Journal of Microbiology

Journal Articles

NEDD4 Regulated Pyroptosis Occurred from Co‑infection between Influenza A Virus and Streptococcus pneumoniae: Jiangzhou You , Linlin Zhou , Xudong San , Hailing Li , Mingyuan Li , Baoning Wang; J. Microbiol. 2023;61(8):777-789. Published online October 4, 2023; DOI: https://doi.org/10.1007/s12275-023-00076-y

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Co-infection of respiratory tract viruses and bacteria often result in excess mortality, especially pneumonia caused by influenza viruses and Streptococcus pneumoniae. However, the synergistic mechanisms remain poorly understood. Therefore, it is necessary to develop a clearer understanding of the molecular basis of the interaction between influenza virus and Streptococcus pneumonia. Here, we developed the BALB/c mouse model and the A549 cell model to investigate inflammation and pyroptotic cell death during co-infection. Co-infection significantly activated the NLRP3 inflammasome and induced pyroptotic cell death, correlated with excess mortality. The E3 ubiquitin ligase NEDD4 interacted with both NLRP3 and GSDMD, the executor of pyroptosis. NEDD4 negatively regulated NLRP3 while positively regulating GSDMD, thereby modulating inflammation and pyroptotic cell death. Our findings suggest that NEDD4 may play a crucial role in regulating the GSDMD-mediated pyroptosis signaling pathway. Targeting NEDD4 represents a promising approach to mitigate excess mortality during influenza pandemics by suppressing synergistic inflammation during co-infection of influenza A virus and Streptococcus pneumoniae.

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Yinqin Qingfei granules alleviate Mycoplasma pneumoniae pneumonia via inhibiting NLRP3 inflammasome-mediated macrophage pyroptosis
Zhe Song, Chengen Han, Guangzhi Luo, Guangyuan Jia, Xiao Wang, Baoqing Zhang
Frontiers in Pharmacology.2024;[Epub] CrossRef
Overexpression of DTX1 inhibits D-GalN/TNF-α-induced pyroptosis and inflammation in hepatocytes by regulating NLRP3 ubiquitination
Mingshui Liu, Jing Gu, Li Chen, Wei Sun, Xiaoping Huang, Jianhe Gan
Toxicology Research.2024;[Epub] CrossRef
NLRP3 Inflammasomes: Dual Function in Infectious Diseases
Yanbo Li, Rui Qiang, Zhengmin Cao, Qingjuan Wu, Jiuchong Wang, Wenliang Lyu
The Journal of Immunology.2024; 213(4): 407. CrossRef

Genome Sequencing Highlights the Plant Cell Wall Degrading Capacity of Edible Mushroom Stropharia rugosoannulata: Mengpei Guo , Xiaolong Ma , Yan Zhou , Yinbing Bian , Gaolei Liu , Yingli Cai , Tianji Huang , Hongxia Dong , Dingjun Cai , Xueji Wan , Zhihong Wang , Yang Xiao , Heng Kang; J. Microbiol. 2023;61(1):83-93. Published online February 1, 2023; DOI: https://doi.org/10.1007/s12275-022-00003-7

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Abstract

The basidiomycetous edible mushroom Stropharia rugosoannulata has excellent nutrition, medicine, bioremediation, and biocontrol properties. S. rugosoannulata has been widely and easily cultivated using agricultural by-products showing strong lignocellulose degradation capacity. However, the unavailable high-quality genome information has hindered the research on gene function and molecular breeding of S. rugosoannulata. This study provided a high-quality genome assembly and annotation from S. rugosoannulata monokaryotic strain QGU27 based on combined Illumina-Nanopore data. The genome size was about 47.97 Mb and consisted of 20 scaffolds, with an N50 of 3.73 Mb and a GC content of 47.9%. The repetitive sequences accounted for 17.41% of the genome, mostly long terminal repeats (LTRs). A total of 15,726 coding gene sequences were putatively identified with the BUSCO score of 98.7%. There are 142 genes encoding plant cell wall degrading enzymes (PCWDEs) in the genome, and 52, 39, 30, 11, 8, and 2 genes related to lignin, cellulose, hemicellulose, pectin, chitin, and cutin degradation, respectively. Comparative genomic analysis revealed that S. rugosoannulata is superior in utilizing aldehyde-containing lignins and is possible to utilize algae during the cultivation.

