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Characterization and genome analysis of two new Aeromonas hydrophila phages, PZL-Ah1and PZL-Ah8

ARCHIVES OF VIROLOGY 2022年第2期167卷 669-673页

作者： Yu, Huabo Feng, Chao Raza, Sayed Haidar Abbas Zhang, Liang Chi, Teng Qi, Yanling Jia, Kaixiang Zhang, Yang Wei, Junfeng Qian, Aidong Sun, wuwen Shan, Xiaofeng Zhang, Lei Jilin Agr Univ Coll Anim Sci & Technol Key Lab Anim Prod & Prod Qual Safety Minist Educ Changchun 130118 Peoples R China Northwest A&F Univ Coll Anim Sci & Technol Yangling 712100 Shanxi Peoples R China

Aeromonas hydrophila (A. hydrophila) is an opportunistic pathogen of fish, humans, and livestock, and has a severe negative impact on aquaculture development. Phage therapy is considered an alternative strategy for controlling bacterial infections and contamination. In this study, we isolated and characterized the genomes of two A. hydrophila-specific phages, PZL-Ah1 and PZL-Ah8, which, based on transmission electron microscopy, were identified as members of the family Podoviridae. Both of these phages had a relatively narrow host range, with lytic activity against Aeromonas spp. strains. Whole-genome sequence analysis revealed that PZL-Ah1 and PZL-Ah8 have a double-stranded DNA genome of 38,641 bp and 40,855 bp in length, with a GC content of 53.68% and 51.89%, respectively. Forty-four open reading frames (ORFs) were predicted in PZL-Ah1, and 52 were predicted in PZL-Ah8. Twenty-eight (63.6%) ORFs in PZL-Ah1 and 29 (55.8%) ORFs in PZL-Ah8 were predicted to encode functional proteins with homologs in the NCBI database, while the remaining ORFs were classified as encoding hypothetical proteins with unknown functions. A comparison with known phage genes suggested that ORF 02, ORF 29, and ORF 04 of PZL-Ah1 and ORF 2 and ORF 4 of PZL-Ah8 are involved in host cell lysis. This study expands the phage genome database and provides good candidates for phage typing applications.

关键词： Virology Medical Microbiology Infectious Diseases

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Comparative genomic analysis of different virulence strains reveals reasons for the increased virulence of Aeromonas veronii

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JOURNAL OF FISH DISEASES 2021年第1期44卷 11-24页

作者： Yang, Bintong Chen, Chong Sun, Yufeng Cao, Linan Zhang, Dongxing Sun, wuwen Zhang, Lei Wang, Guiqin Shan, Xiaofeng Kang, Yuanhuan Qian, Aidong Jilin Agr Univ Key Lab Anim Prod Product Qual & Secur Coll Anim Sci & TechnolJilin Prov Engn Res Ctr A Joint Lab Modern Agr Technol Int CooperatMinist Changchun 130118 Jilin Peoples R China Changchun Sci Tech Univ Coll Life Sci Changchun Peoples R China

Aeromonas veronii is an important zoonotic and aquatic agent. More and more cases have shown that it has caused huge economic losses in the aquaculture industry in addition to threatening human health. But the reasons for the increasing virulence of A. veronii are still unclear. In order to further understand the reasons for the increased virulence of A. veronii, we conducted a comparative analysis of the genomes of A. veronii with different virulence. The analysis revealed that there are multiple virulence factors, such as those related to fimbriae, flagella, toxins, iron ion uptake systems and type II, type III and type VI secretion systems in the virulent strain TH0426 genome. And comparative analysis showed that there were two complete type III secretion systems (API1 and API2), of which the API2 and iron ion transport system were unique to the TH0426 strain. In addition, TH0426 strain also has unique functional gene clusters, which may play important roles in terms of resisting infection, adapting to different environments and genetic evolution. These particular virulence factors and gene clusters may be the important reasons for the increased virulence. These insights will provide a reference for the study of the pathogenesis of A. veronii.

