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The change of Phytophthora infestans Populations in South Korea using Traditional Markers and Genome Analyses

  • Do Hee Kwon;Jin Hee Seo;Yong Ik Jin;Gun Ho Jung;Jang Gyu Choi;Gyu Bin Lee;Kwang Ryong Jo;Jaeyoun Yi;Hwang Bae Sohn;Young Eun Park
    • Proceedings of the Korean Society of Crop Science Conference
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    • 2022.10a
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    • pp.257-257
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    • 2022
  • Late blight, caused by the hemibiotrophic oomycete pathogen Phytophthora infestans, has been the most important disease limiting potato production worldwide. P. infestans undergo major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population. Here, we used molecular markers to divide the 86 South Korea isolates into six clonal lineages: KR_1_A1, KR_2_A2, SIB-1, US-11, SIB-1 like, and KR-2 like. We documented the emergence of a new lineage, termed SIB-1 like, and KR-2 like, and their rapid replacement of other lineages to exceed 35% of the pathogen population across South Korea. Genome analyses of the Korean P. infestans populations revealed extensive genetic polymorphism, particularly in effector genes. Importantly, SIB-1 like isolates carry an intact Avr8 effector gene that triggers resistance in potato carrying the corresponding R immune receptor gene R8 cloned from Solarium demissum. These findings point toward a strategy for deploying genetic resistance to mitigate the impact of the SIB-1 like lineage and illustrate how pathogen population monitoring, combined with genome analysis, informs the management of devastating disease epidemics. Further study is being done on pathogenicity of the SIB-1 like isolates on cultivated potatoes and changes in expression patterns of disease effector genes within the SIB-1 like isolates

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Development of an Automatic PCR System Combined with Magnetic Bead-based Viral RNA Concentration and Extraction

  • MinJi Choi;Won Chang Cho;Seung Wook Chung;Daehong Kim;Il-Hoon Cho
    • Biomedical Science Letters
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    • v.29 no.4
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    • pp.363-370
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    • 2023
  • Human respiratory viral infections such as COVID-19 are highly contagious, so continuous management of airborne viruses is essential. In particular, indoor air monitoring is necessary because the risk of infection increases in poorly ventilated indoors. However, the current method of detecting airborne viruses requires a lot of time from sample collection to confirmation of results. In this study, we proposed a system that can monitor airborne viruses in real time to solve the deficiency of the present method. Air samples were collected in liquid form through a bio sampler, in which case the virus is present in low concentrations. To detect viruses from low-concentration samples, viral RNA was concentrated and extracted using silica-magnetic beads. RNA binds to silica under certain conditions, and by repeating this binding reaction, bulk samples collected from the air can be concentrated. After concentration and extraction, viral RNA is specifically detected through real-time qPCR (quantitative polymerase chain reaction). In addition, based on liquid handling technology, we have developed an automatic machine that automatically performs the entire testing process and can be easily used even by non-experts. To evaluate the system, we performed air sample collection and automated testing using bacteriophage MS2 as a model virus. As a result, the air-collected samples concentrated by 45 times then initial volume, and the detection sensitivity of PCR also confirmed a corresponding improvement.

Development of Enzymatic Recombinase Amplification Assays for the Rapid Visual Detection of HPV16/18

