• Journal of Microbiology and Biotechnology
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• v.19 no.3
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• pp.323-330
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• 2009

Nontuberculous mycobacteria (NTM) are a major cause of opportunistic infections in immunocompromised patients, making the reliable and rapid identification of NTM to the species level very important for the treatment of such patients. Therefore, this study evaluated the usefulness of the novel target genes tuf and tmRNA for the identification of NTM to the species level, using a PCRrestriction fragment length polymorphism analysis (PRA). A total of 44 reference strains and 17 clinical isolates of the genus Mycobacterium were used. The 741 bp or 744 bp tuf genes were amplified, restricted with two restriction enzymes (HaeIII/MboI), and sequenced. The tuf gene-PRA patterns were compared with those for the tmRNA (AvaII), hsp65 (HaeIII/HphI), rpoB (MspI/HaeIII), and 16S rRNA (HaeIII) genes. For the reference strains, the tuf gene-PRA yielded 43 HaeIII patterns, of which 35 (81.4%) showed unique patterns on the species level, whereas the tmRNA, hsp65, rpoB, and 16S rRNA-PRAs only showed 10 (23.3%), 32 (74.4%), 19 (44.2%), and 3 (7%) unique patterns after single digestion, respectively. The tuf gene-PRA produced a clear distinction between closely related NTM species, such as M. abscessus (557-84-58) and M. chelonae (477-84-80-58), and M. kansasii (141-136-80-63-58-54-51) and M. gastri (141-136-117-80-58-51). No difference was observed between the tuf-PRA patterns for the reference strains and clinical isolates. Thus, a diagnostic algorithm using a tuf gene-targeting PRA is a promising tool with more advantages than the previously used hsp65, rpoB, and 16S rRNA genes for the identification of NTM to the species level.

• ALGAE
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• v.31 no.2
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• pp.155-165
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• 2016

Green microalgae from the class Chlorophyceae represent a major biodiversity component of eukaryotic algae in continental water. Identification and classification of this group through morphology is a hard task, since it may present cryptic species and phenotypic plasticity. Despite the increasing use of molecular methods for identification of microorganisms, no single standard barcode marker is yet established for this important group of green microalgae. Some available studies present results with a limited number of chlorophycean genera or using markers that require many different primers for different groups within the class. Thus, we aimed to find a single marker easily amplified and with wide coverage within Chlorophyceae using only one pair of primers. Here, we tested the universality of primers for different genes (tufA, ITS, rbcL, and UCP4) in 22 strains, comprising 18 different species from different orders of Chlorophyceae. The ITS primers sequenced only 3 strains and the UCP primer failed to amplify any strain. We tested two pairs of primers for rbcL and the best pair provided sequences for 10 strains whereas the second one provided sequences for only 7 strains. The pair of primers for the tufA gene presented good results for Chlorophyceae, successfully sequencing 21 strains and recovering the expected phylogeny relationships within the class. Thus, the tufA marker stands out as a good choice to be used as molecular marker for the class.

• Proceedings of the Zoological Society Korea Conference
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• 1998.10b
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• pp.318.1-318
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• 1998

No Abstract, See Full Text

• Proceedings of the Zoological Society Korea Conference
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• 1999.10b
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• pp.257.2-257
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• 1999

No Abstract, See Full Text

• Proceedings of the Zoological Society Korea Conference
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• 1997.10b
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• pp.265.2-265
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• 1997

No Abstract, See Full Text

• Journal of Microbiology and Biotechnology
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• v.31 no.8
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• pp.1154-1162
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• 2021

The transcriptional capacities of target genes are strongly influenced by promoters, whereas few studies have focused on the development of robust, high-performance and cross-species promoters for wide application in different bacteria. In this work, four novel promoters (P_k.rtufB, P_k.r1, P_k.r2, and P_k.r3) were predicted from Ketogulonicigenium robustum and their inconsistency in the -10 and -35 region nucleotide sequences indicated they were different promoters. Their activities were evaluated by using green fluorescent protein (gfp) as a reporter in different species of bacteria, including K. vulgare SPU B805, Pseudomonas putida KT2440, Paracoccus denitrificans PD1222, Bacillus licheniformis and Raoultella ornithinolytica, due to their importance in metabolic engineering. Our results showed that the four promoters had different activities, with P_k.r1 showing the strongest activity in almost all of the experimental bacteria. By comparison with the commonly used promoters of E. coli (tufB, lac, lacUV5), K. vulgare (Psdh, Psndh) and P. putida KT2440 (JE111411), the four promoters showed significant differences due to only 12.62% nucleotide similarities, and relatively higher ability in regulating target gene expression. Further validation experiments confirmed their ability in initiating the target minCD cassette because of the shape changes under the promoter regulation. The overexpression of sorbose dehydrogenase and cytochrome c551 by P_k.r1 and P_k.r2 resulted in a 22.75% enhancement of 2-KGA yield, indicating their potential for practical application in metabolic engineering. This study demonstrates an example of applying bioinformatics to find new biological components for gene operation and provides four novel promoters with broad suitability, which enriches the usable range of promoters to realize accurate regulation in different genetic backgrounds.

