- Volume 53(1); January 2015
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Review
- Minireview] Loop-mediated isothermal amplification (LAMP): principle, features, and future prospects
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Tsugunori Notomi , Yasuyoshi Mori , Norihiro Tomita , Hidetoshi Kanda
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J. Microbiol. 2015;53(1):1-5. Published online January 4, 2015
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DOI: https://doi.org/10.1007/s12275-015-4656-9
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Abstract
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Loop-mediated isothermal amplification (LAMP), a newly developed gene amplification method, combines rapidity, simplicity, and high specificity. Several tests have been developed based on this method, and simplicity is maintained throughout all steps, from extraction of nucleic acids to detection of amplification. In the LAMP reaction, samples are amplified at a fixed temperature through a repetition of two types of elongation reactions occurring at the loop regions: self-elongation of templates from the stem loop structure formed at the 3'-terminal and the binding and elongation of new primers to the loop region. The LAMP reaction has a wide range of possible applications, including point-of-care testing, genetic testing in resource-poor settings (such as in developing countries), and rapid testing of food products and environmental samples.
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Citations
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The American Journal of Tropical Medicine and Hygiene.2020; 103(1): 253. CrossRef - Visual detection of high-risk HPV16 and HPV18 based on loop-mediated isothermal amplification
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Experimental Parasitology.2020; 208: 107809. CrossRef - On-Site Detection of Tissues of Buffalo Origin by Loop-Mediated Isothermal Amplification (LAMP) Assay Targeting Mitochondrial Gene Sequences
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Food Analytical Methods.2020; 13(5): 1060. CrossRef - Rapid detection of pork using alkaline lysis- Loop Mediated Isothermal Amplification (AL-LAMP) technique
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International Microbiology.2019; 22(4): 501. CrossRef - A foldable isothermal amplification microdevice for fuchsin-based colorimetric detection of multiple foodborne pathogens
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BioMed Research International.2019; 2019: 1. CrossRef - Demonstration of a quantitative triplex LAMP assay with an improved probe-based readout for the detection of MRSA
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Food Control.2019; 103: 145. CrossRef - Detection of Potato ring rot Pathogen Clavibacter michiganensis subsp. sepedonicus by Loop-mediated isothermal amplification (LAMP) assay
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Acta Biomedica Scientifica (East Siberian Biomedical Journal).2019; 4(3): 127. CrossRef - A Loop-Mediated Isothermal Amplification Integrated G-Quadruplex Molecular Beacon (LAMP-GMB) Method for the Detection of Staphylococcus aureus in Food
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Infection, Genetics and Evolution.2019; 72: 93. CrossRef - Loop Mediated Isothermal Amplification: A Promising Tool for Screening Genetic Mutations
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Analytical Chemistry.2019; 91(8): 5295. CrossRef - Development of loop-mediated isothermal amplification combined with a chromatographic lateral-flow dipstick for rapid detection of Chattonella marina
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EBioMedicine.2018; 37: 453. CrossRef - Field Evaluation of a Loop-Mediated Isothermal Amplification (LAMP) Platform for the Detection of Schistosoma japonicum Infection in Oncomelania hupensis Snails
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American Journal of Reproductive Immunology.2018;[Epub] CrossRef - Direct and Rapid Detection and Quantification of Oenococcus oeni Cells in Wine by Cells-LAMP and Cells-qLAMP
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Frontiers in Microbiology.2018;[Epub] CrossRef - Laboratory challenges in the diagnosis of hepatitis E virus
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Annals of Laboratory Medicine.2018; 38(2): 119. CrossRef - A field survey using LAMP assay for detection of Schistosoma mansoni in a low-transmission area of schistosomiasis in Umbuzeiro, Brazil: Assessment in human and snail samples
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Research Support, U.S. Gov't, Non-P.H.S.
- Description of Pseudomonas asuensis sp. nov. from biological soil crusts in the Colorado plateau, United States of America
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Gundlapally Sathyanarayana Reddy , # , Ferran Garcia-Pichel
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J. Microbiol. 2015;53(1):6-13. Published online January 4, 2015
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DOI: https://doi.org/10.1007/s12275-015-4462-4
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Abstract
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A Gram-negative, aerobic, non spore-forming, non-motile,
rod-shaped, yellow pigmented bacterium CP155-2T was isolated
from a biological soil crusts sample collected in the
Colorado plateau, USA and subjected to polyphasic taxonomic
characterization. Strain CP155-2T contained summed
feature 3 (C16:1ω5c/C16:1ω7c) and C18:1ω7c as major fatty
acids and diphosphatidylglycerol (DPG) along with phosphatidylethanolamine
(PE) and phosphatidylglycerol (PG)
as major polar lipids. Based on these characteristics CP155-2T
was assigned to the genus Pseudomonas. Phylogenetic analysis
based on 16S rRNA gene sequence further confirmed the
affiliation of CP155-2T to the genus Pseudomonas and showed
a 16S rRNA gene sequence similarity of less than 98.7% with
already described species of the genus. Pseudomonas luteola,
Pseudomonas zeshuii, and Pseudomonas duriflava were identified
as the closest species of the genus Pseudomonas with
16S rRNA gene sequence similarities of 98.7%, 98.6%, and
96.9%, respectively. The values for DNA–DNA relatedness
between CP155-2T and Pseudomonas luteola and Pseudomonas
zeshuii were 23% and 14% respectively a value below
the 70% threshold value, indicating that strain CP155-2T
belongs to a novel taxon of the genus Pseudomonas lineage.