关键词： Aeromonas veronii comparative genomics virulence factor

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Colorimetric biosensing of nopaline synthase terminator using Fe3O4@Au and hemin-functionalized reduced graphene oxide

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ANALYTICAL BIOCHEMISTRY 2020年 602卷 113798-113798页

作者： Cao, Xiaodong Xia, Zihao Yan, wuwen He, Shudong Xu, Xuan Wei, Zhaojun Ye, Yongkang Zheng, Haisong Hefei Univ Technol Sch Food Sci & Biol Engn Hefei 230009 Peoples R China Nanjing Tech Univ Coll Chem & Mol Engn Nanjing 211816 Peoples R China Technol Ctr Hefei Customs Hefei 230032 Peoples R China

In this paper, we present a simple and label-free colorimetric biosensor for detection of the nopaline synthase (NOS) terminator in genetically modified (GM) plants. The "signal on" colorimetric biosensor was developed using a nanocomposite consisted of gold nanoparticles doped magnetic Fe3O4 nanoparticles (Fe3O4@Au NP), capture probe DNA (cDNA), and hemin-functionalized reduced graphene oxide nanosheets (H-GN). The nano-composite was successfully prepared by means of Au-S bonds and the strong pi interactions between cDNA and H-GN. The sensing approach is based on the excellent peroxidase-mimicking activity of H-GN and its different electrostatic interactions with single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). In presence of the target NOS, the cDNA in the nanocomposite will hybridize with its complementary sequence, and form dsDNA structure. Due to the weak pi interactions between dsDNA and H-GN, a portion of H-GN will be released from the surface of Fe3O4@Au NPs and transferred into solution. After magnetic separation was performed, the supernatant was incubated with 3,3',5,5'-tetramethylbenzidine (TMB) in the presence of H2O2. The released HGN can catalyze the oxidation reaction of TMB and turn the colorless solution blue. This "signal-on" colorimetric biosensor shows a broad linear range of 0.5-100 nM for the target NOS, with a 0.19 nM detection limit. The application of the biosensor for determination of NOS segments in samples of GM and non-GM tomatoes shows that it can discriminate between GM and non-GM plants. The reliability of the method for samples of NOS-spiked GM tomato suggests satisfactory recoveries in the range of 93.6%-94.2%.

关键词： Colorimetric biosensor Label-free Genetically modified (GM) plants Peroxidase-mimicking activity

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Chronic cold environment regulates rheumatoid arthritis through modulation of gut microbiota-derived bile acids

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SCIENCE OF THE TOTAL ENVIRONMENT 2023年 903卷 166837页

作者： Liu, Juan Peng, Fu Cheng, Hao Zhang, Dandan Zhang, Yuxi Wang, Lixia Tang, Fei Wang, Jing Wan, Yan Wu, Jing Zhou, Yinlin Feng, wuwen Peng, Cheng Chengdu Univ Tradit Chinese Med Sch Pharm State Key Lab Southwestern Chinese Med Resources Chengdu 611137 Peoples R China Hosp Chengdu Univ Tradit Chinese Med Chengdu 610072 Peoples R China Sichuan Univ West China Sch Pharm Key Lab Drug Targeting & Drug Delivery Syst Educ M Sichuan Engn Lab Plant Sourced Drug Chengdu 610041 Peoples R China Sichuan Univ Sichuan Res Ctr Drug Precis Ind Technol West China Sch Pharm Chengdu 610041 Peoples R China Chengdu Univ Tradit Chinese Med Key Lab Minist Educ Standardizat Chinese Med Chengdu 611137 Peoples R China

