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A report of 31 unrecorded bacterial species belonging to the class Alphaproteobacteria in Korea

  • Kim, Kyung Hyun;Yoon, Jung-Hoon;Kim, Seung-Bum;Jahng, Kwang-Yeop;Cho, Jang-Cheon;Joh, Ki-seong;Cha, Chang-Jun;Seong, Chi-Nam;Bae, Jin-Woo;Im, Wan-Taek;Jeon, Che Ok
    • Journal of Species Research
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    • v.6 no.2
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    • pp.129-140
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    • 2017
  • During a comprehensive investigation of indigenous prokaryotic species in Korea, a total 31 bacterial strains assigned to the class Alphaproteobacteria were isolated from diverse environmental habitats including freshwater, seawater, brackish water, ginseng soil, plant roots, natural caves, and tidal flats. Based on their high 16S rRNA gene sequence similarities(>99.1%) and formation of robust phylogenetic clades with the closest type species, each strain was assigned to an independent and predefined bacterial species. Because there were no published or official reports regarding the isolation of these 31 species in Korea, this study identified three species in two genera in the order Caulobacterales, 12 species in 10 genera in the order Rhodobacterales, three species in two genera in the order Rhizobiales, two species in two genera in the order Rhodospirillales and 11 species in seven genera, all in the order Sphingomonadaceae within the Alphaproteobacteria are reported as new alphaproteobacterial species in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are described in the species description section.

Taguchi Robust Design of Tracked Vehicle for Manganese Nodule Test Miner in Collecting Operation Considering Deep-sea Noise Factors (심해 잡음인자를 고려한 망간단괴 시험집광기의 채집운용시 주행장치 다구치 강건설계)

  • Cho, Su-Gil;Lee, Min-Uk;Lim, Woo-Chul;Choi, Jong-Su;Kim, Hyung-Woo;Lee, Chang-Ho;Hong, Sup;Lee, Tae-Hee
    • Journal of Ocean Engineering and Technology
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    • v.26 no.1
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    • pp.41-46
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    • 2012
  • A deep-sea manganese nodule miner consists of 4 parts: the pickup device, crusher, disposal device, and tracked vehicle. The tracked vehicle is an essential component to keep the self-propelled miner moving across deep-sea soil. The performances of the tracked vehicle are influenced by noise factors: the shear strength of the seafloor, bottom current, seafloor slope, track speed, reaction forces of flexible hose, etc. It is necessary to adopt a robust design method that improves the performances and minimizes the variation caused by noise factors. Taguchi's method, the most widely known robust design method, searches for the robust optimum using an orthogonal array composed of the product of the inner array and outer array. In this paper, we propose a new screening technique to reduce the number of input factors and apply the MRSN (Multi-Response Signal to Noise) ratio to convert multiple performances into single one in order to overcome the difficulties and limitations of using Taguchi's method in a case with many input factors and multiple performances. A test miner was already designed and tested. It has about 1/10 the capacity of a commercial one and was successfully operated at an in-shore area. Taguchi's robust design was applied to the tracked vehicle of the test miner, and design improvements were implemented for the vehicle.

A Evaluation of Standard Support Pattern for Two-Arch Road Tunnel (2-Arch 도로터널에 적용된 표준지보패턴의 적정성 검토)

  • Chun, Byungsik;Choi, Kwangbo;Kim, Hyeyang;Yoo, Junhee
    • Journal of the Korean GEO-environmental Society
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    • v.9 no.7
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    • pp.25-35
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    • 2008
  • In domestic cases, the standard support pattern of 2-lanes road tunnels is presented because construction experience and high degree various data was abundant. But, it is not desirable to apply standard for 2-Arch tunnels that the precedent and measuring data is insufficient existing support pattern blasting plan and interpretation of separate way concerning specific terrain and rock quality. In this study, behavior according to load distribution ratio and Unsymmetrical Pressure about standard support pattern which is applied in design and construction of 2-arch tunnels was analysed and the examination of blasting vibration has influence on the center wall is conducted as a consequence reasonableness of support whether or not with presumed support pressure and ground reaction curve method. In result appropriateness of standard support pattern, support quantity is proper but considers specific terrain and rock quality condition when design and construction of further step 2-arch tunnel standard support pattern must be decided by considering terrains, soil properties and construction condition of the objective tunnel.