The novel taxon status was strengthened by a number of phenotypic
differences wherein CP155-2T was positive for oxidase,
negative for gelatin hydrolysis, could utilize D-cellobiose,
D-raffinose, L-rhamnose, D-sorbitol but not L-aspartic
acid and L-glutamic acid. Based on the collective differences
strain CP155-2T exhibited, it was identified as a novel species
and the name Pseudomonas asuensis sp. nov. was proposed.
The type strain of Pseudomonas asuensis sp. nov. is CP155-
2T (DSM 17866T =ATCC BAA-1264T =JCM13501T =KCTC
32484T).
-
Citations
Citations to this article as recorded by

- Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera
Zaki Saati-Santamaría, Ezequiel Peral-Aranega, Encarna Velázquez, Raúl Rivas, Paula García-Fraile
Biology.2021; 10(8): 782. CrossRef - The current status on the taxonomy of Pseudomonas revisited: An update
Alvaro Peix, Martha-Helena Ramírez-Bahena, Encarna Velázquez
Infection, Genetics and Evolution.2018; 57: 106. CrossRef - Raman‐activated cell sorting and metagenomic sequencing revealing carbon‐fixing bacteria in the ocean
Xiaoyan Jing, Honglei Gou, Yanhai Gong, Xiaolu Su, La Xu, Yuetong Ji, Yizhi Song, Ian P. Thompson, Jian Xu, Wei E. Huang
Environmental Microbiology.2018; 20(6): 2241. CrossRef - Description of Deinococcus oregonensis sp. nov., from biological soil crusts in the Southwestern arid lands of the United States of America
Sathyanarayana Reddy Gundlapally, Ferran Garcia-Pichel
Archives of Microbiology.2017; 199(1): 69. CrossRef - Emended description of the family Chromatiaceae, phylogenetic analyses of the genera Alishewanella, Rheinheimera and Arsukibacterium, transfer of Rheinheimera longhuensis LH2-2T to the genus Alishewanella and description of Alishewanella alkalitolerans sp
Shivaji Sisinthy, Dwaipayan Chakraborty, Harikrishna Adicherla, Sathyanarayana Reddy Gundlapally
Antonie van Leeuwenhoek.2017; 110(9): 1227. CrossRef - Description of Hydrogenophaga laconesensis sp. nov. isolated from tube well water
Soniya Mantri, Mohan Rao Chinthalagiri, Sathyanarayana Reddy Gundlapally
Archives of Microbiology.2016; 198(7): 637. CrossRef - Description of Thalassospira lohafexi sp. nov., isolated from Southern Ocean, Antarctica
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Frontiers in Microbiology.2015;[Epub] CrossRef - List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology
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Journal Article
- Genetic diversity of Clavispora lusitaniae isolated from Agave fourcroydes Lem, as revealed by DNA fingerprinting
-
Daisy Pérez-Brito , Anuar Magaña-Alvarez , Patricia Lappe-Oliveras , Alberto Cortes-Velazquez , Claudia Torres-Calzada , Teófilo Herrera-Suarez , Alfonso Larqué-Saavedra , Raul Tapia-Tussell
-
J. Microbiol. 2015;53(1):14-20. Published online January 4, 2015
-
DOI: https://doi.org/10.1007/s12275-015-4373-4
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50
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11
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Abstract
-
This study characterized Clavispora lusitaniae strains isolated
from different stages of the processing and early fermentation
of a henequen (Agave fourcroydes) spirit produced in
Yucatan, Mexico using a molecular technique. Sixteen strains
identified based on morphological features, obtained from
different substrates, were typed molecularly. Nine different
versions of the divergent D1/D2 domain of the large-subunit
ribosomal DNA sequence were identified among the
C. lusitaniae strains. The greatest degree of polymorphism
was found in the 90-bp structural motif of the D2 domain.
The MSP-PCR technique was able to differentiate 100% of
the isolates. This study provides significant insight into the
genetic diversity of the mycobiota present during the henequen
fermentation process, especially that of C. lusitaniae,
for which only a few studies in plants have been published.
The applied MSP-PCR markers were very efficient in revealing
polymorphisms between isolates of this species.