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Analysis of Gene Regulatory Network and Transcription Factors in Different Tissues of the Stropharia rugosoannulata Fruiting Body
Jia Lu, Jing Yan, Na Lu, Jiling Song, Jiayao Lin, Xiaohua Zhou, Xuebing Ying, Zhen Li, Zufa Zhou, Fangjie Yao
Journal of Fungi.2025; 11(2): 123. CrossRef
Evaluation of Genetic Diversity and Agronomic Traits of Germplasm Resources of Stropharia rugosoannulata
Miao Gu, Qiang Chen, Yan Zhang, Yongchang Zhao, Li Wang, Xiangli Wu, Mengran Zhao, Wei Gao
Horticulturae.2024; 10(3): 213. CrossRef
Molecular Profiling of Rice Straw Degradability Discrepancy in Stropharia rugosoannulata Core Germplasm
Wenbing Gong, Yuyu Zeng, Xinru Li, Zhidong Zhao, Nan Shen, Yan Zhou, Yinbing Bian, Yang Xiao
Journal of Agricultural and Food Chemistry.2024; 72(45): 25379. CrossRef
Genome assembly of M. spongiola and comparative genomics of the genus Morchella provide initial insights into taxonomy and adaptive evolution
Qing Meng, Zhanling Xie, Hongyan Xu, Jing Guo, Qingqing Peng, Yanyan Li, Jiabao Yang, Deyu Dong, Taizhen Gao, Fan Zhang
BMC Genomics.2024;[Epub] CrossRef

Review

The crosstalk between bacteria and host autophagy: host defense or bacteria offense: Lin Zheng , Fang Wei , Guolin Li; J. Microbiol. 2022;60(5):451-460. Published online April 29, 2022; DOI: https://doi.org/10.1007/s12275-022-2009-z

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Abstract

Xenophagy is a specific selective autophagy for the elimination of intracellular bacteria. Current evidence suggests that the processes for host autophagy system to recognize and eliminate invading bacteria are complex, and vary according to different pathogens. Although both ubiquitin-dependent and ubiquitin-independent autophagy exist in host to defense invading bacteria, successful pathogens have evolved diverse strategies to escape from or paralyze host autophagy system. In this review, we discuss the mechanisms of host autophagy system to recognize and eliminate intracellular pathogens and the mechanisms of different pathogens to escape from or paralyze host autophagy system, with a particular focus on the most extensively studied bacteria.

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Complement C3 deposition restricts the proliferation of internalized Staphylococcus aureus by promoting autophagy
Yining Deng, Yunke Zhang, Tong Wu, Kang Niu, Xiaoyu Jiao, Wenge Ma, Chen Peng, Wenxue Wu
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef
Innate immune response of host cells infected with Salmonella
Hongfei Fan, Juane Lu, Hao Wu, Haihua Ruan, Wenjun Song, Y.-T. Yu, P.P. Piccaluga, S. Xie
BIO Web of Conferences.2024; 111: 01022. CrossRef
Exploring the Connections: Autophagy, Gut Microbiota, and Inflammatory Bowel Disease Pathogenesis
Arunkumar Subramanian, Afrarahamed J, Tamilanban T, Vinoth Kumarasamy, M Yasmin Begum, Mahendran Sekar, Vetriselvan Subramaniyan, Ling Shing Wong, Adel Al Fatease
Journal of Inflammation Research.2024; Volume 17: 10453. CrossRef
Programmed cell death and Salmonella pathogenesis: an interactive overview
Yu Zhang, Maodou Xu, Yujiao Guo, Li Chen, Wanwipa Vongsangnak, Qi Xu, Lizhi Lu
Frontiers in Microbiology.2024;[Epub] CrossRef
Bacterial lipoprotein plays an important role in the macrophage autophagy and apoptosis induced by Salmonella typhimurium and Staphylococcus aureus
Shanshan Jiang, Jinyao He, Lijie Zhang, Qiaojiajie Zhao, Shuqi Zhao
Open Life Sciences.2023;[Epub] CrossRef
Xenophagy as a Strategy for Mycobacterium leprae Elimination during Type 1 or Type 2 Leprosy Reactions: A Systematic Review
Débora Dantas Nucci Cerqueira, Ana Letícia Silva Pereira, Ana Elisa Coelho da Costa, Tarcísio Joaquim de Souza, Matheus Santos de Sousa Fernandes, Fabrício Oliveira Souto, Patrícia d’Emery Alves Santos
Pathogens.2023; 12(12): 1455. CrossRef
Brucella BtpB Manipulates Apoptosis and Autophagic Flux in RAW264.7 Cells
Junmei Li, Lin Qi, Ziyang Diao, Mengyu Zhang, Bin Li, Yunyi Zhai, Mingyue Hao, Dong Zhou, Wei Liu, Yaping Jin, Aihua Wang
International Journal of Molecular Sciences.2022; 23(22): 14439. CrossRef

