Journal of Microbiology

Journal Articles

Licochalcone A Protects Vaginal Epithelial Cells Against Candida albicans Infection Via the TLR4/NF-κB Signaling Pathway: Wei Li, Yujun Yin, Taoqiong Li, Yiqun Wang, Wenyin Shi; J. Microbiol. 2024;62(7):525-533. Published online May 31, 2024; DOI: https://doi.org/10.1007/s12275-024-00134-z

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Abstract: Vulvovaginal candidiasis (VVC) is a prevalent condition affecting a significant portion of women worldwide. Licochalcone A (LA), a natural compound with diverse biological activities, holds promise as a protective agent against Candida albicans (C. albicans) infection. This study aims to investigate the potential of LA to safeguard vaginal epithelial cells (VECs) from C. albicans infection and elucidate the underlying molecular mechanisms. To simulate VVC in vitro, VK2-E6E7 cells were infected with C. albicans. Candida albicans biofilm formation, C. albicans adhesion to VK2-E6E7 cells, and C. albicans-induced cell damage and inflammatory responses were assessed by XTT reduction assay, fluorescence assay, LDH assay, and ELISA. CCK-8 assay was performed to evaluate the cytotoxic effects of LA on VK2-E6E7 cells. Western blotting assay was performed to detect protein expression. LA dose-dependently hindered C. albicans biofilm formation and adhesion to VK2-E6E7 cells. Furthermore, LA mitigated cell damage, inhibited the Bax/Bcl-2 ratio, and attenuated the secretion of pro-inflammatory cytokines in C. albicans-induced VK2-E6E7 cells. The investigation into LA's impact on the Toll-like receptor 4 (TLR4)/nuclear factor-kappa B (NF-κB) pathway revealed that LA downregulated TLR4 expression and inhibited NF-κB activation in C. albicans-infected VK2-E6E7 cells. Furthermore, TLR4 overexpression partially abated LA-mediated protection, further highlighting the role of the TLR4/NF-κB pathway. LA holds the potential to safeguard VECs against C. albicans infection, potentially offering therapeutic avenues for VVC management.

Correlation between fat accumulation and fecal microbiota in crossbred pigs: Xin Li , Mengyu Li , Jinyi Han , Chuang Liu , Xuelei Han , Kejun Wang , Ruimin Qiao , Xiu-Ling Li , Xin-Jian Li; J. Microbiol. 2022;60(11):1077-1085. Published online September 9, 2022; DOI: https://doi.org/10.1007/s12275-022-2218-5

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Backfat thickness (BF) is an important indicator of fat deposition capacity and lean meat rate in pigs and is very important in porcine genetics and breeding. Intestinal microbiota plays a key role in nutrient digestion and utilization with a profound impact on fat deposition of livestock animals. To investigate the relationship between the pig gut microbiome and BF, 20 low-BF (L-BF) and 20 high-BF (H-BF) pigs were selected as two groups from Yunong Black pigs in the present study. Fecal samples from pigs were analyzed for microbial diversity, composition, and predicted functionality using 16S rRNA gene sequencing. The results showed that there were significant differences in microbial β diversity between the two groups. LEfSe analysis revealed a number of bacterial features being differentially enriched in either L-BF or H-BF pigs. Spearman correlation analysis identified the abundance of Oscillospira, Peptococcus, and Bulleidia were significantly positive correlations with BF (P < 0.05), while Sutterella and Bifidobacterium were significantly negatively correlated with BF (P < 0.05). Importantly, the bacteria significantly positively correlated with BF mainly belong to Clostridium, which can ferment host-indigestible plant polysaccharides into shortchain fatty acid (SCFA) and promote fat synthesis and deposition. Predictive functional analysis indicated that the pathway abundance of cell motility and glycan biosynthesis were significantly widespread in the microbiota of the H-BF group. The results of this study will be useful for the development of microbial biomarkers for predicting and improving porcine BF, as well as for the investigation of targets for dietary strategies.

