Journal of Microbiology

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Crystal structures of the μ2 subunit of clathrin-adaptor protein 2 in complex with peptides derived from human papillomavirus 16 E7: Sujin Jung, Dahwan Lim, Joon Sig Choi, Ho-Chul Shin, Seung Jun Kim, Bonsu Ku; J. Microbiol. 2025;63(8):e2505003. Published online August 31, 2025; DOI: https://doi.org/10.71150/jm.2505003

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Abstract PDF: Human papillomaviruses (HPVs) cause abnormal cellular proliferation, leading to malignant or benign lesions, such as cervical cancer and warts. The genome of HPV16, the most prevalent high-risk oncogenic genotype within the Alphapapillomavirus genus, encodes two oncoproteins. One of these proteins, E7, interacts with multiple host proteins and modulates their functions through distinct pathways. The CR2 domain of HPV16 E7 was recently reported to interact with the μ2 subunit of clathrin-adaptor protein 2 (AP2-μ2), an adaptor complex involved in cargo internalization during clathrin-mediated endocytosis. In this study, to provide molecular insights into their intermolecular interactions, we determined the crystal structures of AP2-μ2 in complex with the HPV16 E7-derived peptides. Subsequent biochemical analyses revealed that this interaction is primarily maintained by the Y-x-x-Φ motif and further supported by acidic cluster residues of HPV16 E7. Finally, sequence alignment of the E7 CR2 domains from various HPV genotypes showed that the AP2-μ2-binding motif is largely conserved in Alpha-, Beta-, and Mupapillomaviruses, but not in Nu- and Gammapapillomaviruses.

Efficient CRISPR-based genome editing for inducible degron systems to enable temporal control of protein function in large double-stranded DNA virus genomes: Kihye Shin, Eui Tae Kim; J. Microbiol. 2025;63(9):e2504008. Published online August 29, 2025; DOI: https://doi.org/10.71150/jm.2504008

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Abstract PDF: CRISPR-Cas9-based gene editing enables precise genetic modifications. However, its application to human cytomegalovirus (HCMV) remains challenging due to the large size of the viral genome and the essential roles of key regulatory genes. Here, we establish an optimized CRISPR-Cas9 system for precise labeling and functional analysis of HCMV immediate early (IE) genes. By integrating a multifunctional cassette encoding an auxin-inducible degron (AID), a self-cleaving peptide (P2A), and GFP into the viral genome via homology-directed repair (HDR), we achieved efficient knock-ins without reliance on bacterial artificial chromosome (BAC) cloning, a labor-intensive and time-consuming approach. We optimized delivery strategies, donor template designs, and component ratios to enhance HDR efficiency, significantly improving knock-in success rates. This system enables real-time fluorescent tracking and inducible protein degradation, allowing temporal control of essential viral proteins through auxin-mediated depletion. Our approach provides a powerful tool for dissecting the dynamic roles of viral proteins throughout the HCMV life cycle, facilitating a deeper understanding of viral pathogenesis and potential therapeutic targets.

Bacteroides celer sp. nov. and Bacteroides mucinivorans sp. nov., isolated from human feces, and the reclassification of Bacteroides koreensis Shin et al. 2017 and Bacteroides kribbi Shin et al. 2017 as later heterotypic synonyms of Bacteroides ovatus Eggerth and Gagnon 1933 (Approved Lists 1980): Ah-In Yang, Bora Kim, Woorim Kang, Hae-In Joe, Na-Ri Shin; J. Microbiol. 2025;63(6):e2502006. Published online June 30, 2025; DOI: https://doi.org/10.71150/jm.2502006; Correction in: J. Microbiol 2025;63(7):e2507100

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Abstract PDF Supplementary Material: Two novel, Gram-stain-negative, anaerobic, and non-motile bacterial strains, designated KFT8^T and CG01^T, were isolated from the feces of healthy individuals without diagnosed diseases and characterized using a polyphasic approach. Phylogenetic analysis revealed that both strains belong to the genus Bacteroides, with < 99.0% similarity in their 16S rRNA gene sequences to B. facilis NSJ-77^T and B. nordii JCM 12987^T. Within the genus Bacteroides, strain KFT8^T exhibited the highest Orthologous Average Nucleotide Identity value of 94.7% and a digital DNA-DNA hybridization value of 63.7% with B. ovatus ATCC 8483^T, whereas strain CG01^T showed the highest values of 95.3% and 63.3%, respectively, with B. nordii JCM 12987^T. The values between the two novel strains were 74.8% and 21.4%, respectively, which are below the species delineation thresholds, supporting their classification as novel species. The major fatty acid of strain KFT8^T was C_18:1 ω9c, whereas strain CG01^T predominantly contained summed feature 11 (comprising iso-C_17:0 3OH and/or C_18:2 DMA). The only respiratory quinone was MK-11, the major polar lipid was phosphatidylethanolamine. Both strains produced succinic acid and acetic acid as common metabolic end-products of fermentation, while lactic acid and formic acid were detected individually in each strain. Based on polyphasic characterization, strains KFT8^T (= KCTC 15614^T = JCM 36011^T) and CG01^T (= KCTC 15613^T = JCM 36010^T) represent two novel species within the genus Bacteroides, for which the names Bacteroides celer sp. nov. and Bacteroides mucinivorans sp. nov. are proposed, respectively. Additionally, genome-based analyses and phenotypic comparisons revealed that B. koreensis and B. kribbi represent the same strain, showing genomic relatedness to B. ovatus that exceeds the threshold for species delineation. Consequently, we propose the reclassification of B. koreensis Shin et al. 2017 and B. kribbi Shin et al. 2017 as later heterotypic synonyms of B. ovatus Eggerth and Gagnon 1933 (Approved Lists 1980).

Arctic lichen Cladonia borealis-induced cell death is mediated by p53-independent activation of Caspase-9 and PARP-1 signaling in human colorectal cancer cell lines: Ju-Mi Hong, Seul Ki Min, Kyung Hee Kim, Se Jong Han, Joung Han Yim, Sojin Kim, Youn-Jung Kim, Il-Chan Kim; J. Microbiol. 2025;63(4):e2412012. Published online April 29, 2025; DOI: https://doi.org/10.71150/jm.2412012

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Abstract PDF: The anti-cancer effects of Cladonia borealis (an Arctic lichen) methanol extract (CBME) on human colon carcinoma HCT116 cells were investigated for the first time. The proliferation of the HCT116 cells treated with CBME significantly decreased in a dose- and time-dependent manner. Flow cytometry results indicated that treatment with CBME resulted in significant apoptosis in the HCT116 cells. Furthermore, immunoblotting and qRT-PCR results revealed the expression of apoptosis-related marker genes and indicated a significant downregulation of the apoptosis regulator B-cell lymphoma expression and upregulation of the cleaved form of poly (ADP-ribose) polymerase as DNA repair and apoptosis regulators and central tumor suppressor p53. Therefore, CBME significantly inhibited cell proliferation by inducing apoptosis via the mitochondrial apoptotic pathway in colon carcinoma cells. Collectively, these data suggested that CBME contained one or more compounds with anti-cancer effects and could be a potential therapeutic agent. Further studies are required to identify candidate compounds and understand the mechanism of action of CBME.

Journal Articles

Whole Genome Sequence Analysis of Brucella spp. from Human, Livestock, and Wildlife in South Africa: Koketso Desiree Mazwi, Kgaugelo Edward Lekota, Barbara Akofo Glover, Francis Babaman Kolo, Ayesha Hassim, Jenny Rossouw, Annelize Jonker, Justnya Maria Wojno, Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio, Katiuscia Zilli, Anna Janowicz, Francesca Marotta, Giuliano Garofolo, Henriette van Heerden; J. Microbiol. 2024;62(9):759-773. Published online July 22, 2024; DOI: https://doi.org/10.1007/s12275-024-00155-8

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Brucellosis is an economically important zoonotic disease affecting humans, livestock, and wildlife health globally and especially in Africa. Brucella abortus and B. melitensis have been isolated from human, livestock (cattle and goat), and wildlife (sable) in South Africa (SA) but with little knowledge of the population genomic structure of this pathogen in SA. As whole genome sequencing can assist to differentiate and trace the origin of outbreaks of Brucella spp. strains, the whole genomes of retrospective isolates (n = 19) from previous studies were sequenced. Sequences were analysed using average nucleotide identity (ANI), pangenomics, and whole genome single nucleotide polymorphism (wgSNP) to trace the geographical origin of cases of brucellosis circulating in human, cattle, goats, and sable from different provinces in SA. Pangenomics analysis of B. melitensis (n = 69) and B. abortus (n = 56) was conducted with 19 strains that included B. abortus from cattle (n = 3) and B. melitensis from a human (n = 1), cattle (n = 1), goat (n = 1), Rev1 vaccine strain (n = 1), and sable (n = 12). Pangenomics analysis of B. melitensis genomes, highlighted shared genes, that include 10 hypothetical proteins and genes that encodes for acetyl-coenzyme A synthetase (acs), and acylamidase (aam) amongst the sable genomes. The wgSNP analysis confirmed the B. melitensis isolated from human was more closely related to the goat from the Western Cape Province from the same outbreak than the B. melitensis cattle sample from different cases in the Gauteng Province. The B. melitensis sable strains could be distinguished from the African lineage, constituting their own African sub-clade. The sequenced B. abortus strains clustered in the C2 lineage that is closely related to the isolates from Mozambique and Zimbabwe. This study identified genetically diverse Brucella spp. among various hosts in SA. This study expands the limited known knowledge regarding the presence of B. melitensis in livestock and humans in SA, further building a foundation for future research on the distribution of the Brucella spp. worldwide and its evolutionary background.

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Tracing the invisible: Spatial patterns of swine brucellosis in wildlife and domestic pigs of northeast Portugal
Zita Martins Ruano, Teresa Letra Mateus, José Aranha, Eirini Fragkiadaki, Georgia Tzouganatou, Emmanouil Angelakis, Luís Félix, Jorge Pereira, Ana Chorense, Claudia Rocha, Dulce Loureiro, Ricardo Marcos, Madalena Vieira-Pinto
The Veterinary Journal.2025; 314: 106464. CrossRef
Limited genomic diversity and convergent adaptation of Brucella melitensis isolated from human in East China, from 2011 to 2024
Lan Huang, Lu Zhou, Nan Zhang, Weizhong Zhou, Buyun Xu, Jie Hong, Wei Zhang, Ying Zhang, Ke Xu, Changjun Bao, Hai Jiang, Zhongming Tan, Jingxin Li
Frontiers in Microbiology.2025;[Epub] CrossRef
Whole-Genome Sequencing of Brucella melitensis Isolates from Kuwait for the Identification of Biovars, Variants, and Relationship within a Biovar
Abu Salim Mustafa, Mohd Wasif Khan, Nazima Habibi, Wadha Alfouzan
Medical Principles and Practice.2024; 34(2): 152. CrossRef

In Silico Intensive Analysis for the E4 Gene Evolution of Human Adenovirus Species D: Chanhee Lee, Anyeseu Park, Jeong Yoon Lee; J. Microbiol. 2024;62(5):409-418. Published online April 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00132-1

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Abstract PDF: Adenovirus (Ad) is a ubiquitous pathogen capable of infecting a wide range of animals and humans. Human Adenovirus (HAdV) can cause severe infection, particularly in individuals with compromised immune systems. To date, over 110 types of HAdV have been classified into seven species from A to G, with the majority belonging to the human adenovirus species D (HAdV-D). In the HAdV-D, the most significant factor for the creation of new adenovirus types is homologous recombination between viral genes involved in determining the virus tropism or evading immune system of host cells. The E4 gene, consisting of seven Open Reading Frames (ORFs), plays a role in both the regulation of host cell metabolism and the replication of viral genes. Despite long-term studies, the function of each ORF remains unclear. Based on our updated information, ORF2, ORF3, and ORF4 have been identified as regions with relatively high mutations compared to other ORFs in the E4 gene, through the use of in silico comparative analysis. Additionally, we managed to visualize high mutation sections, previously undetectable at the DNA level, through a powerful amino acid sequence analysis tool known as proteotyping. Our research has revealed the involvement of the E4 gene in the evolution of human adenovirus, and has established accurate sequence information of the E4 gene, laying the groundwork for further research.