Journal Article

Proteomic analysis reveals the temperature-dependent presence of extracytoplasmic peptidases in the biofilm exoproteome of Listeria monocytogenes EGD-e: Yue-Jia Lee , Chinling Wang; J. Microbiol. 2020;58(9):761-771. Published online July 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9522-8

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Abstract

The foodborne pathogen Listeria monocytogenes resists environmental stresses by forming biofilms. Because this pathogen transmits between the environment and the host, it must adapt to temperature as an environmental stress. In this study, we aimed to identify which proteins were present depending on the temperature in the biofilms of L. monocytogenes EGD-e. Proteins in the supernatants of biofilms formed at 25°C and 37°C were compared using two-dimensional gel electrophoresis and liquid chromatography with tandem mass spectrometry. The larger number of extracytoplasmic proteins associated with cell wall/membrane/envelop biogenesis was identified from the supernatant of biofilms formed at 25°C (7) than those at 37°C (0). Among the 16 extracytoplasmic proteins detected only at 25°C, three were peptidases, namely Spl, Cwh, and Lmo0186. Moreover, mRNA expression of the three peptidases was higher at 25°C than at 37°C. Interestingly, this adaptation of gene expression to temperature was present in sessile cells but not in dispersed cells. After inhibiting the activity of extracytoplasmic peptidases with a protease inhibitor, we noted that the levels of biofilm biomass increased with higher concentrations of the protease inhibitor only when L. monocytogenes grew biofilms at 25°C and not at 37°C. Overall, our data suggest an effect of temperature on the presence of peptidases in L. monocytogenes biofilms. Additionally, increasing the levels of extracytoplasmic peptidases in biofilms is likely a unique feature for sessile L. monocytogenes that causes a naturally occurring breakdown of biofilms and facilitates the pathogen exiting biofilms and disseminating into the environment.

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Stress Adaptation Responses of a Listeria monocytogenes 1/2a Strain via Proteome Profiling
Federica D’Onofrio, Maria Schirone, Antonello Paparella, Ivanka Krasteva, Manuela Tittarelli, Francesco Pomilio, Luigi Iannetti, Nicola D’Alterio, Mirella Luciani
Foods.2023; 12(11): 2166. CrossRef
How to study biofilms: technological advancements in clinical biofilm research
Leanne Cleaver, James A. Garnett
Frontiers in Cellular and Infection Microbiology.2023;[Epub] CrossRef
Studying the metabolic factors that may impact the growth of co-cultured Listeria monocytogenes strains at low temperature
Maria A. Gkerekou, Eleftheria H. Kaparakou, Petros A. Tarantilis, Panagiotis N. Skandamis
Food Research International.2023; 171: 113056. CrossRef
Exoproteome Perspective on the Bile Stress Response of Lactobacillus johnsonii
Bernadette B. Bagon, Valerie Diane V. Valeriano, Ju Kyoung Oh, Edward Alain B. Pajarillo, Ji Yoon Lee, Dae-Kyung Kang
Proteomes.2021; 9(1): 10. CrossRef

Review

Recent advances in the development of β-lactamase inhibitors: Shivakumar S. Jalde , Hyun Kyung Choi; J. Microbiol. 2020;58(8):633-647. Published online July 27, 2020; DOI: https://doi.org/10.1007/s12275-020-0285-z

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Abstract

β-Lactam antibiotics are the most commonly prescribed antibiotics worldwide; however, antimicrobial resistance (AMR) is a global challenge. The β-lactam resistance in Gram-negative bacteria is due to the production of β-lactamases, including extended-spectrum β-lactamases, metallo-β-lactamases, and carbapenem-hydrolyzing class D β-lactamases. To restore the efficacy of BLAs, the most successful strategy is to use them in combination with β-lactamase inhibitors (BLI). Here we review the medically relevant β-lactamase families and penicillins, diazabicyclooctanes, boronic acids, and novel chemical scaffold-based BLIs, in particular approved and under clinical development.

