• Title/Summary/Keyword: RdRp

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Epidemiological application of the cycle threshold value of RT-PCR for estimating infection period in cases of SARS-CoV-2

  • Soonjong Bae;Jong-Myon Bae
    • Journal of Medicine and Life Science
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    • v.20 no.3
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    • pp.107-114
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    • 2023
  • Epidemiological control of coronavirus disease 2019 (COVID-19) is needed to estimate the infection period of confirmed cases and identify potential cases. The present study, targeting confirmed cases for which the time of COVID-19 symptom onset was disclosed, aimed to investigate the relationship between intervals (day) from symptom onset to testing the cycle threshold (CT) values of real-time reverse transcription-polymerase chain reaction. Of the COVID-19 confirmed cases, those for which the date of suspected symptom onset in the epidemiological investigation was specifically disclosed were included in this study. Interval was defined as the number of days from symptom onset (as disclosed by the patient) to specimen collection for testing. A locally weighted regression smoothing (LOWESS) curve was applied, with intervals as explanatory variables and CT values (CTR for RdRp gene and CTE for E gene) as outcome variables. After finding its non-linear relationship, a polynomial regression model was applied to estimate the 95% confidence interval values of CTR and CTE by interval. The application of LOWESS in 331 patients identified a U-shaped curve relationship between the CTR and CTE values according to the number of interval days, and both CTR and CTE satisfied the quadratic model for interval days. Active application of these results to epidemiological investigations would minimize the chance of failing to identify individuals who are in contact with COVID-19 confirmed cases, thereby reducing the potential transmission of the virus to local communities.

Effect of Stimulus Waveform of Biphasic Current Pulse on Retinal Ganglion Cell Responses in Retinal Degeneration (rd1) mice

  • Ahn, Kun No;Ahn, Jeong Yeol;Kim, Jae-Hyung;Cho, Kyoungrok;Koo, Kyo-In;Senok, Solomon S.;Goo, Yong Sook
    • The Korean Journal of Physiology and Pharmacology
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    • v.19 no.2
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    • pp.167-175
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    • 2015
  • A retinal prosthesis is being developed for the restoration of vision in patients with retinitis pigmentosa (RP) and age-related macular degeneration (AMD). Determining optimal electrical stimulation parameters for the prosthesis is one of the most important elements for the development of a viable retinal prosthesis. Here, we investigated the effects of different charge-balanced biphasic pulses with regard to their effectiveness in evoking retinal ganglion cell (RGC) responses. Retinal degeneration (rd1) mice were used (n=17). From the ex-vivo retinal preparation, retinal patches were placed ganglion cell layer down onto an $8{\times}8$ multielectrode array (MEA) and RGC responses were recorded while applying electrical stimuli. For asymmetric pulses, 1st phase of the pulse is the same with symmetric pulse but the amplitude of 2nd phase of the pulse is less than $10{\mu}A$ and charge balanced condition is satisfied by lengthening the duration of the pulse. For intensities (or duration) modulation, duration (or amplitude) of the pulse was fixed to $500{\mu}s$($30{\mu}A$), changing the intensities (or duration) from 2 to $60{\mu}A$(60 to $1000{\mu}s$). RGCs were classified as response-positive when PSTH showed multiple (3~4) peaks within 400 ms post stimulus and the number of spikes was at least 30% more than that for the immediate pre-stimulus 400 ms period. RGC responses were well modulated both with anodic and cathodic phase-1st biphasic pulses. Cathodic phase-1st pulses produced significantly better modulation of RGC activity than anodic phase-1st pulses regardless of symmetry of the pulse.

