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The new allele C*03:93 showed one nucleotide difference with C*03:04:01 at codon 140 (GCT/ACT)., (© 2011 John Wiley & Sons A/S.)

The structural characterization of glycosaminoglycan (GAG) carbohydrates by mass spectrometry has been a long-standing analytical challenge due to the inherent heterogeneity of these biomolecules, specifically polydispersity, variability in sulfation, and hexuronic acid stereochemistry. Recent advances in tandem mass spectrometry methods employing threshold and electron-based ion activation have resulted in the ability to determine the location of the labile sulfate modification as well as assign the stereochemistry of hexuronic acid residues. To facilitate the analysis of complex electron detachment dissociation (EDD) spectra, principal component analysis (PCA) is employed to differentiate the hexuronic acid stereochemistry of four synthetic GAG epimers whose EDD spectra are nearly identical upon visual inspection. For comparison, PCA is also applied to infrared multiphoton dissociation spectra (IRMPD) of the examined epimers. To assess the applicability of multivariate methods in GAG mixture analysis, PCA is utilized to identify the relative content of two epimers in a binary mixture., (© American Society for Mass Spectrometry, 2011)

A dynamic model of lactic acid fermentation using Lactococcus lactis was constructed, and a metabolic flux analysis (MFA) and metabolic control analysis (MCA) were performed to reveal an intensive metabolic understanding of lactic acid bacteria (LAB). The parameter estimation was conducted with COPASI software to construct a more accurate metabolic model. The experimental data used in the parameter estimation were obtained from an LC-MS/ MS analysis and time-course simulation study. The MFA results were a reasonable explanation of the experimental data. Through the parameter estimation, the metabolic system of lactic acid bacteria can be thoroughly understood through comparisons with the original parameters. The coefficients derived from the MCA indicated that the reaction rate of L-lactate dehydrogenase was activated by fructose 1,6-bisphosphate and pyruvate, and pyruvate appeared to be a stronger activator of L-lactate dehydrogenase than fructose 1,6-bisphosphate. Additionally, pyruvate acted as an inhibitor to pyruvate kinase and the phosphotransferase system. Glucose 6-phosphate and phosphoenolpyruvate showed activation effects on pyruvate kinase. Hexose transporter was the strongest effector on the flux through L-lactate dehydrogenase. The concentration control coefficient (CCC) showed similar results to the flux control coefficient (FCC).

We performed a large case-control study (3,932 cases, 15,562 controls) to investigate the association of hepatitis B virus (HBV) and hepatitis C virus (HCV) with hematopoietic malignancies in Korea, where HBV is endemic. HBV was present in 636 control patients (4.1%), 333 lymphoma patients (12.4%), and 75 leukemia patients (6.0%). HCV infection was present in 173 control patients (1.1%), 76 lymphoma patients (2.8%), and 18 leukemia patients (1.4%). Co-infection of HBV and HCV was present in one (0.007%) control patient, seven lymphoma patients (0.3%), and one leukemia patient (0.08%). HBV infection was associated with increased risks for most subtypes of B and T/NK-cell lymphomas, Hodgkin's lymphoma, and acute myeloid leukemia. HCV infection was associated with increased risks for diffuse large B cell lymphoma, extranodal marginal zone B cell lymphoma, peripheral T cell lymphoma, and acute lymphoid leukemia B cell early pre-B type. HBV seems to have a more important role than HCV in the pathogenesis of specific hematologic malignancies in Korea.

The DRB1*11:95 showed a single nucleotide difference with the DRB1*11:01:01 allele at codon 10 (TAC/TGC)., (© 2010 John Wiley & Sons A/S.)

The new allele B*39:60 showed one nucleotide difference with B*39:01:01 at codon 152 (GTG/GCG)., (© 2010 John Wiley & Sons A/S.)