Citations

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Functional and structural analyses of IMP-27 metallo-β-lactamase: evolution of IMP-type enzymes to overcome Zn(II) deprivation
Yoshiki Kato, Toshio Yamaguchi, Haruka Nakagawa-Kamura, Yoshikazu Ishii, Akiko Shimizu-Ibuka, Pablo Power
Microbiology Spectrum.2024;[Epub] CrossRef
Current Strategy for Targeting Metallo-β-Lactamase with Metal-Ion-Binding Inhibitors
Jessica L. Ortega-Balleza, Lenci K. Vázquez-Jiménez, Eyra Ortiz-Pérez, Guadalupe Avalos-Navarro, Alma D. Paz-González, Edgar E. Lara-Ramírez, Gildardo Rivera
Molecules.2024; 29(16): 3944. CrossRef
Understanding the Functional Dynamics of the TokK Enzyme in Carbapenem Biosynthesis via MD Simulations and QM/MM Calculations
Shakir Ali Siddiqui, Kshatresh Dutta Dubey
Inorganic Chemistry.2024; 63(40): 18963. CrossRef
Recent advances in functionalized macrocyclic polyamines for medicine applications
Hao Chang, Renzhong Qiao, Chao Li
Chinese Chemical Letters.2024; : 110675. CrossRef
Exploring the dynamics of gut microbiota, antibiotic resistance, and chemotherapy impact in acute leukemia patients: A comprehensive metagenomic analysis
Ying Luo, Taha Majid Mahmood Sheikh, Xin Li, YuMeng Yuan, Fen Yao, Meimei Wang, Xiaoling Guo, Jilong Wu, Muhammad Shafiq, Qingdong Xie, Xiaoyang Jiao
Virulence.2024;[Epub] CrossRef
Decrypting biocontrol functions and application modes by genomes data of three Trichoderma Strains/Species
Shida Ji, Bin Liu, Jing Han, Ning Kong, Yongfeng Yang, Yucheng Wang, Zhihua Liu
Fungal Genetics and Biology.2024; 172: 103889. CrossRef
Revisiting the Checkerboard to Inform Development of β-Lactam/β-Lactamase Inhibitor Combinations
Darren J. Bentley
Antibiotics.2024; 13(4): 337. CrossRef
Role of β-Lactamase Inhibitors as Potentiators in Antimicrobial Chemotherapy Targeting Gram-Negative Bacteria
Song Zhang, Xinyu Liao, Tian Ding, Juhee Ahn
Antibiotics.2024; 13(3): 260. CrossRef
The C5α-Methyl-Substituted Carbapenem NA-1-157 Exhibits Potent Activity against Klebsiella spp. Isolates Producing OXA-48-Type Carbapenemases
Clyde A. Smith, Nichole K. Stewart, Marta Toth, Pojun Quan, John D. Buynak, Sergei B. Vakulenko
ACS Infectious Diseases.2023; 9(5): 1123. CrossRef
Phenotypes, genotypes and breakpoints: an assessment of β-lactam/β-lactamase inhibitor combinations against OXA-48
Tomefa E Asempa, Abigail K Kois, Christian M Gill, David P Nicolau
Journal of Antimicrobial Chemotherapy.2023; 78(3): 636. CrossRef
Characteristics of Extended-Spectrum β-Lactamase-Producing Escherichia coli Derived from Food and Humans in Northern Xinjiang, China
Yushuang Wu, Shudi Huang, Donglai Zhang, Hua Ji, Yongqing Ni, Xueling Zhang, Juan Dong, Baokun Li
Foodborne Pathogens and Disease.2023; 20(7): 270. CrossRef