  • Ning Ding;Wanwan Qi;Zihan Wu;Yaqin Zhang;Ruowei Xu;Qiannan Lin;Jin Zhu;Huilin Zhang
    • Journal of Microbiology and Biotechnology
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    • v.33 no.8
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    • pp.1091-1100
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    • 2023
  • Human papillomavirus (HPV) types 16 and 18 are the major causes of cervical lesions and are associated with 71% of cervical cancer cases globally. However, public health infrastructures to support cervical cancer screening may be unavailable to women in low-resource areas. Therefore, sensitive, convenient, and cost-efficient diagnostic methods are required for the detection of HPV16/18. Here, we designed two novel methods, real-time ERA and ERA-LFD, based on enzymatic recombinase amplification (ERA) for quick point-of-care identification of the HPV E6/E7 genes. The entire detection process could be completed within 25 min at a constant low temperature (35-43℃), and the results of the combined methods could be present as the amplification curves or the bands presented on dipsticks and directly interpreted with the naked eye. The ERA assays evaluated using standard plasmids carrying the E6/E7 genes and clinical samples exhibited excellent specificity, as no cross-reaction with other common HPV types was observed. The detection limits of our ERA assays were 100 and 101 copies/µl for HPV16 and 18 respectively, which were comparable to those of the real-time PCR assay. Assessment of the clinical performance of the ERA assays using 114 cervical tissue samples demonstrated that they are highly consistent with real-time PCR, the gold standard for HPV detection. This study demonstrated that ERA-based assays possess excellent sensitivity, specificity, and repeatability for HPV16 and HPV18 detection with great potential to become robust diagnostic tools in local hospitals and field studies.

Impact of combined at-home bleaching and whitening toothpaste use on the surface and color of a composite resin

  • Carolina Meneghin Barbosa;Renata Siqueira Scatolin;Waldemir Francisco Vieira-Junior;Marcia Hiromi Tanaka;Laura Nobre Ferraz
    • Restorative Dentistry and Endodontics
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    • v.48 no.3
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    • pp.26.1-26.12
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    • 2023
  • Objective: This in vitro study aimed to evaluate the effects of different whitening toothpastes on a composite resin during at-home bleaching with 10% carbamide peroxide. Materials and Methods: Sixty samples (7 mm × 2 mm) were used for color and roughness analyses, while another 60 samples (3 mm × 2 mm) were utilized to assess microhardness. The factors analyzed included toothpaste, for which 5 options with varying active agents were tested (distilled water; conventional toothpaste; whitening toothpaste with abrasive agents; whitening toothpaste with abrasive and chemical agents; and whitening toothpaste with abrasive, chemical, and bleaching agents). Brushing and application of whitening gel were performed for 14 days. Surface microhardness (SMH), surface roughness (Ra), and color (ΔL*, Δa*, Δb, ΔE*ab, and ΔE00) were analyzed. The Ra and SMH data were analyzed using mixed generalized linear models for repeated measures, while the color results were assessed using the Kruskal-Wallis and Dunn tests. Results: Between the initial and final time points, all groups demonstrated significant increases in Ra and reductions in SMH. No significant differences were found between groups for SMH at the final time point, at which all groups differed from the distilled water group. Conventional toothpaste exhibited the lowest Ra, while whitening toothpaste with abrasive agent had the highest value. No significant differences were observed in ΔL*, Δa*, and Δb. Conclusions: While toothpaste composition did not affect the color stability and microhardness of resin composite, combining toothbrushing with whitening toothpaste and at-home bleaching enhanced the change in Ra.

Lipase Production by Limtongozyma siamensis, a Novel Lipase Producer and Lipid Accumulating Yeast

  • Varunya Sakpuntoon;Savitree Limtong;Nantana Srisuk
    • Journal of Microbiology and Biotechnology
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    • v.33 no.11
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    • pp.1531-1541
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    • 2023
  • Lipase is a well-known and highly in-demand enzyme. During the last decade, several lipase optimization studies have been reported. However, production costs have always been a bottleneck for commercial-scale microbial enzyme production. This research aimed to optimize the conditions for lipase production by Limtongozyma siamensis DMKU-WBL1-3 via a One-Factor-At-a-Time (OFAT) approach combined with statistical methods while using a low-cost substrate. Results suggest that low-cost substrates can be substituted for all media components. An optimal medium was found, using response surface methodology (RSM) and central composite design (CCD), to consist of 0.50% (w/v) sweet whey, 0.40% (w/v) yeast extract (food grade), and 2.50% (v/v) palm oil with the medium pH adjusted to 4 under shaking flask cultivation. From an economic point of view, this work was successful in reducing production costs while increasing lipase productivity. The medium costs were reduced by 87.5% of the original cost while lipase activity was increased by nearly 6-fold. Moreover, lipase production was further studied in a 2-L stirred-tank fermentor. Its activity was 1,055.6 ± 0.0 U/ml when aeration and agitation rates were adjusted to 1 vvm and 170 rpm, respectively. Interestingly, under this optimal lipase production, the yeast showed accumulated lipids inside the cells. The primary fatty acid is a monounsaturated fatty acid (MUFA) that is typically linked to health benefits. This study hence reveals promising lipase production and lipid accumulation by L. siamensis DMKU-WBL1-3 that are worthy of further study.