Complete genome sequence of Fusarium hypovirus DK2l strain and genomic diversity of dsRNA mycoviruses isolated from Fusarium graminearum

  • Lim, Won-Seok;Chu, Yeon-Mee;Lee, Yin-Won;Kim, Kook-Hyung
    • Proceedings of the Korean Society of Plant Pathology Conference
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    • 2003.10a
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    • pp.117.3-118
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    • 2003
  • We tested for the presence of double-stranded RNA (dsRNA) mycovirus in 827 Fusarium graminearum isolated from diseased barley and maize. dsRNA mycoviruses with various sizes were isolated. Of them, it was previously reported that dsRNA from DK2l isolate had pronounced morphological changes, including reduction in mycelial growth, increased to red pigmentation, reduced virulence and sporulation. (Chu et al., Appl. Environ. Microbiol. 2002). For better understanding of this hypovirulence associated with DK2l dsRNA virus, we determined the complete nucleotide sequence of dsRNA genome and named Fusarium hypovirus DK2l strain (Fhv-DK2l ). Genomic RNA of Fhv-DK2l was determined to be 6625 nucleotides in length excluding the poly (A) tail and contained three putative open reading frame. RNA-dependent RNA polymerase (RdRp) and helicase domain were expected in ORF A, 54 to 4709 nucleotide position. ORE B, 4752 to 5216 nucleotide position, and ORF C, 5475 to 6578 nucleotide position, were predicted to encode 16.7kDa and 41.3kDa protein respectively each. We could not detect any conserved domains from these two proteins. Phylogenetic analysis showed Fhv-DK2l was related to Cryphonectria hypovirus 3. Ten additional isolates were found that were infected with dsRNA mycoviruses. These mycoviruses contain 2 to 4 different segments of dsRNAs with the size range of approximately 1.7 to 10-kbp in length. The presence of dsRNAs isolates did not affect colony morphology and were transmissible through conidia and ascospore with incidence of 30-100%. These results indicate that there is genomic diversity of dsRNA mycoviruses that infect F. graminearum isolates and that impact of virus infection on host's morphology and virulence is determined by the interaction between dsRNAs and the fungal host, not by the mere presence of the dsRNAs

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Changes in the Factors Associated with Decrease of Pungency in ‘Kagdugi’ during Fermentation (깍두기 숙성중 매운맛 감소에 관련된 인자들의 변화)

  • Kim, Mee-Ree;Rhee, Hei-Soo
    • Korean Journal of Food Science and Technology
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    • v.24 no.4
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    • pp.361-366
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    • 1992
  • Studies were carried out on the factors responsible for the change of pungency in 'Kagdugi'. During fermentation, the pH in 'Kagdugi' decreased to around to 4, while acidity increased continuously. In accordance with the decrease of pungency, the content of 4-methylthio-3-butenyl isothiocyanate (MTB-NCS) in the homogenate of 'Kagdugi' decreased gradually and on 3rd day, the optimum period for good flavor, below 5% of that in the homogenate of fresh radish. The decrease of MTB-NCS formation was accompanied by the gradual loss of 4-methylthio-3-butenyl glucosinolate (MTB-glucosinolate), which was found to disappear more rapidly than total glucosinolate. Also, the ascorbic acid-dependent myrosinase activity was observed to decline gradually with the fermentation time, although the ascorbic acid content varied above the concentration required for maximal enzyme activity. Thus, it was suggested that the decline of MTB-NCS may be related to the gradual losses of MTB-glucosinolate content and myrosinase activity which are both susceptible to the effect of acidic pH.

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A New Double-Stranded RNA Mycovirus from Pleurotus ostreatus (ASI 2504)

  • Lee, Jin-Kyung;Lee, Kang-Hyo;Shim, Hye-Kyung;Yang, Joo-Sung;Kim, Gyu-Hyun;Kong, Won-Sik;Yoo, Young-Bok;Kim, Dae-Hyun;Kim, Dong-Giun;Lee, Suk-Chan
    • The Plant Pathology Journal
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    • v.22 no.1
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    • pp.68-74
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    • 2006
  • A new virus with a dsRNA genome was isolated and characterized from the Suhan-:neutari strain (ASI 2504) of Pleurotus ostreatus, which was characterized as long and slightly bent with small caps on the stipe of fruit body. Thirty nm isometric viruses with three dsRNA segments (approximately 2.0, 1.84 and 1.82 kb in sizes) were isolated by ultracentrifugation in sucrose gradients. Western analysis of protein extracted purified viruses with anti-virus polyclonal antibody confirmed that viruses have two specific proteins (36 and 68 kDa). Computer analysis of 2.0 kb segment shows that high. sequence identity with RNA-dependent RNA polymerase (RdRp) of partitiviruses, respectively. When compared to other dsRNA mycoviruses in a phylogenetic analysis, OMDV was most related to Pleurotus ostreatus virus 1.

