Burkholderia thailandensis outer membrane vesicles exert antimicrobial activity against drug-resistant and competitor microbial species

Yihui Wang,Joseph P. Hoffmann,Chau-Wen Chou,Kerstin Höner zu Bentrup,Joseph A. Fuselier,Jacob P. Bitoun,William C. Wimley,Lisa A. Morici 한국미생물학회 2020 The journal of microbiology Vol.58 No.7

Gram-negative bacteria secrete outer membrane vesicles (OMVs) that play critical roles in intraspecies, interspecies, and bacteria-environment interactions. Some OMVs, such as those produced by Pseudomonas aeruginosa, have previously been shown to possess antimicrobial activity against competitor species. In the current study, we demonstrate that OMVs from Burkholderia thailandensis inhibit the growth of drug-sensitive and drug-resistant bacteria and fungi. We show that a number of antimicrobial compounds, including peptidoglycan hydrolases, 4-hydroxy-3-methyl-2-(2-nonenyl)- quinoline (HMNQ) and long-chain rhamnolipid are present in or tightly associate with B. thailandensis OMVs. Furthermore, we demonstrate that HMNQ and rhamnolipid possess antimicrobial and antibiofilm properties against methicillin- resistant Staphylococcus aureus (MRSA). These findings indicate that B. thailandensis secretes antimicrobial OMVs that may impart a survival advantage by eliminating competition. In addition, bacterial OMVs may represent an untapped resource of novel therapeutics effective against biofilm- forming and multidrug-resistant organisms.

Separating paint mist from paint spraying waste gas: mechanism, model and application

Yihui Zhou,Xi He,Wang Li,Tao Xu,Dong Xie,Xin Dai,Zhang Liu,Hanqing Wang,Gang Yu 대한환경공학회 2021 Environmental Engineering Research Vol.26 No.5

The paint spraying waste gas contains a large amount of paint mist, volatile organic compounds (VOCs) and other hazardous materials, which seriously affects human health and atmospheric environment. Paint mist cannot be separated from paint spraying waste gas effectively by the existing dry filtration methods because of the filter blocking. A new separation process and a novel coupling device with high separation efficiency have been developed. A numerical model was established to optimize the structure and operation parameters of the baffle interceptor by hydrodynamics method which verified by the coupling device experiment. From the simulating results, when plate spacing was 20 ㎜, folding angle was 90° and airflow velocity was up to 8 ㎧, the separation efficiency of paint mist with the diameter of 15 ㎛ was 84.7% and the pressure drop of the baffle interceptor was 220.2 ㎩. Experiment was conducted under the above-optimized conditions, and the results showed that the pressure drop of the baffle interceptor was 303.33 ㎩, and the paint mist separation efficiencies of the baffle interceptor and the interception-filtration coupling device were 78.34% and 96.38%, respectively.

Identification and Validation of Novel Biomarkers and Potential Targeted Drugs in Cholangiocarcinoma: Bioinformatics, Virtual Screening, and Biological Evaluation

( Jiena Wang ),( Weiwei Zhu ),( Junxue Tu ),( Yihui Zheng ) 한국미생물생명공학회 2022 Journal of microbiology and biotechnology Vol.32 No.10