-
Citations
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- Clavispora lusitaniae: From a saprophytic yeast to an emergent pathogen
Olga C. Rojas, Alexandra M. Montoya, Rogelio de J. Treviño-Rangel
Fungal Biology.2024; 128(5): 1933. CrossRef - Effect of precursors and stress factors on yeast isolated from fermented maesil extract and their biogenic amine formation
So Hee Yoon, Sanghyeon Lee, Sun-Young Lee, BoKyung Moon
Food Science and Biotechnology.2024; 33(1): 211. CrossRef - Isolation of Clavispora lusitaniae from the Oral Cavity of Immunocompetent Young Adults from the North of Mexico
Olga C. Rojas, Cintia Amaral-Montesino, Soraya Mendoza-Olazaran, Diego Carrión-Alvarez, Rafael González-Álvarez, Alexandra M. Montoya
Indian Journal of Microbiology.2024; 64(2): 475. CrossRef - Influence of the Biotechnological Process of Mezcal Fermentation on Yeast Diversity in Four palenques of Oaxaca, Mexico
Victor Adrian Espinoza-Martinez, Peggy Elizabeth Alvarez-Gutierrez, Felipe de Jesus Palma-Cruz, Raul Enriquez-Valencia, Marcos Pedro Ramirez-Lopez, Claudia Lopez-Sanchez, Hector Gilberto Vazquez-Lopez
Beverages.2023; 9(4): 99. CrossRef - A novel strategy to construct multi-strain starter cultures: an insight to evolve from natural to directed fermentation
J. L. Navarrete-Bolaños, O. Serrato-Joya
Preparative Biochemistry & Biotechnology.2023; 53(10): 1199. CrossRef - Environmental reservoirs of the drug-resistant pathogenic yeast Candida auris
Ayorinde B. Akinbobola, Ryan Kean, Syed Manzoor Ahmed Hanifi, Richard S. Quilliam, N.Luisa Hiller
PLOS Pathogens.2023; 19(4): e1011268. CrossRef - Bioremediation potential and lead removal capacity of heavy metal-tolerant yeasts isolated from Dayet Oum Ghellaz Lake water (northwest of Algeria)
Chahrazed Aibeche, Nawel Selami, Fatima El-Houaria Zitouni-Haouar, Khadidja Oeunzar, Amira Addou, Meriem Kaid-Harche, Abderrezak Djabeur
International Microbiology.2022; 25(1): 61. CrossRef - Phylogeny, evolution, and potential ecological relationship of cytochrome CYP52 enzymes in Saccharomycetales yeasts
Jossue Ortiz-Álvarez, Arturo Becerra-Bracho, Alfonso Méndez-Tenorio, Jazmin Murcia-Garzón, Lourdes Villa-Tanaca, César Hernández-Rodríguez
Scientific Reports.2020;[Epub] CrossRef - Yeast Microbiota during Sauerkraut Fermentation and Its Characteristics
Paweł Satora, Magdalena Skotniczny, Szymon Strnad, Katarína Ženišová
International Journal of Molecular Sciences.2020; 21(24): 9699. CrossRef - Potential production of 2-phenylethanol and 2-phenylethylacetate by non-Saccharomyces yeasts from Agave durangensis
Pablo Jaciel Adame-Soto, Elva Teresa Aréchiga-Carvajal, Mercedes G López, Silvia Marina González-Herrera, Martha Rocio Moreno-Jiménez, Norma Urtiz-Estrada, Olga Miriam Rutiaga-Quiñones
Annals of Microbiology.2019; 69(9): 989. CrossRef - Genetic variation of Colletotrichum magnum isolated from Carica papaya as revealed by DNA fingerprinting
Daisy Pérez-Brito, Alberto Cortes-Velázquez, Teresita Valencia-Yah, Anuar Magaña-Álvarez, Cuauhtémoc Navarro, Blanca Moreno, Steven Quiroga, Raúl Tapia-Tussell
Journal of Microbiology.2018; 56(11): 813. CrossRef
Research Support, Non-U.S. Gov'ts
- Characterization of NpgA, a 4'-phosphopantetheinyl transferase of Aspergillus nidulans, and evidence of its involvement in fungal growth and formation of conidia and cleistothecia for development
-
Jung-Mi Kim , Ha-Yeon Song , Hyo-Jin Choi , Kum-Kang So , Dae-Hyuk Kim , Keon-Sang Chae , Dong-Min Han , Kwang-Yeop Jahng
-
J. Microbiol. 2015;53(1):21-31. Published online January 4, 2015
-
DOI: https://doi.org/10.1007/s12275-015-4657-8
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50
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0
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12
Crossref
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Abstract
-
The null pigmentation mutant (npgA1) in Aspergillus nidulans
results
in a phenotype with colorless organs, decreased branching
growth, delayed of asexual spore development, and
aberrant cell wall structure. The npgA gene was isolated from
A. nidulans to investigate these pleiomorphic phenomena of
npgA1 mutant. Sequencing analysis of the complementing
gene indicated that it contained a 4-phosphopantetheinyl
transferase (PPTase) superfamily domain. Enzymatic assay
of the PPTase, encoded by the npgA gene, was implemented
in vivo and in vitro. Loss-of-function of LYS5, which encoded
a PPTase in Saccharomyces cerevisiae, was functionally complemented
by NpgA, and Escherichia coli-derived NpgA revealed
phosphopantetheinylation activity with the elaboration
of 35-ADP. Deletion of the npgA gene caused perfectly
a lethal phenotype and the absence of asexual/sexual sporulation
and secondary metabolites such as pigments in A.
nidulans. However, a cross feeding effect with A. nidulans wild
type allowed recovery from deletion defects, and phased-culture
filtrate from the wild type were used to verify that the
npgA gene was essential for formation of metabolites needed
for development as well as growth. In addition, forced expression
of npgA promoted the formation of conidia and cleistothecia
as well as growth. These results indicate that the
npgA gene is involved in the phosphopantetheinylation required
for primary biological processes such as growth,
asexual/sexual development, and the synthesis of secondary
metabolites in A. nidulans.
