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Efficient detection of pathogen virus in sand dabs,Paralichthys olivaceus using loop-mediated isothermal amplification(LAMP)

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Acta Oceanologica Sinica 2016年第8期35卷 44-50页

作者： HWANG Jinik PARK So Yun SUH Sung-Suk PARK Mirye lee sukchan lee Taek-Kyun South Sea Environment Research Department Korea Institute of Ocean Science and TechnologyGeoje 53201Republic of Korea Korea University of Science and Technology Daejeon 34113Republic of Korea Department of Genetic Engineering Sungkyunkwan UniversitySuwon 16419Republic of Korea

Viral hemorrhagic septicemia virus（VHSV） and marine birnavirus（MABV） are the causative pathogens for some of the most explosive epidemics of emerging viral diseases in many Asian countries, leading to huge economic losses in aquaculture. Rapid molecular detection for surveillance or diagnosis has been a critical component in reducing the prevalence of pathogen infection. The loop-mediated isothermal amplification（LAMP） of DNA is currently one of the most commonly used molecular diagnostic tools, as it is simple, quick, and easy to amplify target DNA under isothermal conditions. In the present study, a novel and highly specific LAMP assay for the sensitive and rapid detection of VHSV and MABV infection in fish was developed. Using a set of synthesized primers matching a specific region of the genome, the efficiency and specificity of the LAMP assay were optimized in terms of the reaction temperature and DNA polymerase concentration, as they are the main determinants of the sensitivity and specificity of the LAMP assay. In particular, we demonstrated that our assay could be applied to efficient detection of VHSV and MABV infection in the wild fish, Paralichthys olivaceus. Our results demonstrate the simplicity and convenience of this method for the detection of viral infection in aquatic organisms.

关键词： viral hemorrhagic septicaemia virus(VHSV) marine birnavirus(MABV) polymerase chain reaction loop-mediated isothermal amplification

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Biochemical Characterization of Soluble Acid and Alkaline Invertases from Shoots of Etiolated Pea Seedlings

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Journal of Integrative Plant Biology 2010年第6期52卷 536-548页

作者： Donggiun Kim So Yun Park Youngjae Chung Jongbum Park sukchan lee Taek-Kyun lee Department of Biological Science Silla University South Sea Environment Research Department Korea Ocean Research and Development Institute Department of Life Science and Biotechnology Shin Gyeong University Department of Genetic Engineering Sungkyunkwan University

Soluble invertase was purified from pea （Pisum sativum L.） by sequential procedures entailing ammonium sulfate precipitation, DEAE-Sepharose column, Con-A- and Green 19-Sepharose affinity columns, hydroxyapatite column, ultra-filtration, and Sephacryl 300 gel filtration. The purified soluble acid （SAC） and alkaline （SALK） invertases had a pH optimum of 5.3 and 7.3, respectively. The temperature optimum of two invertases was 37 ℃. The effects of various concentrations of Tris-HCI, HgCI2, and CuSO4 on the activities of the two purified enzymes were examined. Tris-HCI and HgCI2 did not affect SAC activity, whereas 10 mM Tris-HCI and 0.05 mM HgCI2 inhibited SALK activity by about 50%. SAC and SALK were inhibited by 4.8 mM and 0.6 mM CuSO4 by 50%, respectively. The enzymes display typical hyperbolic saturation kinetics for sucrose hydrolysis. The Kms of SAC and SALK were determined to be 1.8 and 38.6 mM, respectively. The molecular masses of SAC shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting were 22 kDa and 45 kDa. The molecular mass of SALK was 30 kDa. Iso-electric points of the SAC and SALK were estimated to be about pH 7.0 and pH 5.7, respectively.

关键词： SAC Biochemical Characterization of Soluble Acid and Alkaline Invertases from Shoots of Etiolated Pea Seedlings

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Fatty acid methyl ester profiles and nutritive values of 20 marine microalgae in Korea

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Asian Pacific Journal of Tropical Medicine 2015年第3期8卷 191-196页

作者： Sung-Suk Suh So Jung Kim Jinik Hwang Mirye Park Taek-Kyun lee Eui-Joon Kil sukchan lee South Sea Environment Research Department Korea Institute of Ocean Science and Technology Kyeongbuk Institute for Marine Bio-Industry Department of Genetic Engineering Sungkyunkwan University