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Carboxymethyl chitosan-dialdehyde glucan/polydopamine carrier targeted delivery Bacillus subtilis on enhancing oral utilization and intestinal colonization in mice
Lulu Chu, Luyu Xie, Bingzhi Chen, Yuji Jiang, Wenjie Wang
International Journal of Biological Macromolecules.2024; 280: 135574. CrossRef
Impact of Early Weaning on Development of the Swine Gut Microbiome
Benoit St-Pierre, Jorge Yair Perez Palencia, Ryan S. Samuel
Microorganisms.2023; 11(7): 1753. CrossRef
Comparison of Conjunctival Sac Microbiome between Low and High Myopic Eyes
Kang Xiao, Zhengyu Chen, Qin Long
Journal of Microbiology.2023; 61(5): 571. CrossRef

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

The hrp pathogenicity island of Pseudomonas syringae pv. tomato DC3000 is induced by plant phenolic acids: Jun Seung Lee , Hye Ryun Ryu , Ji Young Cha , Hyung Suk Baik; J. Microbiol. 2015;53(10):725-731. Published online October 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5256-4

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Abstract

Plants produce a wide array of antimicrobial compounds, such as phenolic compounds, to combat microbial pathogens. The hrp PAI is one of the major virulence factors in the plant pathogen, Pseudomonas syringae. A major role of hrp PAI is to disable the plant defense system during bacterial invasion. We examined the influence of phenolic compounds on hrp PAI gene expression at low and high concentrations. There was approximately 2.5 times more hrpA and hrpZ mRNA in PtoDC3000 that was grown in minimal media (MM) supplemented with 10 μM of ortho-coumaric acid than in PtoDC3000 grown in MM alone. On the other hand, a significantly lower amount of hrpA mRNA was observed in bacteria grown in MM supplemented with a high concentration of phenolic compounds. To determine the regulation pathway for hrp PAI gene expression, we performed qRTPCR using gacS, gacA, and hrpS deletion mutants.

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Liebig review: The role of mineral nutrients in the development of Pseudomonas syringae diseases—Lessons learned and implications for disease control in woody plants
Nathalie Soethe, Michelle T. Hulin, Antje Balasus, Gail Preston, Christoph‐Martin Geilfus
Journal of Plant Nutrition and Soil Science.2024; 187(3): 301. CrossRef
Regulation of the Pseudomonas syringae Type III Secretion System by Host Environment Signals
Megan R. O’Malley, Jeffrey C. Anderson
Microorganisms.2021; 9(6): 1227. CrossRef
Quantification of Viable Cells of Pseudomonas syringae pv. tomato in Tomato Seed Using Propidium Monoazide and a Real-Time PCR Assay
A-li Chai, Hai-yan Ben, Wei-tao Guo, Yan-xia Shi, Xue-wen Xie, Lei Li, Bao-ju Li
Plant Disease.2020; 104(8): 2225. CrossRef
Validation of RT-qPCR Approaches to MonitorPseudomonas syringaeGene Expression During Infection and Exposure to Pattern-Triggered Immunity
Amy Smith, Amelia H. Lovelace, Brian H. Kvitko
Molecular Plant-Microbe Interactions®.2018; 31(4): 410. CrossRef
Multidrug Efflux Pumps at the Crossroad between Antibiotic Resistance and Bacterial Virulence
Manuel Alcalde-Rico, Sara Hernando-Amado, Paula Blanco, José L. Martínez
Frontiers in Microbiology.2016;[Epub] CrossRef
Global Analysis of Type Three Secretion System and Quorum Sensing Inhibition of Pseudomonas savastanoi by Polyphenols Extracts from Vegetable Residues
Carola Biancalani, Matteo Cerboneschi, Francesco Tadini-Buoninsegni, Margherita Campo, Arianna Scardigli, Annalisa Romani, Stefania Tegli, Boris Alexander Vinatzer
PLOS ONE.2016; 11(9): e0163357. CrossRef

Effect of Fumarate Reducing Bacteria on In Vitro Rumen Fermentation, Methane Mitigation and Microbial Diversity: Lovelia Mamuad , Seon Ho Kim , Chang Dae Jeong , Yeon Jae Choi , Che Ok Jeon , Sang-Suk Lee; J. Microbiol. 2014;52(2):120-128. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3518-1

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Abstract

The metabolic pathways involved in hydrogen (H2) production, utilization and the activity of methanogens are the important factors that should be considered in controlling methane (CH4) emissions by ruminants. H2 as one of the major substrate for CH4 production is therefore should be controlled. One of the strategies on reducing CH4 is through the use of hydrogenotrophic microorganisms such as fumarate reducing bacteria. This study determined the effect of fumarate reducing bacteria, Mitsuokella jalaludinii, supplementation on in vitro rumen fermentation, CH4 production, diversity and quantity. M. jalaludinii significantly reduced CH4 at 48 and 72 h of incubation and significantly increased succinate at 24 h. Although not significantly different, propionate was found to be highest in treatment containing M. jalaludinii at 12 and 48 h of incubation. These results suggest that supplementation of fumarate reducing bacteria to ruminal fermentation reduces CH4 production and quantity, increases succinate and changes the rumen microbial diversity.