Review

Genomic Evolution and Recombination Dynamics of Human Adenovirus D Species: Insights from Comprehensive Bioinformatic Analysis: Anyeseu Park, Chanhee Lee, Jeong Yoon Lee; J. Microbiol. 2024;62(5):393-407. Published online March 7, 2024; DOI: https://doi.org/10.1007/s12275-024-00112-5

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Human adenoviruses (HAdVs) can infect various epithelial mucosal cells, ultimately causing different symptoms in infected organ systems. With more than 110 types classified into seven species (A-G), HAdV-D species possess the highest number of viruses and are the fastest proliferating. The emergence of new adenovirus types and increased diversity are driven by homologous recombination (HR) between viral genes, primarily in structural elements such as the penton base, hexon and fiber proteins, and the E1 and E3 regions. A comprehensive analysis of the HAdV genome provides valuable insights into the evolution of human adenoviruses and identifies genes that display high variation across the entire genome to determine recombination patterns. Hypervariable regions within genetic sequences correlate with functional characteristics, thus allowing for adaptation to new environments and hosts. Proteotyping of newly emerging and already established adenoviruses allows for prediction of the characteristics of novel viruses. HAdV-D species evolved in a direction that increased diversity through gene recombination. Bioinformatics analysis across the genome, particularly in highly variable regions, allows for the verification or re-evaluation of recombination patterns in both newly introduced and pre-existing viruses, ultimately aiding in tracing various biological traits such as virus tropism and pathogenesis. Our research does not only assist in predicting the emergence of new adenoviruses but also offers critical guidance in regard to identifying potential regulatory factors of homologous recombination hotspots.

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Relationship between adenovirus infection and intussusception via pathological evidence confirms
Lung-Huang Lin, Chi-Jung Huang, Cheng-Yu Lo, Yu-Hsien Lee, Yung-Chuan Chen
Journal of Clinical Pathology.2025; 78(10): 678. CrossRef
In Silico Intensive Analysis for the E4 Gene Evolution of Human Adenovirus Species D
Chanhee Lee, Anyeseu Park, Jeong Yoon Lee
Journal of Microbiology.2024; 62(5): 409. CrossRef

Journal Articles

LAMMER Kinase Governs the Expression and Cellular Localization of Gas2, a Key Regulator of Flocculation in Schizosaccharomyces pombe: Won-Hwa Kang , Yoon-Dong Park , Joo-Yeon Lim , Hee-Moon Park; J. Microbiol. 2024;62(1):21-31. Published online January 5, 2024; DOI: https://doi.org/10.1007/s12275-023-00097-7

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Abstract PDF: It was reported that LAMMER kinase in Schizosaccharomyces pombe plays an important role in cation-dependent and galactose-specific flocculation. Analogous to other flocculating yeasts, when cell wall extracts of the Δlkh1 strain were treated to the wild-type strain, it displayed flocculation. Gas2, a 1,3-β-glucanosyl transferase, was isolated from the EDTA-extracted cell-surface proteins in the Δlkh1 strain. While disruption of the gas2+ gene was not lethal and reduced the flocculation activity of the Δlkh1 strain, the expression of a secreted form of Gas2, in which the GPI anchor addition sequences had been removed, conferred the ability to flocculate upon the WT strain. The Gas2-mediated flocculation was strongly inhibited by galactose but not by glucose. Immunostaining analysis showed that the cell surface localization of Gas2 was crucial for the flocculation of fission yeast. In addition, we identified the regulation of mbx2+ expression by Lkh1 using RT-qPCR. Taken together, we found that Lkh1 induces asexual flocculation by regulating not only the localization of Gas2 but also the transcription of gas2+ through Mbx2.

Prevalence of Indigenous Antibiotic‑Resistant Salmonella Isolates and Their Application to Explore a Lytic Phage vB_SalS_KFSSM with an Intra‑Broad Specificity: Jaein Choe , Su-Hyeon Kim , Ji Min Han , Jong-Hoon Kim , Mi-Sun Kwak , Do-Won Jeong , Mi-Kyung Park; J. Microbiol. 2023;61(12):1063-1073. Published online January 2, 2024; DOI: https://doi.org/10.1007/s12275-023-00098-6

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The consumption of fresh produce has led to increase in antibiotic-resistant (AR) Salmonella outbreaks. In this study, indigenous Salmonella was isolated from a total of two hundred-two samples including fresh produce and agricultural environmental samples in Korea. After biochemical confirmation using the Indole, Methyl Red, Voges-Proskauer, Citrate tests, presumable Salmonella isolates were identified by 16S rRNA sequencing. Identified Salmonella isolates were evaluated for antibiotic susceptibility against twenty-two antibiotics. The specificity and the efficiency of plating (EOP) of vB_SalS_KFSSM were evaluated against fifty-three bacterial strains. Twenty-five suspected Salmonella were isolated and confirmed by the positive
result
for methyl red and citrate, of which ten were identified as Salmonella spp. through 16S rRNA gene sequencing. Eight Salmonella isolates (4.0%, n = 8/202) were resistant to at least one antibiotic, among which five were multi-drug resistant. As a lytic phage against Salmonella spp. CMGS-1, vB_SalS_KFSSM was isolated from cow manure. The phage was observed as a tailed phage belonging to the class Caudoviricetes. It exhibited an intra-broad specificity against four indigenous AR Salmonella isolates, two indigenous Salmonella isolates, and five other Salmonella serotypes with great efficiencies (EOP ≥ 0.75). Thus, this study suggested the potential of vB_SalS_KFSSM to combat indigenous AR Salmonella.

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Functional and Genomic Features of a Lytic Salmonella Phage vB_StyS_KFSST1 for Development as New Feed Additive
Su-Hyeon Kim, In Young Choi, Gyu-Sung Cho, Charles M.A.P. Franz, Mi-Kyung Park
Food Science of Animal Resources.2025; 45(4): 1204. CrossRef

Review

Envelope‑Stress Sensing Mechanism of Rcs and Cpx Signaling Pathways in Gram‑Negative Bacteria: Seung-Hyun Cho , Kilian Dekoninck , Jean-Francois Collet; J. Microbiol. 2023;61(3):317-329. Published online March 9, 2023; DOI: https://doi.org/10.1007/s12275-023-00030-y

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The global public health burden of bacterial antimicrobial resistance (AMR) is intensified by Gram-negative bacteria, which have an additional membrane, the outer membrane (OM), outside of the peptidoglycan (PG) cell wall. Bacterial twocomponent systems (TCSs) aid in maintaining envelope integrity through a phosphorylation cascade by controlling gene expression through sensor kinases and response regulators. In Escherichia coli, the major TCSs defending cells from envelope stress and adaptation are Rcs and Cpx, which are aided by OM lipoproteins RcsF and NlpE as sensors, respectively. In this review, we focus on these two OM sensors. β-Barrel assembly machinery (BAM) inserts transmembrane OM proteins (OMPs) into the OM. BAM co-assembles RcsF, the Rcs sensor, with OMPs, forming the RcsF-OMP complex. Researchers have presented two models for stress sensing in the Rcs pathway. The first model suggests that LPS perturbation stress disassembles the RcsF-OMP complex, freeing RcsF to activate Rcs. The second model proposes that BAM cannot assemble RcsF into OMPs when the OM or PG is under specific stresses, and thus, the unassembled RcsF activates Rcs. These two models may not be mutually exclusive. Here, we evaluate these two models critically in order to elucidate the stress sensing mechanism. NlpE, the Cpx sensor, has an N-terminal (NTD) and a C-terminal domain (CTD). A defect in lipoprotein trafficking
results
in NlpE retention in the inner membrane, provoking the Cpx response. Signaling requires the NlpE NTD, but not the NlpE CTD; however, OM-anchored NlpE senses adherence to a hydrophobic surface, with the NlpE CTD playing a key role in this function.

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Metal-based antimicrobial agents in wound Dressings: Infection management and the challenge of antibiotic resistance
Haoyang Peng, Deqiao Dong, Shiquan Feng, Yueping Guo, Jiaqi Yu, Changran Gan, Xue Hu, Zhenmao Qin, Yan Liu, Yanan Gao
Chemical Engineering Journal.2025; 507: 160726. CrossRef
Bacterial cell wall synthesis and recycling: new antimicrobial targets and vaccine development
Jihyeon Min, Bitnara Kim, Yerim Park, Yongjun Son, Woojun Park
Critical Reviews in Microbiology.2025; : 1. CrossRef
Nitazoxanide inhibits pili assembly by targeting BamB to synergize with polymyxin B against drug-resistant Escherichia coli
Wenwen Li, Bingjie Ji, Boyu Li, Minghui Du, Linwei Wang, Jiale Tuo, Hongmei Zhou, Jian Gong, Yongshan Zhao
Biochimie.2025; 233: 47. CrossRef
Complex interplay between gene deletions and the environment uncovers cellular roles for genes of unknown function in Escherichia coli
Kaat Sondervorst, Kristina Nesporova, Matthew Herdman, Bart Steemans, Joëlle Rosseels, Sander K. Govers, Julia Willett
mSystems.2025;[Epub] CrossRef
Genome-wide characterization of hypothiocyanite stress response in Escherichia coli
Julia D. Meredith, Michael J. Gray, Melissa M. Kendall
Journal of Bacteriology.2025;[Epub] CrossRef
Terminal complement complexes with or without C9 potentiate antimicrobial activity against Neisseria gonorrhoeae
Evan R. Lamb, Alison K. Criss, Mariagrazia Pizza
mBio.2025;[Epub] CrossRef
RcsB and H-NS Both Contribute to the Repression the Expression of the csgDEFG Operon
Hiroshi Ogasawara, Azusa Tomioka, Yuki Kato
Microorganisms.2025; 13(8): 1829. CrossRef
Transcriptome reveals the role of the htpG gene in mediating antibiotic resistance through cell envelope modulation in Vibrio mimicus SCCF01
Zhenyang Qin, Kun Peng, Yang Feng, Yilin Wang, Bowen Huang, Ziqi Tian, Ping Ouyang, Xiaoli Huang, Defang Chen, Weimin Lai, Yi Geng
Frontiers in Microbiology.2024;[Epub] CrossRef
Rcs signal transduction system in Escherichia coli: Composition, related functions, regulatory mechanism, and applications
Zeyu Li, Yingying Zhu, Wenli Zhang, Wanmeng Mu
Microbiological Research.2024; 285: 127783. CrossRef
Identification of genes used by Escherichia coli to mitigate climatic stress conditions
Styliani Roufou, Sholeem Griffin, Lydia Katsini, Monika Polańska, Jan F.M. Van Impe, Panagiotis Alexiou, Vasilis P. Valdramidis
Gene Reports.2024; 36: 101998. CrossRef
The Role of Propionate-Induced Rearrangement of Membrane Proteins in the Formation of the Virulent Phenotype of Crohn’s Disease-Associated Adherent-Invasive Escherichia coli
Olga V. Pobeguts, Maria A. Galyamina, Elena V. Mikhalchik, Sergey I. Kovalchuk, Igor P. Smirnov, Alena V. Lee, Lyubov Yu. Filatova, Kirill V. Sikamov, Oleg M. Panasenko, Alexey Yu. Gorbachev
International Journal of Molecular Sciences.2024; 25(18): 10118. CrossRef
CpxAR two-component system contributes to virulence properties of Cronobacter sakazakii
Tong Jin, Xiangjun Zhan, Liuxin Pang, Bo Peng, Xinpeng Zhang, Wenxiu Zhu, Baowei Yang, Xiaodong Xia
Food Microbiology.2024; 117: 104393. CrossRef
Breaking Barriers: Exploiting Envelope Biogenesis and Stress Responses to Develop Novel Antimicrobial Strategies in Gram-Negative Bacteria
Renu Bisht, Pierre D. Charlesworth, Paola Sperandeo, Alessandra Polissi
Pathogens.2024; 13(10): 889. CrossRef
The protective role of potassium in the adaptation of Pseudomonas protegens SN15-2 to hyperosmotic stress
Jian Wang, Yaping Wang, Shouquan Lu, Haibo Lou, XiaoBing Wang, Wei Wang
Microbiological Research.2024; 289: 127887. CrossRef
Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms’ Complex Regulation
Jin-Won Lee
Journal of Microbiology.2023; 61(3): 273. CrossRef
Physiological and Transcriptomic Analyses of Escherichia coli Serotype O157:H7 in Response to Rhamnolipid Treatment
Shuo Yang, Lan Ma, Xiaoqing Xu, Qing Peng, Huiying Zhong, Yuxin Gong, Linbo Shi, Mengxin He, Bo Shi, Yu Qiao
Microorganisms.2023; 11(8): 2112. CrossRef

