Identifying DNA mismatches at single-nucleotide resolution by probing individual surface potentials of DNA-capped nanoparticles

Lee, Hyungbeen,Lee, Sang Won,Lee, Gyudo,Lee, Wonseok,Nam, Kihwan,Lee, Jeong Hoon,Hwang, Kyo Seon,Yang, Jaemoon,Lee, Hyeyoung,Kim, Sangsig,Lee, Sang Woo,Yoon, Dae Sung The Royal Society of Chemistry 2018 Nanoscale Vol.10 No.2

<P>Here, we demonstrate a powerful method to discriminate DNA mismatches at single-nucleotide resolution from 0 to 5 mismatches (<I>χ</I>0 to <I>χ</I>5) using Kelvin probe force microscopy (KPFM). Using our previously developed method, we quantified the surface potentials (SPs) of individual DNA-capped nanoparticles (DCNPs, ∼100 nm). On each DCNP, DNA hybridization occurs between ∼2200 immobilized probe DNA (<I>p</I>DNA) and target DNA with mismatches (<I>t</I>DNA, ∼80 nM). Thus, each DCNP used in the bioassay (each <I>p</I>DNA-<I>t</I>DNA interaction) corresponds to a single ensemble in which a large number of <I>p</I>DNA-<I>t</I>DNA interactions take place. Moreover, one KPFM image can scan at least dozens of ensembles, which allows statistical analysis (<I>i.e.</I>, an ensemble average) of many bioassay cases (ensembles) under the same conditions. We found that as the <I>χ</I>n increased from <I>χ</I>0 to <I>χ</I>5 in the tDNA, the average SP of dozens of ensembles (DCNPs) was attenuated owing to fewer hybridization events between the <I>p</I>DNA and the <I>t</I>DNA. Remarkably, the SP attenuation <I>vs.</I> the <I>χ</I>n showed an inverse-linear correlation, albeit the equilibrium constant for DNA hybridization exponentially decreased asymptotically as the <I>χ</I>n increased. In addition, we observed a cascade reaction at a 100-fold lower concentration of <I>t</I>DNA (∼0.8 nM); the average SP of DCNPs exhibited no significant decrease but rather split into two separate states (no-hybridization <I>vs.</I> full-hybridization). Compared to complementary <I>t</I>DNA (<I>i.e.</I>, <I>χ</I>0), the ratio of no-hybridization/full-hybridization within a given set of DCNPs became ∼1.6 times higher in the presence of tDNA with single mismatches (<I>i.e.</I>, <I>χ</I>1). The results imply that our method opens new avenues not only in the research on the DNA hybridization mechanism in the presence of DNA mismatches but also in the development of a robust technology for DNA mismatch detection.</P>

In vitro metabolism of a new protective agent, KR-31543 in human an liver microsomes

Lee HyeSuk,Lim Hong,Lee DongHa,Lee SeungSeok,Lee Hongll,Kim SookJin,Ji HyeYoung 大韓藥學會 2003 大韓藥學會 總會 및 學術大會 Vol.2003 No.1

Development of an infant formula certified reference material for the analysis of organic nutrients

Lee, Joonhee,Kim, Byungjoo,Lee, Sun Young,Choi, Jongoh,Kang, Dukjin,Lee, Hwasim,Choi, KiHwan,Lee, Hyeyoung,Sim, Hee-Jung,Baek, Song-Yee,Lee, Honghee,Hyung, Seok-Won,Ahn, Seonghee,Seo, Dongwon,Hwang, J Applied Science Publishers 2019 Food chemistry Vol.298 No.-

<P><B>Abstract</B></P> <P>Infant formula certified reference material (CRM, KRISS CRM 108-02-003) were developed for the analysis of organic nutrients. The CRM is a milk-based infant formula powder, packaged at 14 g per unit. Ten thousand units were prepared and stored at −70 °C. For the certification of each nutrient, ten units were analyzed for simultaneous value-assignment and homogeneity test. Analytical methods used were isotope dilution mass spectrometry (IDMS) based on liquid chromatography mass spectrometer (LC/MS) or gas chromatography mass spectrometer (GC/MS) as higher-order reference methods.13 vitamins, 3 fatty acids, and total cholesterol were certified. The between-unit relative standard deviation of measurement results for each nutrient ranged 0.2% to 2.5%, showing very good homogeneity. The expanded relative uncertainties of the certified values ranged from 1% to 8%, indicating that they have higher-order metrological quality. The values of proximates (proteins, lipids, carbohydrates, water, and ash) were assigned through inter-laboratory comparisons.</P> <P><B>Highlights</B></P> <P> <UL> <LI> An infant formula CRMs for the analysis of organic nutrients was developed. </LI> <LI> Organic nutrients were certified by IDMS approaches as higher-order reference methods. </LI> <LI> Homogeneities and stability of the CRM were evaluated by IDMS approaches. </LI> <LI> Metrological qualities of the certified values were proved by their small uncertainties. </LI> <LI> Five proximates were value-assigned by interlaboratory comparison. </LI> </UL> </P>