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Distinct microbial hydrogen and reductant disposal pathways explain interbreed variations in ruminant methane yield
Qiushuang Li, Zhiyuan Ma, Jiabin Huo, Xiumin Zhang, Rong Wang, Shizhe Zhang, Jinzhen Jiao, Xiyang Dong, Peter H Janssen, Emilio M Ungerfeld, Chris Greening, Zhiliang Tan, Min Wang
The ISME Journal.2024;[Epub] CrossRef
The Effect of Direct-Fed Microbials on In-Vitro Rumen Fermentation of Grass or Maize Silage
Rajan Dhakal, Giuseppe Copani, Bruno Ieda Cappellozza, Nina Milora, Hanne Helene Hansen
Fermentation.2023; 9(4): 347. CrossRef
Alternative pathways for hydrogen sink originated from the ruminal fermentation of carbohydrates: Which microorganisms are involved in lowering methane emission?
Ana Margarida Pereira, Maria de Lurdes Nunes Enes Dapkevicius, Alfredo E. S. Borba
Animal Microbiome.2022;[Epub] CrossRef
Hydrogenosome, Pairing Anaerobic Fungi and H2-Utilizing Microorganisms Based on Metabolic Ties to Facilitate Biomass Utilization
Jing Ma, Pei Zhong, Yuqi Li, Zhanying Sun, Xiaoni Sun, Min Aung, Lizhuang Hao, Yanfen Cheng, Weiyun Zhu
Journal of Fungi.2022; 8(4): 338. CrossRef
Dietary wheat and reduced methane yield are linked to rumen microbiome changes in dairy cows
Keith W. Savin, Peter J. Moate, S. R. O. Williams, Carolyn Bath, Joanne Hemsworth, Jianghui Wang, Doris Ram, Jody Zawadzki, Simone Rochfort, Benjamin G. Cocks, James E. Wells
PLOS ONE.2022; 17(5): e0268157. CrossRef
Effect of Autochthonous Nepalese Fruits on Nutrient Degradation, Fermentation Kinetics, Total Gas Production, and Methane Production in In-Vitro Rumen Fermentation
Rajan Dhakal, Manuel Gonzalez Ronquillo, Einar Vargas-Bello-Pérez, Hanne Helene Hansen
Animals.2022; 12(17): 2199. CrossRef
Reducing Enteric Methanogenesis through Alternate Hydrogen Sinks in the Rumen
Prasanta Kumar Choudhury, Rajashree Jena, Sudhir Kumar Tomar, Anil Kumar Puniya
Methane.2022; 1(4): 320. CrossRef
Methane Emissions Regulated by Microbial Community Response to the Addition of Monensin and Fumarate in Different Substrates
Dan Xue, Huai Chen, Xiaolin Luo
Applied Sciences.2021; 11(14): 6282. CrossRef
Different milk replacers alter growth performance and rumen bacterial diversity of dairy bull calves
Yangdong Zhang, Jing Cheng, Nan Zheng, Yuanqing Zhang, Di Jin
Livestock Science.2020; 231: 103862. CrossRef
Metabolic Hydrogen Flows in Rumen Fermentation: Principles and Possibilities of Interventions
Emilio M. Ungerfeld
Frontiers in Microbiology.2020;[Epub] CrossRef
Rumen fermentation and microbial community composition influenced by live Enterococcus faecium supplementation
Lovelia L. Mamuad, Seon Ho Kim, Ashraf A. Biswas, Zhongtang Yu, Kwang-Keun Cho, Sang-Bum Kim, Kichoon Lee, Sang Suk Lee
AMB Express.2019;[Epub] CrossRef
Advanced estimation and mitigation strategies: a cumulative approach to enteric methane abatement from ruminants
Mahfuzul Islam, Sang-Suk Lee
Journal of Animal Science and Technology.2019; 61(3): 122. CrossRef