Journal Articles

The periplasmic chaperone protein Psg_2795 contributes to the virulence of Pseudomonas savastanoi pv. glycinea: the causal agent of bacterial blight of soybean: Xiuhua Wang , Xiaoyan Zhang , Bao-Hui Lu , Jie Gao; J. Microbiol. 2022;60(5):478-487. Published online March 4, 2022; DOI: https://doi.org/10.1007/s12275-022-1469-5

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Pseudomonas savastanoi pv. glycinea (Psg, also named P. syringae pv. glycinea and P. amygdali pv. glycinea) is the causative agent of bacterial blight in soybean. The identification of virulence factors is essential for understanding the pathogenesis of Psg. In this study, a mini-Tn5 transposon mutant library of Psg strain PsgNC12 was screened on soybean, and one low-virulent mini-Tn5 mutant, designated as 4573, was identified. Sequence analysis of the 4573-mutant revealed that the mini-Tn5 transposon was inserted in the Psg_2795 gene. Psg_2795 encodes a FimC-domain protein that is highly conserved in Pseudomonas. Further analysis revealed that the mutation and knockout of Psg_2795 results in a reduced virulence phenotype on soybean, decreased motility, weakened bacterial attachment to a glass surface and delayed the population growth within soybean leaves. The phenotype of the 4573-mutant could be complemented nearly to wild-type levels using an intact Psg_2795 gene. Collectively, our results demonstrate that Psg_2795 plays an important role in the virulence, motility, attachment and the population growth of PsgNC12 in soybean. This finding provides a new insight into the function of periplasmic chaperone proteins in a type I pilus and provides reference information for identifying Psg_2795 homologues in P. savastanoi and other bacteria.

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Vt35 antitoxin plays a central regulatory role in virulence of Pseudomonas savastanoi pv. glycinea on soybean
Viet Tru Nguyen, Nanami Sakata, Takako Ishiga, Giyu Usuki, Yoshiteru Hashimoto, Yasuhiro Ishiga
Journal of General Plant Pathology.2023; 89(4): 211. CrossRef

Meiotic prophase roles of Pds5 in recombination and chromosome condensation in budding yeast: Jeong Hwan Joo , Hyun Ah Kang , Keun Pil Kim , Soogil Hong; J. Microbiol. 2022;60(2):177-186. Published online February 1, 2022; DOI: https://doi.org/10.1007/s12275-022-1635-9

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Genetic variation in eukaryotes is mediated during meiosis by the exchange of genetic material between homologous chromosomes to produce recombinant chromosomes. Cohesin is essential to promote proper chromosome segregation, chromosome morphogenesis, and recombination in meiotic cells. Cohesin consists of three main subunits–Smc1, Smc3, and the kleisin subunit Mcd1/Scc1 (Rec8 in meiosis)–and cohesin accessory factors. In Saccharomyces cerevisiae, the cohesin regulatory subunit Pds5 plays a role in homolog pairing, meiotic axis formation, and interhomolog recombination. In this study, we examine the prophase functions of Pds5 by performing physical analysis of recombination and three-dimensional high-resolution microscopy analysis to identify its roles in meiosis-specific recombination and chromosome morphogenesis. To investigate whether Pds5 plays a role in mitoticlike recombination, we inhibited Mek1 kinase activity, which
result
ed in switching to sister template bias by Rad51-dependent recombination. Reductions in double-strand breaks and crossover products and defective interhomolog recombination occurred in the absence of Pds5. Furthermore, recombination intermediates, including single-end invasion and double-Holliday junction, were reduced in the absence of Pds5 with Mek1 kinase inactivation compared to Mek1 kinase inactivation cells. Interestingly, the absence of Pds5
result
ed in increasing numbers of chromosomes with hypercompaction of the chromosome axis. Thus, we suggest that Pds5 plays an essential role in recombination by suppressing the pairing of sister chromatids and abnormal compaction of the chromosome axis.

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Recombination-coupled DNA synthesis facilitates post-invasion steps in meiotic crossover and noncrossover formations
Hyungseok Choi, Jun Seo Lee, Jeong H Joo, Soogene Lee, Keun P Kim
Nucleic Acids Research.2025;[Epub] CrossRef
Multiple Autopolyploid Arabidopsis lyrata Populations Stabilized by Long-Range Adaptive Introgression Across Eurasia
Alison D Scott, Uliana K Kolesnikova, Anna Glushkevich, Laura Steinmann, Nikita P Tikhomirov, Ursula Pfordt, Magdalena Bohutínská, Robin Burns, Alexey P Seregin, Filip Kolar, Roswitha Schmickl, Polina Yu Novikova, Kathryn Hodgins
Molecular Biology and Evolution.2025;[Epub] CrossRef
RPA interacts with Rad52 to promote meiotic crossover and noncrossover recombination
Jeong H Joo, Soogil Hong, Mika T Higashide, Eui-Hwan Choi, Seobin Yoon, Min-Su Lee, Hyun Ah Kang, Akira Shinohara, Nancy Kleckner, Keun P Kim
Nucleic Acids Research.2024; 52(7): 3794. CrossRef
Cohesin is required for meiotic spindle assembly independent of its role in cohesion in C. elegans
Karen P. McNally, Elizabeth A. Beath, Brennan M. Danlasky, Consuelo Barroso, Ting Gong, Wenzhe Li, Enrique Martinez-Perez, Francis J. McNally, Sarit Smolikove
PLOS Genetics.2022; 18(10): e1010136. CrossRef
Yeast polyubiquitin unit regulates synaptonemal complex formation and recombination during meiosis
Min-Kyung Jo, Kiwon Rhee, Keun Pil Kim, Soogil Hong
Journal of Microbiology.2022; 60(7): 705. CrossRef

Review

Middle East Respiratory Syndrome coronavirus vaccine development: updating clinical studies using platform technologies: Jung-ah Choi , Jae-Ouk Kim; J. Microbiol. 2022;60(3):238-246. Published online January 28, 2022; DOI: https://doi.org/10.1007/s12275-022-1547-8

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Middle East Respiratory Syndrome coronavirus (MERS-CoV), a contagious zoonotic virus, causes severe respiratory infection with a case fatality rate of approximately 35% in humans. Intermittent sporadic cases in communities and healthcare facility outbreaks have continued to occur since its first identification in 2012. The World Health Organization has declared MERS-CoV a priority pathogen for worldwide research and vaccine development due to its epidemic potential and the insufficient countermeasures available. The Coalition for Epidemic Preparedness Innovations is supporting vaccine development against emerging diseases, including MERS-CoV, based on platform technologies using DNA, mRNA, viral vector, and protein subunit vaccines. In this paper, we review the usefulness and structure of a spike glycoprotein as a MERSCoV vaccine candidate molecule, and provide an update on the status of MERS-CoV vaccine development. Vaccine candidates based on both DNA and viral vectors coding MERSCoV spike gene have completed early phase clinical trials. A harmonized approach is required to assess the immunogenicity of various candidate vaccine platforms. Platform technologies accelerated COVID-19 vaccine development and can also be applied to developing vaccines against other emerging viral diseases.

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Global research hotspots and trends in DNA vaccine research: A bibliometric and visualization study from 2014 to 2024
Juan Zhang, Haiguo Zhang, Cuicui Yao, Lihua Gu, Shasha Dong, Yamei Wu, Lele Miao
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Structure-Guided Design of Potent Coronavirus Inhibitors with a 2-Pyrrolidone Scaffold: Biochemical, Crystallographic, and Virological Studies
Chamandi S. Dampalla, Yunjeong Kim, Alexandria Zabiegala, Dennis J. Howard, Harry Nhat Nguyen, Trent K. Madden, Hayden A. Thurman, Anne Cooper, Lijun Liu, Kevin P. Battaile, Scott Lovell, Kyeong-Ok Chang, William C. Groutas
Journal of Medicinal Chemistry.2024; 67(14): 11937. CrossRef
Role of vaccination in patients with human monkeypox virus and its cardiovascular manifestations
Khawaja Usama Maqbool, Muhammad Talha Akhtar, Shayan Ayub, FNU Simran, Jahanzeb Malik, Maria Malik, Rafia Zubair, Amin Mehmoodi
Annals of Medicine & Surgery.2024; 86(3): 1506. CrossRef
The many facets of CD26/dipeptidyl peptidase 4 and its inhibitors in disorders of the CNS – a critical overview
Hans-Gert Bernstein, Gerburg Keilhoff, Henrik Dobrowolny, Johann Steiner
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Hitesh Chopra, Md. Aminul Islam, Deepak Chandran, Talha B. Emran, Nahed A. El-Shall, Jaffar A. Al-Tawfiq, Kuldeep Dhama
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Journal Articles

Effects of the loss of mismatch repair genes on single-strand annealing between divergent sequences in Saccharomyces cerevisiae: Ye-Seul Lim , Ju-Hee Choi , Kyu-Jin Ahn , Min-Ku Kim , Sung-Ho Bae; J. Microbiol. 2021;59(4):401-409. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-1076-x

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Abstract PDF: Eukaryotic genomes contain many duplicated genes closely located with each other, such as the hexose transporter (HXT) genes in Saccharomyces cerevisiae. They can potentially recombine via single-strand annealing (SSA) pathway. SSA between highly divergent sequences generates heteroduplex DNA intermediates with many mismatches, which can be corrected by mismatch repair (MMR), resulting in recombinant sequences with a single junction point. In this report, we demonstrate that SSA between HXT1 and HXT4 genes in MMR-deficient yeast cells produces recombinant genes with multiple-junctions resulting from alternating HXT1 and HXT4 tracts. The mutations in MMR genes had differential effects on SSA frequencies; msh6Δ mutation significantly stimulated SSA events, whereas msh2Δ and msh3Δ slightly suppressed it. We set up an assay that can identify a pair of recombinant genes derived from a single heteroduplex DNA. As a result, the recombinant genes with multiple-junctions were found to accompany genes with single-junctions. Based on the results presented here, a model was proposed to generate multiple-junctions in SSA pathway involving an alternative short-patch repair system.

Omp16, a conserved peptidoglycan-associated lipoprotein, is involved in Brucella virulence in vitro: Feijie Zhi , Dong Zhou , Junmei Li , Lulu Tian , Guangdong Zhang , Yaping Jin , Aihua Wang; J. Microbiol. 2020;58(9):793-804. Published online September 1, 2020; DOI: https://doi.org/10.1007/s12275-020-0144-y

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Abstract PDF

Brucella, the bacterial agent of common zoonotic brucellosis, primarily infects specific animal species. The Brucella outer membrane proteins (Omps) are particularly attractive for developing vaccine and improving diagnostic tests and are associated with the virulence of smooth Brucella strains. Omp16 is a homologue to peptidoglycan-associated lipoproteins (Pals), and an omp16 mutant has not been generated in any Brucella strain until now. Very little is known about the functions and pathogenic mechanisms of Omp16 in Brucella. Here, we confirmed that Omp16 has a conserved Pal domain and is highly conserved in Brucella. We attempted to delete omp16 in Brucella suis vaccine strain 2 (B. suis S2) without success, which shows that Omp16 is vital for Brucella survival. We acquired a B. suis S2 Omp16 mutant via conditional complementation. Omp16 deficiency impaired Brucella outer membrane integrity and activity in vitro. Moreover, inactivation of Omp16 decreased bacterial intracellular survival in macrophage RAW 264.7 cells. B. suis S2 and its derivatives induced marked expression of IL-1β, IL-6, and TNF-α mRNA in Raw 264.7 cells. Whereas inactivation of Omp16 in Brucella enhanced IL-1β and IL-6 expression in Raw 264.7 cells. Altogether, these findings show that the Brucella Omp16 mutant was obtained via conditional complementation and confirmed that Omp16 can maintain outer membrane integrity and be involved in bacterial virulence in Brucella in vitro and in vivo. These results will be important in uncovering the pathogenic mechanisms of Brucella.