We evaluated a new rapid influenza diagnostic test for the pandemic (H1N1) 2009 influenza virus by using real-time reverse transcription-PCR (rRT-PCR) and viral culture. The sensitivities were 68.5% and 64.5%, and the specificities were 98.4% and 97.6%, respectively. This kit should be used with caution, and negative results should be verified by a confirmative test.

New allele A*31:34 showed one nucleotide difference with A*31:01:02 at codon 166 (GAG/CAG)., (© 2010 John Wiley & Sons A/S.)

Objectives: To characterise the genetic and serological diversity of pathogenic Escherichia coli, we tested 111 E coli strains isolated from diarrhoeal patients in Korea between 2003 and 2006., Methods: The isolates were tested through polymerase chain reaction (PCR) and slide agglutination method for the detection of virulence genes and serotypes, respectively. To compare the expression of Shiga toxin (stx)-1 and stx2 genes, real-time quantitative reverse-transcriptase PCR and rapid exprssion assay, reversed-passive latex agglutination, were performed., Results: Forty-nine Shiga toxin-producing E coli (STEC) strains and 62 non-STEC strains, including 20 enteropathogenic E coli, 20 enterotoxigenic E coli, 20 enteroaggregative E coli, and 2 enteroinvasive E coli were randomly chosen from the strains isolated from diarrhoeal patients in Korea between 2003 and 2006. PCR analysis indicated that locus of enterocyte effacement pathogenicity island, that is, eaeA, espADB, and tir genes were present in STEC, enteropathogenic E coli, and enteroinvasive E coli. Quorum sensing-related gene luxS was detected in most of pathogenic E coli strains. Major serotypes of the STEC strains were O157 (26%) and O26 (20%), whereas the non-STEC strains possessed various serotypes. Especially, all the strains with serotype O157 carried stx2 and the tested virulence factors. Of the STEC strains, the data of real-time quantitative reverse-transcriptase PCR and reversed-passive latex agglutination tests showed that messenger RNA- and protein expression of stx2 gene were higher than those of stx1 gene., Conclusion: Our results provide the epidemiological information regarding the trend of STEC and non-STEC infections in the general population and show the fundamental data in association of serotypes with virulence genes in diarrhoeagenic E coli strains from Korea.

Incompatibility of human leukocyte antigen (HLA) alleles between donors and recipients of unrelated hematopoietic stem cell transplantation (UHSCT) increases the risk of acute graft-versus-host disease (GVHD). We evaluated the positional effect of amino acid substitutions in HLA molecules on severe acute GVHD in Korean pediatric recipients of UHSCT. All of 64 donor-recipient pairs were serologically matched for HLA-A, -B, and -DR loci. Only substitution at residue 9 resulting from an HLA-A*02 polymorphism was significantly associated with the risk of severe acute GVHD in patients (OR=7.0, P=0.033) on multivariate analysis. Recipients of this mismatched HLA also showed shortened overall survival (HR=9.7, P<0.001) and increased risk for transplant-related mortality (HR=9.1, P=0.027). Structural modeling showed that the amino acid substitution could alter the peptide preference of the ligand-binding pocket. A single amino acid substitution at position 9 was a major predictor of severe acute GVHD in Korean pediatric patients., (© 2010 The Authors. Journal compilation © 2010 European Society for Organ Transplantation.)

Human leukocyte antigens (HLAs) are useful markers for anthropological investigations because the allele and haplotype distributions at these loci vary widely among ethnic groups. HLA frequencies in Koreans, however, have not previously been analyzed on a phylogenetic basis. We determined the allele frequencies of four HLA class II (HLA-DRB1, -DQA1, -DQB1, and -DPB1) loci in 149 unrelated Korean individuals using a sequence-based typing method. A total of 29 HLA-DRB1, 17 HLA-DQA1, 16 HLA-DQB1, and 15 HLA-DPB1 alleles were identified. The most common allele at each locus was DRB1*0901, DQA1*0102, DQB1*0301, and DPB1*0501, respectively. Four-locus allelic association analysis showed the existence of 25 DRB1-DQA1-DQB1-DPB1 haplotypes with a frequency greater than 0.010. A dataset comprising ethnicity-specific information from published literature and the dbMHC database, as well as the allele frequencies determined in this study, was subjected to phylogenetic analysis. The analysis showed that Koreans are most closely related to Japanese and Han Chinese from Shandong province. Correspondence analyses showed that the current Korean population is located in a position intermediate between the northern and southern East Asian groups, supporting the theory of a bi- and/or multidirectional route of migration of early Korean settlers. This report can be used for anthropological studies, and may also be of use in the International Hematopoietic Stem Cell Sharing program., (© 2010 John Wiley & Sons A/S.)