• Pediatric Infection and Vaccine
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• v.21 no.3
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• pp.219-224
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• 2014

Invasive infection of the Streptococcus bovis group in a neonate is rare. In cases reported to date, the pathogen of neonatal S. bovis infections is usually Streptococcus gallolyticus subsp. pasteurianus (S. bovis biotype II/2). Streptococcus lutetiensis (S. bovis biotype II/1) was identified using 16S rRNA and tuf gene sequence analysis of the isolates from blood and cerebrospinal fluid (CSF) of a fever-presenting 28-day-old male. Blood culture analysis was performed using automatic equipment (VITEK 2) and identified Streptococcus infantarius supsp. infantarius, yet we were unable to get accurate results from the CSF culture. The fever subsided on the second day of hospitalization, and the patient was discharged without neurologic complication after 14 days of antibiotic therapy. In this case, we were able to accurately identify the pathogen using molecular genetic methods. To our knowledge, this is the first case of late onset neonatal bacteremia and meningitis caused by S. lutetiensis.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.40 no.3
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• pp.128-132
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• 2007

We identified a microsatellite marker, Poli121TUF, which appears to be significantly linked (P<0.001) with a lymphocystis disease virus (LCDV)-resistance gene in the olive flounder, Paralichthys olivaceus. The olive flounder is an economically important food fish, that is widely cultured in Korea, Japan, and China. Lymphocystis disease has spread in these countries and has seriously reduced the economic value of the fish. LCDV causes lymphocystis cells (LC) to form on the body surface, fins, gills, mouth, and intestine. Fish with LC lose commercial value due to their deformed appearance. The identified micro satellite marker can be used as a candidate locus for marker-assisted selection (MAS) in order to enhance the efficiency of selection for LCDV resistance in the olive flounder.

• ALGAE
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• v.29 no.2
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• pp.127-136
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• 2014

Endophytic green algae growing in fronds of Grateloupia spp. were examined for infection frequency from their field populations of Jeju, Wando, and Uljin, Korea in August and September 2013. Three endophytes were isolated in laboratory culture from a G. lanceolata thallus collected in Jeju. Unialgal cultures were made from the endophytes, and their morphological characteristics were observed with light microscopy. In addition, a phylogenetic analysis based on chloroplast-encoded elongation factor tufA gene sequences was performed to identify the G. lanceolata endophytes. Three filamentous green endophytic species, Ulvella leptochaete, Blastophysa rhizopus, and Bolbocoleon piliferum were reported for the first time in Korea. General biological information for the three endophytes was also described.

• Genomics & Informatics
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• v.11 no.4
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• pp.272-276
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• 2013

Sequence analysis of the 16S rRNA gene has been widely used for the classification of microorganisms. However, we have been unable to clearly identify five Flavobacterium species isolated from a freshwater by using the gene as a single marker, because the evolutionary history is incomplete and the pace of DNA substitutions is relatively rapid in the bacteria. In this study, we tried to classify Flavobacterium species through multilocus sequence analysis (MLSA), which is a practical and reliable technique for the identification or classification of bacteria. The five Flavobacterium species isolated from freshwater and 37 other strains were classified based on six housekeeping genes: gyrB, dnaK, tuf, murG, atpA, and glyA. The genes were amplified by PCR and subjected to DNA sequencing. Based on the combined DNA sequence (4,412 bp) of the six housekeeping genes, we analyzed the phylogenetic relationship among the Flavobacterium species. The results indicated that MLSA, based on the six housekeeping genes, is a trustworthy method for the identification of closely related Flavobacterium species.