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Enhancing host defense against Brucella: The immune effect exerted by anti-OMP16 monoclonal antibody
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Brucellosis: Bacteriology, pathogenesis, epidemiology and role of the metallophores in virulence: a review
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Pathogenicity and virulence of Brucella : Strategies for metabolic adaptation and immune evasion
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The (p)ppGpp synthetase Rsh promotes rifampicin tolerant persister cell formation in Brucella abortus by regulating the type II toxin-antitoxin module mbcTA
Xiaofang Liu, Pingping Wang, Ningqiu Yuan, Yunyi Zhai, Yuanhao Yang, Mingyue Hao, Mingxing Zhang, Dong Zhou, Wei Liu, Yaping Jin, Aihua Wang
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Pal Affects the Proliferation in Macrophages and Virulence of Brucella, and as Mucosal Adjuvants, Provides an Effective Protection to Mice Against Salmonella Enteritidis
Yubin Chen, Yanfang Fu, Lingcong Kong, Fengjie Wang, Xiaowei Peng, Zhiqiang Zhang, Qiumei Shi, Qingmin Wu, Tonglei Wu
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Clearance of bacteria from lymph nodes in sheep immunized with Brucella suis S2 vaccine is associated with M1 macrophage activation
Si Chen, Yuanyuan Chen, Zizhuo Jiao, Chengqiang Wang, Dantong Zhao, Yongbin Liu, Wenguang Zhang, Shihua Zhao, Bin Yang, Qinan Zhao, Shaoyin Fu, Xiaolong He, Qiaoling Chen, Churiga Man, Guoying Liu, Xuefeng Wei, Li Du, Fengyang Wang
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A Brucella Omp16 Conditional Deletion Strain Is Attenuated in BALB/c Mice
Feijie Zhi, Jiaoyang Fang, Weifang Zheng, Junmei Li, Guangdong Zhang, Dong Zhou, Yaping Jin, Aihua Wang
Journal of Microbiology and Biotechnology.2022; 32(1): 6. CrossRef
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Hossein Tarrahimofrad, Javad Zamani, Michael R. Hamblin, Maryam Darvish, Hamed Mirzaei
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A LysR Transcriptional Regulator Manipulates Macrophage Autophagy Flux During Brucella Infection
Lu Zhang, Siyuan Yu, Xinnuan Ning, Hui Fang, Jie Li, Feijie Zhi, Junmei Li, Dong Zhou, Aihua Wang, Yaping Jin
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RNA-Seq Analysis Reveals the Role of Omp16 in Brucella-Infected RAW264.7 Cells
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Sequence analysis of the first B5 subgenogroup strain of enterovirus 71 isolated in Korea: Yu Jung Won , Lae Hyung Kang , Ah Ra Lee , Bomina Paik , Hyun Kim , Sung Geun Lee , Seung Won Park , Seung Jin Hong , Soon Young Paik; J. Microbiol. 2020;58(5):422-429. Published online March 28, 2020; DOI: https://doi.org/10.1007/s12275-020-9539-z

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Abstract PDF: Enterovirus A71 (EV71), the main etiological agent of handfoot- mouth disease (HFMD), circulates in many areas of the world and has caused large epidemics since 1997, especially in the Asia-Pacific region. In this study, we determined the full-genome sequence of CMC718, a newly isolated EV71 strain in Korea. The CMC718 genome was 7,415 nucleotides in length and was confirmed by whole-genome phylogenetic analysis to belong to the B5 genotype. In particular, CMC718 demonstrated maximum identity with strain M988 of the B5 genotype and numerous amino acid variants were detected in the 3D domain of the viral protein P3, which is consistent with the mutation pattern of a B5 strain isolated in 2012–2013. Comparison of the CMC718 sequence with other EV71 reference strains confirmed the relationship and genetic variation of CMC718. Our study was a full-genome sequence analysis of the first EV71 strain of the B5 genotype isolated in South Korea. This information will be a valuable reference for the development of methods for the detection of recombinant viruses, the tracking of infections, and the diagnosis of EV71.

Sutterella faecalis sp. nov., isolated from human faeces: Byeong Seob Oh , Ji-Sun Kim , Seung Yeob Yu , Seoung Woo Ryu , Seung-Hwan Park , Se Won Kang , Jam-Eon Park , Seung-Hyeon Choi , Kook-Il Han , Keun Chul Lee , Mi Kyung Eom , Min Kuk Suh , Han Sol Kim , Dong Ho Lee , Hyuk Yoon , Byung-Yong Kim , Je Hee Lee , Jung-Sook Lee , Ju Huck Lee; J. Microbiol. 2020;58(2):99-104. Published online January 29, 2020; DOI: https://doi.org/10.1007/s12275-020-9396-9

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Abstract PDF

An obligately anaerobic, Gram-stain-negative, non-motile, non-spore-forming, and coccobacilli-shaped bacterial strain, designated KGMB03119T, was isolated from human faeces from a Korean. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the genus Sutterella and most closely related to Sutterlla wadsworthensis KCTC 15691T (96.8% 16S rRNA gene sequence similarity). The DNA G + C content of strain KGMB03119T was 58.3 mol% as determined from its whole genome sequence. Strain KGMB03119T was asaccharolytic, catalase-positive, oxidase- and urease-negative. Furthermore, the isolate was positive for alkaline phosphatase, leucine arylamidase, acid phosphatase, arginine arylamidase, alanine arylamidase, and glycine arylamidase. The major cellular fatty acids (> 10%) of the isolate were C18:1ω9c and C16:0. Methylmenaquinone-5 (MMK-5, 100%) was the predominant isoprenoid quinone in the isolate. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain KGMB03119T represents a novel species, for which the name Sutterella faecalis sp. nov. is proposed. The type strain is KGMB03119T (= KCTC 15823T = NBRC 114254T).

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Huilin Deng, Yaozhong Zheng, Qiongyao Wang, Jiaqi Peng, Weibin Bai, Lingmin Tian, Zouyan He, Rui Jiao
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Arianna Carella, Karen C. Carroll, Erik Munson, Romney M. Humphries
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Yan Huang, Yi Feng Wang, Jing Miao, Rui Fang Zheng, Jin Yao Li
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Lauryn Langford, Dhara D. Shah
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Validation List no. 212. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
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Longitudinal Study of the Effects of Flammulina velutipes Stipe Wastes on the Cecal Microbiota of Laying Hens
Jiali Wei, Huanwei Xiao, Yingbo Wei, Ivan Stève Nguepi Tsopmejio, Chang Sun, Haoyuan Wu, Zhouyu Jin, Hui Song, Suzanne Lynn Ishaq, Yunhe Xu
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Development of a neutralization assay based on the pseudotyped chikungunya virus of a Korean isolate: Woo-Chang Chung , Kwang Yeon Hwang , Suk-Jo Kang , Jae-Ouk Kim , Moon Jung Song; J. Microbiol. 2020;58(1):46-53. Published online November 25, 2019; DOI: https://doi.org/10.1007/s12275-020-9384-0

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The Chikungunya virus (CHIKV) belongs to the Alphavirus genus of Togaviridae family and contains a positive-sense single stranded RNA genome. Infection by this virus mainly causes sudden high fever, rashes, headache, and severe joint pain that can last for several months or years. CHIKV, a mosquito- borne arbovirus, is considered a re-emerging pathogen that has become one of the most pressing global health concerns due to a rapid increase in epidemics. Because handling of CHIKV is restricted to Biosafety Level 3 (BSL-3) facilities, the evaluation of prophylactic vaccines or antivirals has been substantially hampered. In this study, we first identified the whole structural polyprotein sequence of a CHIKV strain isolated in South Korea (KNIH/2009/77). Phylogenetic analysis showed that this sequence clustered within the East/ Central/South African CHIKV genotype. Using this sequence information, we constructed a CHIKV-pseudotyped lentivirus expressing the structural polyprotein of the Korean CHIKV isolate (CHIKVpseudo) and dual reporter genes of green fluorescence protein and luciferase. We then developed a pseudovirus-based neutralization assay (PBNA) using CHIKVpseudo. Results from this assay compared to those from the conventional plaque reduction neutralization test showed that our PBNA was a reliable and rapid method to evaluate the efficacy of neutralizing antibodies. More importantly, the neutralizing activities of human sera from CHIKVinfected individuals were quantitated by PBNA using CHIKVpseudo. Taken together, these results suggest that our PBNA for CHIKV may serve as a useful and safe method for testing the neutralizing activity of antibodies against CHIKV in BSL-2 facilities.

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Sofiia N. Rizatdinova, Alina E. Ershova, Irina V. Astrakhantseva
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Yao Yan, Fengyuan Zhang, Meng Zou, Hongyu Chen, Jingwen Xu, Shuaiyao Lu, Hongqi Liu
Acta Biochimica et Biophysica Sinica.2024; 56(10): 1425. CrossRef
Facile quantitative diagnostic testing for neutralizing antibodies against Chikungunya virus
Hui-Chung Lin, Shu-Fen Chang, Chien-Ling Su, Huai-Chin Hu, Der-Jiang Chiao, Yu-Lin Hsu, Hsuan-ying Lu, Chang-Chi Lin, Pei-Yun Shu, Szu-Cheng Kuo
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Development of a Novel Chikungunya Virus-Like Replicon Particle for Rapid Quantification and Screening of Neutralizing Antibodies and Antivirals
Hui-Chung Lin, Der-Jiang Chiao, Pei-Yun Shu, Hui-Tsu Lin, Chia-Chu Hsiung, Chang-Chi Lin, Szu-Cheng Kuo, Juan E. Ludert
Microbiology Spectrum.2023;[Epub] CrossRef
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Anaerotignum faecicola sp. nov., isolated from human faeces: Seung-Hyeon Choi , Ji-Sun Kim , Jam-Eon Park , Keun Chul Lee , Mi Kyung Eom , Byeong Seob Oh , Seung Yeob Yu , Se Won Kang , Kook-Il Han , Min Kuk Suh , Dong Ho Lee , Hyuk Yoon , Byung-Yong Kim , Je Hee Lee , Ju Huck Lee , Jung-Sook Lee , Seung-Hwan Park; J. Microbiol. 2019;57(12):1073-1078. Published online November 4, 2019; DOI: https://doi.org/10.1007/s12275-019-9268-3

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A strictly anaerobic bacterium, designated as strain KGMB- 03357T, was isolated from the faeces of a healthy Korean selected by Bundang Seoul National University based on health status. Cells of strain KGMB03357T are Gram-stain-positive, non-motile, non-spore-forming, and observed as straight or curved rods. The isolate grew at 10–45°C (optimum temperature of 40°C) and a pH range of 5.1–10.5 (optimum pH of 6.8). Analysis of phylogenetic trees based on the 16S rRNA gene sequences revealed that strain KGMB03357T forms a lineage within the genus Anaerotignum, and is most closely related to Anaerotignum lactatifermentans G17T (= KCTC 15066T, 96.1%), Anaerotignum propionicum DSM 1682T (= KCTC 5582T, 94.9%), Anaerotignum neopropionicum DSM 03847T (= KCTC 15564T, 94.9%), and Anaerotignum aminivorans SH021T (= KCTC 15705T, 94.8%). The ANI values between strain KGMB 03357T and members of the genus Anaerotignum were 73.3–71.0%, which are below the ANI criterion for interspecies identity. The DNA G + C content based on the whole-genome sequence is 47.3 mol%. The major cellular fatty acids of strain KGMB03357T are C16:0, C18:0, C18:1 cis 9, and anteiso-C15:0. Strain KGMB03357T contains meso-diaminopimelic acid as the diagnostic amino acid in the cell wall peptidoglycan. Based on the phenotypic, phylogenetic, and genomic properties, strain KGMB 03357T represents a novel species of the genus Anaerotignum, for which the name Anaerotignum faecicola sp. nov. is proposed. The type strain is KGMB03357T (= KCTC 15736T = DSM 107953T).

