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VCS: Tool for Visualizing Copy Number Variation and Single Nucleotide Polymorphism
Kim, HyoYoung,Sung, Samsun,Cho, Seoae,Kim, Tae-Hun,Seo, Kangseok,Kim, Heebal Asian Australasian Association of Animal Productio 2014 Animal Bioscience Vol.27 No.12
Copy number variation (CNV) or single nucleotide phlyorphism (SNP) is useful genetic resource to aid in understanding complex phenotypes or deseases susceptibility. Although thousands of CNVs and SNPs are currently avaliable in the public databases, they are somewhat difficult to use for analyses without visualization tools. We developed a web-based tool called the VCS (visualization of CNV or SNP) to visualize the CNV or SNP detected. The VCS tool can assist to easily interpret a biological meaning from the numerical value of CNV and SNP. The VCS provides six visualization tools: i) the enrichment of genome contents in CNV; ii) the physical distribution of CNV or SNP on chromosomes; iii) the distribution of log2 ratio of CNVs with criteria of interested; iv) the number of CNV or SNP per binning unit; v) the distribution of homozygosity of SNP genotype; and vi) cytomap of genes within CNV or SNP region.
Kim, Jong Min,Kim, Sung,Shin, Dong Hee,Seo, Sang Woo,Lee, Ha Seung,Kim, Ju Hwan,Jang, Chan Wook,Kang, Soo Seok,Choi, Suk-Ho,Kwak, Gyea Young,Kim, Kyung Joong,Lee, Hanleem,Lee, Hyoyoung Elsevier 2018 Nano energy Vol.43 No.-
<P><B>Abstract</B></P> <P>To overcome small- and indirect-bandgap nature of crystalline bulk Si, a lot of efforts have been made to utilize Si quantum dots (SQDs) in optoelectronic devices. By controlling the size of Si quantum dots (SQDs), it is possible to vary the energy bandgap based on quantum confinement effect, which can maximize the power-conversion efficiency (PCE) of solar cells due to the energy harvesting in a broader spectral range. Here, we first employ graphene transparent conductive electrodes (TCEs) for SQDs-based solar cells, showing a maximum PCE of 16.2%, much larger than ever achieved in bulk-Si solar cells with graphene TCEs. In this work, the graphene TCEs are doped with two kinds of materials such as AuCl<SUB>3</SUB> and Ag nanowires for efficient collection of the carriers photo-induced in SQDs. The encapsulation of the doped-graphene TCE with another graphene layer prevents the doping elements from being desorbed or oxidized, thereby making the PCE higher, its doping dependence more evident, and the long-term performance more stable. The observed unique solar cell characteristics prove to be dominated by the trade-off effects between doping-induced variations of diode quality, transmittance/sheet resistance of graphene, energy barrier at the graphene TCE/SQDs interface, and reflectance.</P> <P><B>Highlights</B></P> <P> <UL> <LI> First use of graphene for Si-quantum-dots -based solar cells. </LI> <LI> Maximum power conversion efficiency is 16.2%, largest ever achieved. </LI> <LI> The encapsulation of the graphene electrodes prevents the dopants from being desorbed. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>
Hyoyoung Jang,Hyojoong Kim,Yikweon Jang 한국응용곤충학회 2010 한국응용곤충학회 학술대회논문집 Vol.2010 No.10
Plant penetration by aphids can be monitored electrically by the electrical penetration graph (EPG) technique. To confirm whether some behaviors are correlated to specific graph pattern in EPG, we analyzed the two synchronized data, EPG and video records. We recorded electrical penetration graph (EPG) and behaviors of aphids simultaneously. Then we compared the behaviors of aphids with the recorded EPG waveforms in order to match their visible behaviors and invisible behaviors with stylet. The visible behaviors were categorized for walking, wagging, honeydew production, and reproduction. When the aphids were generally motionless, the EPG denoted feeding-related waveforms (E1, E2, F and G). Whereas, probing waveforms (B and pd) frequently occurred when they were wagging. We aim to present the correlation between observed behaviors and EPG patterns.
Kim, Seong U.,Jo, Eun-Jung,Mun, Hyoyoung,Noh, Yuseon,Kim, Min-Gon American Chemical Society 2018 Journal of agricultural and food chemistry Vol.66 No.19
<P>Here, we report an enhanced colorimetric method using enzymatic amplification with nitroblue tetrazolium (NBT)/5-bromo-4-chloro-3-indolyl phosphate (BCIP) precipitation for the ultrasensitive detection of <I>Escherichia coli</I> O157:H7 through immunomagnetic separation-selective filtration. Biotinylated anti-<I>E. coli</I> O157:H7 antibody and streptavidin-alkaline phosphatase were conjugated to the surface of magnetic nanoparticles, and <I>E. coli</I> O157:H7-conjugates complexes remained on the membrane filter surface. The resultant light brown spots on the membrane filter were amplified with NBT/BCIP solution to yield enzyme-catalyzed precipitation, which increased with an increasing <I>E. coli</I> O157:H7 concentration. <I>E. coli</I> O157:H7 was detected in pure samples with limits of detection of 10 and 6.998 colony-forming units (CFU)/mL through visual observation and measurement of optical density, respectively. The proposed method was applied to a lettuce sample inoculated with selective <I>E. coli</I> O157:H7, which was detected within 55 min without cross-reactivity to non-target bacteria. This enhanced colorimetric method has potential for on-site detection of food contaminants and environmental pollutants.</P> [FIG OMISSION]</BR>
HyoYoung Kim,문선진,김희발 한국유전체학회 2008 Genomics & informatics Vol.6 No.1
Little evidence supports the existence of imprinted genes in chicken. Imprinted genes are thought to be intimately connected with the acquisition of parental resources in mammals; thus, the predicted lack of this type of gene in chicken is not surprising, given that they leave their offspring to their own heritance after conception. In this study, we identified several imprinted genes and their orthologs in human, mouse, and zebrafish, including 30 previously identified human and mouse imprinted genes. Next, using the HomoloGene database, we identified six orthologous genes in human, mouse, and chicken; however, no orthologs were identified for SLC22A18, and mouse Ppp1r9a was not included in the HomoloGene database. Thus, from our analysis, four candidate chicken imprinted genes (IGF2, UBE3A, PHLDA2, and GRB10) were identified. To expand our analysis, zebrafish was included, but no probe ID for UBE3A exists in this species. Thus, ultimately, three candidate imprinted genes (IGF2, PHLDA2, and GRB10) in chicken were identified. GRB10 was not significant in chicken and zebrafish based on the Wilcoxon-Mann- Whitney test, whereas a weak correlation between PHLDA2 in chicken and human was identified from the Spearman's rank correlation coefficient. Significant associations between human, mouse, chicken, and zebrafish were found for IGF2 and GRB10 using the Friedman's test. Based on our results, IGF2, PHLDA2, and GRB10 are candidate imprinted genes in chicken. Importantly, the strongest candidate was PHLDA2.