Summarization of Korean Dialogues through Dialogue Restructuring (대화문 재구조화를 통한 한국어 대화문 요약)

  • Eun Hee Kim;Myung Jin Lim;Ju Hyun Shin
    • Smart Media Journal
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    • v.12 no.11
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    • pp.77-85
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    • 2023
  • After COVID-19, communication through online platforms has increased, leading to an accumulation of massive amounts of conversational text data. With the growing importance of summarizing this text data to extract meaningful information, there has been active research on deep learning-based abstractive summarization. However, conversational data, compared to structured texts like news articles, often contains missing or transformed information, necessitating consideration from multiple perspectives due to its unique characteristics. In particular, vocabulary omissions and unrelated expressions in the conversation can hinder effective summarization. Therefore, in this study, we restructured by considering the characteristics of Korean conversational data, fine-tuning a pre-trained text summarization model based on KoBART, and improved conversation data summary perfomance through a refining operation to remove redundant elements from the summary. By restructuring the sentences based on the order of utterances and extracting a central speaker, we combined methods to restructure the conversation around them. As a result, there was about a 4 point improvement in the Rouge-1 score. This study has demonstrated the significance of our conversation restructuring approach, which considers the characteristics of dialogue, in enhancing Korean conversation summarization performance.

Numerical simulation and experimental study of non-stationary downburst outflow based on wall jet model

  • Yongli Zhong;Yichen Liu;Hua Zhang;Zhitao Yan;Xinpeng Liu;Jun Luo;Kaihong Bai;Feng Li
    • Wind and Structures
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    • v.38 no.2
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    • pp.129-146
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    • 2024
  • Aiming at the problem of non-stationary wind field simulation of downbursts, a non-stationary down-burst generation system was designed by adding a nozzle and program control valve to the inlet of the original wall jet model. The computational fluid dynamics (CFD) method was used to simulate the downburst. Firstly, the two-dimensional (2D) model was used to study the outflow situation, and the database of working conditions was formed. Then the combined superposition of working conditions was carried out to simulate the full-scale measured downburst. The three-dimensional (3D) large eddy simulation (LES) was used for further verification based on this superposition condition. Finally, the wind tunnel test is used to further verify. The results show that after the valve is opened, the wind ve-locity at low altitude increases rapidly, then stays stable, and the wind velocity at each point fluctuates. The velocity of the 2D model matches the wind velocity trend of the measured downburst well. The 3D model matches the measured downburst flow in terms of wind velocity and pulsation characteris-tics. The time-varying mean wind velocity of the wind tunnel test is in better agreement with the meas-ured time-varying mean wind velocity of the downburst. The power spectrum of fluctuating wind ve-locity at different vertical heights for the test condition also agrees well with the von Karman spectrum, and conforms to the "-5/3" law. The vertical profile of the maximum time-varying average wind veloci-ty obtained from the test shows the basic characteristics of the typical wind profile of the downburst. The effectiveness of the downburst generation system is verified.