The pathologies of many diseases are influenced by environmental temperature. As early as the classical Roman age, people believed that exposure to cold weather was bad for rheumatoid arthritis (RA). However, there is no direct evidence supporting this notion, and the molecular mechanisms of the effects of chronic cold exposure on RA remain unknown. Here, in a temperature-conditioned environment, we found that chronic cold exposure aggravates collagen-induced arthritis (CIA) by increasing ankle swelling, bone erosion, and cytokine levels in rats. Furthermore, in chronic cold-exposed CIA rats, gut microbiota dysbiosis was identified, including a decrease in the differential relative abundance of the families Lachnospiraceae and Ruminococcaceae. We also found that an antibiotic cocktail suppressed arthritis severity under cold conditions. Notably, the fecal microbiota transplantation (FMT) results showed that transplantation of cold-adapted microbiota partly recapitulated the microbiota signature in the respective donor rats and phenocopied the cold-induced effects on CIA rats. In addition, cold exposure disturbed bile acid profiles, in particular decreasing gut microbiota-derived taurohyodeoxycholic acid (THDCA) levels. The perturbation of bile acids was also associated with activation of the TGR5-cAMP-PKA axis and NLRP3 inflammasome. Oral THDCA supplementation mitigated the arthritis exacerbation induced by chronic cold exposure. Our findings identify an important role of aberrant gut microbiotaderived bile acids in cold exposure-related RA, highlighting potential opportunities to treat cold-related RA by manipulating the gut microbiota and/or supplementing with THDCA.

关键词： Cold exposure Rheumatoid arthritis Gut microbiota Bile acids Taurohyodeoxycholic acid

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Differential cytokines expression in cervical exfoliated cells of women with implantation after in vitro fertilization

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生物化学与生物物理学报（英文版） 2020年第11期52卷 1281-1284页

作者： Li Li wuwen Zhang Christina (Ling)Tong Hua Yan Ping Yin Kai Li BoonChin Heng Guoqing Tong Reproductive Medicine Center Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese MedicineShanghai 201203China Reproductive Medicine Center Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese MedicineShanghai 201203China School of Public Health and Health Sciences University of MassachusettsAmherstMAUSA Reproductive Medicine Center Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese MedicineShanghai 201203China Reproductive Medicine Center Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese MedicineShanghai 201203China Reproductive Medicine Center Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese MedicineShanghai 201203China School of Stomatology Peking UniversityBeijing 100081China Reproductive Medicine Center Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese MedicineShanghai 201203China

In assisted reproductive technology,the quality of embryo and the receptivity of endometrium are the key components for successful *** endometrial receptivity is an important condition to the attachment of embryo[1].In clinical practice,the endome-trial thickness,serum hormone level,and some gene expressions are always used to evaluate the functional status of endometrium.

关键词： cytokine fertilization in vitro

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高速公路PPP项目回报机制收费定价研究

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河北工业大学学报 2023年第1期52卷 75-80页

作者：宋金华张琳崔武文河北工业大学土木与交通学院天津300401 天津财经大学管理科学和工程学院天津300222

近年来,我国大力推进PPP模式在基础设施服务领域中的应用,而建立科学合理的回报机制是PPP项目的关键,也是政府方、社会资本方和公众方关注的重点。在高速公路PPP项目领域,高速公路具有较好的经营性,从高速公路收费定价的角度研究其投资... 详细信息

近年来,我国大力推进PPP模式在基础设施服务领域中的应用,而建立科学合理的回报机制是PPP项目的关键,也是政府方、社会资本方和公众方关注的重点。在高速公路PPP项目领域,高速公路具有较好的经营性,从高速公路收费定价的角度研究其投资回报机制,站在政府方、社会资本方和公众方的角度进行利益分配,采用多目标规划模型对高速公路项目收费定价构建合理目标函数并建立各方约束条件,由此求解高速公路收费定价最优解,实现项目社会效益最大化,并且在项目的全生命周期内建立定价模型动态调整模式,有助于项目的合理运营,整体把控,以期对政府建立高速公路PPP项目回报机制的收费定价模型提供参考并对高速公路PPP项目的是发展起到促进作用。

关键词：高速公路 PPP项目回报机制收费定价

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Gut microbiota as a target to limit toxic effects of traditional Chinese medicine: Implications for therapy

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BIOMEDICINE & PHARMACOTHERAPY 2021年 133卷 111047-111047页