This study aimed to characterize the replication and pathogenic properties of a Korean pandemic (H1N1) 2009 influenza virus isolate in ferrets and mice. Ferrets infected with A/Korea/01/2009 (H1N1) virus showed mild clinical signs. The virus replicated well in lungs and slightly in brains with no replication in any other organs. Severe bronchopneumonia and thickening of alveolar walls were detected in the lungs. Viral antigens were detected in the bronchiolar epithelial cells, in peribronchial glands with severe peribronchitis and in cells present in the alveoli. A/Korea/01/2009 (H1N1) virus-infected mice showed weight loss and pathological lung lesions including perivascular cuffing, interstitial pneumonia and alveolitis. The virus replicated highly in the lungs and slightly in the nasal tissues. Viral antigens were detected in bronchiolar epithelial cells, pneumocytes and interstitial macrophages. However, seasonal H1N1 influenza virus did not replicate in the lungs of ferrets, and viral antigens were not detected. Thus, this Korean pandemic (H1N1) 2009 isolate infected the lungs of ferrets and mice successfully and caused more pathological lesions than did the seasonal influenza virus.

Background: The prostate-specific antigen (PSA) is considered the most useful among tumor markers currently used. However, its quantitative results are interpreted only qualitatively for the diagnosis of prostate cancer. The recently introduced information theory enables the information of the quantitative results transformed into Shannon's entropy (S) that represents uncertainties and then "1-S" representing diagnostic certainty., Methods: The 882 urological patients enrolled were categorized into 2 groups: a patient group comprising 233 patients with prostate cancer and a disease control group comprising 649 patients with benign prostate disease. The level of PSA in all the patients was tested and was found to be >or=2 ng/mL. The variables like PSA level and age were modeled on logistic regression analysis to predict the probability of prostate cancer and the diagnostic certainty., Results: The mean (SD) of PSA levels in the patient group and the disease control group were 44.5 ng/mL (37.62 ng/mL) and 5.7 ng/mL (3.70 ng/mL), respectively. The logistic regression model fitted well when the age variable was dichotomized at the age of 55 yr. The diagnostic certainty was lowest at a PSA level of 18.90 ng/mL in the <55-yr age group, and 15.45 ng/mL in the >55-yr age group., Conclusions: The diagnostic certainty (1-S) of whether to diagnose prostate cancer or not at a certain PSA level could be obtained using the information theory. The methodology used in this study may help interpret the results of other quantitative tests.

Recent changes in healthcare systems have changed the epidemiologic paradigms in many infectious fields including bloodstream infection (BSI). We compared clinical characteristics of community-acquired (CA), hospital-acquired (HA), and healthcare-associated (HCA) BSI. We performed a prospective nationwide multicenter surveillance study from 9 university hospitals in Korea. Total 1,605 blood isolates were collected from 2006 to 2007, and 1,144 isolates were considered true pathogens. HA-BSI accounted for 48.8%, CA-BSI for 33.2%, and HCA-BSI for 18.0%. HA-BSI and HCA-BSI were more likely to have severe comorbidities. Escherichia coli was the most common isolate in CA-BSI (47.1%) and HCA-BSI (27.2%). In contrast, Staphylococcus aureus (15.2%), coagulase-negative Staphylococcus (15.1%) were the common isolates in HA-BSI. The rate of appropriate empiric antimicrobial therapy was the highest in CA-BSI (89.0%) followed by HCA-BSI (76.4%), and HA-BSI (75.0%). The 30-day mortality rate was the highest in HA-BSI (23.0%) followed by HCA-BSI (18.4%), and CA-BSI (10.2%). High Pitt score and inappropriate empirical antibiotic therapy were the independent risk factors for mortality by multivariate analysis. In conclusion, the present data suggest that clinical features, outcome, and microbiologic features of causative pathogens vary by origin of BSI. Especially, HCA-BSI shows unique clinical characteristics, which should be considered a distinct category for more appropriate antibiotic treatment.