Sequential C−H Methylation Catalyzed by the B12‐Dependent SAM Enzyme TokK: Comprehensive Theoretical Study of Selectivities
Wen‐Hao Deng, Rong‐Zhen Liao
Chemistry – A European Journal.2023;[Epub] CrossRef
CMOS Spectrophotometric Microsystem for Malaria Detection
Gabriel M. Ferreira, Vitória Baptista, Vítor Silva, Maria I. Veiga, Graça Minas, Susana O. Catarino
IEEE Transactions on Biomedical Engineering.2023; 70(8): 2318. CrossRef
Synthesis and β-Lactamase Inhibition Activity of Imidates of Diazabicyclooctane
Lijuan Zhai, Jian Sun, Jingwen Ji, Lili He, Yuanyu Gao, Jinbo Ji, Yuanbai Liu, Yangxiu Mu, Xueqin Ma, Dong Tang, Haikang Yang, Zafar Iqbal, Zhixiang Yang
Russian Journal of Bioorganic Chemistry.2022; 48(5): 1059. CrossRef
Recent Developments to Cope the Antibacterial Resistance via β-Lactamase Inhibition
Zafar Iqbal, Jian Sun, Haikang Yang, Jingwen Ji, Lili He, Lijuan Zhai, Jinbo Ji, Pengjuan Zhou, Dong Tang, Yangxiu Mu, Lin Wang, Zhixiang Yang
Molecules.2022; 27(12): 3832. CrossRef
Retracted and replaced: Phenotypes, genotypes and breakpoints: an assessment of β-lactam/ β-lactamase inhibitor combinations against OXA-48
Tomefa E Asempa, Abigail K Kois, Christian M Gill, David P Nicolau
Journal of Antimicrobial Chemotherapy.2022; 77(10): 2622. CrossRef
Carbapenemase producing Klebsiella pneumoniae: implication on future therapeutic strategies
Ilias Karaiskos, Irene Galani, Vassiliki Papoutsaki, Lamprini Galani, Helen Giamarellou
Expert Review of Anti-infective Therapy.2022; 20(1): 53. CrossRef
Antimicrobial Activity of Dihydroisocoumarin Isolated from Wadi Lajab Sediment-Derived Fungus Penicillium chrysogenum: In Vitro and In Silico Study
Raha Orfali, Shagufta Perveen, Mohamed Fahad AlAjmI, Safina Ghaffar, Md Tabish Rehman, Abdullah R. AlanzI, Saja Bane Gamea, Mona Essa Khwayri
Molecules.2022; 27(11): 3630. CrossRef
The Odd Couple(s): An Overview of Beta-Lactam Antibiotics Bearing More Than One Pharmacophoric Group
Margherita De Rosa, Anna Verdino, Annunziata Soriente, Anna Marabotti
International Journal of Molecular Sciences.2021; 22(2): 617. CrossRef
Drugs That Changed Society: History and Current Status of the Early Antibiotics: Salvarsan, Sulfonamides, and β-Lactams
Søren Brøgger Christensen
Molecules.2021; 26(19): 6057. CrossRef
In Crystallo Time-Resolved Interaction of the Clostridioides difficile CDD-1 enzyme with Avibactam Provides New Insights into the Catalytic Mechanism of Class D β-lactamases
Nichole K. Stewart, Marta Toth, Anastasiya Stasyuk, Sergei B. Vakulenko, Clyde A. Smith
ACS Infectious Diseases.2021; 7(6): 1765. CrossRef
Inhibition of the Clostridioides difficile Class D β-Lactamase CDD-1 by Avibactam
Nichole K. Stewart, Marta Toth, Anastasiya Stasyuk, Mijoon Lee, Clyde A. Smith, Sergei B. Vakulenko
ACS Infectious Diseases.2021; 7(5): 1164. CrossRef

