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author:("Kim, jinyun")
1.  Significance of 40-, 45-, and 48-kDa Proteins in the Moderate-to-Severe Clinical Symptoms of Buckwheat Allergy 
This study was aimed to investigate the relationship between the allergen components and moderate-to-severe allergic reactions in patients with buckwheat allergy.
Fifteen patients with a history of buckwheat ingestion and a buckwheat specific IgE level≥0.35 kU/L were enrolled. They were divided into 2 groups according to clinical severity scores, with 0-1 being asymptomatic-to-mild and 2-4 being moderate-to-severe symptoms. Immunoblotting was performed to investigate IgE reactivity toward buckwheat allergens and to measure intensity of each component by using a reflective densitometer.
The proportions of positive band to the 16 kDa (62.5% vs 0%, P=0.026) and 40-50 kDa (87.5% vs 28.6%, P=0.041) buckwheat allergens in the grade 2-4 group were higher than those in grade 0-1 group. The level of buckwheat specific IgE of grade 2-4 group was higher than that of grade 0-1 group (41.3 kU/L vs 5.5 kU/L, P=0.037). The median optical densities (ODs) of IgE antibody binding to 40-50 kDa protein were higher in the grade 2-4 group, compared with those in the grade 0-1 group (130% OD vs 60.8% OD, P=0.037).
The 40-50 kDa protein is implicated as an important allergen to predict moderate-to-severe clinical symptoms in Korean children with buckwheat allergy.
PMCID: PMC4274468  PMID: 25553261
Food allergy; buckwheat; allergen; severity; component; immunoblotting
2.  Long-Term Outcomes and Dynamics of Mutants Associated with Lamivudine-Adefovir Rescue Therapy in Patients with Lamivudine-Resistant Chronic Hepatitis B 
Gut and Liver  2015;9(1):103-108.
To investigate the association between the baseline profiles and dynamics of hepatitis B virus (HBV) DNA polymerase gene mutations and the long-term virological response of lamivudine (LAM)-adefovir (ADV) combination therapy in patients with LAM-resistant chronic hepatitis B.
Seventy-five patients who received LAM-ADV combination therapy for more than 12 months were analyzed. Restriction fragment mass polymorphism assays were used to detect and monitor the dynamics of LAM- and ADV-resistant mutations.
The median duration of LAM-ADV combination therapy was 26 months (range, 12 to 58 months). The baseline mutation profiles, rtM204I (p=0.992), rtM204I/V (p=0.177), and rtL180M (p=0.051), were not correlated with the cumulative virological response, and the baseline HBV DNA level (p=0.032) was the only independent predictive factor for cumulative virological response. Tests for LAM- and ADV-resistant mutations were performed in 12 suboptimal responders in weeks 48 and 96. The population of rtM204 mutants persisted or increased in 8 of 12 patients, and rtA181T mutants newly emerged as a minor population in four patients until 96 weeks. Nevertheless, the viral loads progressively decreased during rescue therapy, and these dynamics did not correlate with virological response.
The baseline profile and dynamics of LAM-resistant mutations during LAM-ADV combination therapy are not associated with a virological response.
PMCID: PMC4282849  PMID: 25287170
Hepatitis B virus; Lamivudine resistance; Restriction fragment mass polymorphism; Mutation
3.  Characterization of age signatures of DNA methylation in normal and cancer tissues from multiple studies 
BMC Genomics  2014;15(1):997.
DNA methylation (DNAm) levels can be used to predict the chronological age of tissues; however, the characteristics of DNAm age signatures in normal and cancer tissues are not well studied using multiple studies.
We studied approximately 4000 normal and cancer samples with multiple tissue types from diverse studies, and using linear and nonlinear regression models identified reliable tissue type-invariant DNAm age signatures. A normal signature comprising 127 CpG loci was highly enriched on the X chromosome. Age-hypermethylated loci were enriched for guanine–and-cytosine-rich regions in CpG islands (CGIs), whereas age-hypomethylated loci were enriched for adenine–and-thymine-rich regions in non-CGIs. However, the cancer signature comprised only 26 age-hypomethylated loci, none on the X chromosome, and with no overlap with the normal signature. Genes related to the normal signature were enriched for aging-related gene ontology terms including metabolic processes, immune system processes, and cell proliferation. The related gene products of the normal signature had more than the average number of interacting partners in a protein interaction network and had a tendency not to interact directly with each other. The genomic sequences of the normal signature were well conserved and the age-associated DNAm levels could satisfactorily predict the chronological ages of tissues regardless of tissue type. Interestingly, the age-associated DNAm increases or decreases of the normal signature were aberrantly accelerated in cancer samples.