Device-associated infections (DAIs) have been the major causes of morbidity and mortality of patients in intensive care units (ICUs). This study evaluated the risk factors for DAIs in ICUs. Ninety-six medical or surgical ICUs of 56 hospitals participated in the Korean Nosocomial Infections Surveillance System between July 2007 and June 2008. The occurrence of catheter-associated urinary tract infection (CAUTI), central line-associated bloodstream infection (CABSI), and ventilator-associated pneumonia (VAP) were monitored and DAI rates were calculated. Data associated with ICU characteristics were collected and Poisson regression was used for statistical analysis. Rates of CAUTI, CABSI, and VAP were 3.87 per 1000 urinary catheter days, 2.23 per 1000 central line days, and 1.89 per 1000 mechanical ventilator days, respectively. Rates of CAUTI were higher in ICUs in Seoul (P=0.032) and ICUs of major teaching hospitals (P=0.010). The ICUs of university-affiliated hospitals showed lower CAUTI rates (P=0.013). CABSI rates were higher in Seoul (P=0.001) and in medical ICUs (P=0.026). VAP rates were lower in ICUs of hospitals with more than 900 beds compared with hospitals with 400-699 beds (P=0.026). VAP rates were higher in surgical ICUs (P<0.0001) and increased 1.13-fold with each 100-unit increase in beds per infection control professional (P=0.003). The organisational and institutional characteristics of ICUs may influence DAI rates and there is a need for improvement in the incidence of VAP, CAUTI or CABSI., (Copyright 2010. Published by Elsevier Ltd.)

Influenza epidemics arise through the accumulation of viral genetic changes, culminating in a novel antigenic type that is able to escape host immunity. Following an outbreak of the A/Fujian/411/2002-like strains in Asia, including China, Japan, and South Korea, in 2002, Australia and New Zealand experienced substantial outbreaks of the same strains in 2003, and subsequently worldwide outbreaks occurred in the 2003-2004 season. The emergence of A/Fujian/411/2002-like strains coincided with a higher level of influenza-like illness in South Korea than what is seen at the peak of a normal season, and there was at least a year's difference between South Korea and the United States. Genetic evolution of human influenza A/H3N2 viruses was monitored by sequence analysis of hemagglutinin (HA) genes collected in Asia, including 269 (164 new) HA genes isolated in South Korea from 1999 to 2007. The Fujian-like influenza strains were disseminated with rapid sequence variation across the antigenic sites of the HA1 domain, which sharply distinguished between the A/Moscow/10/1999-like and A/Fujian/411/2002-like strains. This fast variation, equivalent to approximately 10 amino acid changes within a year, occurred in Asia and would be the main cause of the disappearance of the reassortants, although the reassortant and nonreassortant Fujian-like strains circulated simultaneously in Asia.