Allexivirus Transmitted by Eriophyid Mites in Garlic Plants

  • Kang, Sang-Gu;Koo, Bong-Jin;Lee, Eun-Tag;Chang, Moo-Ung
    • Journal of Microbiology and Biotechnology
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    • v.17 no.11
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    • pp.1833-1840
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    • 2007
  • Viruses in garlic plants (Allium sativum L.) have accumulated and evolved over generations, resulting in serious consequences for the garlic trade around the world. These viral epidemics are also known to be caused by aphids and eriophyid mites (Aceria tulipae) carrying Potyviruses, Carlaviruses, and Allexiviruses. However, little is known about viral epidemics in garlic plants caused by eriophyid mites. Therefore, this study investigated the infection of garlic plants with Allexiviruses by eriophyid mites. When healthy garlic plants were cocultured with eriophyid mites, the leaves of the garlic plants developed yellow mosaic strips and became distorted. In extracts from the eriophyid mites, Allexiviruses were observed using immunosorbent electron microscopy (ISEM). From an immunoblot analysis, coat proteins against an Allexivirus garlic-virus antiserum were clearly identified in purified extracts from collected viral-infected garlic plants, eriophyid mites, and garlic plants infected by eriophyid mites. A new strain of GarV-B was isolated and named GarV-B Korea isolate 1 (GarV-B1). The ORF1 and ORF2 in GarV-B1 contained a typical viral helicase, RNA-directed RNA polymerase (RdRp), and triple gene block protein (TGBp) for viral movement between cells. The newly identified GarV-B1 was phylogenetically grouped with GarV-C and GarV-X in the Allexivirus genus. All the results in this study demonstrated that eriophyid mites are a transmitter insect species for Allexiviruses.

Identification of Two Novel Amalgaviruses in the Common Eelgrass (Zostera marina) and in Silico Analysis of the Amalgavirus +1 Programmed Ribosomal Frameshifting Sites

  • Park, Dongbin;Goh, Chul Jun;Kim, Hyein;Hahn, Yoonsoo
    • The Plant Pathology Journal
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    • v.34 no.2
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    • pp.150-156
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    • 2018
  • The genome sequences of two novel monopartite RNA viruses were identified in a common eelgrass (Zostera marina) transcriptome dataset. Sequence comparison and phylogenetic analyses revealed that these two novel viruses belong to the genus Amalgavirus in the family Amalgaviridae. They were named Zostera marina amalgavirus 1 (ZmAV1) and Zostera marina amalgavirus 2 (ZmAV2). Genomes of both ZmAV1 and ZmAV2 contain two overlapping open reading frames (ORFs). ORF1 encodes a putative replication factory matrix-like protein, while ORF2 encodes a RNA-dependent RNA polymerase (RdRp) domain. The fusion protein (ORF1+2) of ORF1 and ORF2, which mediates RNA replication, was produced using the +1 programmed ribosomal frameshifting (PRF) mechanism. The +1 PRF motif sequence, UUU_CGN, which is highly conserved among known amalgaviruses, was also found in ZmAV1 and ZmAV2. Multiple sequence alignment of the ORF1+2 fusion proteins from 24 amalgaviruses revealed that +1 PRF occurred only at three different positions within the 13-amino acid-long segment, which was surrounded by highly conserved regions on both sides. This suggested that the +1 PRF may be constrained by the structure of fusion proteins. Genome sequences of ZmAV1 and ZmAV2, which are the first viruses to be identified in common eelgrass, will serve as useful resources for studying evolution and diversity of amalgaviruses.

