The Attenuation Mechanism and Live Vaccine Potential of a Low-Virulence Edwardsiella ictaluri Strain Obtained by Rifampicin Passaging Culture

Wang Shuyi,Hao Jingwen,Yang Jicheng,Zhang Qianqian,Li Aihua 한국미생물·생명공학회 2023 Journal of microbiology and biotechnology Vol.33 No.2

The rifampicin-resistant strain E9-302 of Edwardsiella ictaluri strain 669 (WT) was generated by continuous passage on BHI agar plates containing increasing concentrations of rifampicin. E9-302 was attenuated significantly by 119 times to zebrafish Danio rerio compared to WT in terms of the 50% lethal dose (LD50). Zebrafish vaccinated with E9-302 via intraperitoneal (IP) injection at a dose of 1 × 103 CFU/fish had relative percentage survival (RPS) rates of 85.7% when challenged with wild-type E. ictaluri via IP 14 days post-vaccination (dpv). After 14 days of primary vaccination with E9-302 via immersion (IM) at a dose of 4 × 107 CFU/ml, a booster IM vaccination with E9-302 at a dose of 2 × 107 CFU/ml exhibited 65.2% RPS against challenge with wild-type E. ictaluri via IP 7 days later. These results indicated that the rifampicin-resistant attenuated strain E9-302 had potential as a live vaccine against E. ictaluri infection. A previously unreported amino acid site change at position 142 of the RNA polymerase (RNAP) β subunit encoded by the gene rpoB associated with rifampicin resistance was identified. Analysis of the whole-genome sequencing results revealed multiple missense mutations in the virulence-related genes esrB and sspH2 in E9-302 compared with WT, and a 189 bp mismatch in one gene, whose coding product was highly homologous to glycosyltransferase family 39 protein. This study preliminarily explored the molecular mechanism underlying the virulence attenuation of rifampicin-resistant strain E9-302 and provided a new target for the subsequent study of the pathogenic mechanism of E. ictaluri.

Identification of Dominant Microbial Community and Diversity in Continuously Cropped Pepper Fields

Hui Wang,Li Liu,Shuyi Yu,Tianshu Guan,Baihong Li,Qi Wang,Changyuan Liu 한국원예학회 2021 원예과학기술지 Vol.39 No.4

Pepper blight is the most significant soil-borne disease affecting the continuous cropping of peppers. To identify the effect of Phytophthora capsici infection on microbial flora, we isolated and counted the microorganisms collected from the rhizosphere soil of P. capsici-affected farms that continuously cropped pepper for 3, 6, and 9 years in Liaoning Province, China. The colony and cell morphology, physiological and biochemical characteristics, and 16S rDNA sequence of bacteria and actinomycetes were documented. In addition, colony and microscopic morphology of fungi and the rDNA-ITS sequence were analysed for classification. We observed that healthy and diseased peppers had the largest number of bacteria in the rhizosphere followed by actinomycetes and fungi. After infection, the number of bacteria and actinomycetes decreased with a corresponding increase in the number of fungi, leading to a reduction in the ratio of bacteria/fungi to actinomycetes/fungi. We identified 15 dominant bacterial strains, of which Bacillus represented the most abundant genus consisting of 7 strains followed by Flavobacterium and Staphylococcus. Furthermore, 15 of the 17 actinomycetes strains belonged to the genus Streptomyces. Among the six fungal strains, we found P. infestans, Fusarium, and Penicillium consisting of two strains each. This study elucidated the impact of pathogenic P. capsici on the composition of soil microbes over time and characterized several cultivatable dominant bacterial groups, which can provide a basis for practical intervention strategies to improve soil conditions for continuous cropping.

Research progress of single-atom coating and its application prospect in protective coatings

Chijia Wang,Qianqian Yin,Shuyi Liu,Jianxin Wang,Weihao Fan,Zhanjian Liu,Fatang Liu,Yize Liu,Huaiyuan Wang 한국공업화학회 2023 Journal of Industrial and Engineering Chemistry Vol.128 No.-

Coating technology is the most economical and efficient approach to retard metal corrosion, and newcomposite coatings prepared by adding monoatomic fillers to a polymer matrix have excellent corrosionresistance and good mechanical properties. The single-atom coating formed by the immobilization ofmetal atoms alone on the matrix or filler represents the maximum utilization of atoms at the presentstage, which has unique coordination properties, active sites, and synergistic effects with the support. Compared with traditional fillers, single-atom fillers not only have the advantages of supporting fillersbut can also provide monatomic metals to form passivation films, promote the progress of catalytic passivationreactions, and combine organic compounds to generate new composite materials. This paperfocuses on the preparation methods and mechanisms of single-atom coatings in the field of batteriesand catalysts as well as the application of composite materials prepared by combining single-atom materialswith polymer matrices in the field of metal protection. The preparation methods, application prospects,and coating characteristics of various single-atom composites were summarized. In addition,we discuss the potential applications of single-atom coatings in the design of future composite coatings.