These tissue type-invariant DNAm age signatures in normal and cancer can be used to address important questions in developmental biology and cancer research.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-997) contains supplementary material, which is available to authorized users.
PMCID: PMC4289351  PMID: 25406591
DNA methylation; Epigenetics; Age signature; Aging; Meta-analysis; Systems biology; Cancer
4.  Relationship Between Indoor Air Pollutant Levels and Residential Environment in Children With Atopic Dermatitis 
This study was aimed to investigate the relationship between indoor air pollutant levels and residential environment in children with atopic dermatitis (AD) living in Seoul.
A total of 150 children with AD were included. Residential environment was assessed by questionnaires which were completed by their parents. To evaluate the level of exposure to the indoor air pollutants, concentrations of the indoor air pollutants including particulate matter with diameter less than 10 µm (PM10), formaldehyde, carbon dioxide (CO2), carbon monoxide (CO), nitrogen dioxide (NO2), Total Volatile Organic Compound (TVOC), benzene, toluene, ethyl-benzene, xylene, styrene, bacterial aerosols, and airborne fungi were measured.
A significant difference was exhibited in the levels of PM10 in case of visible fungus on the walls (P=0.047). There was relationship between the construction year of the house, moving to a newly constructed building within 1 year and formaldehyde level. With the use of artificial air freshener, the differences were found in the concentrations of TVOC (P=0.003), benzene (P=0.015), toluene (P=0.012) and ethyl-benzene (P=0.027). The concentration of xylene was significantly high when oil was used as heating fuel (P=0.015). Styrene exhibited differences depending on building type and its concentrations were significantly high in a residential and commercial complex building (P=0.005). The indoor concentration of bacterial aerosols was significantly low with the use of air cleaner (P=0.045). High NO2, benzene concentrations were present in case of almost no ventilation (P=0.028 and P=0.028, respectively).
Individual residential environments are closely related with the levels of the indoor air pollutants. To alleviate AD symptoms, simple questions about residential environments such as visible fungus on the walls and the use of artificial air freshener are helpful to assess the possibility of increased indoor air pollutant levels when direct measurement is not available.
PMCID: PMC4214972  PMID: 25374751
Atopic dermatitis; environment; childhood; air pollution; pollutant
5.  Characterizing the Secondary Protein Structure of Black Widow Dragline Silk Using Solid-State NMR & X-ray Diffraction 
Biomacromolecules  2013;14(10):3472-3483.
This study provides a detailed secondary structural characterization of major ampullate dragline silk from Latrodectus hesperus (black widow) spiders. X-ray diffraction results show that the structure of black widow major ampullate silk fibers is comprised of stacked β-sheet nanocrystallites oriented parallel to the fiber axis and an amorphous region with oriented (anisotropic) and isotropic components. The combination of two-dimensional (2D) 13C-13C through-space and through-bond solid-state NMR experiments provide chemical shifts that are used to determine detailed information about amino acid motif secondary structure in black widow spider dragline silk. Individual amino acids are incorporated into different repetitive motifs that make up the majority of this protein-based biopolymer. From the solid-state NMR measurements, we assign distinct secondary conformations to each repetitive amino acid motif and hence to the amino acids that make up the motifs. Specifically, alanine is incorporated in β-sheet (poly(Alan) and poly(Gly-Ala)), 31-helix (poly(Gly-Gly-Xaa), and α-helix (poly(Gln-Gln-Ala-Tyr)) components. Glycine is determined to be in β-sheet (poly(Gly-Ala)) and 31-helical (poly(Gly-Gly-Xaa)) regions, while serine is present in β-sheet (poly(Gly-Ala-Ser)), 31-helix (poly(Gly-Gly-Ser)), and β-turn (poly(Gly-Pro-Ser)) structures. These various motif-specific secondary structural elements are quantitatively correlated to the primary amino acid sequence of major ampullate spidroin 1 and 2 (MaSp1 and MaSp2) and are shown to form a self-consistent model for black widow dragline silk.