Objecive:To screen the fatty acid(FA) composition of 20 marine microalgae species,including seven Diophyceae,six Bacillariophyeae four Chlorophyceae,two Haptophyceae and one Raphidophyceae ***:Microalgal cells cultured at the Korea Institute of Ocean Science & Technology were harvested during the late exponential growth phase and the FA composition ***:The FA composition of microalgae was *** example,seven different species of Dinophyceae were composed primarily of C14:0,C16:0.C18:0.C20:4n-6.C20:5n-3 and C22:*** C14:0.C16:0,C16:1.C18:0.C20:5n-3 and C22:6n-3 were abundant FAs in six species of *** addition,four Chlurophyceae,two Haptopkyeeae and one Raphidophyceae species all contained a high degree of C16:1 n-7[(9.2R-34.91)%and(34.48-35.04)%].C14:0[(13.34-25.96)%]and[(26.69-Z8.24)%],and C16:0[(5.89-29.15)%]and[(5.70-16.81)%].Several factors contribute to the nutritional value of *** the polyunsaturated FA content and n-3 to n-6 FA ratio,which could be used to assess the nutritional quality of ***:This study is the first comprehensive assessment of the FA composition and nutritional value of microalgae species in South Korea,and identifies the potential utility of FAs as species-specific biomarkers.

关键词： Microalgae PUFA Nutritive values DHA EPA

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Detection of coat protein gene of nervous necrosis virus using loopmediated isothermal amplification

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Asian Pacific Journal of Tropical Medicine 2016年第3期9卷 230-235页

作者： Jinik Hwang Sung-Suk Suh Mirye Park Myung-Joo Oh Jong-Oh Kim sukchan lee Taek-Kyun lee South Sea Environment Research Department Korea Institute of ocean science & technology Korea University of Science and Technology Department of Aqualife Medicine Chonnam National University Department of Genetic Engineering Sungkyunkwan University

Objective:To establish a novel and highly specific loop-mediated isothermal amplification(LAMP) assay for the identification of nervous necrosis virus(NNV) ***:A set of synthesized primers was used to match the sequences of a specific region of the nnr gene from the National Center for Biotechnology Information database,not originating from NNV-infected fish,the efficiency and specificity of LAMP were measured dependent on the concentration of DNA polymerase and the reaction temperature and *** addition,to determine species-specific LAMP primers,cross reactivity testing was applied to the reaction between NVV and other virus families including viral hemorrhagic septicemia virus and marine ***:The optimized LAMP reaction carried out at 64 ℃ for 60 min,and above 4 U Bst DNA *** sensitivity of LAMP for the detection of nnv was thus about 10 times greater than the sensitivity of polymerase chain *** LAMP assay primers were specific for the detection NNV infection in Epinephelus ***:The development of LAMP primers based on genetic information from a public database,not virus-infected samples,may provide a very simple and convenient method to identify viral infection in aquatic organisms.

关键词： Nervous necrosis virus Nodaviridae Polymerase chain reaction Loop-mediated isothermal Amplification

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Expression Analysis of Proline Metabolism-related Genes From Halophyte Arabis stelleri under Osmotic Stress Conditions

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Journal of Integrative Plant Biology 2010年第10期52卷 891-903页

作者： Yuchul Jung Jungan Park Yunjung Choi Jin-Gweon Yang Donggiun Kim Beom-Gi Kim Kyunghee Roh Dong-Hee lee Chung-Kyoon Auh sukchan lee Department of Genetic Engineering Sungkyunkwan University Institute of Life Science and Technology Sungkyunkwan University National Academy of Agricultural Science Rural Development Administration Department of Life Science Ewha Womans University Department of Biological Sciences Mokpo National University

Arabis stelleri var. japonica evidenced stronger osmotic stress tolerance than Arabidopsis thaliana. Using an A. thaliana microarray chip, we determined changes in the expression of approximately 2 800 genes between A. stelleri plants treated with 0.2 M mannitol versus mock-treated plants. The most significant changes in the gene expression patterns were in genes defining cellular components or in genes associated with the endomembrane system, stimulus response, stress response, chemical stimulus response, and defense response. The expression patterns of three de novo proline biosynthesis enzymes were evaluated in A. stelleri var. japonica seedlings treated with 0.2 M mannitol, 0.2 M sorbitol, and 0.2 M NaCI. The expression of At-pyrroline-5-carboxylate synthetase was not affected by NaCI stress but was similarly induced by mannitol and sorbitol. The proline dehydrogenase gene, which is known to be repressed by dehydration stress and induced by free L-proline, was induced at an early stage by mannitol treatment, but the level of proline dehydrogenase was increased later by treatment with both mannitol and NaCI. The level of free L-proline accumulation increased progressively in response to treatments with mannitol, sorbitol, and NaCI. Mannitol induced L-proline accumulation more rapidly than NaCI or sorbitol. These findings demonstrate that the osmotic tolerance of the novel halophyte, Arabis stelleri, is associated with the accumulation of L-proline.