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Journal of the Science of Food and Agriculture.2023; 103(4): 1885. CrossRef
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International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
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Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021
Erik Munson, Karen C. Carroll, Romney M. Humphries
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Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum
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List of new names and new combinations previously effectively, but not validly, published
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IgG and IgM responses to human papillomavirus L1 virus-like particle as a function of dosing schedule and vaccine formulation: Min-Hye Park , Ji Won You , Hyoung Jin Kim , Hong-Jin Kim; J. Microbiol. 2019;57(9):821-827. Published online August 27, 2019; DOI: https://doi.org/10.1007/s12275-019-9308-z

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Most commercialized virus-like particle (VLP) vaccines use aluminum salt as adjuvant, even though VLPs provoke adequate antibody responses without adjuvant. We do not have detailed knowledge of how adjuvant affects the profile of anti- VLP antibodies. Meanwhile, there is evidence that differences between vaccination protocols influence the glycosylation of antibodies, which may alter their effector functions. In the present study a murine model was used to investigate the effects of dosing schedule and adjuvant on the antibody profiles and glycosylation levels of antigen-specific antibody responses to human papillomavirus type 16 L1 (HPV16 L1) VLPs. Mice received subcutaneously 2,000 ng of antigen divided into 4 or 7 doses. The HPV16 L1 VLPs elicited > 4 log10 anti-HPV16 L1 IgG titers without adjuvant, and aluminum hydroxide as adjuvant increased IgG titers 1.3- to 4-fold and reduced the anti-HPV16 L1 IgG2a / anti-HPV16 L1 IgG1 ratio value (use of aluminum hydroxide reduced the ratio of the IgG2a). Immunization with HPV16 L1 VLPs in combination with Freund’s adjuvant enhanced IgG titers 5- to 12- fold. Seven-dose immunization markedly increased anti- HPV16 L1 IgM titers compared to four-dose immunization, as well as increasing the proportion of glycosylated antibodies. Our results suggest that antibody glycosylation can be controlled immunologically, and IgG and IgM profiles and glycosylation profiles of the vaccine-induced antibodies can be used as indicators reflecting the vaccine characteristics. These
results
indicate that the HPV16 L1 VLP dosing schedule can affect the quality of antigen-specific antibody responses. We suggest that dosing schedules should be noted in vaccination protocols for VLP-based vaccines.

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Mediterraneibacter butyricigenes sp. nov., a butyrate-producing bacterium isolated from human faeces: Ji-Sun Kim , Keun Chul Lee , Min Kuk Suh , Kook-Il Han , Mi Kyung Eom , Ju Huck Lee , Seung-Hwan Park , Se Won Kang , Jam-Eon Park , Byeong Seob Oh , Seung Yeob Yu , Seung-Hyeon Choi , Dong Ho Lee , Hyuk Yoon , Byung-Yong Kim , Seung-Jo Yang , Jung-Sook Lee; J. Microbiol. 2019;57(1):38-44. Published online December 29, 2018; DOI: https://doi.org/10.1007/s12275-019-8550-8

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A Gram-stain-positive, obligately anaerobic, non-motile, nonspore- forming, and rod-shaped bacterial strain, designated KGMB01110T, was isolated from a faecal sample of a healthy male in South Korea. Phylogenetic analysis based on 16S rRNA gene showed that strain KGMB01110T belonged to Clostridium cluster XIVa and was most closely related to Mediterraneibacter glycyrrhizinilyticus KCTC 5760T (95.9% 16S rRNA gene sequence similarity). The DNA G + C content of strain KGMB01110T based on its whole genome sequence was 44.1 mol%. The major cellular fatty acids (> 10%) of the isolate were C14:0 and C16:0. The strain KGMB01110T was positive for arginine dihydrolase, β-galactosidase-6-phosphatase, and alkaline phosphatase. The strain KGMB01110T also produced acid from D-glucose and D-rhamnose, and hydrolyzed gelatin and aesculin. Furthermore, HPLC analysis and UV-tests of culture supernatant revealed that the strain KGMB01110T produced butyrate as the major end product of glucose fermentation. Based on the phylogenetic and phenotypic characteristics, strain KGMB01110T represent a novel species of the genus Mediterraneibacter in the family Lachnospiraceae. The type strain is KGMB01110T (= KCTC 15684T = CCUG 72830T).

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Prevalence of human Norovirus by genotype in contaminated groundwater in Korea over the last decade (2007–2016): Siwon Lee , Junhyeong Jang , Kyungseon Bae , Wonseok Lee , Hyenmi Chung , Sangjung Park; J. Microbiol. 2018;56(12):926-931. Published online November 27, 2018; DOI: https://doi.org/10.1007/s12275-018-8340-8

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This study investigated the occurrence of human Norovirus (HuNoV) by genotype in 1,486 groundwater samples collected from 843 groundwater wells suspected of contamination during 2007–2016, in South Korea. We identified and genotyped 186 HuNoV sequences in 178 HuNoV-positive samples using the RIVM-NoroNet norovirus genotyping tool (NGT) and phylogenetic tree analysis based on RIVM-NoroNet reference sequences. HuNoV GII was more prevalent than GI. The major genotypes detected were HuNoV GII.4 (43.0%), GII.22 (15.6%), GI.5 (10.2%), and GI.1 (8.6%); several genotypes accounted for < 5.0% of all HuNoVs, including GII.17, GI.6, GI.4, GII.6, GI.8, GII.3, GII.13, GI.3, GI.7, GI.2, GI.9, GII.1, GII.8, and GII.10. The prevalence of HuNoVs and number of genotypes detected has drastically decreased over the last decade. HuNoV GII.17, the emerging genotype worldwide including Europe and Asia, appeared in Korean groundwater from 2010, dominated in 2013–2014, and continued to be observed. HuNoV GII.4, the major type occurred last decade from Korean groundwater except 2013–2014, continued to be detected and prevalent similar to HuNoV GII.17 in 2016.

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Water-based extracts of Zizania latifolia inhibit Staphylococcus aureus infection through the induction of human beta-defensin 2 expression in HaCaT cells: Bo Yeon Kang , Seung-Su Lee , Myun-Ho Bang , Hyoik Jeon , Hangeun Kim , Dae Kyun Chung; J. Microbiol. 2018;56(12):910-916. Published online November 27, 2018; DOI: https://doi.org/10.1007/s12275-018-8307-9

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Zizania latifolia is a perennial herb belonging to the family Gramineae that has been used as a health food in Asian countries. In this study, we investigated the antimicrobial effect of Z. latifolia, which increased human beta-defensin 2 (hBD2) expression in HaCaT cells. hBD2 expression was further increased in cells treated with Z. latifolia extracts and subsequently infected with Staphylococcus aureus. Inversely, S. aureus infection decreased after treatment. The induction of hBD2 in HaCaT cells was mediated by the Toll-like receptor 2 (TLR2) signaling pathway, including the activation of extracellular signal-regulated kinase (ERK) and activator protein 1 (AP-1). Further study using siRNA revealed that hBD2 played an important role in the inhibition of S. aureus infection in HaCaT cells. Our data suggest that Z. latifolia extracts can be used as an antimicrobial ingredient for skin treatment formulas.

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Reovirus safety study for proliferation and differentiation of human adipose-derived mesenchymal stem cells: Jeong-Soo Park , Manbok Kim; J. Microbiol. 2017;55(1):75-79. Published online December 30, 2016; DOI: https://doi.org/10.1007/s12275-017-6542-0

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Naturally occurring reoviruses are live replication-proficient viruses specifically infecting human cancer cells while sparing the normal counterparts. Stem cells can be highly susceptible to viral infection due to their innate high proliferation potential and other active signaling pathways of cells that might be involved in viral tropism. In the previous study, we showed that reoviruses could adversely affect murine embryonic stem cells’ integrity in vitro and in vivo. Oncolytic viruses, delivered systemically face many hurdles that also impede their localization and infection of, metastatic tumors, due to a variety of immune and physical barriers. To overcome such hurdles to systemic delivery, several studies supported the idea that certain types of cells, including mesenchymal stem cells, might play a role as cell carriers for oncolytic viruses. Thus, it would be interesting to examine whether human adult stem cells such as human adipose-derived mesenchymal stem cells could be saved by the reoviral challenge. In this study, we report that biological activities such as proliferation and multipotency of human adipose-derived stem cells are not affected by wild-type reovirus challenge as evidenced by survival, osteogenic and adipogenic differentiation potential assays following treatment with reoviruses. Therefore, unlike murine embryonic stem cells, our study strongly suggests that human adipose-derived adult stem cells could be spared in vivo during wild-type reoviral anti-cancer therapeutics in a clinical setting. Furthermore, the results support the possible clinical use of human adipose-derived stem cells as an effective cell carrier of oncolytic reovirus to maximize their tumor tropism and anti-tumor activity.

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Epidemiological relationships of Campylobacter jejuni strains isolated from humans and chickens in South Korea: Jae-Young Oh , Yong-Kuk Kwon , Bai Wei , Hyung-Kwan Jang , Suk-Kyung Lim , Cheon-Hyeon Kim , Suk-Chan Jung , Min-Su Kang; J. Microbiol. 2017;55(1):13-20. Published online December 30, 2016; DOI: https://doi.org/10.1007/s12275-017-6308-8

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Thirty-nine human isolates of Campylobacter jejuni obtained from a national university hospital during 2007–2010 and 38 chicken isolates of C. jejuni were collected from poultry farms during 2009–2010 in South Korea were used in this study. Campylobacter genomic species and virulence-associated genes were identified by PCR. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were performed to compare their genetic relationships. All isolates were highly resistant to ciprofloxacin, nalidixic acid, and tetracycline. Of all isolates tested, over 94% contained seven virulence associated genes (flaA, cadF, racR, dnaJ, cdtA, cdtB, and cdtC). All isolates were classified into 39 types by PFGE clustering with 90% similarity. Some chicken isolates were incorporated into some PFGE types of human isolates. MLST analysis for the 39 human isolates and 38 chicken isolates
result
ed in 14 and 23 sequence types (STs), respectively, of which 10 STs were new. STs overlapped in both chicken and human isolates included ST-21, ST-48, ST-50, ST-51, and ST-354, of which ST-21 was the predominant ST in both human and chicken isolates. Through combined analysis of PFGE types and STs, three chicken isolates were clonally related to the three human isolates associated with food poisoning (VII-ST-48, XXII-ST-354, and XXVIII-ST-51). They were derived from geographically same or distinct districts. Remarkably, clonal spread of food poisoning pathogens between animals and humans was confirmed by population genetic analysis. Consequently, contamination of campylobacters with quinolone resistance and potential virulence genes in poultry production and consumption may increase the risk of infections in humans.