PMCID: PMC3914425  PMID: 24024617
6.  Genome Information of Methylobacterium oryzae, a Plant-Probiotic Methylotroph in the Phyllosphere 
PLoS ONE  2014;9(9):e106704.
Pink-pigmented facultative methylotrophs in the Rhizobiales are widespread in the environment, and many Methylobacterium species associated with plants produce plant growth-promoting substances. To gain insights into the life style at the phyllosphere and the genetic bases of plant growth promotion, we determined and analyzed the complete genome sequence of Methylobacterium oryzae CBMB20T, a strain isolated from rice stem. The genome consists of a 6.29-Mb chromosome and four plasmids, designated as pMOC1 to pMOC4. Among the 6,274 coding sequences in the chromosome, the bacterium has, besides most of the genes for the central metabolism, all of the essential genes for the assimilation and dissimilation of methanol that are either located in methylotrophy islands or dispersed. M. oryzae is equipped with several kinds of genes for adaptation to plant surfaces such as defense against UV radiation, oxidative stress, desiccation, or nutrient deficiency, as well as high proportion of genes related to motility and signaling. Moreover, it has an array of genes involved in metabolic pathways that may contribute to promotion of plant growth; they include auxin biosynthesis, cytokine biosynthesis, vitamin B12 biosynthesis, urea metabolism, biosorption of heavy metals or decrease of metal toxicity, pyrroloquinoline quinone biosynthesis, 1-aminocyclopropane-1-carboxylate deamination, phosphate solubilization, and thiosulfate oxidation. Through the genome analysis of M. oryzae, we provide information on the full gene complement of M. oryzae that resides in the aerial parts of plants and enhances plant growth. The plant-associated lifestyle of M. oryzae pertaining to methylotrophy and plant growth promotion, and its potential as a candidate for a bioinoculant targeted to the phyllosphere and focused on phytostimulation are illuminated.
PMCID: PMC4161386  PMID: 25211235
7.  Anti-Helicobacter pylori activities of FEMY-R7 composed of fucoidan and evening primrose extract in mice and humans 
Laboratory Animal Research  2014;30(3):131-135.
Helicobacter pylori-eliminating effects of FEMY-R7, composed of fucoidan and evening primrose extract, were investigated in mice and humans. Male C57BL/6 mice were infected with the bacteria by intragastric inoculation (1×109 CFU/mouse) 3 times at 2-day intervals, and simultaneously, orally treated twice a day with 10 or 100 mg/kg FEMY-R7 for 2 weeks. In Campylobcter-like organism-detection test, FEMY-R7 markedly reduced the urease-positive reactivity. In a clinical sudy, human subjects, confirmed to be infected with Helicobacter pylori, were orally administered twice a day with a capsule containing 150 mg FEMY-R7 for 8 weeks. FEMY-R7 significantly decreased both the Delta over baseline-value in urea breath test and the serum pepsinogens I and II levels. The results indicate that FEMY-R7 not only eliminates H. pylori from gastric mucosa of animals and humans, but also improves gastric function.
PMCID: PMC4188832  PMID: 25324874
Helicobacter pylori; FEMY-R7; fucoidan; evening primrose extract; Campylobcter-like organism-detection test; urea breath test; pepsinogen
8.  Identification of a Novel Mutation in the CYBB Gene, p.Asp378Gly, in a Patient With X-linked Chronic Granulomatous Disease 
Chronic granulomatous disease (CGD) is a rare immunodeficiency disease, which is characterized by the lack of a functional nicotinamide adenine dinucleotide phosphate (NADPH) oxidase in phagocytes. The disease presents leukocytosis, anemia, hypergammaglobulinemia, and granuloma formation of the skin, lung, or lymph nodes. The mutation of the CYBB gene encoding gp91phox, located on chromosome Xp21.1 is one of the causes of CGD. We report a patient with X-linked CGD who carried a novel mutation, a c.1133A>G (paAsp378Gly) missense mutation, in the CYBB gene.
PMCID: PMC4077965  PMID: 24991462
Chronic granulomatous disease; immunodeficiency; CYBB gene; mutation
9.  Application of Damage Control Resuscitation Strategies to Patients with Severe Traumatic Hemorrhage: Review of Plasma to Packed Red Blood Cell Ratios at a Single Institution 
Journal of Korean Medical Science  2014;29(7):1007-1011.