作者： Feng, wuwen Liu, Juan Huang, Lihua Tan, Yuzhu Peng, Cheng Chengdu Univ Tradit Chinese Med Sch Pharm Chengdu Peoples R China Chengdu Univ Tradit Chinese Med State Key Lab Characterist Chinese Med Resources Chengdu Peoples R China

Traditional Chinese medicines (TCMs) are medicines that are widely used in oriental countries under the guidance of ancient Chinese medicinal philosophies. With thousands of years of experiences in fighting against diseases, TCMs are gaining increasing importance in the world. Although the efficacy of TCMs is well recognized in clinic, the toxicity of TCMs has become a serious issue around the world in recent years. In general, the toxicity of TCMs is caused by the toxic medicinal compounds and contaminants in TCMs such as pesticides, herbicides, and heavy metals. Recent studies have demonstrated that gut microbiota can interact with TCMs and thus influence the toxicity of TCMs. However, there is no focused review on gut microbiota and the toxicity of TCMs. Here, we summarized the influences of the gut microbiota on the toxicity of medicinal compounds in TCMs and the corresponding mechanisms were offered. Then, we discussed the relationships between gut microbiota and the TCM contaminants. In addition, we discussed the methods of manipulating gut microbiota to reduce the toxicity of TCMs. At the end of this review, the perspectives on gut microbiota and the toxicity of TCMs were also discussed.

关键词： Gut microbiota Traditional Chinese medicine Toxicity Contaminant

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MB2: Decomposed Behavior Modeling for Self-Driving Database Management Systems 21

MB2: Decomposed Behavior Modeling for Self-Driving Database ...

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ACM SIGMOD International Conference on Management of Data (SIGMOD)

作者： Ma, Lin Zhang, William Jiao, Jie Wang, wuwen Butrovich, Matthew Lim, Wan Shen Menon, Prashanth Pavlo, Andrew Carnegie Mellon Univ Pittsburgh PA 15213 USA

ISBN: (纸本)9781450383431

Database management systems (DBMSs) are notoriously difficult to deploy and administer. The goal of a self-driving DBMS is to remove these impediments by managing itself automatically. However, a critical problem in achieving full autonomy is how to predict the DBMS's runtime behavior and resource consumption. These predictions guide a self-driving DBMS's decision-making components to tune and optimize all aspects of the system. We present the ModelBot2 end-to-end framework for constructing and maintaining prediction models using machine learning (ML) in self-driving DBMSs. Our approach decomposes a DBMS's architecture into fine-grained operating units that make it easier to estimate the system's behavior for configurations that it has never seen before. ModelBot2 then provides an offline execution environment to exercise the system to produce the training data used to train its models. We integrated ModelBot2 in an in-memory DBMS and measured its ability to predict its performance for OLTP and OLAP workloads running in dynamic environments. We also compare ModelBot2 against state-of-the-art ML models and show that our models are up to 25x more accurate in multiple scenarios.

关键词： self-driving database autonomous database database administration

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骨创伤患者发生下肢深静脉血栓的危险因素及其诊断效能分析

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中华创伤杂志 2024年第9期40卷 809-816页

作者：赵婷孙颖昕张武文周思源周鑫叠冯同保张平南京医科大学附属常州第二人民医院医学检验科常州213000 南京医科大学附属常州第二人民医院创伤骨科常州213000 南京医科大学常州医学中心常州213000

目的探讨骨创伤患者发生下肢深静脉血栓(DVT)的危险因素及其诊断效能。方法采用回顾性队列研究分析2023年10月至2024年2月南京医科大学附属常州第二人民医院收治的108例骨创伤患者的临床资料,其中男61例,女47例;年龄17~96岁[(55.2±... 详细信息