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Research Support, Non-U.S. Gov'ts

Anti-tumor effect of Cordyceps militaris in HCV-infected human hepatocarcinoma 7.5 cells: Seulki Lee , Hwan Hee Lee , Jisung Kim , Joohee Jung , Aree Moon , Choon-Sik Jeong , Hyojeung Kang , Hyosun Cho; J. Microbiol. 2015;53(7):468-474. Published online June 27, 2015; DOI: https://doi.org/10.1007/s12275-015-5198-x

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Abstract

Cordyceps extract has been reported to have various pharmacological activities including an anti-cancer effect. We investigated the inhibitory effect of Cordyceps militaris on hepatitis C virus-infected human hepatocarcinoma 7.5 cells (J6/JFH1-huh 7.5 cells). The huh7.5 cells with or without HCV infection were treated with various concentrations of ethanol extract of Cordyceps militaris (CME) for 48 h and the cytotoxicity was measured by CCK-8 assay. Both J6/JFH1- huh7.5 cells and huh7.5 cells were highly susceptible to CME. To examine the molecular mechanisms of the inhibitory effect on huh7.5 cells, the effect of CME on cell apoptosis was measured using flow cytometry and the expressions of p53, Bim, Bax, PARP, (cleaved) caspase-9, and (cleaved) caspase- 3 in huh 7.5 cells were detected by western blot assays. CME significantly increased early apoptosis and up-regulated the expression of Bim, Bax, cleaved PARP, cleaved caspase 9 and cleaved caspase-3. We also found the decrease of HCV Core or NS3 protein by CME in HCV-infected huh 7.5 cells.

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Anti-Cancer Effect of Quercetin in Xenograft Models with EBV-Associated Human Gastric Carcinoma
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Therapeutic potential of an AcHERV-HPV L1 DNA vaccine: Hee-Jung Lee , Jong Kwang Yoon , Yoonki Heo , Hansam Cho , Yeondong Cho , Yongdae Gwon , Kang Chang Kim , Jiwon Choi , Jae Sung Lee , Yu-Kyoung Oh , Young Bong Kim; J. Microbiol. 2015;53(6):415-420. Published online May 30, 2015; DOI: https://doi.org/10.1007/s12275-015-5150-0

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Abstract

Cervical cancer is strongly associated with chronic human papillomavirus infections, among which HPV16 is the most common. Two commercial HPV vaccines, Gardasil and Cervarix are effective for preventing HPV infection, but cannot be used to treat existing HPV infections. Previously, we developed a human endogenous retrovirus (HERV)-enveloped recombinant baculovirus capable of delivering the L1 genes of HPV types 16, 18, and 58 (AcHERV-HP16/18/58L1, AcHERV-HPV). Intramuscular administration of AcHERVHPV vaccines induced a strong cellular immune response as well as a humoral immune response. In this study, to examine the therapeutic effect of AcHERV-HPV in a mouse model, we established an HPV16 L1 expressing tumor cell line. Compared to Cervarix, immunization with AcHERVHPV greatly enhanced HPV16 L1-specific cytotoxic T lymphocytes (CTL) in C57BL/6 mice. Although vaccination could not remove preexisting tumors, strong CTL activity retarded the growth of inoculated tumor cells. These results indicate that AcHERV-HPV could serve as a potential therapeutic DNA vaccine against concurrent infection with HPV 16, 18, and 58.

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Genotyping, Morphology and Molecular Characteristics of a Lytic Phage of Neisseria Strain Obtained from Infected Human Dental Plaque: Ahmed N Aljarbou , Mohamad Aljofan; J. Microbiol. 2014;52(7):609-618. Published online May 30, 2014; DOI: https://doi.org/10.1007/s12275-014-3380-1

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The lytic bacteriaphage (phage) A2 was isolated from human dental plaques along with its bacterial host. The virus was found to have an icosahedron-shaped head (60±3 nm), a sheathed and rigid long tail (~175 nm) and was categorized into the family Siphoviridae of the order Caudovirales, which are dsDNA viral family, characterised by their ability to infect bacteria and are nonenveloped with a noncontractile tail. The isolated phage contained a linear dsDNA genome having 31,703 base pairs of unique sequence, which were sorted into three contigs and 12 single sequences. A latent period of 25 minutes and burst size of 24±2 particles was determined for the virus. Bioinformatics approaches were used to identify ORFs in the genome. A phylogenetic analysis confirmed the species inter-relationship and its placement in the family.

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Prediction of Bacterial microRNAs and Possible Targets in Human Cell Transcriptome: Amir Shmaryahu , Margarita Carrasco , Pablo D.T. Valenzuela; J. Microbiol. 2014;52(6):482-489. Published online May 29, 2014; DOI: https://doi.org/10.1007/s12275-014-3658-3

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Recent studies have examined gene transfer from bacteria to humans that would result in vertical inheritance. Bacterial DNA appears to integrate into the human somatic genome through an RNA intermediate, and such integrations are detected more frequently in tumors than normal samples and in RNA than DNA samples. Also, vertebrate viruses encode products that interfere with the RNA silencing machinery, suggesting that RNA silencing may indeed be important for antiviral responses in vertebrates. RNA silencing in response to virus infection could be due to microRNAs encoded by either the virus or the host. We hypothesized that bacterial expression of RNA molecules with secondary structures is potentially able to generate miRNA molecules that can interact with the human host mRNA during bacterial infection. To test this hypothesis, we developed a pipelinebased bioinformatics approach to identify putative micro-RNAs derived from bacterial RNAs that may have the potential to regulate gene expression of the human host cell. Our results suggest that 68 bacterial RNAs predicted from 37 different bacterial genomes have predicted secondary structures potentially able to generate putative microRNAs that may interact with messenger RNAs of genes involved in 47 different human diseases. As an example, we examined the effect of transfecting three putative microRNAs into human embryonic kidney 293 (HEK293) cells. The results show that the bacterially derived microRNA sequence can significantly regulate the expression of the respective target human gene. We suggest that the study of these predicted microRNAs may yield important clues as to how the human host cell processes involved in human diseases like cancer, diabetes, rheumatoid arthritis, and others may respond to a particular bacterial environment.

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Lactobacillus paracasei subsp. paracasei LC01 Positively Modulates Intestinal Microflora in Healthy Young Adults: Hao Zhang , Jing Sun , Xianting Liu , Chuan Hong , Yuanbo Zhu , Aiping Liu , Siqi Li , Huiyuan Guo , Fazheng Ren; J. Microbiol. 2013;51(6):777-782. Published online December 19, 2013; DOI: https://doi.org/10.1007/s12275-013-3279-2

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Lactobacillus paracasei subsp. paracasei LC01 (LC01) can tolerate intestinal stresses and has antioxidant activity. To evaluate the effect of the bacterium on human intestinal microflora, a randomized, double-blind, placebo-controlled human trial was carried out. Fifty-two healthy adult volunteers were randomized equally to two groups. One group consumed 12% (wt/vol) skimmed milk supplemented with 1010 CFU of LC01 each day for the 4-week treatment period, and then consumed placebo in the next treatment period, separated by a 2-week washout. The other group followed the reverse order. Group-specific real-time PCR and biochemical analyses was used to determine the intestinal bacterial composition of fecal samples collected at the end of every period, and the concentration of short-chain fatty acids and ammonia. A significant inhibition in fecal Escherichia coli and increase in Lactobacillus, Bifidobacterium, and Roseburia intestinalis were observed after consumption of LC01. Acetic acid and butyric acid were significantly higher in the probiotic stage and fecal ammonia was significantly lower. The results indicated a modulation effect of LC01 on the intestinal microflora of young adults, suggesting a beneficial effect on bowel health. LC01 may have potential value as a probiotic.

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Although cytology screening has reduced the incidence and mortality rate of cervical cancer significantly, its usefulness is limited to samples from the site of the lesion, resulting in its low sensitivity and unsuitability for use in medical checkups. The purpose of the present study was to evaluate the prevalence of HPV infection using genotype distribution and to analyze the correlation of the HPV DNA test results with cytological results. We also evaluated the benefits of quantitative information obtained from cyclic-catcher melting temperature analysis (CMTA) in screening for cervical cancer. We performed cyclic-CMTA using AnyplexTM II HPV28 Detection in combination with cervical cytology for 2,181 subjects. The following HPV positivity types were detected using cyclic-CMTA and HPV positivity was found to increase together with the severity of the cytology results: (1) For 419 HPV positive specimens, HPV DNA was detected in 18.1% of normal specimens, 78.3% of ASCUS, and all of LSIL and HSIL; (2) high-risk HPV DNAs were detected in 63.3% of normal (N=547), 65.9% of ASCUS (N=41), 76.9% of LSIL (N=13), and 88.9% of HSIL (N=9) among total detected HPV DNA regardless multiple detection; (3) multiple HPV genotypes were detected in 4.8% of normal specimens (N=2,146), 52.2% of ASCUS (N=23), 57.1% of LSIL (N=7), and 40.0% of HSIL (N=5). In addition, a high level of viral DNA was observed using cyclic-CMTA in all specimens beyond the LSIL stage according to cytology, while only 6% of specimens with normal cytology showed a correlation with viral quantitation by cyclic-CMTA. The combination of HPV genotyping with a quantitative assay and cytology will allow for a more accurate diagnosis of cervical cancer.

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Candida albicans ENO1 Null Mutants Exhibit Altered Drug Susceptibility, Hyphal Formation, and Virulence: Hui-Ching Ko , Ting-Yin Hsiao , Chiung-Tong Chen , Yun-Liang Yang; J. Microbiol. 2013;51(3):345-351. Published online June 28, 2013; DOI: https://doi.org/10.1007/s12275-013-2577-z

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Abstract PDF

We previously showed that the expression of ENO1 (enolase) in the fungal pathogen Candida albicans is critical for cell growth. In this study, we investigate the contribution of the ENO1 gene to virulence. We conducted our functional study of ENO1 in C. albicans by constructing an eno1/eno1 null mutant strain in which both ENO1 alleles in the genome were knockouted with the SAT1 flipper cassette that contains the nourseothricin-resistance marker. Although the null mutant failed to grow on synthetic media containing glucose, it was capable of growth on media containing yeast extract, peptone, and non-fermentable carbon sources. The null mutant was more susceptible to certain antifungal drugs. It also exhibited defective hyphal formation, and was avirulent in BALB/c mice.

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The Production and Immunogenicity of Human Papillomavirus Type 58 Virus-like Particles Produced in Saccharomyces cerevisiae: Hye-Lim Kwag , Hyoung Jin Kim , Don Yong Chang , Hong-Jin Kim; J. Microbiol. 2012;50(5):813-820. Published online November 4, 2012; DOI: https://doi.org/10.1007/s12275-012-2292-1

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Abstract

Human papillomavirus (HPV) is the cause of most cases of cervical cancer. HPV type 58 (HPV58) is the second most frequent cause of cervical cancer and high-grade squamous intraepithelial lesions (HSIL) in Asia and South / Central America, respectively. However, there is no vaccine against HPV58, although there are commercially available vaccines against HPV16 and 18. In this study, we produced HPV58 L1 protein from Saccharomyces cerevisiae, and investigated its immunogenicity. We first determined the optimum period of culture for obtaining HPV58 L1. We found that a considerable portion of the HPV58 L1 resulting from 48 h culture cannot be recovered by purification, while the HPV58 L1 resulting from 144 h culture is recovered efficiently: the yield of HPV58 L1 finally recovered from 144 h culture was 2.3 times higher than that from 48 h culture, although the production level of L1 protein from 144 h culture was lower than that from 48 h culture. These results indicate that the proportion of functional L1 protein from 144 h-cultured cells is significantly higher than that of 48 h-cultured cells. The HPV58 L1 purified from the 144 h culture was correctly assembled into structures similar to naturally occurring HPV virions. Immunization with the HPV58 L1 efficiently elicited anti-HPV58 neutralizing antibodies and antigen-specific CD4+ and CD8+ T cell proliferations, without the need for adjuvant. Our findings provide a convenient method for obtaining substantial amounts of highly immunogenic HPV58 L1 from S. cerevisiae.