When treating trauma patients with severe hemorrhage, massive transfusions are often needed. Damage control resuscitation strategies can be used for such patients, but an adequate fresh frozen plasma: packed red blood cell (FFP:PRBC) administration ratio must be established. We retrospectively reviewed the medical records of 100 trauma patients treated with massive transfusions from March 2010 to October 2012. We divided the patients into 2 groups according to the FFP:PRBC ratio: a high-ratio (≥0.5) and a low-ratio group (<0.5). The patient demographics, fluid and transfusion quantities, laboratory values, complications, and outcomes were analyzed and compared. There were 68 patients in the high-ratio and 32 in the low-ratio group. There were statistically significant differences between groups in the quantities of FFP, FFP:PRBC, platelets, and crystalloids administered, as well as the initial diastolic blood pressure. Bloodstream infections were noted only in the high-ratio group, and the difference was statistically significant (P=0.028). Kaplan-Meier plots revealed that the 24-hr survival rate was significantly higher in the high-ratio group (71.9% vs. 97.1%, P<0.001). In severe hemorrhagic trauma, raising the FFP:PRBC ratio to 0.5 or higher may increase the chances of survival. Efforts to minimize bloodstream infections during the resuscitation must be increased.
Graphical Abstract
PMCID: PMC4101768  PMID: 25045236
Resuscitation; Transfusion; Blood Product Ratio; Survival; Trauma
10.  Dendritic Cell Expression of the Signaling Molecule TRAF6 is Critical for Gut Microbiota-Dependent Immune Tolerance 
Immunity  2013;38(6):1211-1222.
The intracellular signaling molecule TRAF6 is critical for Toll-like receptor (TLR)-mediated activation of dendritic cells (DCs). We now report that DC-specific deletion of TRAF6 (TRAF6ΔDC) resulted, unexpectedly, in loss of mucosal tolerance, characterized by spontaneous development of T helper 2 (Th2) cells in the lamina propria, and eosinophilic enteritis and fibrosis in the small intestine. Loss of tolerance required the presence of gut commensal microbiota, but was independent of DC-expressed MyD88. Further, TRAF6ΔDC mice exhibited decreased regulatory T (Treg) cell numbers in the small intestine, and diminished induction of iTreg cells in response to model antigen. Evidence suggested this defect was associated with diminished DC expression of interleukin-2 (IL-2). Finally, we demonstrate that aberrant Th2 cell-associated responses in TRAF6ΔDC mice could be mitigated via restoration of Treg cell activity. Collectively, our findings reveal a role for TRAF6 in directing DC maintenance of intestinal immune tolerance through balanced induction of Treg versus Th2 cell immunity.
PMCID: PMC3715143  PMID: 23791643
11.  An ethanolic extract of Angelica gigas improves atherosclerosis by inhibiting vascular smooth muscle cell proliferation 
Laboratory Animal Research  2014;30(2):84-89.
The effects of an ethanolic extract of Angelica gigas (EAG) on the vascular smooth muscle cell (VSMC) proliferation and high-cholesterol diet-induced hypercholesterolemia and atherosclerosis were investigated. Rat aortic VSMCs were stimulated with platelet-derived growth factor-BB (25 ng/mL) for the induction of DNA synthesis and cell proliferation. EAG (1-10 µg/mL) significantly inhibited both the thymidine incorporation and cell proliferation in a concentration-dependent manner. Hypercholesterolemia was induced by feeding male New Zealand white rabbits with 0.5% cholesterol in diet for 10 weeks, during which EAG (1% in diet) was given for the final 8 weeks after 2-week induction of hypercholesterolemia. Hypercholesterolemic rabbits exhibited great increases in serum total cholesterol and low-density lipoproteins (LDL) levels, and finally severe atheromatous plaque formation covering 28.4% of the arterial walls. EAG significantly increased high-density lipoproteins (HDL), slightly decreased LDL, and potentially reduced the atheroma area to 16.6%. The results indicate that EAG attenuates atherosclerosis not only by inhibiting VASC proliferation, but also by increasing blood HDL levels. Therefore, it is suggested that EAG could be an alternative or an adjunct therapy for the improvement of hypercholesterolemia and atherosclerosis.
PMCID: PMC4079836  PMID: 24999363
Hypercholesterolemia; atherosclerosis; vascular smooth muscle cell proliferation; Angelica gigas
12.  Musicians Show General Enhancement of Complex Sound Encoding and Better Inhibition of Irrelevant Auditory Change in Music: An ERP Study 
The European journal of neuroscience  2013;37(8):1295-1307.