Comparison of clinical diagnostic performance between commercial RRT-LAMP and RT-qPCR assays for SARS-CoV-2 detection

  • Kim, Hye-Ryung;Park, Jonghyun;Han, Hyung-Soo;Kim, Yu-Kyung;Jeon, Hyo-Sung;Park, Seung-Chun;Park, Choi-Kyu
    • Korean Journal of Veterinary Service
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    • v.44 no.3
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    • pp.163-168
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    • 2021
  • The rapid and reliable detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a key role in isolating infected patients and preventing further viral transmission. In this study, we evaluated the clinical diagnostic performances of a commercial real-time reverse transcription loop-mediated isothermal amplification (RRT-LAMP) assay (Isopollo® COVID-2 assay, M-monitor, Daegu, Korea) using eighty COVID-19 suspected clinical samples and compared these with the results of a commercial real-time reverse transcription polymerase chain reaction (RT-qPCR) assay (AllplexTM 2019-nCoV rRT-QPCR Assay, SeeGene, Seoul, Korea). The results of the RRT-LAMP assay targeting the N or RdRp gene of SARS-CoV-2 showed perfect agreement with the RT-qPCR assay results in terms of detection. Furthermore, the RRT-LAMP assay was completed in just within a 20-min reaction time, which is significantly faster than about the 2 h currently required for the RT-qPCR assay, thus enabling prompt decision making regarding the isolation of infected patients. The RRT-LAMP assay will be a valuable tool for rapid, sensitive, and specific detection of SARS-CoV-2 in human or unexpected animal clinical cases.

The Effects of Rainbow Power Therapy on Neck Pain Patients (Rainbow Power Therapy의 경항통에 대한 효과)

  • Seo, Jung-Chul;Seo, Bo-Myung;Kim, Sung-Woong;Lee, Kyung-Min;Yun, Jong-Seok;Lee, Sea-Youn;Kim, Kyung-Woon;Lee, Yoon-Kyung;Lim, Seong-Chul;Jung, Tae-Young;Hwang, Jae-Wok;Han, Sang-Won
    • Korean Journal of Acupuncture
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    • v.21 no.2
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    • pp.147-159
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    • 2004
  • Objective : This study was designed to estimate the effects of Rainbow Power therapy on neck pain patients by using Visual Analogue Scale(VAS) and pressure algometer. Methods : Rainbow Power therapy group consisted of 18 patients and acupuncture therapy group consisted of 7 patients. The degree of improvement of neck pain was evaluated by VAS and pain pressure threshold(at the points of Jianjing GB21 and Jianwaishu SI14) before treatment, before 3rd treatment and before 5th treatment. Rainbow Power therapy was performed at the points of Jianjing GB21, Zhongfu LU1, Yangxi LI5, Ganshu BL18, Weishu BL21 and Shenshu, BL23. Each points were stimulated with RP-UM103(Rainbow Power therapy instrument) for 20 seconds. The points of acupuncture therapy were Jeonggeun, Jeongjong, Sangbaekn and Hegu LI4 and acupuncture was maintained for 15 minutes. After above therapy dry cupping was performed at the points of Jianjing GB21, Jianwaishu SI14, Gaohuang BL43, Tianzong, SI11 and Bingfeng SI12 for 5 minutes. Results : There was no significant difference between the two groups in VAS, pain threshold of Jianjing GB21 and Jianwaishu SI14 following treatment. In the two groups VAS was significantly decreased. In Rainbow Power therapy group the pain threshold of the two points was significantly increased. But there was no significant increase in acupuncture therapy groups about the pain threshold of Jianwaishu SI14. Conclusions : The effectiveness of Rainbow Power therapy on neck pain was shown through VAS and pressure algometer. These imply that Rainbow Power therapy may be useful for neck pain. Further study is needed about Rainbow Power therapy.