반달가슴곰 캐릭터 디자인 컨셉 개발 연구

이현주(Lee Hyun-Ju),박영순(Park YoungSoon),이성식(Lee SungSik),이지현(Lee Jeehyun),정의철(Jung EuiChul),주혜영(Chu HyeYoung),김소연(Kim SoYoun),박영진(Park YoungJin),홍자경(Hong JaKyung),한유진(Han YuJin),오세환(Oh Sehwan),이주형(Lee Ju 한국디자인학회 2008 한국디자인학회 학술발표대회 논문집 Vol.- No.-

Use of PCR-restriction fragment length polymorphism for the identification of zoonotic mycobacteriosis in zebrafish caused by <i>Mycobacterium abscessus</i> and <i>Mycobacterium chelonae</i>

Seok, Seung-Hyeok,Koo, Hye Cheong,Kasuga, Asako,Kim, Yeun,Lee, Eun Gae,Lee, Hyeyoung,Park, Jong-Hwan,Baek, Min-Won,Lee, Hui-Young,Kim, Dong-Jae,Lee, Byeung-Hee,Lee, Yong-Soon,Cho, Sang-Nae,Park, Jae-H Elsevier 2006 Veterinary microbiology Vol.114 No.3

<P><B>Abstract</B></P><P>Skin ulcers, scoliosis, and dropsy-like scale edema were observed in laboratory-maintained zebrafish. Affected fish had multifocal granulomas not only in internal organs such as the liver, intestine, genital organs, kidney, muscle, and spleen but also in the fin, epithelium, gills, and sclera of the eyes. Large numbers of acid-fast-rod-shaped bacteria were observed within the necrotic centers of well-demarcated, multifocal granulomas with Gram's stain and Ziehl–Neelson's stain. The size of the <I>Mycobacterium</I> spp. was 1–2μm×2–3μm with a double-layered cell wall, based upon electron-microscopical features. Definitive diagnosis of these outbreaks was obtained by culture on selective media followed by PCR-restriction fragment length polymorphism analysis (PRA) of the <I>rpoB</I> gene for species identification. The amplified 360-bp products of the <I>rpoB</I> gene of mycobacteria isolated from zebrafish were digested with <I>Msp</I>I restriction enzyme, which revealed unique band patterns matching those of <I>Mycobacterium abscessus</I> and <I>Mycobacterium chelonae</I> which are responsible for skin and soft tissue infection caused by rapidly growing mycobacteria in humans. This is the first documentation of the precise identification of zoonotic non-tuberculous mycobacteria isolated from laboratory-maintained zebrafish by the PRA of the <I>rpoB</I> gene; this study thus provides a great deal of useful epidemiological information and reduces the likelihood that epizootics will occur.</P>

HiComet: a high-throughput comet analysis tool for large-scale DNA damage assessment

Lee, Taehoon,Lee, Sungmin,Sim, Woo Young,Jung, Yu Mi,Han, Sunmi,Won, Joong-Ho,Min, Hyeyoung,Yoon, Sungroh BioMed Central 2018 BMC bioinformatics Vol.19 No.-

<P><B>Background</B></P><P>DNA damage causes aging, cancer, and other serious diseases. The comet assay can detect multiple types of DNA lesions with high sensitivity, and it has been widely applied. Although comet assay platforms have improved the limited throughput and reproducibility of traditional assays in recent times, analyzing large quantities of comet data often requires a tremendous human effort. To overcome this challenge, we proposed HiComet, a computational tool that can rapidly recognize and characterize a large number of comets, using little user intervention.</P><P><B>Results</B></P><P>We tested HiComet with real data from 35 high-throughput comet assay experiments, with over 700 comets in total. The proposed method provided unprecedented levels of performance as an automated comet recognition tool in terms of robustness (measured by precision and recall) and throughput.</P><P><B>Conclusions</B></P><P>HiComet is an automated tool for high-throughput comet-assay analysis and could significantly facilitate characterization of individual comets by accelerating its most rate-limiting step. An online implementation of HiComet is freely available at https://github.com/taehoonlee/HiComet/.</P>

Survival Benefit of Liver Resection in BCLC-B Stage Hepatocellular Carcinoma : A Korean Nationwide Multicenter Study with Propensity Score Matching