Using electrophysiology, we have examined two questions in relation to musical training – namely, whether it enhances sensory encoding of the human voice and whether it improves the ability to ignore irrelevant auditory change. Participants performed an auditory distraction task, in which they identified each sound as either short (350 ms) or long (550 ms) and ignored a change in sounds’ timbre. Sounds consisted of a male and a female voice saying a neutral sound [a], and of a cello and a French Horn playing an F3 note. In some blocks, musical sounds occurred on 80% of trials, while voice sounds on 20% of trials. In other blocks, the reverse was true. Participants heard naturally recorded sounds in half of experimental blocks and their spectrally-rotated versions in the other half. Regarding voice perception, we found that musicians had a larger N1 ERP component not only to vocal sounds but also to their never before heard spectrally-rotated versions. We, therefore, conclude that musical training is associated with a general improvement in the early neural encoding of complex sounds. Regarding the ability to ignore irrelevant auditory change, musicians’ accuracy tended to suffer less from the change in sounds’ timbre, especially when deviants were musical notes. This behavioral finding was accompanied by a marginally larger re-orienting negativity in musicians, suggesting that their advantage may lie in a more efficient disengagement of attention from the distracting auditory dimension.
PMCID: PMC3628406  PMID: 23301775
musical training; auditory perception in musicians; timbre perception; auditory change; auditory distraction
13.  Stem Cell Research Funding Policies and Dynamic Innovation: A Survey of Open Access and Commercialization Requirements 
Stem Cell Reviews  2014;10(4):455-471.
This article compares and contrasts the pressures of both open access data sharing and commercialization policies in the context of publicly funded embryonic stem cell research (SCR). First, normative guidelines of international SCR organizations were examined. We then examined SCR funding guidelines and the project evaluation criteria of major funding organizations in the EU, the United Kingdom (UK), Spain, Canada and the United States. Our survey of policies revealed subtle pressures to commercialize research that include: increased funding availability for commercialization opportunities, assistance for obtaining intellectual property rights (IPRs) and legislation mandating commercialization. In lieu of open access models, funders are increasingly opting for limited sharing models or “protected commons” models that make the research available to researchers within the same region or those receiving the same funding. Meanwhile, there still is need for funding agencies to clarify and standardize terms such as “non-profit organizations” and “for-profit research,” as more universities are pursuing for-profit or commercial opportunities.
PMCID: PMC4127440  PMID: 24676713
Stem cell research (SCR); Human embryonic stem cells (hESC); Induced pluripotent stem cells (iPSC); Open access; Data sharing; Commercialization
14.  Prevalence of Immediate-Type Food Allergy in Early Childhood in Seoul 
There are scanty epidemiologic data on the prevalence of food allergy (FA) among preschool children in Asia. We performed this study to determine the prevalence and causative foods of immediate-type FA in early childhood in Korea.
A questionnaire-based, cross-sectional study was performed between September and October 2011. Children aged 0-6 years were recruited from 301 public child care centers in Seoul. Parents were asked to complete a questionnaire on FA. Children with FA were classified into "perceived FA, ever," "immediate-type FA, ever," and "immediate-type FA, current" according to the algorithm.
A total of 16,749 children were included in this study. The prevalence of "perceived FA, ever," "immediate-type FA, ever," and "immediate-type FA, current" was 15.1%, 7.0%, and 3.7%, respectively. "Immediate-type FA, current" was reported by 182 (4.9%) out of 3,738 children aged ≤2 years, 262 (3.4%) of 7,648 children aged 3-4 years, and 177 (3.3%) of 5,363 children aged 5-6 years. Hen's egg (126/621) was the most frequent cause as the individual food item, followed by cow's milk (82/621) and peanut (58/621). Among the food groups, fruits (114/621), tree nuts (90/621) and crustaceans (85/621) were the most common offending foods. The three leading causes of food-induced anaphylaxis were hen's egg (22/47), cow's milk (15/47), and peanut (14/47).
The prevalence of immediate-type FA in early childhood is 3.7%, and is higher in younger children. The most common offending foods differed with age.
PMCID: PMC3936041  PMID: 24587949
Immediate hypersensitivity; child; food allergy; prevalence
15.  Perilla oil improves blood flow through inhibition of platelet aggregation and thrombus formation 
Laboratory Animal Research  2014;30(1):21-27.