Crashworthiness design of bionic-shell thin-walled tube under axial impact

Lingyun Qin,Shuyi Yang,Hongzhou Li,Juchuan Dai,Guosheng Wang,Qihui Ling,Zhewu Chen 대한기계학회 2023 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.37 No.7

Bionic structures have been widely utilized in the crashworthiness design of thin-walled structures due to their superior energy absorption capabilities. This study constructed a bionic-shell thin-walled tube (BST) with excellent crashworthiness based on the structural bionic principle using the shell shape cross-section as the prototype. First, the theoretical model of the mean crushing force (MCF) for BST under axial compression was developed. An experiment was conducted and the reliability of the finite element model was verified. Then, the effects of structural parameters, such as the number of ribs, wall thickness, and inner tube diameter on the crashworthiness of the BST were investigated using the finite element method. Finally, to obtain the ideal configuration of structural parameters, the BST was optimized using the response surface method (RSM) with specific energy absorption (SEA) and crushing force efficiency (CFE) as the optimization objectives and peak crushing force (PCF) as the constraint condition. The results showed that the BST with six ribs exhibited the best crashworthiness under the same mass. The optimized BST-6 was found to have better energy absorption performance than the double circular tube (DCT) and the bionic-horsetail thin-walled tube (BHT). Compared with the DCT, the SEA and CFE increased by 35.15 % and 32.23 %, respectively.

Engineering a Highly Thermostable and Stress Tolerant Superoxide Dismutase by N-terminal Modification and Metal Incorporation

Mingchang Li,Shuyi Guo,Xiaomin Li,Quan Wang,Lin Zhu,Chunyan Yin,Wei Wang 한국생물공학회 2017 Biotechnology and Bioprocess Engineering Vol.22 No.6

Thermophilic or hyperthermophilic SODs (superoxide dismutase) usually offer substantial biotechnological advantages over mesophilic SODs. Previously a 244-amino acid N-terminal domain (NTD) from a heatresistant SOD of Geobacillus thermodenitrificans NG80-2 was discovered and demonstrated to be able to confer thermostability to homologous mesophilic SODs, which revealed a new type of heat resistance mechanism. To further improve the heat resistance and stress tolerance of thermophilic cambialistic superoxide dismutase (Fe/Mn- SODAp) from Aeropyrum pernix K1 through metal incorporation and fusion with the newly found peptide NTD for broadening its industrial application, the wildtype SODAp and NTD-fused ntdSODAp were expressed in E. coli BL21 and incorporated with metal cofactors by two ways. Recombinant fusion SOD obtained by in vitro reconstitution (Mn-rec ntdSODAp) exhibited improved optimum temperature at 70oC and dramatically enhanced thermostability especially at 110oC with enhanced pH stability from 4 to 10 and higher tolerance for denaturants and organic media than Mn-rec SODAp. To the best of our knowledge, Mn-rec ntdSODAp could be the most heat resistant SOD. In addition, metal incorporation of SODAp and ntdSODAp via in vivo modification have been developed and proved to be more practical for industrial use. These results indicate that fusion with NTD along with metal incorporation can generate superimposed effect and be applied to enhance the stability of cambialistic thermophilic SODs, thus providing a universal and convenient bioengineering method for generating extremely stable SODs.