Recent insight and future techniques to enhance rumen fermentation in dairy goats
Lovelia L. Mamuad, Sung Sill Lee, Sang Suk Lee
Asian-Australasian Journal of Animal Sciences.2019; 32(8): 1321. CrossRef
Effects of illite supplementation on in vitro and in vivo rumen fermentation, microbial population and methane emission of Hanwoo steers fed high concentrate diets
Ashraf A. Biswas, Sung‐Sill Lee, Lovelia L. Mamuad, Seon‐Ho Kim, Yeon‐Jae Choi, Chanhee Lee, Kichoon Lee, Gui‐Seck Bae, Sang‐Suk Lee
Animal Science Journal.2018; 89(1): 114. CrossRef
Effect of different concentrate diet levels on rumen fluid inoculum used for determination of in vitro rumen fermentation, methane concentration, and methanogen abundance and diversity
Seon-Ho Kim, Lovelia L. Mamuad, Eun-Joong Kim, Ha-Guyn Sung, Gui-Seck Bae, Kwang-Keun Cho, Chanhee Lee, Sang-Suk Lee
Italian Journal of Animal Science.2018; 17(2): 359. CrossRef
Methanobacterium formicicum as a target rumen methanogen for the development of new methane mitigation interventions: A review
P Chellapandi, M Bharathi, C Sangavai, R Prathiviraj
Veterinary and Animal Science.2018; 6: 86. CrossRef
Rumen prokaryotic communities of ruminants under different feeding paradigms on the Qinghai-Tibetan Plateau
Dan Xue, Huai Chen, Xinquan Zhao, Shixiao Xu, Linyong Hu, Tianwei Xu, Lin Jiang, Wei Zhan
Systematic and Applied Microbiology.2017; 40(4): 227. CrossRef
Increased propionate concentration inLactobacillus mucosae-fermented wet brewers grains and duringin vitrorumen fermentation
L.L. Mamuad, S.H. Kim, Y.J. Choi, A.P. Soriano, K.K. Cho, K. Lee, G.S. Bae, S.S. Lee
Journal of Applied Microbiology.2017; 123(1): 29. CrossRef
Use of Lysozyme as a Feed Additive on In vitro Rumen Fermentation and Methane Emission
Ashraf A. Biswas, Sung Sill Lee, Lovelia L. Mamuad, Seon-Ho Kim, Yeon-Jae Choi, Gui-Seck Bae, Kichoon Lee, Ha-Guyn Sung, Sang-Suk Lee
Asian-Australasian Journal of Animal Sciences.2016; 29(11): 1601. CrossRef
Quantification of organic acids in ruminal in vitro batch culture fermentation supplemented with fumarate using a herb mix as a substrate
J. Pisarčíková, Z. Váradyová, K. Mihaliková, S. Kišidayová, J. Plaizier
Canadian Journal of Animal Science.2016; 96(1): 60. CrossRef
Rumen fermentation and performance of Hanwoo steers fed total mixed ration with Korean rice wine residue
Chang-Dae Jeong, Lovelia L. Mamuad, Jong Youl Ko, Ha Guyn Sung, Keun Kyu Park, Yoo Kyung Lee, Sang-Suk Lee
Journal of Animal Science and Technology.2016;[Epub] CrossRef
Limits to Dihydrogen Incorporation into Electron Sinks Alternative to Methanogenesis in Ruminal Fermentation
Emilio M. Ungerfeld
Frontiers in Microbiology.2015;[Epub] CrossRef
Effect of Soybean Meal and Soluble Starch on Biogenic Amine Production and Microbial Diversity Using In vitro Rumen Fermentation
Chang-Dae Jeong, Lovelia L. Mamuad, Seon-Ho Kim, Yeon Jae Choi, Alvin P. Soriano, Kwang Keun Cho, Che-Ok Jeon, Sung Sil Lee, Sang-Suk Lee
Asian-Australasian Journal of Animal Sciences.2014; 28(1): 50. CrossRef