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- Regulators of the Asexual Life Cycle of Aspergillus nidulans
Ye-Eun Son, Jae-Hyuk Yu, Hee-Soo Park
Cells.2023; 12(11): 1544. CrossRef - De novo biosynthesis of carminic acid in Saccharomyces cerevisiae
Qian Zhang, Xinglong Wang, Weizhu Zeng, Sha Xu, Dong Li, Shiqin Yu, Jingwen Zhou
Metabolic Engineering.2023; 76: 50. CrossRef - Expanding luciferase reporter systems for cell-free protein expression
Wakana Sato, Melanie Rasmussen, Christopher Deich, Aaron E. Engelhart, Katarzyna P. Adamala
Scientific Reports.2022;[Epub] CrossRef - Biosynthesis of fungal polyketides by collaborating and trans-acting enzymes
Elizabeth Skellam
Natural Product Reports.2022; 39(4): 754. CrossRef - Liamocins biosynthesis, its regulation in Aureobasidium spp., and their bioactivities
Xin-Xin Kang, Shu-Lei Jia, Xin Wei, Mei Zhang, Guang-Lei Liu, Zhong Hu, Zhe Chi, Zhen-Ming Chi
Critical Reviews in Biotechnology.2022; 42(1): 93. CrossRef - Shimalactone Biosynthesis Involves Spontaneous Double Bicyclo‐Ring Formation with 8π‐6π Electrocyclization
Isao Fujii, Makoto Hashimoto, Kaori Konishi, Akiko Unezawa, Haruka Sakuraba, Kenta Suzuki, Harue Tsushima, Miho Iwasaki, Satsuki Yoshida, Akane Kudo, Rina Fujita, Aika Hichiwa, Koharu Saito, Takashi Asano, Jun Ishikawa, Daigo Wakana, Yukihiro Goda, Ayumi
Angewandte Chemie.2020; 132(22): 8542. CrossRef - Shimalactone Biosynthesis Involves Spontaneous Double Bicyclo‐Ring Formation with 8π‐6π Electrocyclization
Isao Fujii, Makoto Hashimoto, Kaori Konishi, Akiko Unezawa, Haruka Sakuraba, Kenta Suzuki, Harue Tsushima, Miho Iwasaki, Satsuki Yoshida, Akane Kudo, Rina Fujita, Aika Hichiwa, Koharu Saito, Takashi Asano, Jun Ishikawa, Daigo Wakana, Yukihiro Goda, Ayumi
Angewandte Chemie International Edition.2020; 59(22): 8464. CrossRef - Genomic analysis of a riboflavin-overproducing Ashbya gossypii mutant isolated by disparity mutagenesis
Tatsuya Kato, Junya Azegami, Ami Yokomori, Hideo Dohra, Hesham A. El Enshasy, Enoch Y. Park
BMC Genomics.2020;[Epub] CrossRef - Genetic evidences for the core biosynthesis pathway, regulation, transport and secretion of liamocins in yeast-like fungal cells
Si-Jia Xue, Guang-Lei Liu, Zhe Chi, Zhi-Chao Gao, Zhong Hu, Zhen-Ming Chi
Biochemical Journal.2020; 477(5): 887. CrossRef - A Novel Rapid Fungal Promoter Analysis System Using the Phosphopantetheinyl Transferase Gene,npgA, inAspergillus nidulans
Ha-Yeon Song, Dahye Choi, Dong-Min Han, Dae-Hyuk Kim, Jung-Mi Kim
Mycobiology.2018; 46(4): 429. CrossRef - Both a PKS and a PPTase are involved in melanin biosynthesis and regulation of Aureobasidium melanogenum XJ5-1 isolated from the Taklimakan desert
Hong Jiang, Guang-Lei Liu, Zhe Chi, Jian-Ming Wang, Ly-Ly Zhang, Zhen-Ming Chi
Gene.2017; 602: 8. CrossRef - Identification of a Polyketide Synthase Gene in the Synthesis of Phleichrome of the Phytopathogenic Fungus Cladosporium phlei
Kum-Kang So, Yun-Jo Chung, Jung-Mi Kim, Beom-Tae Kim, Seung-Moon Park, Dae-Hyuk Kim
Molecules and Cells.2015; 38(12): 1105. CrossRef
- Crystal structure of the bacterial type VI secretion system component TssL from Vibrio cholerae
-
Jeong Ho Chang , Yeon-Gil Kim
-
J. Microbiol. 2015;53(1):32-37. Published online December 4, 2014
-
DOI: https://doi.org/10.1007/s12275-015-4539-0
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51
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10
Crossref
-
Abstract
-
The type VI secretion system (T6SS), commonly found in
Gram-negative bacteria, is responsible for exporting effector
proteins. The T6SS has been reported to be cytotoxic to host
cells. While the components and assembly of the T6SS complex
have been largely assessed, structural data on T6SS components
from virulent bacteria is remarkably insufficient.
Here, we report the crystal structure of Vibrio cholerae TssL
(VcTssL), a core component of T6SS. In spite of a relatively
low sequence identity, the overall structure of VcTssL is largely
similar to those from other bacterial homologs except
for several differences found in local structural elements. A
unique feature attributed to the C-terminal fragment of Vc-
TssL is a crystallographic artifact. This incidental feature of
VcTssL may provide insights into screening of molecular
partners for the cytoplasmic domain of TssL. Additionally,
our results may help in the design of molecular probes for a
detailed understanding of the functional relationship between
TssL and other T6SS components.