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Developement of novel enzyme system for production of enantiomerically pure ${\beta}-amino$ acids : Kinetic resolution of racemic 3-amino-n-butanoic acid using transaminase from Alcaligenes denitrificans Y2k-2

  • Im, Seong-Yeop;Jo, Byeong-Gwan;Kim, Byeong-Gi
    • 한국생물공학회:학술대회논문집
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    • 2000.11a
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    • pp.579-582
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    • 2000
  • (R,S)-3-amino-n-butanoic acid$(DL-\;{\beta}\;-homoalanine)$ has been kinetically resolved using Alcaligenes denitrificans Y2k-2 as a biocatalyst, which was isolated from soil by enrichment culture, which was carried out with minimal media containing (R,S)-3-amino-n-butanoic acid as a sole nitrogen source. The enzyme which peformed this kinetic resolution assumed to belong to the ${\omega}-transaminase$ family, because A. denitrificans used pyruvate as amino acceptor and its transaminase activity was inhibited by gabaculine, aminooxy acetic acid and hydroxylamine. In whole cell reaction, (R,S)-3-amino-n-butanoic acid was kinetically resolved to the corresponding (R)-3-amino-n-butanoic acid with excellent E (>100) in the presence of pyruvate as an amino acceptor at $37^{\circ}C$. (S-specific) We observed the substrate inhibition for pyruvate at 100mM. In this study, characteristics of transaminase activity of Alcaligenes denitrificans Y2k-2, such as substrate specificity and thermostability, are carried out for the development of (R)-3- amino-n-butanoic acid production system.

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Identification of Heterodera glycines (Tylenchida; Heteroderidae) Using qPCR

  • Ko, Hyoung-Rai;Kang, Heonil;Park, Eun-Hyoung;Kim, Eun-Hwa;Lee, Jae-Kook
    • The Plant Pathology Journal
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    • v.35 no.6
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    • pp.654-661
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    • 2019
  • The soybean cyst nematode, Heterodera glycines, is a major plant-parasitic nematode that has caused important economic losses to Korea's soybean production. Four species of cyst nematodes, H. schachtii, H. glycines, H. trifolii, and H. sojae, all belong to schachtii group are coexist in field soil in Korea. The rapid identification of the nematode is crucial for preventing crop damage and in decision making for controlling this nematode. This study aimed to develop a species-specific primer set for quantitative PCR (qPCR) assay of H. glycines. The specific primer set (HGF1 and HGR1) for H. glycines was designed based on the cytochrome c oxidase subunit I (COI) sequence of mitochondrial DNA. After optimization, it is possible to identify the H. glycines using a qPCR assay with DNA extracted from a single cyst and single second-stage juvenile (J2). The specificity was confirmed by the absence of SYBR fluorescent signals of three other Heterodera species. A serial dilution of DNA extracted from a single cyst was obtained for the sensitivity test. The result showed that the standard curve of the test had a highly significant linearity between DNA concentration and Ct value (R2 = 0.996, slope = -3.49) and that the detection limit concentration of DNA of the primer set was 10 pg of DNA per reaction. Our findings suggested that H. glycines could be distinguished from H. sojae and other Heterodera species when a qPCR assay is used with a specific primer set.