目的探讨骨创伤患者发生下肢深静脉血栓(DVT)的危险因素及其诊断效能。方法采用回顾性队列研究分析2023年10月至2024年2月南京医科大学附属常州第二人民医院收治的108例骨创伤患者的临床资料,其中男61例,女47例;年龄17~96岁[(55.2±19.5)岁]。根据入院后96 h内的下肢彩色多普勒超声结果,将患者分为DVT组(58例)和非DVT组(50例)。其中DVT组骨创伤后7 d内发生下肢DVT 42例,7 d后发生下肢DVT 16例。收集两组基本临床资料,包括性别、年龄、体重指数(BMI)、基础疾病、致伤原因、骨折部位、是否手术、入院时Caprini评分和实验室检查指标,包括凝血常规[凝血酶原时间(PT)、国际标准化比值(INR)、凝血酶时间(TT)、活化部分凝血活酶时间(APTT)、纤维蛋白原(FBG)、D‑二聚体(D‑D)]和血栓四项[血浆凝血酶‑抗凝血酶Ⅲ复合物(TAT)、血栓调节蛋白(TM)、组织型纤溶酶原激活剂‑抑制剂1复合体(tPAIC)、纤溶酶α2纤溶酶抑制剂复合体(PIC)]。采用单因素分析和多因素二元Logistic回归分析评估上述指标与骨创伤患者发生下肢DVT的相关性并确定其独立危险因素。对相关危险因素进行受试者工作特征(ROC)曲线及曲线下面积(AUC)分析,评价并比较各危险因素对骨创伤患者发生下肢DVT的诊断效能,并进一步评价各危险因素对骨创伤后7 d内发生DVT的诊断效能。结果单因素分析结果显示,性别、年龄、Caprini评分、D‑D、TAT、TM和PIC与骨创伤患者发生下肢DVT有一定的相关性(P<0.01)。多因素二元Logistic回归分析结果表明,Caprini评分(OR=1.36,95%CI 1.12,1.65,P<0.01)、TAT(OR=1.05,95%CI 1.00,1.10,P<0.05)和TM(OR=1.34,95%CI 1.02,1.77,P<0.05)与骨创伤患者发生下肢DVT显著相关。ROC曲线分析结果表明,TAT(AUC=0.76,95%CI 0.67,0.86)的诊断效能最大,TM(AUC=0.72,95%CI 0.62,0.81)和Caprini评分(AUC=0.72,95%CI 0.62,0.82)的诊断效能次之。将各危险因素进行联合分析能有效提高对DVT的诊断效能(AUC=0.84,95%CI 0.77,0.92)。另外,TAT(AUC=0.81,95%CI 0.71,0.91)对骨创伤后7 d内发生下肢DVT的诊断效能更优,且高于Caprini评分(AUC=0.72,95%CI 0.61,0.83)和TM(AUC=0.71,95%CI 0.60,0.83);同时,将各危险因素联合分析也能有效提高对骨创伤后7 d内发生下肢DVT的诊断效能(AUC=0.85,95%CI 0.77,0.93)。结论Caprini评分、TAT和TM是骨创伤患者发生下肢DVT的独立危险因素,且三者对发生下肢DVT均具有较好的诊断效能。将三者联合分析能显著提高诊断效能,较单独使用各指标的诊断效能更高。同时,TAT对骨创伤后7 d内发生下肢DVT的诊断效能更优,将各危险因素进行联合分析同样能提高其诊断效能。

关键词：静脉血栓形成,诊断下肢骨折危险因素

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An Optimization Framework for Two-tier Cellular Network Resource Allocation and Handover

An Optimization Framework for Two-tier Cellular Network Reso...

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作者： Li, wuwen University of California Los Angeles

学位级别：Ph.D.

The Orthogonal Frequency Division Multiplexing Access (OFDMA) and macro-femto two-tier heterogrneous network are the core technologies used in 4G and 5G cellular networks. These pose new challanges and optimization potential for network resource allocation with consideration of fairness as well as for user equiptment (UE) handoff with consideration of resource allocation. This thesis studies both problems, and analyses the inherent difficulties in the problem domain. Then several optimization algorithms are proposed to solve the problem. An optimization framework is proposed to integrate the algorithms together.

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