-
Citations
Citations to this article as recorded by

- Structural Characterization of TssL from Acinetobacter baumannii: a Key Component of the Type VI Secretion System
Federico M. Ruiz, Juvenal Lopez, C. Gastón Ferrara, Elena Santillana, Yanis R. Espinosa, Mario F. Feldman, Antonio Romero, Ann M. Stock
Journal of Bacteriology.2020;[Epub] CrossRef -
In situ
and high‐resolution cryo‐
EM
structure of a bacterial type
VI
secretion system membrane complex
Chiara Rapisarda, Yassine Cherrak, Romain Kooger, Victoria Schmidt, Riccardo Pellarin, Laureen Logger, Eric Cascales, Martin Pilhofer, Eric Durand, Rémi Fronzes
The EMBO Journal.2019;[Epub] CrossRef - Crystal Structure of the Type VI Secretion System Accessory Protein TagF from Pseudomonas Aeruginosa
Chang-Kyu Ok, Jeong Ho Chang
Protein & Peptide Letters.2019; 26(3): 204. CrossRef - Structure and Activity of the Type VI Secretion System
Yassine Cherrak, Nicolas Flaugnatti, Eric Durand, Laure Journet, Eric Cascales, Maria Sandkvist, Peter J. Christie
Microbiology Spectrum.2019;[Epub] CrossRef - Crystal structure of the periplasmic domain of TssL, a key membrane component of Type VI secretion system
Xiangbei Wang, Bo Sun, Mengxue Xu, Shenshen Qiu, Dongqing Xu, Tingting Ran, Jianhua He, Weiwu Wang
International Journal of Biological Macromolecules.2018; 120: 1474. CrossRef - Tryptophan-mediated Dimerization of the TssL Transmembrane Anchor Is Required for Type VI Secretion System Activity
Abdelrahim Zoued, Jean-Pierre Duneau, Eric Durand, Alexandre P. España, Laure Journet, Françoise Guerlesquin, Eric Cascales
Journal of Molecular Biology.2018; 430(7): 987. CrossRef - Structure–Function Analysis of the TssL Cytoplasmic Domain Reveals a New Interaction between the Type VI Secretion Baseplate and Membrane Complexes
Abdelrahim Zoued, Chloé J. Cassaro, Eric Durand, Badreddine Douzi, Alexandre P. España, Christian Cambillau, Laure Journet, Eric Cascales
Journal of Molecular Biology.2016; 428(22): 4413. CrossRef - Aim, Load, Fire: The Type VI Secretion System, a Bacterial Nanoweapon
Francesca R. Cianfanelli, Laura Monlezun, Sarah J. Coulthurst
Trends in Microbiology.2016; 24(1): 51. CrossRef - Biogenesis and structure of a type VI secretion membrane core complex
Eric Durand, Van Son Nguyen, Abdelrahim Zoued, Laureen Logger, Gérard Péhau-Arnaudet, Marie-Stéphanie Aschtgen, Silvia Spinelli, Aline Desmyter, Benjamin Bardiaux, Annick Dujeancourt, Alain Roussel, Christian Cambillau, Eric Cascales, Rémi Fronzes
Nature.2015; 523(7562): 555. CrossRef - Type VI secretion system: secretion by a contractile nanomachine
Marek Basler
Philosophical Transactions of the Royal Society B: Biological Sciences.2015; 370(1679): 20150021. CrossRef
- Performance of a real-time PCR assay for the rapid identification of Mycobacterium species
-
Hye-young Wang , Hyunjung Kim , Sunghyun Kim , Do-kyoon Kim , Sang-Nae Cho , Hyeyoung Lee
-
J. Microbiol. 2015;53(1):38-46. Published online January 4, 2015
-
DOI: https://doi.org/10.1007/s12275-015-4495-8
-
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43
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18
Crossref
-
Abstract
-
Mycobacteria cause a variety of illnesses that differ in severity
and public health implications. The differentiation of
Mycobacterium tuberculosis (MTB) from nontuberculous
mycobacteria (NTM) is of primary importance for infection
control and choice of antimicrobial therapy. The diagnosis
of diseases caused by NTM is difficult because NTM species
are prevalent in the environment and because they have fastidious
properties. In the present study, we evaluated 279
clinical isolates grown in liquid culture provided by The
Catholic University of Korea, St. Vincent’s Hospital using
real-time PCR based on mycobacterial rpoB gene sequences.
The positive rate of real-time PCR assay accurately discriminated
100% (195/195) and 100% (84/84) between MTB and
NTM species. Comparison of isolates identified using the
MolecuTech REBA Myco-ID? and Real Myco-ID? were completely
concordant except for two samples. Two cases that
were identified as mixed infection (M. intracellulare-M. massiliense
and M. avium-M. massiliense co-infection) by PCRREBA
assay were only detected using M. abscessus-specific
probes by Real Myco-ID?. Among a total of 84 cases, the
most frequently identified NTM species were M. intracellulare
(n=38, 45.2%), M. avium (n=18, 23.7%), M. massiliense
(n=10, 13.2%), M. fortuitum (n=5, 6%), M. abscessus
(n=3, 3.9%), M. gordonae (n=3, 3.9%), M. kansasii (n=2,
2.4%), M. mucogenicum (n=2, 2.4%), and M. chelonae (n=
1, 1.2%). Real Myco-ID? is an efficient tool for the rapid detection
of NTM species as well as MTB and sensitive and
specific and comparable to conventional methods.