Effect of different water levels on the photosynthetic pigments of crops

  • Ryu, Hee-La;Jeong, Eun-Ju;Lee, Won-Hee;Lee, In-Jung
    • Proceedings of the Korean Society of Crop Science Conference
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    • 2017.06a
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    • pp.205-205
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    • 2017
  • An excess soil water condition is one of the major problems for the field crops growing in paddy fields because of their poor drainage and less availability for oxygen uptake which leads to adversely affect the photosynthesis. Therefore, the current study was undertaken with aim to investigate the effects groundwater level on the photosynthetic response of soy bean (Urum), red bean (Arari), sesame (Geonbaek), perilla (Dayu) after the transplanting to the lysimeter to investigate the plant-water relation and their effect on photosynthesis. The chlorophyll content of the crops according to the humid conditions of the soy bean, sesame and the perilla was found to be 5%, 6.89 % and 13.7% higher than that of the groundwater treated at 40cm, respectively. On the other hand, the chlorophyll content of adzuki bean decreased 6.6% from the groundwater level of 40cm, and the sorghum decreased by 5.7%. As a result of investigating the Fv / Fm value of groundwater, the adzuki bean at 20cm above groundwater was lower than that of groundwater by 40cm immediately before flowering. The Fv / Fm value of soy bean and sesame at 40cm above groundwater were lowered by flowering under groundwater 20 cm and Fv / Fm value of sorghum is increased at 40 cm treatment immediately before flowering while the Fv / Fm values of the perilla had no significant difference in comparison to those at 20 cm and 40 cm of groundwater. In the case of chlorophyll fluorescence reaction, it is known that the when the absolute value is closer to 0.82, the stress is considered less. As a result of comparing the numerical values of the crops, it was found that the sorghum was the most stressed followed by adzuki bean and sesame, while the soy beans and perilla was found on the average, as they received less stress.

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Development of Microfluidic Chip for Enrichment and DNA Extraction of Bacteria Using Concanavalin A Coated Magnetic Particles (Concanavalin A가 코팅 된 자성 입자를 이용한 미생물 농축 및 유전자 추출 칩 개발)

  • Kwon, Kirok;Gwak, Hogyeong;Hyun, Kyung-A;Jung, Hyo-Il
    • Journal of Sensor Science and Technology
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    • v.27 no.4
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    • pp.237-241
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    • 2018
  • The real-time enrichment and detection of pathogens are serious issues and rapidly evolving field of research because of the ability of these pathogens to cause infectious diseases. In general, bacterial detection is accomplished by conventional colony counting or by polymerase chain reaction (PCR) after DNA extraction. As colony counting requires considerable time to cultivate, PCR is an attractive method for rapid detection. A small number of pathogens can cause diseases. Hence, a pretreatment process, such as enrichment is essential for detecting bacteria in an actual environment. Thus, in this study, we developed a microfluidic chip capable of performing rapid enrichment of bacteria and the extraction of their genes. A lectin, i.e., Concanavalin A (ConA), which shows binding affinity to the surface of most bacteria, was coated on the surface of magnetic particles to nonspecifically capture bacteria. It was subsequently concentrated through magnetic forces in a microfluidic channel. To lyse the captured bacteria, magnetic particles were irradiated by a wavelength of 532nm. The photo-thermal effect on the particles was sufficient for extracting DNA, which was consequently utilized for the identification of bacteria. Our device will help monitor the existence of bacteria in various environmental situations such as water, air, and soil.