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Nutrient Utilization, Body Composition and Lactation Performance of First Lactation Bali Cows (Bos sondaicus) on Grass-Legume Based Diets

  • Sukarini, I.A.M.;Sastradipradja, D.;Sutardi, T.;Mahardika, IG.;Budiarta, IG.A.
    • Asian-Australasian Journal of Animal Sciences
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    • v.13 no.12
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    • pp.1681-1690
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    • 2000
  • A study on energy and protein utilization, and milk production of Bali cows on grass-legume diets was carried out using 12 first lactation cows (initial BW $263.79{\pm}21.66kg$) during a period of 16 weeks starting immediately post calving. The animals were randomly allotted into 4 dietary treatment groups R1, R2, R3 and R4, receiving from the last 2 months of pregnancy onwards, graded improved rations based on a mixture of locally available grass and legume feed ad libitum. R1 contained on a DM basis 70% elephant grass (PP, Penisetum purpureum) plus 30% Gliricidia sepia leaves (GS), R2 was 30% PP plus 55% GS supplemented with 15% Hibiscus tilliactus leaves (HT, defaunating effect), R3 and R4 were 22.5% PP+41.25% GS+11.25% HT+25% concentrate, where R3 was not and R4 supplemented with zinc di-acetate. TDN, CP and zinc contents of the diets were 58.2%, 12.05% and 18.3 mg/kg respectively for R1, 65.05%, 16.9% and 25.6 mg/kg respectively for R2, 66.03%, 16.71% and 29.02 mg/kg respectively for R3 and 66.03%, 16.71% and 60.47 mg/kg respectively for R4. Milk production and body weight were monitored throughout the experimental period. In vivo body composition by the urea space technique validated by the body density method and supported by carcass data was estimated at the start and termination of the experiment. Nutrient balance and rumen performance characteristics were measured during a balance trial of 7 days during the 3rd and 4th week of the lactation period. Results indicated that quality of ration caused improvement of ruminal total VFA concentration, increments being 52 to 65% for R2, R3 and R4 above R1, with increments of acetate being less (31 to 48%) and propionate being proportionally more in comparison to total VFA increments. Similarly, ammonia concentrations increased to 5.24 to 7.07 mM, equivalent to 7.34 to 9.90 mg $NH_3-N/100ml$ rumen fluid. Results also indicated that feed quality did not affect DE and ME intakes, and heat production (HP), but increased GE, UE, energy in milk and total retained energy (RE total) in body tissues and milk. Intake-, digestible- and catabolized-protein, and retained-protein in body tissues and milk (Rprot) were all elevated increasing the quality of ration. Similar results were obtained for milk yield and components with mean values reaching 2.085 kg/d (R4) versus 0.92 kg/d (R1) for milk yield, and 170.22 g/d (R4) vs 71.69 g/d (R1), 105.74 g/d (R4) vs 45.35 g/d (R1), 101.34 g/d (R4) vs 46.36 g/d (R1) for milk-fat, -protein, and -lactose, respectively. Relatively high yields of milk production was maintained longer for R4 as compared to the other treatment groups. There were no significant effects on body mass and components due to lactation. From the relationship $RE_{total}$ (MJ/d)=12.79-0.373 ME (MJ/d); (r=0.73), it was found that $ME_{m}=0.53MJ/kgW^{0.75}.d$. Requirement of energy to support the production of milk, ranging from 0.5 to 3.0 kg/d, follows the equation: Milk Prod. ($Q_{mp}$, kg/d)=[-2.48+4.31 ME($MJ/kg^{0.75}.d$)]; (r=0.6) or $Q_{mp}$=-3.4+[0.08($ME-RE_{body\;tissue}$)]MJ/d]; (r=0.94). The requirement for protein intake for maintenance ($IP_m$) equals $6.19 g/kg^{0.75}.d$ derived from the relationship RP=-47.4+0.12 IP; (r=0.74, n=9). Equation for protein requirement for lactation is $Q_{nl}$=[($Q_{mp}$)(% protein in milk)($I_{mp}$)]/100, where $Q_{nl}$ is g protein required for lactation, $Q_{mp}$ is daily milk yield, Bali cow's milk-protein content av. 5.04%, and $I_{mp}$ is metabolic increment for milk production ($ME_{lakt}/ME_{m}=1.46$).