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- Evaluation of Nanopore Sequencing for Diagnosing Pulmonary Tuberculosis Using Negative Smear Clinical Specimens
Guocan Yu, Yanqin Shen, Liwei Yao, Xudong Xu
Infection and Drug Resistance.2024; Volume 17: 673. CrossRef - Preclinical murine models for the testing of antimicrobials against Mycobacterium abscessus pulmonary infections: Current practices and recommendations
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Tuberculosis.2024; 147: 102503. CrossRef -
Durlobactam to boost the clinical utility of standard of care β-lactams against
Mycobacterium abscessus
lung disease
Dereje A. Negatu, Wassihun Wedajo Aragaw, Tewodros T. Gebresilase, Sindhuja Paruchuri, Firat Kaya, Sung Jae Shin, Peter Sander, Véronique Dartois, Thomas Dick, Jared A. Silverman
Antimicrobial Agents and Chemotherapy.2024;[Epub] CrossRef - Epidemiology and laboratory detection of non-tuberculous mycobacteria
Nuo Xu, Lihong Li, Shenghai Wu
Heliyon.2024; 10(15): e35311. CrossRef - Molecular identification of non-tuberculous mycobacterial species isolated from extrapulmonary samples using real-time PCR and rpoB sequence analysis
Mohammad Hashemzadeh, Aram Asarehzadegan Dezfuli, Azar Dokht Khosravi, Maryam Moradi Bandbal, Atousa Ghorbani, Mahtab Hamed, Soolmaz Khandan Dezfuli
AMB Express.2023;[Epub] CrossRef - TO ANALYZE THE TB-PCR POSITIVITY RATE USING REAL-TIME PCR FOR EARLY DETECTION OF TUBERCULOSIS
DEEPAK SAWANT, LOKHANDE CD, SHARMA RK, CHOUGULE RA
Asian Journal of Pharmaceutical and Clinical Research.2023; : 167. CrossRef - Factors Associated with the Performance of Direct PCR Detection of Mycobacteria in Clinical Specimens: Retrospective Real-world Data
Chang-Hun Park
Laboratory Medicine Online.2023; 13(3): 205. CrossRef - Evaluation of a new assay for nontuberculous mycobacteria species identification in diagnostic material and cultures
Tatiana Smirnova, Vera Ustinova, Sofya Andreevskaya, Elena Larionova, Ekaterina Kiseleva, Larisa Chernousova, Dmitry Varlamov, Dmitry Sochivko, Atadzhan Ergeshov
Tuberculosis.2021; 130: 102124. CrossRef -
Cas12a/Guide RNA-Based Platform for Rapid and Accurate Identification of Major
Mycobacterium
Species
Guohui Xiao, Xing He, Su Zhang, Yaya Liu, Zhihang Liang, Houming Liu, Juanjuan Zhang, Min Ou, Shuhao Cai, Wenjie Lai, Tianyu Zhang, Lili Ren, Guoliang Zhang, Yi-Wei Tang
Journal of Clinical Microbiology.2020;[Epub] CrossRef - Diagnostic Performance of the GENEDIA MTB/NTM Detection Kit for Detecting Mycobacterium tuberculosis and Nontuberculous Mycobacteria With Sputum Specimens
Sunghwan Shin, In Young Yoo, Hyang Jin Shim, On Kyun Kang, Byung Woo Jhun, Won-Jung Koh, Hee Jae Huh, Nam Yong Lee
Annals of Laboratory Medicine.2020; 40(2): 169. CrossRef - Diagnostic performance of real time PCR and MALDI-TOF in the detection of nontuberculous mycobacteria from clinical isolates
Ellappan Kalaiarasan, Kalpana Thangavelu, Krishnakumariamma Krishnapriya, Muthaiah Muthuraj, Maria Jose, Noyal Mariya Joseph
Tuberculosis.2020; 125: 101988. CrossRef - Comparison of the Three Molecular Diagnostic Assays for Molecular Identification ofMycobacterium tuberculosisand Nontuberculous Mycobacteria Species in Sputum Samples
Jinyoung Bae, Sung-Bae Park, Ji-Hoi Kim, Mi Ran Kang, Kyung Eun Lee, Sunghyun Kim, Hyunwoo Jin
Biomedical Science Letters.2020; 26(3): 170. CrossRef -
Rapid Identification of Clinically Relevant
Mycobacterium
Species by Multicolor Melting Curve Analysis
Ye Xu, Bin Liang, Chen Du, Xueshan Tian, Xingshan Cai, Yanjie Hou, Hui Li, Rongrong Zheng, Junlian Li, Yuqin Liu, Kaili Wang, Muhammad Ammar Athar, Yaoju Tan, Qingge Li, Melissa B. Miller
Journal of Clinical Microbiology.2019;[Epub] CrossRef - Mycobacterium abscessus Complex Cutaneous Infection
Ruben Porudominsky, Eduardo H. Gotuzzo
Current Tropical Medicine Reports.2018; 5(3): 170. CrossRef - The assessment of host and bacterial proteins in sputum from active pulmonary tuberculosis
Hsin-Chih Lai, Yu-Tze Horng, Pen-Fang Yeh, Jann-Yuan Wang, Chin-Chung Shu, Chia-Chen Lu, Jang-Jih Lu, Jen-Jyh Lee, Po-Chi Soo
Journal of Microbiology.2016; 54(11): 761. CrossRef - Efectos adversos de terapia inmunosupresora en paciente reumatológico: infección por micobacterias no tuberculosas
Jean Sebastian Hurtado Hurtado
Reumatología Clínica.2016; 12(2): 118. CrossRef - Adverse Effects of Immunosuppressive Therapy in Rheumatic Patients: Non-tuberculous Mycobacterial Infection
Jean Sebastian Hurtado Hurtado
Reumatología Clínica (English Edition).2016; 12(2): 118. CrossRef - Nontuberculous Mycobacterial Lung Disease Caused byMycobacterium shinjukuense: The First Reported Case in Korea
Seong Mi Moon, Su-Young Kim, Myung Jin Chung, Seung Heon Lee, Sung Jae Shin, Won-Jung Koh
Tuberculosis and Respiratory Diseases.2015; 78(4): 416. CrossRef
- Oral administration of Lactobacillus plantarum lysates attenuates the development of atopic dermatitis lesions in mouse models
-
Hangeun Kim , Hye Rim Kim , Na-Ra Kim , Bong Jun Jeong , Jong Suk Lee , Soojin Jang , Dae Kyun Chung
-
J. Microbiol. 2015;53(1):47-52. Published online December 4, 2014
-
DOI: https://doi.org/10.1007/s12275-015-4483-z
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-
49
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0
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26
Crossref
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Abstract
-
Lactobacillus plantarum is a well-documented probiotic that
has been used in clinical trials for the regulation of the immune
system and treatment of gastrointestinal diseases. In
this study, we evaluated the effects of L. plantarum cell lysates
on the immune regulation through the in vitro and in vivo
studies. L. plantarum lysates were prepared by sonication
method
, and we observed that the repetition of disruption
step increased indicator components within the bacterial
lysates. Indicator components might affect TNF-α production.
