• Journal of Microbiology and Biotechnology
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• v.18 no.4
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• pp.624-630
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• 2008

Terminal restriction fragment length polymorphism (T-RFLP) is a method that has been frequently used to survey the microbial diversity of environmental samples and to monitor changes in microbial communities. T-RFLP is a highly sensitive and reproducible procedure that combines a PCR with a labeled primer, restriction digestion of the amplified DNA, and separation of the terminal restriction fragment (T-RF). The reliable identification of T-RF requires the information of nucleotide sequences as well as the size of T-RF. However, it is difficult to obtain the information of nucleotide sequences because the T-RFs are fragmented and lack a priming site of 3'-end for efficient cloning and sequence analysis. Here, we improved on the T-RFLP method in order to analyze the nucleotide sequences of the distinct T-RFs. The first method is to selectively amplify the portion of T-RF ligated with specific oligonucleotide adapters. In the second method, the termini of T-RFs were tailed with deoxynucleotides using terminal deoxynucleotidyl transferase (TdT) and amplified by a second round of PCR. The major T-RFs generated from reference strains and from T-RFLP profiles of activated sludge samples were efficiently isolated and identified by using two modified T-RFLP methods. These methods are less time consuming and labor-intensive when compared with other methods. The T-RFLP method using TdT has the advantages of being a simple process and having no limit of restriction enzymes. Our results suggest that these methods could be useful tools for the taxonomic interpretation of T-RFs.

• The Korean Journal of Malacology
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• v.27 no.3
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• pp.273-282
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• 2011

The ultrastructural characteristics of germ cells during spermatogenesis and mature sperm morphology in male Pinctada martensii were investigated by transmission electron microscope observation. The morphologies of the sperm nucleus and the acrosome of this species are the oval shape and cone shape, respectively. Spermatozoa are approximately $47-50{\mu}m$ in length including a sperm nucleus (about $1.24{\mu}m$ in length), an acrosome (about $0.60{\mu}m$ in length), and tail flagellum (about $45-47{\mu}m$). The axoneme of the sperm tail shows a 9+2 structure. In P. martensii in Pteriidae, a special substructure showing a thick and wide triangular shape which is composed of electron-dense opaque material (occupied about 50% of all, the upper part of the acrosomal vesicle), appeared in the upper region (part) of the acrosomal vesicle, while the lower region (part) of the acrosomal vesicle is composed of electron-lucent material. Thus, this special structure, which exist in the upper part of the acrosomal vesicle in P. martensii, is somewhat different from those of other subacrosomal vesicle in other families in subacrosomal vesicles. Therefore, we assume that the existence of a special substructure showing a thick and wide triangular shape in the acrosomal vesicle of the spermatozoon can be used as a key characteristic for identification of P. martensii or other species in Pteriidae in subclass Pteriomorphia. The number of mitochondria in the midpiece of the sperm of this species are five (exceptionally sometimes four), as one of common characteristics appear the same number of mitochondria in the same families of superfamilyies. This species in Pteriidae does not contain the axial rod and satellite fibres which appear in the species in Ostreidae in subclass Pteriomorphia. These characteristics can be used for the taxonomic analysis of the family or superfamily levels as a systematic key or tools.

• Korean journal of applied entomology
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• v.56 no.3
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• pp.229-239
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• 2017

The South Korean hermit beetle has previously been identified as Osmoderma opicum, which is distributed in Japan. Because of its rarity, this species is classified as an endangered species. To date, however, the identity of this species in South Korea has not been conclusively confirmed. To assess the taxonomic status of the hermit beetle occurring in South Korea, we performed a comparative study with the beetle's Eurasian congeners, based on morphological examination and molecular analysis using COI gene sequences. The results clearly showed that the South Korean hermit beetle is identical to Osmoderma caeleste, which has been described from the Russian Far East. Therefore, we suggest that the taxonomic identity of the South Korean hermit beetle is O. caeleste.