NOTE] Next-Generation Sequencing-Based Transcriptome Analysis of L-Lysine-Producing Corynebacterium glutamicum ATCC 21300 Strain: Hong-Il Kim , Jae-Young Nam , Jae-Yong Cho , Chang-Soo Lee , Young-Jin Park; J. Microbiol. 2013;51(6):877-880. Published online December 19, 2013; DOI: https://doi.org/10.1007/s12275-013-3236-0

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Abstract

In the present study, 151 genes showed a significant change in their expression levels in Corynebacterium glutamicum ATCC 21300 compared with those of C. glutamicum ATCC 13032. Of these 151 genes, 56 genes (2%) were up-regulated and 95 genes (3%) were down-regulated. RNA sequencing analysis also revealed that 11 genes, involved in the L-lysine biosynthetic pathway of C. glutamicum, were up- or downregulated compared with those of C. glutamicum ATCC 13032. Of the 151 genes, 10 genes were identified to have mutations including SNP (9 genes) and InDel (1 gene). This information will be useful for genome breeding of C. glutamicum to develop an industrial amino acid-producing strain with minimal mutation.

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Review of the Proteomics and Metabolic Properties of Corynebacterium glutamicum
Juhwan Park, Sooa Lim
Microorganisms.2024; 12(8): 1681. CrossRef
Transcriptome analysis of l-leucine-producing Corynebacterium glutamicum under the addition of trimethylglycine
Jian Wang, Xuesong Wang, Qing Liang, Deheng Li, Dawei Li, Qunqun Guo
Amino Acids.2022; 54(2): 229. CrossRef
RETRACTED ARTICLE: Comparative analysis of the Corynebacterium glutamicum transcriptome in response to changes in dissolved oxygen levels
Xiuxia Liu, Sun Yang, Fen Wang, Xiaofeng Dai, Yankun Yang, Zhonghu Bai
Journal of Industrial Microbiology and Biotechnology.2017; 44(2): 181. CrossRef
Transcriptome and Gene Ontology (GO) Enrichment Analysis Reveals Genes Involved in Biotin Metabolism That Affect l-Lysine Production in Corynebacterium glutamicum
Hong-Il Kim, Jong-Hyeon Kim, Young-Jin Park
International Journal of Molecular Sciences.2016; 17(3): 353. CrossRef

Simultaneous Detection of Waterborne Viruses by Multiplex Real-Time PCR: Lae-Hyung Kang , Se-hwan Oh , Jeong-Woong Park , Yu-Jung Won , Sangryeol Ryu , Soon-Young Paik; J. Microbiol. 2013;51(5):671-675. Published online September 14, 2013; DOI: https://doi.org/10.1007/s12275-013-3199-1

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Abstract

Norovirus, Rotavirus group A, the Hepatitis A virus, and Coxsackievirus are all common causes of gastroenteritis. Conventional diagnoses of these causative agents are based on antigen detection and electron microscopy. To improve the diagnostic potential for viral gastroenteritis, internally controlled multiplex real-time polymerase chain reaction (PCR) methods have been recently developed. In this study, individual real-time PCRs were developed and optimized for specific detections of Norovirus genogroup I, Norovirus genogroup II, Rotavirus group A, the Hepatitis A virus, and Coxsackievirus group B1. Subsequently, individual PCRs were combined with multiplex PCR reactions. In general, multiplex real-time PCR assays showed comparable sensitivities and specificities with individual assays. A retrospective clinical evaluation showed increased pathogen detection in 29% of samples using conventional PCR methods. Prospective clinical evaluations were detected in 123 of the 227 (54%) total samples used in the multiplex realtime PCR analysis. The Norovirus genogroup II was found most frequently (23%), followed by Rotavirus (20%), the Hepatitis A virus (4.5%), Coxsackievirus (3.5%), and Norovirus genogroup I (2.6%). Internally controlled multiplex real-time PCR assays for the simultaneous detection of Rotavirus, Coxsackievirus group B, the Hepatitis A virus, and Norovirus genogroups I and II showed significant improvement in the diagnosis of viral gastroenteritis.