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Reliability of Non-Culturable Virus Monitoring by PCR-Based Detection Methods in Environmental Waters Containing Various Concentrations of Target RNA: Eung Seo Koo , Chang-Hoon Yoo , Youjin Na , Soo Young Park , Hey Rhyoung Lyoo , Yong Seok Jeong; J. Microbiol. 2012;50(5):726-734. Published online November 4, 2012; DOI: https://doi.org/10.1007/s12275-012-2279-y

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Abstract: Owing to the lack of practical cell culture system for human noroviruses (HuNoV), various detection methods based on conventional reverse transcription-PCR (RT-PCR) and the quantitative real-time PCR have been major tools for monitoring environmental water safety. In this study, we showed that the proportion of water sample concentrates used for one-step RT-PCR significantly influences false-negative findings of the non-culturable viruses. In total, 59 archived samples of previously analyzed water concentrates were reexamined for HuNoV RNA by the one-step RT-PCR and semi-nested PCR. Using new aliquots for RNA extraction for every trial, up to 20 PCR trials were performed for each archive to determine whether the crosscheck results supported the previous determinations. We reconfirmed that 27.6% (8/29) of the samples were HuNoV-positive samples: 6.7% (1/15) from groundwater, 33.3% (3/9) from river water, and 80% (4/5) from treated sewage effluent (TSE). These results corresponded to the ratio of previously negative HuNoV samples now identified as positive (8/30): 6.7% (1/15) from groundwater, 20% (1/5) from river water, and 60% (6/10) from TSE. To elucidate the cause of these results, 16 different concentrations of murine norovirus (MNV) RNA (from 2×102 to 8×103 copies, divided into 10 tubes for each concentration) were subjected to one-step RT-PCR. The detection frequency and reproducibility decreased sharply when the number of MNV RNA copies fell below threshold levels. These observations suggest that the proportion of water concentrate used for PCR-based detection should be considered carefully when deciding viral presence in certain types of environmental water, particularly in regard with legal controls.

Remodeling of the Glycosylation Pathway in the Methylotrophic Yeast Hansenula polymorpha to Produce Human Hybrid-Type N-Glycans: Seon Ah Cheon , Hyunah Kim , Doo-Byoung Oh , Ohsuk Kwon , Hyun Ah Kang; J. Microbiol. 2012;50(2):341-348. Published online April 27, 2012; DOI: https://doi.org/10.1007/s12275-012-2097-2

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Abstract PDF

As a step forward to achieve the generation of human complex- type N-glycans in the methylotrophic yeast Hansenula polymorpha, we here report the modification of the yeast glycosylation pathway by heterologous expression of the human gene encoding β-1,2-N-acetylglucosaminyltransferase I (GnTI). For the optimal expression of human GnTI in the yeast Golgi compartment, the catalytic domain of the GnTI was fused to various N-terminal leader sequences derived from the yeast type II membrane proteins. The vectors containing GnTI fusion constructs were introduced into the H. polymorpha och1Δ single and och1Δalg3Δ double mutant strains expressing the ER-targeted Aspergillus saitoi α-1,2 mannosidase, respectively. Both of the glycoengineered Hpoch1Δ and Hpoch1ΔHpalg3Δ strains were shown to produce successfully the hybrid-type glycans with a monoantennary N-acetylglucosamine (GlcNAc1Man5GlcNAc2 and GlcNAc1Man3GlcNAc2, respectively) by N-glycan profile analysis of cell wall proteins. Furthermore, by comparative analysis of byproduct formation and the glycosylation site occupancy, we propose that the Hpoch1Δ strain would be more suitable than the Hpoch1ΔHpalg3Δ strain as a host for the production of recombinant proteins with humanized glycans.

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Cultured Bacterial Diversity and Human Impact on Alpine Glacier Cryoconite: Yung Mi Lee , So-Yeon Kim , Jia Jung , Eun Hye Kim , Kyeung Hee Cho , Franz Schinner , Rosa Margesin , Soon Gyu Hong , Hong Kum Lee; J. Microbiol. 2011;49(3):355-362. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-0232-0

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The anthropogenic effect on the microbial communities in alpine glacier cryoconites was investigated by cultivation and physiological characterization of bacteria from six cryoconite samples taken at sites with different amounts of human impact. Two hundred and forty seven bacterial isolates were included in Actinobacteria (9%, particularly Arthrobacter), Bacteroidetes (14%, particularly Olleya), Firmicutes (0.8%), Alphaproteobacteria (2%), Betaproteobacteria (16%, particularly Janthinobacterium), and Gammaproteobacteria (59%, particularly Pseudomonas). Among them, isolates of Arthrobacter were detected only in samples from sites with no human impact, while isolates affiliated with Enterobacteriaceae were detected only in samples from sites with strong human impact. Bacterial isolates included in Actinobacteria and Bacteroidetes were frequently isolated from pristine sites and showed low maximum growth temperature and enzyme secretion. Bacterial isolates included in Gammaproteobacteria were more frequently isolated from sites with stronger human impact and showed high maximum growth temperature and enzyme secretion. Ecotypic differences were not evident among isolates of Janthinobacterium lividum, Pseudomonas fluorescens, and Pseudomonas veronii, which were frequently isolated from sites with different degrees of anthropogenic effect.

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Temperatures beyond the community optimum promote the dominance of heat-adapted, fast growing and stress resistant bacteria in alpine soils
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Genome Sequence Analysis of H5N1 Influenza A Virus Isolated from a Vietnamese in 2007: Dieu Linh Tran , Kangmo Kim , Jae Yoo Choi , Hyun Dong Paik , Si-Woo Choi , Jin Yeul Ma , Sung-Soon Kim , Sung Joon Ahn , Young Bong Kim; J. Microbiol. 2011;49(2):274-279. Published online May 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0311-2

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Highly pathogenic H5N1 avian influenza A virus (AIV) crossed the species barrier and caused a number of deaths in humans in Vietnam and 14 other countries. Since the last report of human H5N1 infection in November 2005, the first documented H5N1 human infection was reported in June 2007 in Vietnam and was followed by 7 more cases, including 5 fatalities. In this study, we isolated and analyzed the full length of the H5N1 genome from a sample from the first patient in 2007. Phylogenetic analysis of eight genomic segments of the H5N1 virus strain (A/Vietnam/HN/2007, VNH07) revealed that this strain appears to be of genotype V and contains the HA gene, which is classified into clade 2.3.4. The deduced amino acid sequence of the HA protein has a typical affinity sequence for α2,3 linkage (SAα2,3-Gal) receptors and typical multibasic cleavage sequences. Compared with other H5N1 isolates, VNH07 showed that the possible reassortments for the NA and NP segments occurred between A/goose/Guangxi/3017/2005-like isolates (2.3.2) and A/human/Zhejiang/16/2006-like isolates (2.3.4).

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Rethinking Approaches to Improve the Utilization of Nucleic Acid Amplification Tests for Detection and Characterization of Influenza A in Diagnostic and Reference Laboratories
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Enhancement of Immunotherapeutic Effects of HPV16E7 on Cervical Cancer by Fusion with CTLA4 Extracellular Region: Yi Zheng , Yijuan Zhang , Jun Wan , Chaofan Shi , Laiqiang Huang; J. Microbiol. 2008;46(6):728-736. Published online December 24, 2008; DOI: https://doi.org/10.1007/s12275-008-0087-1

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Cervical cancer is caused by infection by high-risk human papillomavirus (HPV), especially HPV16. Limitations in current treatments of cervical cancers call for the development of new and improved immunotherapies. This study aims at investigating the efficacy of a novel vaccine consisting of modified HPV 16E7 fused with human cytotoxic T-lymphocyte antigen 4 (CTLA4). The regions in HPV16 E7 gene associated with its transformation and CTL-enhanced response were modified; the resultant HPV16mE7 was fused with extracellular region of CTLA4 to generate HPVm16E7-eCTLA4 fusion protein. Binding of this fusion protein to B7 molecules expressed on antigen presenting-cells (APCs) was demonstrated. C57BL/6 (H-2b) mice immunized with low dose of the fusion protein (10 μg) produced higher titer antibody and stronger specific CTL response, and expressed higher levels of IFN-γ and IL-12, compared with those immunized with HPVm16E7 only or admixture of HPVm16E7 and CTLA4, or PBS; and were protected from lethal dose tumor challenge. Tumor growth was retarded and survival prolonged in mouse models with the fusion protein treatment. Our results demonstrate that fusion of HPV16 E7 with eCTLA4 targeting APCs resulted in enhanced immunity, and that this fusion protein may be useful for improving the efficacy of immunotherapeutic treatments of cervical cancer and other HPV16 infection-associated tumors.

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Bacterial, Archaeal, and Eukaryal Diversity in the Intestines of Korean People: Young-Do Nam , Ho-Won Chang , Kyoung-Ho Kim , Seong Woon Roh , Min-Soo Kim , Mi-Ja Jung , Si-Woo Lee , Jong-Yeol Kim , Jung-Hoon Yoon , Jin-Woo Bae; J. Microbiol. 2008;46(5):491-501. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0199-7

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The bacterial, archaeal, and eukaryal diversity in fecal samples from ten Koreans were analyzed and compared by using the PCR-fingerprinting method, denaturing gradient gel electrophoresis (DGGE). The bacteria all belonged to the Firmicutes and Bacteroidetes phyla, which were known to be the dominant bacterial species in the human intestine. Most of the archaeal sequences belonged to the methane-producing archaea but several halophilic archarea-related sequences were also detected unexpectedly. While a small number of eukaryal sequences were also detected upon DGGE analysis, these sequences were related to fungi and stramenopiles (Blastocystis hominis). With regard to the bacterial and archaeal DGGE analysis, all ten samples had one and two prominent bands, respectively, but many individual-specific bands were also observed. However, only five of the ten samples had small eukaryal DGGE bands and none of these bands was observed in all five samples. Unweighted pair group method and arithmetic averages clustering algorithm (UPGMA) clustering analysis revealed that the archaeal and bacterial communities in the ten samples had relatively higher relatedness (the average Dice coefficient values were 68.9 and 59.2% for archaea and bacteria, respectively) but the eukaryal community showed low relatedness (39.6%).

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Affinity Maturation of an Anti-Hepatitis B Virus PreS1 Humanized Antibody by Phage Display: Gi-Hyeok Yang , Sun Ok Yoon , Myung Hee Jang , Hyo Jeong Hong; J. Microbiol. 2007;45(6):528-533.; DOI: https://doi.org/2640 [pii]

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Abstract PDF: In a previous study we generated an anti-Hepatitis B Virus (HBV) preS1 humanized antibody (HzKR127) that showed in vivo HBV-neutralizing activity in chimpanzees. However, the antigen-binding affinity of the humanized antibody may not be sufficient for clinical use and thus affinity maturation is required for better therapeutic efficacy. In this study, phage display technique was employed to increase the affinity of HzKR127. All six amino acid residues (Glu95-Tyr96-Asp97-Glu98-Ala99-Tyr100) in the heavy (H) chain complementarydetermining region 3 (HCDR3) of HzKR127 were randomized and phage-displayed single chain Fv (scFv) library was constructed. After three rounds of panning, 12 different clones exhibiting higher antigen-binding activity than the wild type ScFv were selected and their antigen-binding specificity for the preS1 confirmed. Subsequently, five ScFv clones were converted to whole IgG and subjected to affinity determination. The results showed that two clones (B3 and A19) exhibited an approximately 6 fold higher affinities than that of HzKR127. The affinity-matured humanized antibodies may be useful in anti-HBV immunotherapy.

Generation and Characterization of a Monoclonal Antibody with Specificity for Mycoplasma arginini: Yeon Sung Son , Hyo Jeong Hong; J. Microbiol. 2007;45(6):547-552.; DOI: https://doi.org/2610 [pii]

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Abstract PDF: Previously, we generated monoclonal antibodies (MAbs) that bound to the surface of human embryonic stem cells (hESCs) in an attempt to discover new hESC-specific surface markers. In this study, MAb 47-235 (IgG1, κ) was selected for further characterization. The MAb bound to the surface of undifferentiated hESCs but did not bind to mouse ESCs or mouse embryonic fibroblast cells in flow cytometric analysis. The antibody immunoprecipitated a 47 kDa protein from the lysates of cell surface-biotinylated hESCs. Identification of the protein by quadrupole time of flight tandem mass spectrometry revealed that 47-235 binds to Ag 243-5 protein of Mycoplasma arginini. BM-Cyclin treatment of the hESCs that reacted with 47-235 resulted in loss of mycoplasma DNA and the reactivity to 47-235. Nevertheless, the hESCs that were reactive to 47-235 maintained self-renewal and pluripotency and thus could be differentiated into three embryonic germ layers.