• The Bulletin of The Korean Astronomical Society
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• v.43 no.1
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• pp.42.1-42.1
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• 2018

Deep Ecliptic Patrol of the Southern Sky (DEEP-South) observation is being made during the off-season for exoplanet survey, using Korea Microlensing Telescope Network (KMTNet). An optimal combination of its prime focus optics and the 0.3 billion pixel CCD provides a four square degrees field of view with 0.4 arcsec/pixel plate scale which is also best suited for small body studies. Normal operation of KMTNet started in October 2015, and a significant portion of the allocated telescope time for DEEP-South is dedicated to targeted observation, Opposition Census (OC), of near-Earth asteroids for physical and taxonomic characterization. This is effectively achieved through multiband, time series photometry using Johnson-Cousins BVRI filters. Uninterrupted monitoring of the southern sky with KMTNet is optimized for spin characterization of a broad spectrum of asteroids ranging from the near-Earth space to the main-belt, including binaries, asteroids with satellites, slow/fast- and non-principal axis-rotators, and thus is expected to facilitate the debiasing of previously reported lightcurve observations. Our software subsystem consists of an automated observation scheduler, a pipelined data processing system for differential photometry, and an easy-to-use lightcurve analysis toolkit. Lightcurves, spin periods and provisional determination of class of asteroids to which the lightcurve belongs will be presented, using the dataset from first year operation of KMTNet. Our new taxonomic classification scheme for asteroids will also be summarized.

• Korean Journal of Microbiology
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• v.37 no.2
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• pp.114-119
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• 2001

Many isolates from different forest soil layers did not show appreciable growth on full strength of the conventional nutrient broth (NB medium) but grow on its 100-fold dilution (DNB medium). These isolates were divided into four types according to organic nutrient concentration in the growth medium from $1^{-1}\;to\;10^{-4}$dilution of normal NB medium. Oligotrophic bacteria were type II and type IV which grew in $10^{-4}$ dilution of NB (1 mg C/l) medium. Sixty strains were isolated for obligate oligotrophic bacteria. Chemotaxonomic and phylogenetic characteristics of eleven isolates of acetylene-reducing (nitrogen-fixing) oligotrophic bacteria from forest soil were investigated. They showed similar characteristics: the cellular fatty acid mainly consisted of straight-chain unsaturated $C_{18:1}$ (60-84% of total fatty acids). Ubiquinone Q-10 and a high guanine plus-cytosine content(61-64 mol%) were found. Eleven isolates of nitrogen-fixing oligotrophic bacteria were found to be closely related by full 16S rDNA sequence simility and many common taxonomic traits. Analysis of full 16S rDNA sequences of eleven isolates indicated that they were more closely related to Bradyrhizobium (similarity values: 98.1-98.8%), Agromonas, Nitrobacter, and Afipia.

• Journal of Microbiology and Biotechnology
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• v.27 no.7
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• pp.1288-1299
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• 2017

Composting is widely used to transform waste into valuable agricultural organic fertilizer. Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the global nitrogen cycle, but their role in composting remains poorly understood. In the present study, the community structure, diversity, and abundance of anammox bacteria were analyzed using cloning and sequencing methods by targeting the 16S rRNA gene and the hydrazine oxidase gene (hzo) in samples isolated from compost produced from cow manure and rice straw. A total of 25 operational taxonomic units were classified based on 16S rRNA gene clone libraries, and 14 operational taxonomic units were classified based on hzo gene clone libraries. The phylogenetic tree analysis of the 16S rRNA gene and deduced HZO protein sequences from the corresponding encoding genes indicated that the majority of the obtained clones were related to the known anammox bacteria Candidatus "Brocadia," Candidatus "Kuenenia," and Candidatus "Scalindua." The abundances of anammox bacteria were determined by quantitative PCR, and between $2.13{\times}10^5$ and $1.15{\times}10^6$ 16S rRNA gene copies per gram of compost were found. This study provides the first demonstration of the existence of anammox bacteria with limited diversity in cow manure composting.