Background: The Abbott RealTime hepatitis C virus (HCV) Genotype II (Abbott Molecular Inc.) for HCV genotyping, which uses real-time PCR technology, has recently been developed., Methods: Accuracy and sensitivity of detection were assessed using the HCV RNA PHW202 performance panel (SeraCare Life Sciences). Consistency with restriction fragment mass polymorphism (RFMP) data, cross-reactivity with other viruses, and the ability to detect minor strains in mixtures of genotypes 1 and 2 were evaluated using clinical samples., Results: All performance panel viruses were correctly genotyped at levels of >500 IU/mL. Results were 100% concordant with RFMP genotypic data (66/66). However, 5% (3/66) of the samples examined displayed probable genotypic cross reactivity. No cross reactivity with other viruses was evident. Minor strains in the mixtures were not effectively distinguished, even at quantities higher than the detection limit., Conclusions: The Abbott RealTime HCV Genotype II assay was very accurate and yielded results consistent with RFMP data. Although the assay has the advantages of automation and short turnaround time, we suggest that further improvements are necessary before it is used routinely in clinical practice. Efforts are needed to decrease cross reactivity among genotypes and to improve the ability to detect minor genotypes in mixed infections.

The hepatitis C virus (HCV) genotype is the most important factor in predicting the outcome of chronic hepatitis C treatment. Therefore, convenient and accurate HCV genotyping methods for routine laboratory testing are needed. In this study, to identify the HCV genotypes, an oligonucleotide DNA chip was designed using 15 probes from the 5'-untranslated region. Reverse transcription was combined with asymmetric polymerase chain reaction (PCR) to obtain an amplified product for hybridization without the need for a denaturation step. In addition, a biotin-labeled PCR product and streptavidin-Cy3 conjugate were cohybridized simultaneously. Clinical sera from Korean and French patients (n=112) were used to compare the chip results with those obtained by direct sequencing. The DNA chip showed 100% accuracy for the commercial panels and had a lower detection limit of 2.8x10(2) IU/ml. Agreement levels between the chip and sequencing results at the genotype and subgenotype levels were 100% and 94.6% (106/112), respectively. By the combined reverse transcription-asymmetric PCR and cohybridization methods, the DNA chip reduced assay time and was convenient to use. This DNA chip may be useful for identifying HCV genotypes in clinical laboratories., (2009 Elsevier B.V. All rights reserved.)

Major histocompatibility complex (MHC) class I chain-related gene A (MICA) is located within the human MHC, centromeric to HLA-B and telomeric to HLA-DRB1. The location of MICA in the MHC indicates the presence of linkage disequilibrium with human leukocyte antigen (HLA). Like HLA, MICA is highly polymorphic; however, the information available for MICA polymorphisms is not as comprehensive as that for HLA polymorphisms. We estimated the allelic frequencies of MICA and haplotypes with HLA-B and HLA-DRB1 at high-resolution in a population of 139 unrelated Korean individuals by applying the newly developed method of sequence-based typing (SBT). A total of 17 MICA alleles were identified. The most frequent allele was MICA*010 (19.4%), followed by alleles *00201 (17.6%), *00801 (14.7%), *01201 (9.4%), *004 (8.3%) and *049 (7.9%). The most common two- and three-locus haplotypes were HLA-B*1501-MICA*010 (10.4%), MICA*010-HLA-DRB1*0406 (5.8%) and HLA-B*1501-MICA*010-HLA-DRB1*0406 (5.8%). This is the first study to provide such high-resolution information on the distribution of haplotypes comprising MICA, HLA-B and HLA-DRB1 in Korean individuals, a level of resolution made possible by use of the SBT method. The results of this study should help determine the mechanisms underlying diseases associated with MICA polymorphisms in Korean individuals.