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Microbiological quality of irrigation water for cultivation of fruits and vegetables: An overview of available guidelines, water testing strategies and some factors that influence compliance.
Oluwadara Alegbeleye, Anderson S. Sant’Ana
Environmental Research.2023; 220: 114771. CrossRef
Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality
Lisa Paruch
International Journal of Environmental Research and Public Health.2022; 19(9): 5128. CrossRef
Development and Evaluation of a SYBR Green-Based, Real-time Polymerase Chain Reaction for Rapid and Specific Detection of Human Coxsackievirus B5
Kyu Bong Cho
Biomedical Science Letters.2020; 26(4): 302. CrossRef
Multiplex qPCR for serodetection and serotyping of hepatitis viruses: A brief review
Mohammad Irshad, Priyanka Gupta, Dhananjay Singh Mankotia, Mohammad Ahmad Ansari
World Journal of Gastroenterology.2016; 22(20): 4824. CrossRef
Quantification and Genotyping of Rotavirus A within Two Wastewater Treatment Processes
Chourouk Ibrahim, Nadia Cherif, Salah Hammami, Pierre Pothier, Abdennaceur Hassen
CLEAN – Soil, Air, Water.2016; 44(4): 393. CrossRef
Microfluidic Quantitative PCR for Simultaneous Quantification of Multiple Viruses in Environmental Water Samples
Satoshi Ishii, Gaku Kitamura, Takahiro Segawa, Ayano Kobayashi, Takayuki Miura, Daisuke Sano, Satoshi Okabe, C. A. Elkins
Applied and Environmental Microbiology.2014; 80(24): 7505. CrossRef

Cloning, Annotation and Expression Analysis of Mycoparasitism-Related Genes in Trichoderma harzianum 88: Lin Yao , Qian Yang , Jinzhu Song , Chong Tan , Changhong Guo , Li Wang , Lianhai Qu , Yun Wang; J. Microbiol. 2013;51(2):174-182. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2545-7

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Abstract: Trichoderma harzianum 88, a filamentous soil fungus, is an effective biocontrol agent against several plant pathogens. High-throughput sequencing was used here to study the mycoparasitism mechanisms of T. harzianum 88. Plate confrontation tests of T. harzianum 88 against plant pathogens were conducted, and a cDNA library was constructed from T. harzianum 88 mycelia in the presence of plant pathogen cell walls. Randomly selected transcripts from the cDNA library were compared with eukaryotic plant and fungal genomes. Of the 1,386 transcripts sequenced, the most abundant Gene Ontology (GO) classification group was “physiological process”. Differential expression of 19 genes was confirmed by real-time RT-PCR at different mycoparasitism stages against plant pathogens. Gene expression analysis revealed the transcription of various genes involved in mycoparasitism of T. harzianum 88. Our study provides helpful insights into the mechanisms of T. harzianum 88-plant pathogen interactions.

Development and Evaluation of Multiplex Real-time RT-PCR Assays for Seasonal, Pandemic A/H1pdm09 and Avian A/H5 Influenza Viruses Detection: Jang-Hoon Choi , Mi-Seon Kim , Joo-Yeon Lee , Nam-Joo Lee , Donghyok Kwon , Min Gu Kang , Chun Kang; J. Microbiol. 2013;51(2):252-257. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2452-y

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Abstract: Since the pandemic influenza A (H1N1) 2009 ((H1N1)pdm09) virus spread all over the world, the (H1N1)pdm09 virus has been circulating with seasonal influenza viruses. We developed rapid and sensitive one-step multiplex real-time RTPCR assays (rRT-PCR) for simultaneous detection of influenza viruses currently circulating in humans, and the avian A/H5 virus. The detection limit of each assay was 4.8 to 1 copies per reaction and no cross-reactivity with other major respiratory pathogens was found. Analytical positive predictive value (PPV), negative predictive value (NPV) sensitivity and specificity were 100%, 94.1%, 93.7% and 100%, respectively. Clinical evaluation revealed that 1,976 (16.5%) of 11,963 throat swabs from patients with respiratory symptoms were confirmed as 1,651 (83.6%) A/H1pdm09, 308 (15.6%) A/H3 and 17 (0.8%) B virus during the 2010-2011 influenza season. Collectively, the multiplex rRT-PCR assays described here provide a practical tool for reliable implementation of influenza surveillance and diagnosis.

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.