( Hyeyoung Kim ),( Sung-woo Ahn ),( Suk Kyun Hong ),( Kyung Chul Yoon ),( Hyo-sin Kim ),( Jin Yong Choi ),( Youngrok Choi ),( Hae Won Lee ),( Nam-joon Yi ),( Kwang-woong Lee ),( Kyung-suk Suh ) 대한간학회 2016 춘·추계 학술대회 (KASL) Vol.2016 No.1

Purpose: The recent evidence supporting the survival benefit of liver resection (LR) for Barcelona Clinic Liver Cancer B hepatocellular carcinoma (BCLC-B HCC) is increasing, but remains controversial. Therefore, well designed comparative studies about the results of LR vs. non-surgical treatment for BCLC-B HCC are difficult and still uncommon. The aim of this study was to compare the survival benefit of treatment including LR vs. only non-surgical treatment for BCLC-B HCC between well-matched patient groups. Methods: We reviewed the database of the Korean Liver Cancer Study Group (KLCSG) selected using random sampling from the nationwide multicenter HCC cohort. The registered patients were diagnosed with HCC between 2003 and 2005 (n=4,520) or between 2008 and 2010 (n=4,966). Among the total 887 patients of BCLC-B HCC (multinodular asymptomatic tumors without an invasive pattern), 83 patients underwent LR as the first or second treatment within 2 years after initial diagnosis (LR group; 9.4%). Control was the group of 599 patients who underwent only non-surgical treatment within 2 years after initial diagnosis (non-LR group; 67.5%). To select well-matched patient groups, propensity score matching was used at 1:1 ratio with covariates at the time of diagnosis including registered timing, gender, age, child class, MELD score, tumor number, tumor size, and under lying liver disease. The survival outcomes were compared between the matched groups. Results: The two groups were well balanced by propensity score matching and 80 patients were matched respectively. In LR group, the patients showed significantly better outcome than in non-LR group. The 1-, 2-, 3-, and 5-year overall survivals were 90.1% vs. 78.7%, 87.6% vs. 47.5%, 75.2% vs. 35.1%, and 54.7% vs. 20.2% in LR vs. non-LR group, each (p<0.001). Multivariate Cox proportional hazards regression analysis revealed non-surgical treatments (hazard ratio, 2.974; 95% confidence interval, 1.937 to 4.565, p<0.001), low albumin level (≤3.0 g/dl) at the time of diagnosis (hazard ratio, 2.347; 95% confidence interval, 1.014 to 5.433, p=0.046), and the largest tumor size greater than 5.5cm (hazard ratio, 1.677; 95% confidence interval, 1.109 to 2.535, p=0.014) were significant independent risk factors for overall survival in BCLC-B stage HCC. Conclusion: In BCLC-B stage HCC, treatment with LR offers a significant overall survival benefit compared with non-surgical treatments.

Discovery of Novel High-Molecular Weight Oligosaccharides Containing <i>N</i>-Acetylhexosamine in Bovine Colostrum Whey Permeate Hydrolyzed with <i>Aspergillus oryzae</i> β-Galactosidase

Lee, Hyeyoung,Nobrega de Moura Bell, Juliana Maria Leite,Barile, Daniela American Chemical Society 2019 Journal of agricultural and food chemistry Vol.67 No.12

<P>Bovine milk oligosaccharides (BMOs) that resemble human milk oligosaccharides are found in whey permeate, indicating that dairy streams can be used as a potential source of bioactive oligosaccharides. Recovery of oligosaccharides from whey permeate is hindered by their low abundance and high concentration of lactose. In the present work, lactose in bovine colostrum whey permeate was hydrolyzed by <I>Aspergillus oryzae</I> β-galactosidase to facilitate subsequent monosaccharide removal by membrane separation. Chromatographic separation coupled with high-resolution mass spectrometry revealed β-galactosidase degradation of several β-linkage-containing BMOs and production of novel oligosaccharides that ranged in size from 5 to 11 monosaccharide units containing several galactose repeating units and <I>N</I>-acetylhexosamine at their reducing ends. Optimization of BMO hydrolysis and separation methodology could generate high amounts of hetero-oligosaccharides for improved recovery of potentially biotherapeutic oligosaccharides.</P> [FIG OMISSION]</BR>

Clinical Significance of HLA-DQ Antibodies in the Development of Chronic Antibody-Mediated Rejection and Allograft Failure in Kidney Transplant Recipients

Lee, Hyeyoung,Min, Ji Won,Kim, Ji-Il,Moon, In-Sung,Park, Ki-Hyun,Yang, Chul Woo,Chung, Byung Ha,Oh, Eun-Jee Williams & Wilkins Co 2016 Medicine Vol.95 No.11