Sputum Processing Method for Lateral Flow Immunochromatographic Assays to Detect Coronaviruses

  • Aram Kang;Minjoo Yeom;Hyekwon Kim;Sun-Woo Yoon;Dae-Gwin Jeong;Hyong-Joon Moon;Kwang-Soo Lyoo;Woonsung Na;Daesub Song
    • IMMUNE NETWORK
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    • v.21 no.1
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    • pp.11.1-11.10
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    • 2021
  • Coronavirus causes an infectious disease in various species and crosses the species barriers leading to the outbreak of zoonotic diseases. Due to the respiratory diseases are mainly caused in humans and viruses are replicated and excreted through the respiratory tract, the nasal fluid and sputum are mainly used for diagnosis. Early diagnosis of coronavirus plays an important role in preventing its spread and is essential for quarantine policies. For rapid decision and prompt triage of infected host, the immunochromatographic assay (ICA) has been widely used for point of care testing. However, when the ICA is applied to an expectorated sputum in which antigens are present, the viscosity of sputum interferes with the migration of the antigens on the test strip. To overcome this limitation, it is necessary to use a mucolytic agent without affecting the antigens. In this study, we combined known mucolytic agents to lower the viscosity of sputum and applied that to alpha and beta coronavirus, porcine epidemic diarrhea virus (PEDV) and Middle East respiratory syndrome coronavirus (MERS-CoV), respectively, spiked in sputum to find optimal pretreatment conditions. The pretreatment method using tris(2-carboxyethyl)phosphine (TCEP) and BSA was suitable for ICA diagnosis of sputum samples spiked with PEDV and MERS-CoV. This sensitive assay for the detection of coronavirus in sputum provides an useful information for the diagnosis of pathogen in low respiratory tract.

Treatment of Skin Diseases in Hyungsang Medicine (피부병의 형상의학적 치료)

  • Suk Min He;Hwang Won Duek;Jung Haeng Gyu;Lee Yong Tae
    • Journal of Physiology & Pathology in Korean Medicine
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    • v.18 no.3
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    • pp.646-669
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    • 2004
  • By treating skin diseases with Hyungsang medicine and reviewing the clinical cases of them through classifying skin diseases into general care and into Hyungsang medical care, the writer came to the conclusion as followings. The skin is a house of Kyungnak, and it' s a place which Ki comes in and out, which human body controls conditions of his physiological function and which doctors can make a diagnosis from seeing it. The skin is subject to lung and large intestine in the point of organ, but in the point of movement, to spleen and stomach. Skin diseases come from unbalance of Ki and Hyul, mostly from fever in blood and also from Dam, Wind, Dampness and Dryness because of including fire. Generally skin diseases are treated according to classifying into distinctive symptoms, region, cause or time being occurred, and concomitant symptoms. After being divided into man and woman, age and youth, fatness and leanness, Jung Ki Shin Hyul type, visceral figures, Yukkyung shapes on Hyungsang medicine method, the remedy of skin diseases which is combined common meditation with Hyungsang medical method is efficacious. In distinguishing into man and woman, age and youth, man gets sick mainly by drinking liquor and exhausting Jung, woman is taken ill generally by indigestion and Damwha, especially by drinking liquor. Young child gets ill mostly from inherent weakness, but in many cases he is occurred by disturbed digestion, so he must be taken care of ingesting food. The aged becomes ill from weakening, so he must be treated according to reasons of diseases. To fatness and leanness, skin diseases are showed symptoms by weakened Yang, insufficient Yin or excess fever on the theory of upper and lower parts, by unbalance of Ki and Hyul on the theory of left and right, by Dryness and Dampness on the theory of front and rear and by insufficiency of vitality and combined fever on the theory of inside and outside. Therefore doctors must cure the symptoms according to the theory of upper and lower, left and right, front and rear and inside and outside. In type of Jung Ki Shin Hyul, the balances between Jung-Hyul and Shin-Ki are important points. Concretely Jung type comes to easily shortage of Jung or gathering abnormally Dampness and Dam, Ki type is easy to make a mass with Ki or to be deficient of Ki, Shin type comes to press seven emotions togather or to be insufficient of Yin and fever inside, and Hyul type is inclined to be deficient of Hyul and to become feverish or to be deficient of Ki. Therefore on the ground of the above reasons skin diseases come into existence. Inclusively in Jung-Hyul type , Ki must be moved on the base of full Jung-Hyul, so Wukmijiwhangtang or Samultang is prescribed basically. In Shin-Ki type , Jung-Hyul is saved on the base of moving Ki, so Hyangsosan or Yijintang is the proper prescription. Considering the visceral figures, doctors judge for diagnosis and remedy by putting together the elements, that is, great and small sizes of a set of features (eye, ear, mouth, nose), color and temper. The yukkyung types are classified according to many or few of Ki-Hyul, and then skin diseases appear by being inclined toward one side between Ki and hyul, or among the six atmospheric elements(wind, cold, heat, dampness, dryness, and fire). Especially because Yangmyung type is full of much Ki and Hyul, and also has much fever in stomach, he gets skin symptoms frequently. So his prescription is based on taking off fever in stomach, and also he must be careful about regimen certainly.