L. plantarum lysates did not induce TNF-α production,
while LPS-induced TNF-α production was dramatically inhibited
in a sonication-dependent manner in THP-1 cells.
Oral administration of L. plantarum lysates effectively attenuated
the horny layer formation and decreased epidermal
thickening in NC/Nga mice skin. The damage to barrier function
after the 8 weeks oral administration was reduced by L.
plantarum lysates as compared to that in the atopic dermatitis
(AD) mice. Further study revealed that L. plantarum lysates
polarized Th1 response via induction of IL-12 and IFN-γ
production and inhibition of IL-4 and IgE production in
NC/Nga mice. Together, our results suggest that L. plantarum
lysates are remarkable material for host homeostasis and it
could be used for the treatment of inflammatory diseases.
-
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Ece Tüsüz Önata, Öner Özdemir
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Mi Eun Kim, Jun Sik Lee
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Does
Lactobacillus plantarum-
ATCC8014 alleviate inflammation?
In vitro
and
in vivo
appraisal
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- Effect of carbonyl cyanide 3-chlorophenylhydrazone (CCCP) on killing Acinetobacter baumannii by colistin
-
Young Kyoung Park , Kwan Soo Ko
-
J. Microbiol. 2015;53(1):53-59. Published online January 4, 2015
-
DOI: https://doi.org/10.1007/s12275-015-4498-5
-
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51
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45
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Abstract
-
We investigated the effect of cyanide 3-chlorophenylhydrazone
(CCCP) and other efflux pump inhibitors (EPIs) on the
colistin susceptibility in Acinetobacter baumannii. While minimum
inhibitory concentrations (MICs) of colistin in all
colistin-resistant strains decreased significantly with 25 μM
of CCCP and 2,4-dinitrophenol (DNP), phenyl-arginine-β-
naphthylamide (PAβN), and reserpine did not decrease the
colistin MICs. However, CCCP and DNP as well as PAβN
and reserpine did not have a significant effect on the MICs of
the other agents. Efflux pump gene expressions in colistinresistant
strains were not increased compared with those in
colistin-susceptible strains. When only 5X MIC of colistin (5
mg/L) was provided to a colistin-susceptible A. baumannii
strain, the bacterial cell number was reduced by 9 h after exposure
to colistin, but regrowth was observed. When CCCP
was added to colistin, bacterial cells were completely killed
after 24 to 48 h of incubation, which was not due to the toxicity
of CCCP itself. Colistin resistance in A. baumannii may
not be due to efflux pumps. Our present study suggests that
bacterial cells with reduced metabolic activity by CCCP are
more susceptible to colistin in A. baumannii. It may show
the possibility that combined therapy with colistin and other
antimicrobial agents could effective against A. baumannii
infections.
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Citations
Citations to this article as recorded by

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- Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform
-
Yoon-Seong Jeon , Sang-Cheol Park , Jeongmin Lim , Jongsik Chun , Bong-Soo Kim
-
J. Microbiol. 2015;53(1):60-69. Published online January 4, 2015
-
DOI: https://doi.org/10.1007/s12275-015-4601-y
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-
53
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0
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34
Crossref
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Abstract
-
The cost of DNA sequencing has decreased due to advancements
in Next Generation Sequencing. The number of sequences
obtained from the Illumina platform is large, use of
this platform can reduce costs more than the 454 pyrosequencer.
However, the Illumina platform has other challenges,
including bioinformatics analysis of large numbers
of sequences and the need to reduce erroneous nucleotides
generated at the 3-ends of the sequences. These erroneous
sequences can lead to errors in analysis of microbial communities.
Therefore, correction of these erroneous sequences
is necessary for accurate taxonomic identification. Several
studies that have used the Illumina platform to perform metagenomic
analyses proposed curating pipelines to increase
accuracy. In this study, we evaluated the likelihood of obtaining
an erroneous microbial composition using the MiSeq
250 bp paired sequence platform and improved the pipeline
to reduce erroneous identifications. We compared different
sequencing conditions by varying the percentage of control
phiX added, the concentration of the sequencing library, and
the 16S rRNA gene target region using a mock community
sample composed of known sequences. Our recommended
method
corrected erroneous nucleotides and improved identification
accuracy. Overall, 99.5% of the total reads shared
95% similarity with the corresponding template sequences
and 93.6% of the total reads shared over 97% similarity. This
indicated that the MiSeq platform can be used to analyze microbial
communities at the genus level with high accuracy.
The improved analysis method recommended in this study
can be applied to amplicon studies in various environments
using high-throughput reads generated on the MiSeq platform.