<▼1><P>Supplemental Digital Content is available in the text</P></▼1><▼2><P><B>Abstract</B></P><P>With the development of the single antigen beads assay, the role of donor specific alloantibody (DSA) against human leukocyte antigens in kidney transplantation (KT) has been highlighted. This study aimed to investigate the clinical significance of DQ-DSA detected at renal allograft biopsy. We evaluated 263 KT recipients who underwent allograft biopsy and DSA detection at the same time. Among them, 155 patients who were nonsensitized before transplantation were selected to investigate the role of de-novo DQ-DSA. Both the total and nonsensitized subgroup was categorized into 4 groups each according to DSA results as: DQ only, DQ + non-DQ, non-DQ, and no DSA. In the total patient group, post-KT DSA was positive in 79 (30.0%) patients and DQ-DSA was most prevalent (64.6%). In the nonsensitized subgroup, de-novo DSAs were detected in 45 (29.0%) patients and DQ-DSA was also most prevalent (73.3%). The DQ only group showed a significantly longer post-KT duration compared to the other groups (<I>P</I> < 0.05). The overall incidence of antibody-mediated rejection (AMR) was 17.9%. B-DSA, DR-DSA, and DQ-DSA were associated with AMR (<I>P</I> < 0.05), but in the analysis for chronic AMR, only DQ-DSA showed significance in both the total and the nonsensitized subgroup (<I>P</I> < 0.05). On comparison of Banff scores among groups, those representing humoral immunity were significantly dominant in all DSA positive groups compared to the no DSA group (<I>P</I> < 0.05), and higher scores of markers representing chronic tissue injury were more frequently detected in the groups with DQ-DSA. The worst postbiopsy survival was seen in the DQ + non-DQ group of the total patient group, and patients with de-novo DQ-DSA showed poorer graft survival in the nonsensitized subgroup compared to the no DSA group (<I>P</I> < 0.05). In the multivariate analysis, de-novo DQ-DSA was the only significant risk factor associated with late allograft failure (<I>P</I> < 0.05). Our study is the first to demonstrate the association of DQ-DSA with detailed histological findings representing chronic AMR. These findings suggest that the detection of DQ-DSA in nonsensitized patients is significantly associated with the development of chronic AMR and late allograft failure. Therefore monitoring of DQ-DSA not only in sensitized patients, but also nonsensitized patients may be necessary to improve long-term allograft outcomes.</P></▼2>

LSRSL

( Hyeyoung Kim ),( Kwang-woong Lee ),( Nam-joon Yi ),( Hae Won Lee ),( Youngrok Choi ),( Hyo-sin Kim ),( Kyung Chul Yoon ),( Suk Kyun Hong ),( Rovgaliyev B. ),( Kyung-suk Suh ) 대한간학회 2016 춘·추계 학술대회 (KASL) Vol.2016 No.1

Aims: The patient with large splenorenal shunt (LSRS) is challenging at liver transplantation (LT), irrespective of organizing portal vein (PV) thrombus. Here, we report the clinical outcomes of 17 patients who received direct LSRS ligation during LT. Methods: We reviewed patients who underwent LT and intraoperative direct ligation of LSRS between Jan. 2010 and Jun. 2013. Results: Among 580 recipients, 17 patients underwent intraoperative direct ligation of LSRS. Pre-LT MELD score was 15.4 ± 6.6 (7 - 33). Main PV diameter on preoperative imaging was mean 7.6 ± 3.1 (3.0 - 13.9) mm. PV thrombectomy was done in 41.2% of patients (n = 7). Except one hospital mortality, 16 patients showed favorable outcome (94.1%). The mortality was related with sepsis, but not with liver dysfunction. There were 2 patients (11.8%) of major complication (Clavien-Dindo grade ≥ IIIa): splenic artery embolization for massive ascites control (#1), and reoperation due to ligation of left renal vein instead of LSRS at the time of LT. Including the patient of splenic artery embolization (#1), massive and prolonged ascites after LT was in 23.5% of patients (n = 4) with small diameter of PV (< 7.5mm). They were living donor recipients, and not related with pre-LT ascites. Except the patient (#1), in the other three, ascites was tolerable and well controlled by conservative manage. After the patient (#1), we performed test clamp of LSRS before direct ligation in small diameter of PV, and applied PV pressure monitoring in patients who showed a sign of portal hypertension such as bowel edema. Three patients underwent total or partial ligation under PV pressure monitoring (within 8mmHg of pressure difference before and after ligation of LSRS). Total 16 patients have maintained normal liver function until last follow-up (94.1%). Conclusions: Direct ligation of LSRS during LT is a safe and effective method to overcome the effects of LSRS. However, meticulous care is needed in isolation and ligation of LSRS. Selective simultaneous intraoperative portal pressure monitoring can be helpful for prevention of severe portal hypertension.