NOTE] Molecular Characterization of Two Strains of Porcine Group C Rotavirus: Sung-Geun Lee , Soo-Hyun Youn , Mi-Hwa Oh , Ok-Jae Rhee , Sangsuk Oh , Soon-Young Paik; J. Microbiol. 2011;49(6):1058-1062. Published online December 28, 2011; DOI: https://doi.org/10.1007/s12275-011-1088-z

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Abstract: Group C rotaviruses are an important cause of acute gastroenteritis in humans and animals. Fecal samples were collected from a porcine herd in July, 2009. Group C rotavirus RNA was detected using RT-PCR for the VP6 gene. The identified strain was further characterized by sequencing and phylogenetic analysis of the partial VP4, and complete VP6 and VP7 gene sequences. The partial VP4 and complete VP6 gene sequences of the CUK-5 strain were most closely related to those of the CUK-6 strain of group C rotaviruses. Phylogenetic analysis of the VP7 gene of the 2 strains (CUK-5 and CUK-6) and reference strains of group G rotavirus by the neighbor-joining method also confirmed that CUK-5 and CUK-6 belonged to type G5 and G1 strains, respectively. This study provides useful data for the prediction of newly appearing variants of porcine group C rotaviruses in neighboring countries through comparisons with GCRVs and fundamental research for vaccine development.

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

Transcriptional Control of Genes Involved in Yeast Phospholipid Biosynthesis: Roshini Wimalarathna , Chen-Han Tsai , Chang-Hui Shen; J. Microbiol. 2011;49(2):265-273. Published online May 3, 2011; DOI: https://doi.org/10.1007/s12275-011-1130-1

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Abstract: Phospholipid biosynthetic genes encode enzymes responsible for phospholipid biosynthesis. They are coordinately regulated by the availability of phospholipid precursors through the inositol-sensitive upstream activating sequence (UASINO). However, not all phospholipid genes are UASINO-containing genes and not all UASINO-containing genes have the same response to the phospholipid precursors. Therefore, the transcriptional regulation of phospholipid genes in response to the availability of phospholipid precursors is still unclear. Here, 22 out of 47 phospholipid biosynthetic genes were identified as UASINO-containing genes, including EKI1, EPT1, INM1, IPK2, KCS1, PAH1, and PIK1 which have never been reported before. We also showed, using qRTPCR technique, that 12 UASINO-containing genes are down-regulated by 100 μM inositol in the wild type cells and up-regulated by 100 μM inositol in the ino2Δ cells. Therefore, it is possible that these genes are transcriptionally regulated by the UASINO through the negative response of Ino2p to inositol. One other UASINO-containing gene might be regulated by the positive response of Ino2p to 100 μM inositol. Surprisingly, we found 9 UASINO-containing genes are not dependent on the response of Ino2p to 100 μM inositol, indicating that they may be regulated by other pathway. Furthermore, we identified 9 and 3 non-UASINO-containing genes that are possibly regulated by the negative and positive response of Ino2p to 100 μM inositol, respectively. Therefore, these observations provide insight into the understanding of the co-regulated phospholipid biosynthetic genes expression.

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

Evaluation of the Sensitivity and Specificity of Primer Pairs and the Efficiency of RNA Extraction Procedures to Improve Noroviral Detection from Oysters by Nested Reverse Transcription-Polymerase Chain Reaction: Cheonghoon Lee , Sooryun Cheong , Hee-Jung Lee , Miye Kwon , Ilnam Kang , Eun-Gyoung Oh , Hong-Sik Yu , Soon-Bum Shin , Sang-Jong Kim; J. Microbiol. 2010;48(5):586-593. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0047-4

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Abstract: Noroviruses (NoV) are the key cause of acute epidemic gastroenteritis, and oysters harvested from NoVpolluted sea areas are considered as the significant vectors of viral transmission. To improve NoV detection from oyster using nested reverse transcription-polymerase chain reaction (RT-PCR), we evaluated the sensitivity and specificity of previously published primer pairs and the efficiency of different RNA extraction procedures. Among the primer pairs used for RT-PCR, the sensitivity of GIF1/GIR1-GIF2/GIR1 and GIIF1/GIIR1-GIIF2/GIIR1 was higher than that of other primer pairs used in nested RT-PCR for the detection of NoV genogroup I (NoV GI) and NoV GII from both NoV-positive stool suspension and NoVseeded oyster concentrates, respectively; the resulting products showed neither unspecific bands in the positive samples nor false-positive bands in the negative controls. The extraction of NoV RNA from oyster samples using a QIAamp? Viral RNA Mini kit with a QIAshredderTM Homogenizer pretreatment afforded more efficient recovery (mean recovery for NoV GI and GII, 6.4%) and the procedure was less time consuming (<30 min) than most other RNA extraction procedures. The results of RNA extraction procedure and primer pairs evaluated by nested RT-PCR assay in this study can be useful for monitoring NoV contamination in oysters, which is an indicator of possible public health risks.