• Korean Journal of Ichthyology
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• v.26 no.4
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• pp.249-258
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• 2014

To examine the taxonomic status of Acheilognathus sp. specimens from the Geum River, morphological and genetical characteristics of A. sp., A. yamatsutae and A. majusculus were investigated and compared in detail. Specimens of A. sp. could be distinguished from the other two species by the combination of some morphological characters such as nuptial color, vertebrae, gillrakers and etc. Males of A. sp. had red bands on the outer margin of dorsal and anal fins and a white band on the outer margin of ventral fin in breeding season. A. sp. had larger maximum body length and somewhat more vertebrae than A. yamatsutae, and had fewer gillrakers than A. majusculus. A. sp. appeared as a monophyletic group with A. majusculus and A. cyanostigma based on genetic analysis. In addition, it had even more close relationship with other congeners than A. yamatsutae. Therefore it is presumed that A. sp. from the Geum River may be a distinct species in genus Acheilognathus.

• Applied Biological Chemistry
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• v.38 no.3
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• pp.196-201
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• 1995

Chemo- and numerical taxonomic studies on the isolate SL-387 producing novel aminopeptidase M inhibitors MR-387A and B were carried out The genus of the isolate was determined as Streptomyces by cultural and morphological data and chemical indices. Forty one taxonomic unit characters were tested for determining the species of the isolate, and the data were analyzed numerically using a computer program as called TAXON. The isolate was best matched to Streptomyces neyagawaensis in the major cluster 18 of Streptomyces with $S_{SM}$ value of 75.67%. On the base of chemotaxonomic data and TAXON analysis, the isolate SL-387 was identified to be a member of Streptomyces neyagawaensis.

• Mycobiology
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• v.45 no.4
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• pp.392-400
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• 2017

Peanut yield and quality are seriously affected by pod rot pathogens worldwide, especially in China in recent years. The goals of this study are to analyze the structure of fungal communities of peanut pod rot in soil in three peanut cultivars and the correlation of pod rot with environmental variables using 454 pyrosequencing. A total of 46,723 internal transcribed spacer high-quality sequences were obtained and grouped into 1,706 operational taxonomic units at the 97% similarity cut-off level. The coverage, rank abundance, and the Chao 1 and Shannon diversity indices of the operational taxonomic units were analyzed. Members of the phylum Ascomycota were dominant, such as Fusarium, Chaetomium, Alternaria, and Sordariomycetes, followed by Basidiomycota. The results of the heatmap and redundancy analysis revealed significant variation in the composition of the fungal community among the three cultivar samples. The environmental conditions in different peanut cultivars may also influence on the structure of the fungal community. The results of this study suggest that the causal agent of peanut pod rot may be more complex, and cultivars and environmental conditions are both important contributors to the community structure of peanut pod rot fungi.

• Biomolecules & Therapeutics
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• v.31 no.6
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• pp.674-681
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• 2023

Bile pigment, bilirubin, and biliverdin concentrations may change as a results of biliary tract cancer (BTC) altering the mechanisms of radical oxidation and heme breakdown. We explored whether changes in bile pigment components could help distinguish BTC from benign biliary illness by evaluating alterations in patients with BTC. We collected bile fluid from 15 patients with a common bile duct stone (CBD group) and 63 individuals with BTC (BTC group). We examined the bile fluid's bilirubin, biliverdin reductase (BVR), heme oxygenase (HO-1), and bacterial taxonomic abundance. Serum bilirubin levels had no impact on the amounts of bile HO-1, BVR, or bilirubin. In comparison to the control group, the BTC group had considerably higher amounts of HO-1, BVR, and bilirubin in the bile. The areas under the curve for the receiver operating characteristic curve analyses of the BVR and HO-1 were 0.832 (p<0.001) and 0.891 (p<0.001), respectively. Firmicutes was the most prevalent phylum in both CBD and BTC, according to a taxonomic abundance analysis, however the Firmicutes/Bacteroidetes ratio was substantially greater in the BTC group than in the CBD group. The findings of this study showed that, regardless of the existence of obstructive jaundice, biliary carcinogenesis impacts heme degradation and bile pigmentation, and that the bile pigment components HO-1, BVR, and bilirubin in bile fluid have a diagnostic significance in BTC. In tissue biopsies for the diagnosis of BTC, particularly for distinguishing BTC from benign biliary strictures, bile pigment components can be used as additional biomarkers.