Cholangiocarcinoma (CCA) is a complex and refractor type of cancer with global prevalence. Several barriers remain in CCA diagnosis, treatment, and prognosis. Therefore, exploring more biomarkers and therapeutic drugs for CCA management is necessary. CCA gene expression data was downloaded from the TCGA and GEO databases. KEGG enrichment, GO analysis, and protein-protein interaction network were used for hub gene identification. miRNA were predicted using Targetscan and validated according to several GEO databases. The relative RNA and miRNA expression levels and prognostic information were obtained from the GEPIA. The candidate drug was screened using pharmacophore-based virtual screening and validated by molecular modeling and through several in vitro studies. 301 differentially expressed genes (DEGs) were screened out. Complement and coagulation cascades-related genes (including AHSG, F2, TTR, and KNG1), and cell cycle-related genes (including CDK1, CCNB1, and KIAA0101) were considered as the hub genes in CCA progression. AHSG, F2, TTR, and KNG1 were found to be significantly decreased and the eight predicted miRNA targeting AHSG, F2, and TTR were increased in CCA patients. CDK1, CCNB1, and KIAA0101 were found to be significantly abundant in CCA patients. In addition, Molport-003-703-800, which is a compound that is derived from pharmacophores-based virtual screening, could directly bind to CDK1 and exhibited anti-tumor activity in cholangiocarcinoma cells. AHSG, F2, TTR, and KNG1 could be novel biomarkers for CCA. Molport-003-703-800 targets CDK1 and work as potential cell cycle inhibitors, thereby having potential for consideration for new chemotherapeutics for CCA.

Numerical simulation in time domain to study cross-flow VIV of catenary riser subject to vessel motion-induced oscillatory current

Liu, Kun,Wang, Kunpeng,Wang, Yihui,Li, Yulong The Society of Naval Architects of Korea 2020 International Journal of Naval Architecture and Oc Vol.12 No.-

The present study proposes a time domain model for the Vortex-induced Vibration (VIV) simulation of a catenary riser under the combination of the current and oscillatory flow induced by vessel motion. In this model, the hydrodynamic force of VIV comprises excitation force, hydrodynamic damping and added mass, which are taken as functions of the non-dimensional frequency and amplitude ratio. The non-dimensional frequency is related with the response frequency, natural frequency, lock-in range and the fluid velocity. The relatively oscillatory flow induced by vessel motion is taken into account in the fluid velocity. Considering that the added mass coefficient and the non-dimensional frequency can affect each other, an iterative analysis is conducted at each time step to update the added mass coefficient and the natural frequency. This model is in detail validated against the published test models. The results show that the model can reasonably reflect the effect of the added mass coefficient on the VIV, and can well predict the riser's VIV under stationary and oscillatory flow induced by vessel motion. Based on the model, this study carries out the VIV simulation of a catenary riser with harmonic vessel motion. By analyzing the bending moment near the touchdown point, it is found that under the combination of the ocean current and oscillatory flow the vessel motion may decrease the VIV response, while increase the excited frequencies. In addition, the decreasing rate of the VIV under vessel surge is larger than that under vessel heave at small vessel motion velocity, while the situation becomes opposite at large vessel motion velocity.

Numerical simulation in time domain to study cross-flow VIV of catenary riser subject to vessel motion-induced oscillatory current

Liu, Kun,Wang, Kunpeng,Wang, Yihui,Li, Yulong The Society of Naval Architects of Korea 2020 International Journal of Naval Architecture and Oc Vol.12 No.1

The present study proposes a time domain model for the Vortex-induced Vibration (VIV) simulation of a catenary riser under the combination of the current and oscillatory flow induced by vessel motion. In this model, the hydrodynamic force of VIV comprises excitation force, hydrodynamic damping and added mass, which are taken as functions of the non-dimensional frequency and amplitude ratio. The non-dimensional frequency is related with the response frequency, natural frequency, lock-in range and the fluid velocity. The relatively oscillatory flow induced by vessel motion is taken into account in the fluid velocity. Considering that the added mass coefficient and the non-dimensional frequency can affect each other, an iterative analysis is conducted at each time step to update the added mass coefficient and the natural frequency. This model is in detail validated against the published test models. The results show that the model can reasonably reflect the effect of the added mass coefficient on the VIV, and can well predict the riser's VIV under stationary and oscillatory flow induced by vessel motion. Based on the model, this study carries out the VIV simulation of a catenary riser with harmonic vessel motion. By analyzing the bending moment near the touchdown point, it is found that under the combination of the ocean current and oscillatory flow the vessel motion may decrease the VIV response, while increase the excited frequencies. In addition, the decreasing rate of the VIV under vessel surge is larger than that under vessel heave at small vessel motion velocity, while the situation becomes opposite at large vessel motion velocity.