The poly-gamma-d-glutamic acid (PGA) capsule is one of the major virulence factors of Bacillus anthracis, which causes a highly lethal infection. The antiphagocytic PGA capsule disguises the bacilli from immune surveillance and allows unimpeded growth of bacilli in the host. Recently, efforts have been made to include PGA as a component of anthrax vaccine; however, the innate immune response of PGA itself has been poorly investigated. In this study, we characterized the innate immune response elicited by PGA in the human monocytic cell line THP-1, which was differentiated into macrophages with phorbol 12-myristate 13-acetate (PMA) and human monocyte-derived dendritic cells (hMoDCs). PGA capsules were isolated from the culture supernatant of either the pXO1-cured strain of B. anthracis H9401 or B. licheniformis ATCC 9945a. PGA treatment of differentiated THP-1 cells and hMoDCs led to the specific extracellular release of interleukin-1beta (IL-1beta) in a dose-dependent manner. Evaluation of IL-1beta processing by Western blotting revealed that cleaved IL-1beta increased in THP-1 cells and hMoDCs after PGA treatment. Enhanced processing of IL-1beta directly correlated with increased activation of its upstream regulator, caspase-1, also known as IL-1beta-converting enzyme (ICE). The extracellular release of IL-1beta in response to PGA was ICE dependent, since the administration of an ICE inhibitor prior to PGA treatment blocked induction of IL-1beta. These results demonstrate that B. anthracis PGA elicits IL-1beta production through activation of ICE in PMA-differentiated THP-1 cells and hMoDCs, suggesting the potential for PGA as a therapeutic target for anthrax.

Ultraviolet (UV) photodissociation (PD) experiments using 266 nm light were performed for a series of phosphopeptide cations in a Fourier transform mass spectrometer. The objective of the experiments was to determine whether 266 nm UV irradiation on the phosphopeptide cations would induce unique peptide backbone dissociation. In addition, the general behavior of the phosphate loss (-80 or -98 Da) was monitored, particularly for those phosphopeptides with a phosphotyrosine residue that itself is a UV chromophore. For phosphopeptides with a UV chromophore, their photodissociation behavior was very similar to that of low-energy sustained off-resonance irradiation collisionally activated dissociation (SORI-CAD), with a few exceptions. For example, b- and y-type peptide backbone fragments were prevalent, and their dephosphorylation behavior was consistent with that of the SORI-CAD results. For phosphoserine peptides, the loss of a phosphate group was always observed. On the other hand, for phosphotyrosine peptides, the phosphate loss was found to be dependent on the presence of a basic amino group in the sequence and the charge state of the precursor ions, in agreement with the CAD results in the literature. However, hydrogen atom loss or aromatic side chain loss, which is known to be the excited state specific fragmentation pathway, was rarely observed in our 266 nm UV PD experiments, in contrast to the previous UV PD literature (particularly at 220 nm). The mechanism for these observations is described in terms of dominant internal conversion followed by intramolecular vibrational energy redistribution (IVR)., (Copyright 2009 John Wiley & Sons, Ltd.)

Anthrax is a lethal infectious disease caused by the spore-forming Bacillus anthracis. The two major virulence factors of B. anthracis are exotoxin and the poly-gamma-d-glutamic acid (PGA) capsule. The three components of the exotoxin, protective antigen (PA), lethal factor and edema factor act in a binary combination, which results in massive edema and organ failure in the progress of anthrax disease. The antiphagocytic PGA capsule disguises the bacilli from immune surveillance and allows unimpeded growth of bacilli in the host. Because PA can elicit a protective immune response, it has been a target of the anthrax vaccine. In addition to PA, efforts have been made to include PGA as a component of the anthrax vaccine. In this study, we report that PA-PGA conjugates induce expressions of anti-PA, anti-PGA and toxin-neutralizing antibodies in guinea-pigs and completely protect guinea-pigs against a 50 x LD(50) challenge with fully virulent B. anthracis spores. Polyclonal rabbit antisera produced against either PA or ovalbumin conjugated to a PGA-15mer offer a partial passive protection to guinea-pigs against B. anthracis infection, indicating that anti-PGA antibodies play a protective role. Our results demonstrate that PA-PGA conjugate vaccines are effective in the guinea-pig model, in addition to the previously reported mouse model.