-
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- Hypermethylation of the interferon regulatory factor 5 promoter in Epstein-Barr virus-associated gastric carcinoma
-
Seung Myung Dong , Hyun Gyu Lee , Sung-Gyu Cho , Seung-Hyun Kwon , Heejei Yoon , Hyun-Jin Kwon , Ji Hae Lee , Hyemi Kim , Pil-Gu Park , Hoguen Kim , S. Diane Hayward , Jeon Han Park , Jae Myun Lee
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J. Microbiol. 2015;53(1):70-76. Published online January 4, 2015
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DOI: https://doi.org/10.1007/s12275-014-4654-3
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Abstract
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Interferon regulatory factor-5 (IRF-5), a member of the mammalian
IRF transcription factor family, is regulated by p53,
type I interferon and virus infection. IRF-5 participates in
virus-induced TLR-mediated innate immune responses and
may play a role as a tumor suppressor. It was suppressed in
various EBV-infected transformed cells, thus it is valuable to
identify the suppression mechanism. We focused on a promoter
CpG islands methylation, a kind of epigenetic regulation
in EBV-associated Burkitt’s lymphomas (BLs) and gastric
carcinomas. IRF-5 is not detected in most of EBV-infected
BL cell lines due to hypermethylation of IRF-5 distal
promoter (promoter-A), which was restored by a demethylating
agent, 5-aza-2-deoxycytidine. Hypomethylation of
CpG islands in promoter-A was observed only in EBV type III
latent infected BL cell lines (LCL and Mutu III). Similarly,
during EBV infection to Akata-4E3 cells, IRF-5 was observed
at early time periods (2 days to 8 weeks), concomitant unmethylation
of promoter-A, but suppressed in later infection
periods as observed in latency I BL cell lines. Moreover, hypermethylation
in IRF-5 promoter-A region was also observed
in EBV-associated gastric carcinoma (EBVaGC) cell lines or
primary gastric carcinoma tissues, which show type I latent
infection. In summary, IRF-5 is suppressed by hypermethylation
of its promoter-A in most of EBV-infected transformed
cells, especially BLs and EBVaGC. EBV-induced carcinogenesis
takes an advantage of proliferative effects of TLR
signaling, while limiting IRF-5 mediated negative effects in
the establishment of EBVaGCs.
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Journal Article
- Extended stability of cyclin D1 contributes to limited cell cycle arrest at G1-phase in BHK-21 cells with Japanese encephalitis virus persistent infection
-
Ji Young Kim , Soo Young Park , Hey Rhyoung Lyoo , Eung Seo Koo , Man Su Kim , Yong Seok Jeong
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J. Microbiol. 2015;53(1):77-83. Published online January 4, 2015
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DOI: https://doi.org/10.1007/s12275-015-4661-z
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Abstract
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There is increasing evidence that many RNA viruses manipulate
cell cycle control to achieve favorable cellular environments
for their efficient replication during infection. Although
virus-induced G0/G1 arrest often delays early apoptosis temporarily,
a prolonged replication of the infected virus leads
host cells to eventual death. In contrast, most mammalian
cells with RNA virus persistent infection often escape cytolysis
in the presence of productive viral replication. In this study,
we demonstrated that the extended endurance of cyclin D1
was clearly associated with the suppression of glycogen synthase
kinase-3β (GSK-3β) expression in BHK-21 cells that are
persistently infected with Japanese encephalitis virus (JEV).
The G0/G1 arrest of these cells turned much loose compared
to the normal BHK-21 cells with JEV acute infection. After
cycloheximide treatment, cyclin D1 in the persistently infected
cells lasted several hours longer than those in acutely
infected cells. Furthermore, both p21Cip1 and p27Kip1, positive
regulators for cyclin D1 accumulation in the nucleus, were
suppressed in their expression, which contrasts with those
in JEV acute infection. Inhibition of the GSK-3β by lithium
chloride treatment rescued a significant number of cells from
cytolysis in JEV acute infection, which coincided with the
levels of cyclin D1 that escaped from proteolysis. Therefore,
the limitation of G1/S arrest in the BHK-21 cells with JEV persistent
infection is associated with the suppression of GSK-3β
expression, resulting in the extended duration of cyclin D1.
-
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Research Support, Non-U.S. Gov't
- Note] Analysis of a draft genome sequence of Kitasatospora cheerisanensis KCTC 2395 producing bafilomycin antibiotics
-
Jae Yoon Hwang , Soo Hee Kim , Hye Ryeung Oh , Eunju Kwon , Doo Hyun Nam
-
J. Microbiol. 2015;53(1):84-89. Published online December 4, 2014
-
DOI: https://doi.org/10.1007/s12275-015-4340-0
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58
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7
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Abstract
-
Kitasatospora cheerisanensis KCTC 2395, producing bafilomycin
antibiotics belonging to plecomacrolide group, was
isolated from a soil sample at Mt. Jiri, Korea. The draft genome
sequence contains 8.04 Mb with 73.6% G+C content
and 7,810 open reading frames. All the genes for aerial mycelium
and spore formations were confirmed in this draft
genome. In phylogenetic analysis of MurE proteins (UDPN-
acetylmuramyl-L-alanyl-D-glutamate:DAP ligase) in a conserved
dcw (division of cell wall) locus, MurE proteins of
Kitasatospora species were placed in a separate clade between
MurEs of Streptomyces species incorporating LL-diaminopimelic
acid (DAP) and MurEs of Saccharopolyspora erythraea
as well as Mycobacterium tuberculosis ligating meso-
DAP. From this finding, it was assumed that Kitasatospora
MurEs exhibit the substrate specificity for both LL-DAP and
meso-DAP. The bafilomycin biosynthetic gene cluster was
located in the left subtelomeric region. In 71.3 kb-long gene
cluster, 17 genes probably involved in the biosynthesis of
bafilomycin derivatives were deduced, including 5 polyketide
synthase (PKS) genes comprised of 12 PKS modules.
-
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Frontiers in Microbiology.2015;[Epub] CrossRef
Published Erratum
- Erratum] Protective Role of Gut Commensal Microbes against Intestinal Infections
-
My Young Yoon , Keehoon Lee , Sang Sun Yoon
-
J. Microbiol. 2015;53(1):90-90.
-
DOI: https://doi.org/10.1007/s12275-015-0705-7
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47
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Abstract
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In the article by Yoon et al. published in Journal of Microbiology 2014; 52, 983-989. First author name should be changed as Mi Young Yoon
-
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