A new reconfigurable liquid-metal-antenna-based sensor

Xiao-Ping Zhou,Yihui Fu,Hantao Zhu,Zihao Yu,Shanyong Wang 국제구조공학회 2022 Smart Structures and Systems, An International Jou Vol.30 No.4

In this paper, a new sensor chip with frequency reconstruction range of 2.252 GHz ~ 2.450 GHz is designed and fabricated. On this basis, a self-designed "T-shaped" shell is added to overcome the disadvantage of uneven deformation of the traditional steel shell, and the range of the sensor chip is expanded to 0 kN ~ 96 kN. The liquid metal antenna is used to carry out a step-by-step loading test, and the relationship between the antenna resonance frequency and the pressure load is analyzed. The results show that there is a good linear relationship between the pressure load and the resonant frequency. Therefore, the liquid metal antenna can be regarded as a pressure sensor. The cyclic loading and unloading experiments of the sensor are carried out, and different loading rates are used to explore the influence on the performance of the sensor. The loading and unloading characteristic curves and the influence characteristic curves of loading rate are plotted. The experimental results show that the sensor has no residual deformation during the cycle of loading and unloading. Moreover, the influence of temperature on the performance of the sensor is studied, and the temperature correction formula is derived.

The cytoplasmic loops of AgrC contribute to the quorum-sensing activity of Staphylococcus aureus

Huang Qian,Xie Yihui,Yang Ziyu,Cheng Danhong,He Lei,Wang Hua,Liu Qian,Li Min 한국미생물학회 2021 The journal of microbiology Vol.59 No.1

In Staphylococcus aureus, the accessory gene regulator (agr) quorum-sensing system is thought to play an important role in biofilm formation. The histidine kinase AgrC is one of the agr system components and activated by the self-generated auto-inducing peptide (AIP), which is released continuously into the extracellular environment during bacterial growth. The extracellular loops (Extra-loops) of AgrC are crucial for AIP binding. Here, we reported that the cytoplasmic loops (Cyto-loops) of AgrC are also involved in Agr activity. We identified S. aureus ST398 clinical isolates containing a naturally occurring single amino acid substitution (lysine to isoleucine) at position 73 of an AgrC Cyto-loop that exhibited significantly stronger biofilm formation and decreased Agr activity compared to the wild-type strain. A constructed strain containing the K73I point mutation in AgrC Cyto-loop continued to show a growth dependent induction of the agr system, although the growth dependent induction was delayed by about 6 h compared to the wild-type. In addition, a series of strains containing deletion mutants of the AgrC Cyto- and Extra-loops were constructed and revealed that the removal of the two Cyto-loops and Extra-loops 2 and 3 totally abolished the Agr activity and the growth-dependence on the agr system induction. Remarkably, the Extra-loop 1 deletion did not affect the Agr activity. In conclusion, the AgrC Cyto-loops play a crucial role in the S. aureus quorum-sensing activity.

Whole-genome sequence association study identifies cyclin dependent kinase 8 as a key gene for the number of mummified piglets

Wu Pingxian,Chen Dejuan,Wang Kai,Wang Shujie,Liu Yihui,Jiang Anan,Xiao Weihang,Jiang Yanzhi,Zhu Li,Xu Xu,Qiu Xiaotian,Li Xuewei,Tang Guoqing 아세아·태평양축산학회 2023 Animal Bioscience Vol.36 No.1