Comparative Proteomic Analysis of Virulent Korean Mycobacterium tuberculosis K-strain with Other Mycobacteria Strain Following Infection of U-937 Macrophage: Sung Weon Ryoo , Young Kil Park , Sue-Nie Park , Young Soo Shim , Hyunjeong Liew , Seongman Kang , Gill-Han Bai; J. Microbiol. 2007;45(3):268-271.; DOI: https://doi.org/2532 [pii]

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Abstract PDF: In Korea, the Mycobacterium tuberculosis K-strain is the most prevalent clinical isolates and belongs to the Beijing family. In this study, we conducted comparative porteomics of expressed proteins of clinical isolates of the K-strain with H37Rv, H37Ra as well as the vaccine strain of Mycobacterium bovis BCG following phagocytosis by the human monocytic cell line U-937. Proteins were analyzed by 2-D PAGE and MALDITOF-MS. Two proteins, Mb1363 (probable glycogen phosphorylase GlgP) and MT2656 (Haloalkane dehalogenase LinB) were most abundant after phagocytosis of M. tuberculosis K-strain. This approach provides a method to determine specific proteins that may have critical roles in tuberculosis pathogenesis.

Comparison of Bacterial Composition between Human Saliva and Dental Unit Water System: Eun-Hyoung Jeon , Ji-Hye Han , Tae-Young Ahn; J. Microbiol. 2007;45(1):1-5.; DOI: https://doi.org/2500 [pii]

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Abstract PDF: The bacterial compositions between the dental unit water system and human saliva were characterized and compared by direct sequence analysis of 16S rDNA clone libraries. Based on the species richness estimation, bacterial diversity in the dental unit water system (DUW) was more diverse than that of the human saliva (HS). The Chao1 estimates of species richness in HS and DUW samples were 12.0 and 72.4, respectively. The total numbers of OTUs observed in the combined libraries accounted for 83% (HS) and 59% (DUW) of the Chao1 diversity estimate as defined at the 80% similarity threshold. Based on the sequence analysis, the phylum Proteobacteria was the major group in both clone libraries at phylum level. DUW clone library contained 80.0% Proteobacteria, 8.0% Bacteroides, 4.0% Nitrospira, 4.0% Firmicutes, 2.0% Planctomycetes and 2.0% Acidobacteria. On the other hand, human saliva (HS) clone library contained 55.5% Proteobacteria, 36.1% Firmicutes and 8.4% Bacteroides. The majority of bacteria identified belonged to phylum Proteobacteria in both samples. In dental unit water system (DUW), Alphaproteobacteria was detected as the major group. There was no evidence of the bacterial contamination due to a dental treatment. Most sequences were related to microorganisms derived from biofilm in oligotrophic environments.

Bacterial Diversity in the Human Saliva from Different Ages: Jung-Gyu Kang , Seong Hwan Kim , Tae-Young Ahn; J. Microbiol. 2006;44(5):572-576.; DOI: https://doi.org/2438 [pii]

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Abstract PDF: To obtain primary idea on oral bacterium species that are generally present in periodotally healthy Koreans, the oral bacterial flora in the saliva of four periodontally healthy Koreans at different ages (5, 32, 35, 65) was investigated in this study. For this investigation, 16SrRNA gene clone libraries were generated from the saliva of the four healthy Koreans, and 50 clones were randomly selected from each saliva clone library and sequenced. Totally, 37 different kinds of bacterial 16S rRNA gene sequences were identified based on sequence homology search through GenBank database. The 37 kinds of saliva clone sequences were classified to 14 genera and 2 uncultured and 1 unidentified bacteria. Among the 14 identified genera, Streptococcus, Prevotella, and Veillonella were common genera, and Streptococcus was dominant genus that accounted for 7 different species. Among the seven Streptococcus species, S. salivarius appeared as the most common species. More numbers of species belonging to the genera Streptococcus and Prevotella was present in saliva from ages 32 and 35. While saliva from ages 5 and 65 showed more numbers of species belonging to the genera Rothia, including potential pathogenic species. Overall, saliva of a young child and a senior showed higher bacterial diversity than that of young adults.

Finding the Sources of Korean Salmonella enterica Serovar Enteritidis PT4 Isolates by Pulsed-field Gel Electrophoresis: Yong-Ku Woo; J. Microbiol. 2005;43(5):424-429.; DOI: https://doi.org/2280 [pii]

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Abstract PDF: In previous studies, it has been reported that both S. enteritidis, the most common serotype, and S. enteritidis Phage Type 4 (SEPT 4) isolates were identified as the most prevalent PT in domestic poultry and also in humans in Korea until 2002. The aim of this study was to analyze the genetic diversity and epidemiological properties of both PT isolates, and also to trace the source of SEPT 4 isolates from domestic poultry and humans by Pulsed-field gel electrophoresis (PFGE). In order to understand the molecular epidemiologic properties of SEPT 4 isolates, which have very similar phenotypic properties to our preliminary investigations (serotyping, phage typing, large plasmids and antibiograms), PFGE analysis with XbaI enzyme was performed on the representative SEPT 4 isolates. Thirty-six SEPT 4 isolates were analyzed and differentiated with 10 pulsed-field profiles (PFP) expressing very high discriminative ability (SID: 0.921). In PFP, SEPT 4 isolates from human patients showed a perfect genetic match with those from broiler chickens and meats. Therefore, this study was able to successfully trace the major source of SEPT 4 isolates and also to determine the usefulness of the PFGE method for genetic analysis of epidemic strains.

Growth of Staphylococcus aureus with Defective Siderophore Production in Human Peritoneal Dialysate Solution: Ra-Young Park , Hui-Yu Sun , Mi-Hwa Choi , Young-Hoon Bae , Sung-Heui Shin; J. Microbiol. 2005;43(1):54-61.; DOI: https://doi.org/2137 [pii]

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Abstract PDF: In this study, we attempted to determine the effects of iron-availability and the activity of the bacterial iron-uptake system (IUS) on the growth of Staphylococcus aureus in human peritoneal dialysate (HPD) solution. A streptonigrin-resistant S. aureus (SRSA) strain, isolated from S. aureus ATCC 6538, exhibited defective siderophore production, thereby resulting in ineffective uptake of iron from low iron-saturated transferrin. The growth of both strains was stimulated in HPD solution supplemented with FeCl_3 and holotransferrin, but growth was inhibited in HPD solution which had been supplemented with apotransferrin and dipyridyl. The SRSA strain grew less robustly than did its parental strain in both iron-supplemented HPD solution and regular HPD solution. These results indicate that iron-availability and siderophore-mediated IUS activity in particular, the ability to produce siderophores and thus capture iron from low iron-saturated transferrin play critical roles in the growth of S. aureus in HPD solution. Our results also indicated that the possibility of using iron chelators as therapeutic or preventive agents warrants further evaluation.

Review

Strategies Against Human Papillomavirus Infection and Cervical Cancer: Woon-Won Jung , Taehoon Chun , Donggeun Sul , Kwang Woo Hwang , Hyung-Sik Kang , Duck Joo Lee , In-Kwon Han; J. Microbiol. 2004;42(4):255-266.; DOI: https://doi.org/2112 [pii]

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Abstract PDF: Papillomaviruses infect a wide variety of animals, including humans. The human papillomavirus (HPV), in particular, is one of the most common causes of sexually transmitted disease. More than 200 types of HPV have been identified by DNA sequence data, and 85 HPV genotypes have been well characterized to date. HPV can infect the basal epithelial cells of the skin or inner tissue linings, and are, accordingly, categorized as either cutaneous or mucosal type. HPV is associated with a panoply of clinical conditions, ranging from innocuous lesions to cervical cancer. In the early 1980s, studies first reported a link between cervical cancer and genital HPV infection. Genital HPV infections are now recognized to be a major risk factor in at least 95% of cervical cancers. 30 different HPV genotypes have been identified as causative of sexually transmitted diseases, most of which induce lesions in the cervix, vagina, vulva, penis, and anus, as the result of sexual contact. There is also direct evidence demonstrating that at least four of these genotypes are prerequisite factors in cervical cancer. The main aim of this review was to evaluate the current literature regarding the pathovirology, diagnostics, vaccines, therapy, risk groups, and further therapeutic directions for HPV infections. In addition, we reviewed the current status of HPV infections in South Korean women, as evidenced by our data.

Retraction of Publication

Retraction Note to: Cryptic prophages in a blaNDM‑1‑bearing plasmid increase bacterial survival against high NaCl concentration, high and low temperatures, and oxidative and immunological stressors: So Yeon Kim , Kwan Soo Ko; J. Microbiol. 2023;61(4):481-481.; DOI: https://doi.org/10.1007/s12275-023-00049-1

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Abstract PDF: Retraction Note to: Journal of Microbiology (2020) Vol. 58, No. 6, pp. 483–488 https://doi.org/10.1007/s12275-020-9605-6 The Editor-in-Chief has retracted this article at the request of the authors. After publication concerns were raised that prophage sequences do not exist in the genome of the plasmid pNDM-A1 used in this study. The authors have not been able to confirm the existence of prophage sequences in the plasmid. As a result, the Editor-in-Chief no longer has confidence in the results and conclusions presented in this article. Kwan Soo Ko agrees with this retraction. So Yeon Kim has not responded to correspondence from the Editor-in-Chief about this retraction.

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

EDITORIAL] Human fungal pathogens: Why should we learn?: Jeong-Yoon Kim; J. Microbiol. 2016;54(3):145-148.; DOI: https://doi.org/10.1007/s12275-016-0647-8

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71 Crossref

Abstract PDF

Human fungal pathogens that cause invasive infections are hidden killers, taking lives of one and a half million people every year. However, research progress in this field has not been rapid enough to effectively prevent or treat life-threatening fungal diseases. To update recent research progress and promote more active research in the field of human fungal pathogens, eleven review articles concerning the virulence mechanisms and host interactions of four major human fungal pathogens–Candida albicans, Cryptococcus neoformans, Aspergillus fumigatus, and Histoplasma capsulatum–are presented in this special issue.

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Nitric oxide in human cytomegalovirus replication and gene expression: Lee, Jee Yeon , Lee, Chan Hee; J. Microbiol. 1997;35(2):152-157.

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Abstract PDF: Infection of human fibroblast (HF) cells with human cytomegalovirus (HCMV) result in changes in the intracellular level of second messengers. Since nitric oxide (NO) production has been known to be related with other second messengers, it is probable that HCMV infection of HF cells may involve NO. To test this possibility, the amount of NO was measured following HCMV infection but we were not able to detect significant change in the production of NO. Exogenous addition of NO generators such as sodium nitroprusside (SNP) or S-nitroso-N-a-cetylpenicillamine (SNAP) immediately after HCMV infection, however, inhibited virus multiplication. Furthermore, immunoblot experiment using monoclonal antibody to HCMV major immediate early (MIE) proteins or CAT assay using pCMVIE/CAT (plasmid containing CAT gene driven by HCMV MIE promoter) revealed that SNP or SNAP blocked the MIE gene expression. SNP was more effective than SNAP in hibiting HCMV multiplication or MIE gene expression. SNP produced more NO than SNAP in inhibiting HCMV multiplication or MIE gene expression. SNP produced more NO than SNAP. Although the mechanism for the inhibition of HCMV multiplication and MIE gene expression by NO is still elusive some correlation with NO-mediated inhibition of HCMV-induced increase in cytosolic free Ca^2+ concentration ([Ca^2+]) was observed. The increase of [Ca^2+] following HCMV infection was inhibited by SNP, and less effectively by SNAP. Raising [Ca^2+ with bromo-A23187 partially reversed the SNP block of MIE gene expression. Thus, there appear to e some relationships among NO. [Ca^2+], and HCMV MIE gene expression.

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