To investigate the frequency of amantadine resistance among influenza A viruses isolated in Korea during the 2003-2009 seasons, 369 (16.8%) 2199 A/H1N1 viruses and 780 (14.8%) of 5263 A/H3N2 viruses were randomly selected. The M2 and HA1 genes of each isolate were amplified by reverse transcription-polymerase chain reaction and followed by nucleotide sequencing. The results showed that the resistance rate to amantadine among A/H1N1 viruses increased significantly from 2004-2005 (33.3%) to 2007-2008 (97.8%) and then decreased dramatically in 2008-2009 (1.9%). The A/H1N1 isolates recently detected in 2008-2009 turned amantadine-sensitive containing two new substitutions at specific sites (S141N, G185A) in HA1. Compared with A/H1N1 viruses, the amantadine resistance among the A/H3N2 viruses increased from 2003-2004 (9.7%) to 2005-2006 (96.7%) and decreased in 2006-2007 (57.4%). During 2006-2007, both of amantadine-resistant and -sensitive A/H3N2 viruses co-circulated but clustered in different branches phylogenetically. All of A/H3N2 isolates tested during 2007-2009 appeared to cluster in the same group being resistant to amantadine.

Lethal toxin (LT), produced by the gram-positive bacterium Bacillus anthracis, was identified as a major etiologic agent causing anthrax due to its strong immunotoxicity. Gram-positive bacteria express lipoteichoic acid (LTA), which is considered as a counterpart to lipopolysaccharide (LPS) of gram-negative bacteria, but differs from LPS in the structure and function. Since dendritic cells (DCs) are essential for the appropriate initiation of immune response, we investigated the effect of LT on LTA-induced DC maturation using immature DCs prepared by differentiation of C57BL/6 mouse bone marrow cells. When immature DCs were matured with LTA in the presence of LT, the expression of representative markers for DC maturation such as CD80, CD83, and CD86 together with MHC class I and II molecules was inhibited. LT ameliorated the attenuation of endocytic capacity during DC maturation by LTA while such effect was not observed in LPS-matured DCs. Furthermore, exposure to LT resulted in a decrease in the expression of pro-inflammatory cytokines including IL-6, TNF-alpha, and IL-12p40 in LTA-stimulated DCs as in LPS-stimulated DCs. Interestingly, LT showed a minimal change in LTA-induced IL-1beta expression while LT highly enhanced the LPS-induced IL-1beta expression. Those inhibitory effects might be associated with LT interference of LTA-signaling pathways mediated through mitogen-activated protein kinases (MAPKs) since LT suppressed phosphorylation of MAPK, which was induced by LTA. Meanwhile, no change was observed in the expression of putative anthrax toxin receptors, TEM8 and CMG2, or Toll-like receptor 2. These results suggest that LT suppresses the maturation and activation of DCs stimulated with LTA, similar to the suppression in the LPS-stimulated DCs, but via a distinct mechanism.

Background: Many immunochromatography (ICA) kits for anti-human immunodeficiency virus type (HIV) antibody (Ab) have been introduced to improve the accessibility of HIV Ab tests. However, qualified evaluation reports for HIV rapid tests are not enough to validate their performances. Meta-analysis for the performances of the HIV Ab rapid tests was performed in this study., Methods: PubMed database was searched with combination of search terms, 'human immunodeficiency virus', 'HIV Ab', 'rapid test', 'immunochromatography', 'performance', 'sensitivity', and 'specificity'. Criteria of inclusion were performance studies for HIV ICA kits with serum or EDTA whole blood. Methodological qualities were evaluated with standards for reporting of diagnostic accuracy studies (STARD) checklists by two investigators. Homogeneity among selected studies was evaluated and then pooled sensitivity and specificity were calculated. Positive and negative predictive values were simulated with presumed HIV prevalence in Korea., Results: Twenty-three studies were selected from 12 high-qualified papers with STARD checklists. The performance of 23 studies were found to be heterogeneous (P<0.1) and random effect model was used. Pooled sensitivity was 99.71% (95% CI: 99.45-99.97%) and pooled specificity was 99.27% (95% CI: 98.83-99.70%). With HIV prevalence of 0.03%, positive and negative predictive values were presumed to be 3.936% and 99.999%, respectively., Conclusions: This meta-analysis for HIV ICA rapid tests showed good performance. In consideration of low positive predictive values of HIV rapid tests, confirmation by enzyme immunoassay or Western blot is still needed. This study would be helpful in evaluating and establishing proper performance guideline for those kits not fully evaluated.