关键词： Expression Analysis of Proline Metabolism-related Genes From Halophyte Arabis stelleri under Osmotic Stress Conditions

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An Effective Integrated Machine Learning Framework for Identifying Severity of Tomato Yellow Leaf Curl Virus and Their Experimental Validation

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Research 2023年第3期2023卷 91-104页

作者： Nattanong Bupi Vinoth Kumar Sangaraju Le Thi Phan Aamir Lal Thuy Thi Bich Vo Phuong Thi Ho Muhammad Amir Qureshi Marjia Tabassum sukchan lee Balachandran Manavalan Department of Integrative Biotechnology College of Biotechnology and BioengineeringSungkyunkwan UniversitySuwon 16419.Gyeonggi-doRepublic of Korea Computational Biology and Bioinformatics Laboratory Department of Integrative BiotechnologyCollege of Biotechnology and Bioengineering.Sungkyunkwan UniversitySuwon 16419Gyeonggi-doRepublic of Korea

Tomato yellow leaf curl virus(TYLCV)dispersed across different countries,specifically to subtropical regions,associated with more severe *** TYLCV was first isolated in 1931,it has been a menace to tomato industrial production worldwide over the past *** groups were newly isolated from TYLCV-resistant tomatoes in 2022;however,their functions are *** development of machine learning(ML)-based models using characterized sequences and evaluating blind predictions is one of the major challenges in interdisciplinary *** purpose of this study was to develop an integrated computational framework for the accurate identification of symptoms(mild or severe)based on TYLCV sequences(isolated in Korea).For the development of the framework,we first extracted 11 different feature encodings and hybrid features from the training data and then explored 8 different classifiers and developed their respective prediction models by using randomized 10-fold ***,we carried out a systematic evaluation of these 96 developed models and selected the top 90 models,whose predicted class labels were combined and considered as reduced *** the basis of these features,a multilayer perceptron was applied and developed the final prediction model(IML-TYLCVs).We conducted blind prediction on 3 groups using IML-TYLCVs,and the results indicated that 2 groups were severe and 1 group was ***,we confirmed the prediction with virus-challenging experiments of tomato plant phenotypes using infectious clones from 3 *** virologists and plant breeding professionals can access the user-friendly online IML-TYLCVs web server at https://***/IML-TYLCVs,which can guide them in developing new protection strategies for newly emerging viruses.

关键词： breeding fir prediction

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T-type Ca2+ channels in thalamic control of behavior

T-type Ca2+ channels in thalamic control of behavior

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中国神经科学学会第四次会员代表大会暨第八届全国学术会议

作者： sukchan lee Soojung lee Huisu Kim Guk Bae Kim Ingie Hong Sukwoo Choi Sung-Yon Kim Sang Jeong Kim Hee-Sup Shin Department of Physiology SeoulNational University College of Medicine and Neuroscience Research Institute Medical Research CenterKorea School of Biological Sciences College of Natural SciencesSeoul National UniversityKorea Department of Physiology Seoul National University College of Medicine and Neuroscience Research Institute Medical Research CenterKorea

Objective The Mediodorsal thalamus(MD) is a part of the limbic system and connects reciprocally with the prefrontal cortex,the amygdala and the hippocampus,which comprise a network of structures involved in fear memory. However,the contribution of the MD to fear behavior is poorly *** C(PLC) b4 is expressed intensely in the MD but very lightly in the prefrontal cortex and the amygdala,the two key regions known to regulate fear *** Here,we examined a role of the MD using the PLCb4 knock-out(PLCb4) mice in the formation and extinction of auditory-conditioned *** The PLCb4 mice showed normal acquisition and long-term memory of auditory-conditioned ***,the mutant was severely impaired in fear *** clamp recording on the mutant MD neurons in thalamic slices showed an increase of low threshold Ca currents mediated via T-type Ca channels compared to the wild *** infusion in vivo of T-type channel blocker into the MD ameliorated the impaired extinction phenotype in PLCb4 and facilitated the extinction in wild type *** These results suggest that the mediodorsal thalamus is involved in the control of fear extinction and T-type Ca channels play an inhibitory role in this process.

关键词： T-type Ca2+ channels mediodorsal nucleus thalamus fear extinction

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