The inhibitory effects of perilla oil on the platelet aggregation in vitro and thrombosis in vivo were investigated in comparison with aspirin, a well-known blood flow enhancer. Rabbit platelet-rich plasma was incubated with perilla oil and aggregation inducers collagen or thrombin, and the platelet aggregation rate was analyzed. Perilla oil significantly inhibited both the collagen- and thrombin-induced platelet aggregations, in which the thromboxane B2 formation from collagen-activated platelets were reduced in a concentration-dependent manner. Rats were administered once daily by gavage with perilla oil for 1 week, carotid arterial thrombosis was induced by applying 35% FeCl3-soaked filter paper for 10 min, and the blood flow was monitored with a laser Doppler probe. Perilla oil delayed the FeCl3-induced arterial occlusion in a dose-dependent manner, doubling the occlusion time at 0.5 mL/kg. In addition, a high dose (2 mL/kg) of perilla oil greatly prevented the occlusion, comparable to the effect of aspirin (30 mg/kg). The results indicate that perilla oil inhibit platelet aggregation by blocking thromboxane formation, and thereby delay thrombosis following oxidative arterial wall injury. Therefore, it is proposed that perilla oil could be a good candidate without adverse effects for the improvement of blood flow.
PMCID: PMC3973807  PMID: 24707301
Platelet aggregation; thromboxane B2; thrombosis; perilla oil
16.  In vitro and in vivo anti-Helicobacter pylori activities of FEMY-R7 composed of fucoidan and evening primrose extract 
Laboratory Animal Research  2014;30(1):28-34.
Effects of FEMY-R7, composed of fucoidan and evening primrose extract, on the bacterial growth and intragastric infection of Helicobacter pylori as well as gastric secretion were investigated in comparison with a proton-pump inhibitor pantoprazole. For in vitro anti-bacterial activity test, H. pylori (1×108 CFU/mL) was incubated with a serially-diluted FEMY-R7 for 3 days. As a result, FEMY-R7 fully inhibited the bacterial growth at 100 µg/mL, which was determined to be a minimal inhibitory concentration. In addition, 6-hour incubation with H. pylori, FEMY-R7 inhibited urease activity in a concentration-dependent manner, showing a median inhibitory concentration of 1,500 µg/mL. In vivo elimination study, male C57BL/6 mice were infected with the bacteria by intragastric inoculation (5×109 CFU/mouse) 3 times at 2-day intervals, and simultaneously, orally treated twice a day with 10, 30 or 100 mg/kg FEMY-R7 for 7 days. In Campylobcter-like organism-detection test and bacterial identification, FEMY-R7 exerted a high bacteria-eliminating capacity at 30-100 mg/kg, comparably to 30 mg/kg pantoprazole. In contrast to a strong antacid activity of pantoprazole in a pylorus-ligation study, FEMY-R7 did not significantly affect gastric pH, free HCl, and total acidity, although it significantly decreased fluid volume at a low dose (10 mg/kg). The results indicate that FEMY-R7 eliminate H. pylori from gastric mucosa by directly killing the bacteria and preventing their adhesion and invasion, rather than by inhibiting gastric secretion or mucosal damage.
PMCID: PMC3973808  PMID: 24707302
Helicobacter pylori; FEMY-R7; fucoidan; evening primrose extract; minimal inhibitory concentration (MIC); CLO test; gastric secretion
17.  Small Private Key PKS on an Embedded Microprocessor 
Sensors (Basel, Switzerland)  2014;14(3):5441-5458.
Multivariate quadratic ( ) cryptography requires the use of long public and private keys to ensure a sufficient security level, but this is not favorable to embedded systems, which have limited system resources. Recently, various approaches to cryptography using reduced public keys have been studied. As a result of this, at CHES2011 (Cryptographic Hardware and Embedded Systems, 2011), a small public key scheme, was proposed, and its feasible implementation on an embedded microprocessor was reported at CHES2012. However, the implementation of a small private key scheme was not reported. For efficient implementation, random number generators can contribute to reduce the key size, but the cost of using a random number generator is much more complex than computing on modern microprocessors. Therefore, no feasible results have been reported on embedded microprocessors. In this paper, we propose a feasible implementation on embedded microprocessors for a small private key scheme using a pseudo-random number generator and hash function based on a block-cipher exploiting a hardware Advanced Encryption Standard (AES) accelerator. To speed up the performance, we apply various implementation methods, including parallel computation, on-the-fly computation, optimized logarithm representation, vinegar monomials and assembly programming. The proposed method reduces the private key size by about 99.9% and boosts signature generation and verification by 5.78% and 12.19% than previous results in CHES2012.