Detection of Hepatitis A Virus from Oyster by Nested PCR Using Efficient Extraction and Concentration Method: Duwoon Kim , Seok-Ryel Kim , Ki-Sung Kwon , Ji-Won Lee , Myung-Joo Oh; J. Microbiol. 2008;46(4):436-440. Published online August 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0131-1

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Abstract: The molecular methods using polymerase chain reaction have been proposed as useful tools for the identification of viral pathogens in food and water. However, the PCR-based methods are highly dependent on the methods of virus concentration and nucleic acid purification due to the low sensitivity of PCR in the presence of PCR inhibitors. We developed TPTT [tris elution buffer-PEG-TRIzol-poly(dT) magnetic bead] protocol in order to detect hepatitis A virus (HAV) inoculated in oyster digestive glands. The detection limit of HAV precipitated with zirconium hydroxide was 105 fold less sensitive in a nested PCR than that precipitated the HAV supernatant twice with PEG/NaCl (16% polyethylene glycol 6,000, 0.525 M NaCl) in a 1:2 (v/v) ratio, which provided an efficient detection of 0.0148 PFU/g from approximately 0.05 g of oyster homogenate. This method is efficient for potential use in the detection of HAV from shellfish and is more sensitive than most currently published tests.

Cyanobacterial Hybrid Kinase Sll0043 Regulates Phototaxis by Suppressing Pilin and Twitching Motility Protein: Bong-Jeong Shin , Jeehyun Oh , Sungsoo Kang , Young-Ho Chung , Young Mok Park , Young Hwan Kim , Seungil Kim , Jong Bhak , Jong-Soon Choi; J. Microbiol. 2008;46(3):300-308. Published online July 5, 2008; DOI: https://doi.org/10.1007/s12275-007-0212-6

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Abstract: The unicellular cyanobacterium Synechocystis sp. PCC 6803 glides toward a light source through the interplay of positive phototaxis genes and proteins. In genetic analysis, the complete disruption of the hybrid sensory kinase sll0043 produced negative phototaxis. Furthermore, Sll0043 was found to be a hub protein by in silico prediction of protein-protein interaction, in which Sll0043 was predominantly linked to seven two-component proteins with high confidence. To understand the regulation and networking of positive phototaxis proteins, the proteomic profile of the sll0043 mutant was compared to that of wild-type. In the sll0043 mutant, 18 spots corresponding to 15 unique proteins were altered by 1.3 to 59 fold; the spots were identified by 2-DE/MALDI-MS analysis. Down-regulated proteins in the sll0043 null-mutant included chaperonins, superoxide dismutase, and phycocyanin β-subunit. In contrast, nine proteins involved in photosynthesis, translation, regulatory function, and other functions were up-regulated. In particular, a twitching motility protein (PilT1) was induced over 2-fold in sll0043 mutant. Moreover, semiquantitative and quantitative RT-PCR analysis revealed that pilin (pilA1), pili motor (pilT1), and pili switch gene (pilT2) were significantly increased in sll0043 mutant. These results suggest that the hybrid kinase Sll0043 regulates positive phototaxis by suppressing the expression of pili biosynthesis and regulatory genes and through the interplay with positive phototaxis/motility two-component proteins.

Sequence Analysis of NS4 Region of HCV Isolated from Korean Patient: Paik, Sang Hoon , Lee, Young Ik , Kim, Won Bae , Yang, Jai Myung; J. Microbiol. 1995;33(3):260-266.

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Abstract: Hepatitis C virus (HCV) has been considered as a major causative agent of post-transfusion related non-A, non-B hepatitis. In this study, the cDNA sequence of NS4 region of HCV (HCV-S) obtained from a Korean patient's plasma was determined. Comparative nucleotide sequence analysis between to type II. 67.2% homology to type III, and 66.4% homology to type IV. The putative amino acid sequence homologies to types I, II, III, and IV were 82.8-84.7%, 92.5-95.1%. 72.5% and 71.1% respectively. This data strongly suggests that HCV-S should be classified as type II. Significant similarities of hydrophobicity profiles and putative transmembranous domains were found in HCV-S and four major prototypes, indicating that the protein structure is similar in spite of the heterogeneities of intertype homologies at the level of the primary nucleotide and amino acid sequences.

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