Activating Temperature of Kaolin As a Cement Admixture

  • Park, Hee-Yong;Hwang, Hey-Zoo;Kim, Moo-Han;Kim, Moon-Han
    • KCI Concrete Journal
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    • v.13 no.1
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    • pp.3-9
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    • 2001
  • This research concerns the effect of kaolin as material of cement admixture. which has the advantage of low price and high adaptability. Kaolin, a kind of soil, is well known as a raw material of pottery. which is widely scat-tered on the earth (especially in Korea). This research shows the method and process for activating kaolin to have the properties of a cement admixture through experiment. In the experiments, kaolin is baked in high temperature and then cooled suddenly to be activated. The temperature zone and time span, on which kaolin is activated are examined. The research looks over the effect of the activated kaolin based on several criteria regarding to chemical and physical characteristic of general admixtures. The results of this research are as follows; kaolin start activation at the temperature above 50$0^{\circ}C$ and make ends of activation at the temperature below 95$0^{\circ}C$ and there was little effect by the change of duration. It is concluded that compressive strength can be increased by putting activated kaolin in the concrete and the activated kaolin is good for water resistance and anti-chemical , and that it is effective for protecting the leakage of hazardous article like Cl- and for protecting damage by an organic salt like acid. The activated kaolin of proper temperature and time is effective in compressive strength, salt resistance and acid resistance. The adaptability of activated kaolin as a cement admixture was shown through this research.

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Transformation of Korean Ginseng (Panax ginseng C.A. Meyer) with Salt Toleranc SAL1 Gene (염류내성관련 SAL1 유전자에 의한 인삼 형질전환)

  • In, Jun-Gyo;Yang, Deok-Chun
    • Korean Journal of Medicinal Crop Science
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    • v.13 no.1
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    • pp.57-62
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    • 2005
  • Salt-tolerant transgenic Panax ginseng plants were produced by introducing the SAL1 geue (3'(2'), 5'-bis-phosphate nucleotidase) that confers tolerance to the salts through Agrobacterium tumefaciens co-cultivation. Cotyledon explants of immature ginseng zygotic embryos cultured on Murashige and Skoog medium lacking growth regulators formed somatic embryos directly with below 10%, but the 74% tranformation rate were observed at the treatment of phytohormone with 1.0 mg/l 2,4-D and 0.5 mg/l kinetin. Somatic embryos were initially cultured on MS medium supplemented with 250 mg/l cefotaxime for 3 weeks and subsequently subcultured five times to a medium containing 100 mg/l kanamycin and 250 mg/l cefotaxime. Upon development into the cotyledonary stage, these somatic embryos were transferred to on the medium containing 50 mg/l kanamycin and 10 mg/l gibberellic acid to induce germination and strong selection. Integration of the transgene into the plants was confirmed by polymerase chain reaction with specific primers. The ginseng transformants with well-developed shoots and roots were successfully acclimatized in a greenhouse when they were planted in soil.

A report of 39 unrecorded bacterial species in Korea, belonging to the Betaproteobacteria and Gammaproteobacteria

  • Choi, Ahyoung;Bae, Jin-Woo;Cha, Chang-Jun;Chun, Jongsik;Im, Wan-Taek;Jahng, Kwang Yeop;Jeon, Che Ok;Joh, Kiseong;Kim, Seung Bum;Seong, Chi Nam;Yoon, Jung-Hoon;Cho, Jang-Cheon
    • Journal of Species Research
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    • v.4 no.2
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    • pp.109-126
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    • 2015
  • As a subset study to discover indigenous prokaryotic species in Korea, a total of 39 bacterial strains assigned to the classes Betaproteobacteria and Gammaproteobacteria were isolated from diverse environmental samples collected from soil, tidal flat, freshwater, seawater, seaweed, wetland, plant roots, guts of insects, and fermented foods. From the high 16S rRNA gene sequence similarity (>99.1%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 39 species have been described in Korea; therefore 4 species of 4 genera in the order Burkholderiales and 1 species in the order Neisseriales within the class Betaproteobacteria, and 10 species of 6 genera in the order Alteromonadales, 11 species of 3 genera in the order Pseudomonadales, 4 species of 4 genera in the order Enterobacteriales, 2 species of 2 genera in the order Vibrionales, 1 species in the order Aeromonadales, 3 species of 3 genera in the order Oceanospirillales, 2 species of 2 genera in the order Xanthomonadales, and 1 species in the order Chromatiales within the Gammaproteobacteia are reported for proteobacterial species found in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are also described in the species description section.