Research Support, Non-U.S. Gov't

Pseudomonas aeruginosa-induced IL-1β Production is Inhibited by Sophora flavescens via the NF-κB/inflammasome Pathways: Jung-Hoon Lee , Heesung Shin , Yong-Jae Kim , Se-Hwan Paek , Shouguang Jin , Un-Hwan Ha; J. Microbiol. 2014;52(12):1044-1049. Published online November 29, 2014; DOI: https://doi.org/10.1007/s12275-014-4512-3

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Abstract

The proinflammatory cytokine interleukin-1β plays an important role in protecting the host against airway infection; however, it can also trigger a massive influx of neutrophils into the airways, causing tissue damage. Anti-inflammatory treatments are particularly in demand for patients suffering from chronic inflammatory diseases. Sophora flavescens is a traditional herbal medicine used to reduce inflammation, but no study has examined its ability to block IL-1β production. Here, we show that S. flavescens reduced the Pseudomonas aeruginosa-induced expression of IL-1β by lung epithelial cells and macrophages. S. flavescens was also effective at reducing IL-1β production induced by either Staphylococcus aureus or phorbol 12-myristate 13-acetate, indicating that the effect is generalizable to diverse inflammatory stimuli. In addition, S. flavescens blocked the phosphorylation of IKKα/β, key upstream kinases involved in the degradation of IκBα, and the cleavage of caspase-1, a key component of the inflammasome. Thus, this study demonstrates that S. flavescens exerts its anti-inflammatory effects by blocking P. aeruginosa-mediated NF-κB/inflammasome activation and the subsequent production of IL-1β.

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Effects of Sophora flavescens ethanol extract supplementation in high soybean meal diets on growth, intestinal antioxidant status and immune response in Pearl Gentian grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂)
Xin Lu, Yinhui Peng, Kianann Tan, Bingxiang Zhou, Qingfang Gong, Peng Xu, Xueying Liang, Wenjie Liu, Kit Yue Kwan, Yingrui Wu, Xiaohui Cai
Aquaculture International.2025;[Epub] CrossRef
Maackiain: A comprehensive review of its pharmacology, synthesis, pharmacokinetics and toxicity
Waqas Haider, Wei Pan, Dayang Wang, Waqas Niaz, Muhammad Kashif Zaman, Raza Ullah, Shakir Ullah, Muhammad Rafiq, Bing Yu, Hailin Cong
Chemico-Biological Interactions.2025; 405: 111294. CrossRef
Antimicrobial Effects of Sophora flavescens Alkaloids on Metronidazole-Resistant Gardnerella vaginalis in Planktonic and Biofilm Conditions
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Current Microbiology.2023;[Epub] CrossRef
Chemical diversity, biological activities and Traditional uses of and important Chinese herb Sophora
Peng Sun, Wenjie Zhao, Qi Wang, Lele Chen, Kunkun Sun, Zhaoshuang Zhan, Jiafeng Wang
Phytomedicine.2022; 100: 154054. CrossRef
Effect and Safety of Kangfuyan Capsules (抗妇炎胶囊) for Relieving Chronic Pelvic Pain: A Multicenter, Randomized, Controlled, Double-Blind, Parallel-Group Clinical Trial
Zhao-hui Liu, Zhe Jin, Hong Zhao, Yao Lu, Hui Zhen, Ting Zou
Chinese Journal of Integrative Medicine.2021; 27(12): 883. CrossRef
Maackiain, a compound derived from Sophora flavescens, increases IL‐1β production by amplifying nigericin‐mediated inflammasome activation
Jin‐Won Huh, Jung‐Hoon Lee, Eekhyoung Jeon, Hyung Won Ryu, Sei‐Ryang Oh, Kyung‐Seop Ahn, Hyun Sik Jun, Un‐Hwan Ha
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Integrative Medicine Research.2019; 8(4): 240. CrossRef
The Pseudomonas aeruginosa HSP70-like protein DnaK induces IL-1β expression via TLR4-dependent activation of the NF-κB and JNK signaling pathways
Jung-Hoon Lee, Jisu Jeon, Fang Bai, Shouguang Jin, Weihui Wu, Un-Hwan Ha
Comparative Immunology, Microbiology and Infectious Diseases.2019; 67: 101373. CrossRef
Effects of alkaloids from Sophora flavescens on osteoblasts infected with Staphylococcus aureus and osteoclasts
Xuping Wang, Rongzong Zheng, Xiaowen Huang, Zhujun Mao, Nani Wang, Hongyu Li, Chengping Wen, Dan Shou
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Attenuation of Pseudomonas aeruginosa quorum sensing, virulence and biofilm formation by extracts of Andrographis paniculata
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Antibacterial and synergistic effects of the n-BuOH fraction of Sophora flavescens root against oral bacteria
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