De novo Assembly and Analysis of Amur Sturgeon (Acipenser schrenckii) Transcriptome in Response to Mycobacterium Marinum Infection to Identify Putative Genes Involved in Immunity

( Qianqian Zhang ),( Xiehao Wang ),( Defeng Zhang ),( Meng Long ),( Zhenbing Wu ),( Yuqing Feng ),( Jingwen Hao ),( Shuyi Wang ),( Qian Liao ),( Aihua Li ) 한국미생물생명공학회(구 한국산업미생물학회) 2019 Journal of microbiology and biotechnology Vol.29 No.8

Fish mycobacteriosis is a common bacterial disease in many species of freshwater and marine fish and has caused severe loss of fish production. Mycobacterium marinum has been the most prevalent pathogen observed in several outbreaks of mycobacteriosis of farmed sturgeons in China. However, the immune responses and pathology of sturgeons in mycobacterial infection are rarely studied. Therefore, we used the Illumina RNA-seq method to analyze the transcriptome profile of Acipenser schrenckii challenged with Mycobacterium marinum. To begin, 168,220 non-redundant contigs were acquired from the infection and control groups, and among these, 33,225 contigs have acquired annotations. A total of 4,043 differently expressed (DE) contigs between the two groups were identified, and among these, 2479 were upregulated and 1564 were down-regulated in the infected fish. A total of 1,340 DE contigs with acquired annotations in KEGG were enriched for 124 pathways including the TNF signaling pathway, and the Toll-like receptor signaling pathway. The roles of DE genes involved in significant pathways and other processes were discussed. The 2,209 DE contigs that have yet to acquire proper annotation may represent candidate genes associated with infection in sturgeons and are expected to serve as immunogenetic resources for further study. To our best knowledge, this is the first transcriptome study on sturgeons under bacterial infection.

A SCHEME OF REAL-TIME COMPUTER ARCHITECTURE FOR SPACE INTELLIGENT ROBOT

Bingrong Hong,Hong liu,Chengfa Wang,Shuyi Wang 대한전자공학회 1993 ICEIC:International Conference on Electronics, Inf Vol.1993 No.8

A Scheme of Real-Time Computer Architecture for Space Intelligent Robot

Bingrong Hong,Hong Liu,Chengfa Wang,Shuyi Wang 대한전자공학회 1993 International Conference on Electronics, Informati Vol.2 No.1

Multi-study Integration of Brain Cancer Transcriptomes Reveals Organ-Level Molecular Signatures

Sung, Jaeyun,Kim, Pan-Jun,Ma, Shuyi,Funk, Cory C.,Magis, Andrew T.,Wang, Yuliang,Hood, Leroy,Geman, Donald,Price, Nathan D. Public Library of Science 2013 PLoS computational biology Vol.9 No.7

<▼1><P>We utilized abundant transcriptomic data for the primary classes of brain cancers to study the feasibility of separating all of these diseases simultaneously based on molecular data alone. These signatures were based on a new method reported herein – Identification of Structured Signatures and Classifiers (ISSAC) – that resulted in a brain cancer marker panel of 44 unique genes. Many of these genes have established relevance to the brain cancers examined herein, with others having known roles in cancer biology. Analyses on large-scale data from multiple sources must deal with significant challenges associated with heterogeneity between different published studies, for it was observed that the variation among individual studies often had a larger effect on the transcriptome than did phenotype differences, as is typical. For this reason, we restricted ourselves to studying only cases where we had at least two independent studies performed for each phenotype, and also reprocessed all the raw data from the studies using a unified pre-processing pipeline. We found that learning signatures across multiple datasets greatly enhanced reproducibility and accuracy in predictive performance on truly independent validation sets, even when keeping the size of the training set the same. This was most likely due to the meta-signature encompassing more of the heterogeneity across different sources and conditions, while amplifying signal from the repeated global characteristics of the phenotype. When molecular signatures of brain cancers were constructed from all currently available microarray data, 90% phenotype prediction accuracy, or the accuracy of identifying a particular brain cancer from the background of all phenotypes, was found. Looking forward, we discuss our approach in the context of the eventual development of organ-specific molecular signatures from peripheral fluids such as the blood.</P></▼1><▼2><P><B>Author Summary</B></P><P>From a multi-study, integrated transcriptomic dataset, we identified a marker panel for differentiating major human brain cancers at the gene-expression level. The ISSAC molecular signatures for brain cancers, composed of 44 unique genes, are based on comparing expression levels of pairs of genes, and phenotype prediction follows a diagnostic hierarchy. We found that sufficient dataset integration across multiple studies greatly enhanced diagnostic performance on truly independent validation sets, whereas signatures learned from only one dataset typically led to high error rate. Molecular signatures of brain cancers, when obtained using all currently available gene-expression data, achieved 90% phenotype prediction accuracy. Thus, our integrative approach holds significant promise for developing organ-level, comprehensive, molecular signatures of disease.</P></▼2>