Correlation Between Primary Tuberculous Pleurisy and NRAMP1 Genetic Polymorphism (결핵성 흉막염 환자에서 NRAMP1 유전자 다형성에 대한 연구)

  • Kim, Je-Hyeong;Kim, Byung-Gyu;Jung, Ki-Hwan;Park, Sang-Myun;Lee, Sang-Youb;Lee, Sin-Hyung;Sin, Cheol;Cho, Jae-Youn;Shim, Jae-Jeong;In, Kwang-Ho;Yoo, Se-Hwa;Kang, Kyung-Ho
    • Tuberculosis and Respiratory Diseases
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    • v.48 no.2
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    • pp.155-165
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    • 2000
  • Background: The phagolysosomal function of alveolar macrophage against M. tuberculosis infection is influenced by Nramp1, which is encoded by the NRAMP1 gene. There are several genetic polymorphisms in NRAMP1, and these polymorphisms affect the innate host resistance through the defect in production and function of Nramp1. To investigate this relationship, the NRAMP1 genetic polymorphism in patients with primary tuberculous pleurisy was determined. Methods: Fifty-six primary tuberculous pleurisy patient, who were diagnosed by pleural biopsy, were designated to the pleurisy group and 45 healthy adults were designated to the healthy control group. Three genetic polymorphisms of NRAMP1, such as a single point mutation in intron 4(469+14G/C, INT4), a nonconservative single-base substitution at codon 543 that changes aspartic acid to asparagine(D543N) and a TGTG deletion in the 3' untranslated region(1729+55delI4, 3'UTR), were determined. Polymerase chain reaction(PCR) and polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP) were used. Results: The frequencies of mutant genotypes of INT4 and 3'UTR were significantly high in pleurisy group(p=0.001, p=0.023). But the frequencies of D543N were not significantly different between the two groups(p=0.079). The odds ratios, which are a comparison with wild genotype for determining mutant genotypes, were 8. 022(95% confidence interval=2.422-26.572) for INT4 and 5.733(95% confidence interval = 1.137~28.916) for 3'UTR ; these were statistically significant But the ratio for D543N was not significant In the combined analysis of the INT4 and 3'UTR polymorphisms, the odds ratios were 6.000(95% confidence interval = 1.461~24.640) for GC/++ genotype and 14.000(95% confidence interval=1.610~121.754) for GC/+del when compared with GG/++ homozygotes ; these were statistically significant. Conclusion: Among the NRAMP1 genetic polymorphisms, a single point mutation in intron 4(469+14G/C, INT4) and a TGTG deletion in the 3' untranslated region(1729+55del4, 3'UTR) were closely related to the primary tuberculous pleurisy.

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