Objective: Pigs, an ideal biomedical model for human diseases, suffer from about 50% early embryonic and fetal death, a major cause of fertility loss worldwide. However, identifying the causal variant remains a huge challenge. This study aimed to detect single nucleotide polymorphisms (SNPs) and candidate genes for the number of mummified (NM) piglets using the imputed whole-genome sequence (WGS) and validate the potential candidate genes. Methods: The imputed WGS was introduced from genotyping-by-sequencing (GBS) using a multi-breed reference population. We performed genome-wide association studies (GWAS) for NM piglets at birth from a Landrace pig populatiGWAS peak located on SSC11: 0.10 to 7.11 Mbp (Top SNP, SSC11:1,889,658 bp; p = 9.98E-13) was identified in cyclin dependent kinase on. A total of 300 Landrace pigs were genotyped by GBS. The whole-genome variants were imputed, and 4,252,858 SNPs were obtained. Various molecular experiments were conducted to determine how the genes affected NM in pigs. Results: A strong GWAS peak located on SSC11: 0.10 to 7.11 Mbp (Top SNP, SSC11:1,889,658 bp; p = 9.98E-13) was identified in cyclin dependent kinase 8 (CDK8) gene, which plays a crucial role in embryonic retardation and lethality. Based on the molecular experiments, we found that Y-box binding protein 1 (YBX1) was a crucial transcription factor for CDK8, which mediated the effect of CDK8 in the proliferation of porcine ovarian granulosa cells via transforming growth factor beta/small mother against decapentaplegic signaling pathway, and, as a consequence, affected embryo quality, indicating that this pathway may be contributing to mummified fetal in pigs. Conclusion: A powerful imputation-based association study was performed to identify genes associated with NM in pigs. CDK8 was suggested as a functional gene for the proliferation of porcine ovarian granulosa cells, but further studies are required to determine causative mutations and the effect of loci on NM in pigs.

Genetic parameter estimation for reproductive traits in QingYu pigs and comparison of carcass and meat quality traits to Berkshire×QingYu crossbred pigs

Luo Jia,Yang Yiting,Liao Kun,Liu Bin,Chen Ying,Shen Linyuan,Chen Lei,Jiang An’an,Liu Yihui,Li Qiang,Wang Jinyong,Li Xuewei,Zhang Shunhua,Zhu Li 아세아·태평양축산학회 2020 Animal Bioscience Vol.33 No.8

Objective: The QingYu pig is well known for its excellent meat quality attributes in Sichuan province, China. In order to improve its production efficiency, the determination of genetic factors contributing to quantifiable economic traits of livestock is important. Moreover, the cross-breeding of QingYu pigs with western breeds possessing strong growth attributes is an efficient way to improve the performance of this breed. Methods: Here, the genetic parameters of several important reproductive traits of QingYu pigs were estimated, include total number born (TNB), number born alive, litter birth weight, individual birth weight, number of piglets weaned, litter weaning weight, and individual weaning weight. The data was analyzed using the ASReml 3.0 software (NSW Inc., Sydney, Australia). Furthermore, the effects of crossing Berkshire with QingYu (BQ) pigs on carcass and meat quality traits, as well as the effects of slaughter weight on carcass and meat quality of BQ were characterized. Results: QingYu pigs exhibited superior reproductive traits. The TNB available to QingYu pigs was more than 8 per parity. The observed repeatability of the reproductive traits of the QingYu pigs was between 0.10 and 0.23. The significantly correlated genetic and phenotypic of reproduction traits were consistent. Interestingly, the BQ pigs exhibited improved carcass quality, with a significant increase in loin muscle area, lean percentage and reduction in sebum percentage. As a result, BQ had higher L45min, lower cooking scores, and lower drip loss. In addition, the loin muscle area, body length, and sebum percentage were significantly higher in 90 and 100 kg animals. Cooking loss showed a significant increase at 80 kg, and marbling increased significantly from 90 kg. Conclusion: The results of this study suggest that QingYu pigs exhibit excellent reproductive properties and heritability of these traits. Crossing with Berkshire is an efficient strategy to improve the carcass and meat quality of QingYu pigs for commercial operations. Furthermore, it appears as though the optimal slaughter weight of BQ pigs is at approximately 90 kg.