PMCID: PMC4004000  PMID: 24651722
public key cryptography; small private key; multivariate quadratic cryptography; embedded microprocessor; efficient software implementation; ATxmega128a1; AES accelerator; random number generator; signature generation
18.  Identification of a novel mutation in the CHD7 gene in a patient with CHARGE syndrome 
Korean Journal of Pediatrics  2014;57(1):46-49.
CHARGE syndrome has been estimated to occur in 1:10,000 births worldwide and shows various clinical manifestations. It is a genetic disorder characterized by a specific and a recognizable pattern of anomalies. The major clinical features are ocular coloboma, heart malformations, atresia of the choanae, growth retardation, genital hypoplasia, and ear abnormalities. The chromodomain helicase DNA-binding protein 7 (CHD7) gene, located on chromosome 8q12.1, causes CHARGE syndrome. The CHD7 protein is an adenosine triphosphate (ATP)-dependent chromatin remodeling protein. A total of 67% of patients clinically diagnosed with CHARGE syndrome have CHD7 mutations. Five hundred twenty-eight pathogenic and unique CHD7 alterations have been identified so far. We describe a patient with a CHARGE syndrome diagnosis who carried a novel de novo mutation, a c.3896T>C (p. leu1299Pro) missense mutation, in the CHD7 gene. This finding will provide more information for genetic counseling and expand our understanding of the pathogenesis and development of CHARGE syndrome.
PMCID: PMC3935113  PMID: 24578717
CHARGE syndrome; CHD7; Mutation
19.  Nattokinase improves blood flow by inhibiting platelet aggregation and thrombus formation 
Laboratory Animal Research  2013;29(4):221-225.
The effects of nattokinase on the in vitro platelet aggregation and in vivo thrombosis were investigated in comparison with aspirin. Rabbit platelet-rich plasma was incubated with nattokinase and aggregation inducers collagen and thrombin, and the platelet aggregation rate was analyzed. Nattokinase significantly inhibited both the collagen- and thrombin-induced platelet aggregations. Nattokinase also reduced thromboxane B2 formation from collagen-activated platelets in a concentration-dependent manner. Rats were orally administered with nattokinase for 1 week, and their carotid arteries were exposed. Arterial thrombosis was induced by applying 35% FeCl3-soaked filter paper for 10 min, and the blood flow was monitored with a laser Doppler probe. Nattokinase delayed the FeCl3-induced arterial occlusion in a dose-dependent manner, doubling the occlusion time at 160 mg/kg. In addition, a high dose (500 mg/kg) of nattokinase fully prevented the occlusion, as achieved with aspirin (30 mg/kg). The results indicate that nattokinase extracted from fermented soybean inhibit platelet aggregation by blocking thromboxane formation, and thereby delay thrombosis following oxidative arterial wall injury. Therefore, it is suggested that nattokinase could be a good candidate without adverse effects for the improvement of blood flow.
PMCID: PMC3879341  PMID: 24396387
Platelet aggregation; thromboxane B2; thrombosis; nattokinase
20.  Inhibitory effects of a β-dunnione compound MB12662 on gastric secretion and ulcers 
Laboratory Animal Research  2013;29(3):178-181.
The effects of a β-dunnione compound MB12662 on the gastric secretion and ulcers were investigated in rats. In order to assess the effects of MB12662 on the gastric secretion and acidity, rats were subjected to pylorus ligation operation, and 6 hours later, gastric fluid was collected. Treatment with MB12662 reduced the gastric fluid volume to 47.3% of control level and increased pH. In an alcohol-induced ulcer model, rats were orally administered 3 mL/kg of ethanol, and 1 hour later, the ulcer lesions ware measured under a stereomicroscope. MB12662 reduced ulcer index in a dose-dependent manner which was much stronger than a proton-pump inhibitor pantoprazole. In a stress-induced ulcer model, rats were subjected to water-immersion restraint stress, and 5 hours later, the ulcer lesions ware examined. MB12662 also attenuated the stress-induced gastric lesions, although the efficacy of MB12662 was lower than that of pantoprazole. Therefore, it is suggested that MB12662 could be a candidate compound for the prevention or treatment of gastric ulcers induced by gastric over-secretion and alcoholic hangover.
