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Comparison of digital PCR platforms using the molecular marker
Cherl-Joon Lee,Wonseok Shin,Minsik Song,Seung-Shick Shin,Yujun Park,Kornsorn Srikulnath,Dong Hee Kim,Kyudong Han Korea Genome Organization 2023 Genomics & informatics Vol.21 No.2
Assays of clinical diagnosis and species identification using molecular markers are performed according to a quantitative method in consideration of sensitivity, cost, speed, convenience, and specificity. However, typical polymerase chain reaction (PCR) assay is difficult to quantify and have various limitations. In addition, to perform quantitative analysis with the quantitative real-time PCR (qRT-PCR) equipment, a standard curve or normalization using reference genes is essential. Within the last a decade, previous studies have reported that the digital PCR (dPCR) assay, a third-generation PCR, can be applied in various fields by overcoming the shortcomings of typical PCR and qRT-PCR assays. We selected Stilla Naica System (Stilla Technologies), Droplet Digital PCR Technology (Bio-Rad), and Lab on an Array Digital Real-Time PCR analyzer system (OPTOLANE) for comparative analysis among the various droplet digital PCR platforms currently in use commercially. Our previous study discovered a molecular marker that can distinguish Hanwoo species (Korean native cattle) using Hanwoo-specific genomic structural variation. Here, we report the pros and cons of the operation of each dPCR platform from various perspectives using this species identification marker. In conclusion, we hope that this study will help researchers to select suitable dPCR platforms according to their purpose and resources.
Soft sweep development of resistance in Escherichia coli under fluoroquinolone stress
Xianxing Xie,Ruichen Lv,Chao Yang,Yajun Song,Yanfeng Yan,Yujun Cui,Ruifu Yang 한국미생물학회 2019 The journal of microbiology Vol.57 No.12
We employed a stepwise selection model for investigating the dynamics of antibiotic-resistant variants in Escherichia coli K-12 treated with increasing concentrations of ciprofloxacin (CIP). Firstly, we used Sanger sequencing to screen the variations in the fluoquinolone target genes, then, employed Illumina NGS sequencing for amplicons targeted regions with variations. The results demonstrated that variations G81C in gyrA and K276N and K277L in parC are standing resistance variations (SRVs), while S83A and S83L in gyrA and G78C in parC were emerging resistance variations (ERVs). The variants containing SRVs and/or ERVs were selected successively based on their sensitivities to CIP. Variant strain 1, containing substitution G81C in gyrA, was immediately selected following ciprofloxacin exposure, with obvious increases in the parC SRV, and parC and gyrA ERV allele frequencies. Variant strain 2, containing the SRVs, then dominated the population following a 20× increase in ciprofloxacin concentration, with other associated allele frequencies also elevated. Variant strains 3 and 4, containing ERVs in gyrA and parC, respectively, were then selected at 40× and 160× antibiotic concentrations. Two variants, strains 5 and 6, generated in the selection procedure, were lost because of higher fitness costs or a lower level of resistance compared with variants 3 and 4. For the second induction, all variations/indels were already present as SRVs and selected out step by step at different passages. Whatever the first induction or second induction, our results confirmed the soft selective sweep hypothesis and provided critical information for guiding clinical treatment of pathogens containing SRVs.
Jianping Shen,Siwei Zhang,Wei Wang,Shuguang Li,Song Zhang,Yujun Wang 한국광학회 2021 Current Optics and Photonics Vol.5 No.3
A tapered As 2 S 3 photonic crystal fiber (PCF) with four layers of air holes in a hexagonal array around the core is designed in this paper. Numerical simulation shows that the dispersion D decreases and the nonlinearity coefficient γ increases from the thick to the thin end along the tapered PCF. We simulate the midinfrared pulse compression in the tapered As 2 S 3 PCF using the adaptive split-step Fourier method. Initial Gaussian pulses of 4.4 ps and a central wavelength of 2.5 μm propagating in the tapered PCF arelocated in the anomalous dispersion region. With an average power of assumed input pulses at 3 mW and a repetition frequency of 81.0 MHz, we theoretically obtain a pulse duration of 56 fs and a compression factor of 78 when the pulse propagates from the thick end to the thin end of the tapered PCF. When confinement loss in the tapered PCF is included in the simulation, the minimum pulse duration reaches 72 fs; correspondingly, the maximum compression factor reaches 61. The results show that in the anomalous-dispersion region, midinfrared pulses can be efficiently compressed in a dispersion-decreasing and nonlinearity-increasing tapered As 2 S 3 PCF. Due to confinement loss in the tapered fiber, the efficiency of pulse compression is suppressed.
Jinlong Zhang,Jingkun Lu,Bing Liu,Qiuyue Liu,Fan Jin,Miaojun Zhang,Yerong Liu,Yujun Song,Chenhui Dong,Wanyi Zhang,Ningxu Han,Xu Deng,Feng Xing 한양대학교 세라믹연구소 2019 Journal of Ceramic Processing Research Vol.20 No.S1
Quantification of viable spores is a time taking task due to the lack of rapid, efficient and accurate methods. This studypresented a simple spectrophotometric method for the detection of viable spores based on spore’s property of losing refractivityduring the germination process. By comparison of the results obtained by both spectrophotometric method and colonycounting method, a good linear correlation (R2 = 0.99) was achieved between viable spore concentration and OD loss underappropriate conditions. To avoid interference from ungerminable spores and vegetative cells, a turbidity complementationstrategy of keeping the initial concentration of spore suspensions at the same and relatively lower level was required. Thecalibration equation developed could be used to predict the viable spore yield produced in a series of fermentation experiments. The experimental results proved that this novel spectrophotometric method was sensitive, rapid, and easy to performcompared to conventional colony counting method.