attractive route for the synthesis of (S,S)-2,8-diazobicyclo[4.3.0]nonane, an important chiral intermediate of the fluoroquinolone antibiotic, moxifloxacin. In our previous study, a lipase from Sporisorium reilianum (SRL) was identified to possess excellent thermostability and pH stability. However, the low enzymatic activity of the SRL is a challenge that must be addressed. A rational design was initially employed for SRL tailoring according to the engineered Candida antarctica lipase B (CALB), resulting in a beneficial variant called SRL-I194N/V195L. Subsequently, two key amino acid residues in loop 6, L145 and L154, which might modulate the lid conformation between open and closed, were identified. A tetra-site variant, SRL-I194N/V195L/L145V/L154G (V13), with a significantly enhanced activity of 87.8 U∙mg−1 was obtained; this value was 2195-fold higher than that of wild-type SRL. Variant V13 was used to prepare optically pure (2S,3R)-dimethyl 1-acetylpiperidine-2,3-dicarboxylate ((2S,3R)-1), resolving 1 mol∙L−1 cis-(±)-1 with a conversion of 49.9% in 2 h and absolute stereoselectivity (E > 200). Excellent stability with a half-life of 92.5 h was also observed at 50 °C. Overall, the study findings reveal a lipase with high activity toward cis-(±)-1 at an industrial level and may offer a general strategy for enhancing the enzyme activity of other lipases and other classes of enzymes with a lid moiety.

Keywords： Lipase     Sporisorium reilianum     Site-directed mutagenesis     Molecular dynamics simulation     Rational design     Moxifloxacin    

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High-Affinity Decoy PD-1 Mutant Screened from an Epitope-Specific Cell Library Article

Hao Liu, Chunxia Qiao, Naijing Hu, Zhihong Wang, Jing Wang, Jiannan Feng, Beifen Shen, Yuanfang Ma, Longlong Luo

Engineering 2021, Volume 7, Issue 11,   Pages 1557-1565 doi: 10.1016/j.eng.2020.11.011

Abstract:

Immunotherapy with anti-programmed cell death protein-1 (PD-1)/programmed cell death ligand-1 (PD-L1) monoclonal antibodies has become routine in the treatment of many kinds of human cancers, such as lung cancer, intestinal cancer, and melanoma. The PD-1/PD-L1 pathway inhibits T cell activation in the micro-environment, making it an attractive target against cancer. Wild-type (WT) PD-1 ectodomain has been shown to have difficulty blocking PD-1/PD-L1 mixture formation due to its low affinity. The present work uses three-dimensional (3D) crystal complex structures to analyze the interaction by which PD-1 binds to PD-L1 or PD-L2. It also reports on a theoretical study of the binding mode between PD-1 and its clinical antibody Opdivo. Based on the theoretical binding analysis of PD-1 and its ligands (i.e., PD-L1 and PD-L2) or antibody (Opdivo), a small-content, epitope-oriented mammalian cell library was established for PD-1. After three rounds of cell sorting, the decoy PD-1 mutant 463, which presented a higher affinity than WT PD-1 to the PD-L1 (the affinity has increased by almost three orders of magnitude) was screened out. It exhibited an inhibitory effect against PD-1 to prevent it from forming mixtures with PD-L1, which was similar to the effect of the commercial anti-PD-L1 antibody atezolizumab (ATE). The median effective concentration (EC50) value of the decoy mutant was 0.031 μg·mL−1 in comparison with 0.063 μg·mL−1 for ATE; both values were much lower than that of WT PD-1, at 2.571 μg·mL−1. The 463 decoy mutant reversed the inhibitory function of PD-1 in T cell activation; furthermore, 10 mg·kg−1 of 463 inhibited about 75% of tumor growth in vivo in a MC38 transgenic xenograft mice model, which was similar to the activity of ATE. More interestingly, an even lower dose of 463 (2 mg·kg−1) showed a better effect than 10 mg·kg−1 of WT PD-1. This work offers the decoy 463 with an improved curative effect, which holds potential to become a good option against PD-1/PD-L1-related cancers.

Keywords： Decoy PD-1     PD-L1     Mammalian cell library     Epitope-oriented    

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Title Author Date Type Operation

Genomic Mutations within the Host Microbiome: Adaptive Evolution or Purifying Selection

Jiachao Zhang,Rob Knight,

Journal Article

A multi-functional dynamic state estimator for error validation: measurement and parameter errors and sudden load changes

Mehdi AHMADI JIRDEHI,Reza HEMMATI,Vahid ABBASI,Hedayat SABOORI

Journal Article

Bio-inspired cryptosystem on the reciprocal domain: DNA strands mutate to secure health data

S. Aashiq Banu, Rengarajan Amirtharajan,aashiqbanu@sastra.ac.in,amir@ece.sastra.edu

Journal Article

Rational Design, Over-expression and Characterization of a Novel Staphylokinase with Lower Tendency of Polymerization

Song Gang,Yu Min,Mo Wei,Song Houyan

Journal Article

Firefly algorithm with division of roles for complex optimal scheduling

Jia Zhao, Wenping Chen, Renbin Xiao, Jun Ye,zhaojia925@163.com,chen_9731@163.com,rbxiao@hust.edu.cn,yejun68@sina.com

Journal Article

Efficient Activity Enhancement of a Lipase from Sporisorium reilianum for the Synthesis of a Moxifloxacin Chiral Intermediate via Rational Design

Xue Cai, Jiang-Wei Shen, Yu Qiang, Jing Hua, Zhang-Qi Ma, Zhi-Qiang Liu, Yu-Guo Zheng

Journal Article

High-Affinity Decoy PD-1 Mutant Screened from an Epitope-Specific Cell Library

Hao Liu, Chunxia Qiao, Naijing Hu, Zhihong Wang, Jing Wang, Jiannan Feng, Beifen Shen, Yuanfang Ma, Longlong Luo

Journal Article