PMCID: PMC3791353  PMID: 24106514
Gastric secretion; ulcer; alcohol; stress; β-dunnione; MB12662
21.  Draft Genome Sequence of the Antifungal-Producing Plant-Benefiting Bacterium Burkholderia pyrrocinia CH-67 
Journal of Bacteriology  2012;194(23):6649-6650.
Burkholderia pyrrocinia CH-67 was isolated from forest soil as a biocontrol agent to be utilized in agriculture. Here, we report the 8.05-Mb draft genome sequence of this bacterium. Its genome contains genes involved in biosynthesis of secondary metabolites and plant growth promotion, which may contribute to probiotic effects on plants.
PMCID: PMC3497489  PMID: 23144399
22.  Genome Sequence of the Agar-Degrading Marine Bacterium Alteromonadaceae sp. Strain G7 
Journal of Bacteriology  2012;194(24):6961-6962.
Here, we present the high-quality draft genome sequence of the agar-degrading marine gammaproteobacterium Alteromonadaceae sp. strain G7, which was isolated from coastal seawater to be utilized as a bioresource for production of agar-derived biofuels. The 3.91-Mb genome contains a number of genes encoding algal polysaccharide-degrading enzymes such as agarases and sulfatases.
PMCID: PMC3510564  PMID: 23209220
23.  Genome Sequence of the Thermotolerant Yeast Kluyveromyces marxianus var. marxianus KCTC 17555 
Eukaryotic Cell  2012;11(12):1584-1585.
Kluyveromyces marxianus is a thermotolerant yeast that has been explored for potential use in biotechnological applications, such as production of biofuels, single-cell proteins, enzymes, and other heterologous proteins. Here, we present the high-quality draft of the 10.9-Mb genome of K. marxianus var. marxianus KCTC 17555 (= CBS 6556 = ATCC 26548).
PMCID: PMC3536290  PMID: 23193140
24.  Complete Genome Sequence of the Probiotic Bacterium Bifidobacterium bifidum Strain BGN4 
Journal of Bacteriology  2012;194(17):4757-4758.
Bifidobacterium bifidum, a common endosymbiotic inhabitant of the human gut, is considered a prominent probiotic microorganism that may promote health. We completely decrypted the 2.2-Mb genome sequence of B. bifidum BGN4, a strain that had been isolated from the fecal sample of a healthy breast-fed infant, and annotated 1,835 coding sequences.
PMCID: PMC3415514  PMID: 22887663
25.  Construction and Manipulation of a New Kaposi's Sarcoma-Associated Herpesvirus Bacterial Artificial Chromosome Clone 
Journal of Virology  2012;86(18):9708-9720.
Efficient genetic modification of herpesviruses such as Kaposi's sarcoma-associated herpesvirus (KSHV) has come to rely on bacterial artificial chromosome (BAC) technology. In order to facilitate this approach, we generated a new KSHV BAC clone, called BAC16, derived from the rKSHV.219 virus, which stems from KSHV and Epstein-Barr virus-coinfected JSC1 primary effusion lymphoma (PEL) cells. Restriction enzyme and complete sequencing data demonstrate that the KSHV of JSC1 PEL cells showed a minimal level of sequence variation across the entire viral genome compared to the complete genomic sequence of other KSHV strains. BAC16 not only stably propagated in both Escherichia coli and mammalian cells without apparent genetic rearrangements, but also was capable of robustly producing infectious virions (∼5 × 107/ml). We also demonstrated the utility of BAC16 by generating deletion mutants of either the K3 or K5 genes, whose products are E3 ligases of the membrane-associated RING-CH (MARCH) family. While previous studies have shown that individual expression of either K3 or K5 results in efficient downregulation of the surface expression of major histocompatibility complex class I (MHC-I) molecules, we found that K5, but not K3, was the primary factor critical for the downregulation of MHC-I surface expression during KSHV lytic reactivation or following de novo infection. The data presented here demonstrate the utility of BAC16 for the generation and characterization of KSHV knockout and mutant recombinants and further emphasize the importance of functional analysis of viral genes in the context of the KSHV genome besides the study of individual gene expression.
PMCID: PMC3446615  PMID: 22740391

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