Collisional activation of 2-[(2,2,6,6-tetramethylpiperidin-1-yloxy)methyl]benzoic acid (TEMPO-Bz)-conjugated peptide cations, prepared by attaching a TEMPO-derived precursor 1 to an N-terminal amino group or a lysine side chain, resulted in the formation of radical species. The subsequent tandem mass spectrometry on the radical cations exhibited odd-electron peptide backbone dissociations in the same manner as that observed by electron capture dissociation (ECD) or electron transfer dissociation (ETD). For example, a-, x-, or z-types of ions were major fragments and the disulfide bond was readily cleaved. The TEMPO-FRIPS (free radical initiated peptide sequencing) was also applicable to characterizing even singly protonated peptides, in contrast to ECD or ETD in which only doubly or highly protonated cations are responsive. The TEMPO-FRIPS approach also has universality in that it can be used in any type of a tandem mass spectrometer.

Background: We investigated hepatitis B virus (HBV) infection cases, who were HBsAg negative by radioimmunoassay (RIA) and HBV DNA positive for their clinical characteristics, the S gene mutation of hepatitis B virus (HBV), and usefulness of other HBsAg immunoassay., Methods: Among the patients requested for HBV DNA quantification, 16 patients positive in HBV DNA but negative in HBsAg RIA (BNIBT HBsAg Kit, China) were enrolled. The "a" determinant of HBV S gene was sequenced and clinical characteristics were reviewed. Additional HBsAg assay was performed using Architect HBsAg kit (Abbott laboratories, USA) employing chemiluminescent immunoassay method., Results: Eleven of the 16 patients showed multiple mutations in the "a" determinant. These patients received liver transplantation several years ago and have been treated with hepatitis B immune globulin (HBIG) and antiviral drugs. G145R mutation was found in 8 patients and G145K, D144G, and D144A were also frequently found. Among 9 of the 11 patients tested for HBsAg by Architect HBsAg kit, 8 showed positive results. Among 4 of the remaining 5 patients, only 2 showed weak positive results (< or = 1 IU/mL) in Architect HBsAg kit., Conclusions: HBV DNA-positive/HBsAg RIA-negative results were mostly observed in the patients treated with HBIG after liver transplantation, in whom HBIG escape mutations were found. Majority of these cases were positive in Architect HBsAg assay, and it is recommended to use other HBsAg immunoassay methods that are more sensitive than RIA in the detection limit as well as in the detection of escape mutant in hospitals performing liver transplantation.

In this work, we investigated the surface processes involved in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS), which produce intact characteristic ions, typically in disulfide form, from self-assembled monolayers (SAMs) of alkanethiolates on gold. For the study, SAMs decorated with peptides and a THAP matrix were employed. Using two-laser MS, it was previously found that irradiation with a UV laser gave rise to the direct desorption of SAM molecules from alkanethiol SAMs on gold, producing disulfide species in vacuum. However, a closer examination of this study suggests that the MALDI process in which the matrix is used may not be the case. Instead, the results indicate that the treatment of the matrix solution is responsible for the characteristic ion formation in MALDI MS. We propose that the matrix solution dissolves alkanethiolate molecules from SAMs, leading to the generation of characteristic disulfide species in the solution. The disulfides are then cocrystallized with matrix molecules and subsequently detected by MALDI MS. Because MALDI MS is a powerful tool for biopolymers with high molecular weights, it has been successfully applied to SAMs presenting large biomolecules. This understanding of the MALDI process in the surface MS of alkanethiol SAMs on gold may allow advances in the biomolecular application of SAMs in combination with mass spectrometric analysis.

Background: Hepatitis B virus (HBV) detected in Korean patients almost belongs to genotype C, which is subdivided into subgenotype C1 (or Cs) and C2 (or Ce). It was recently reported that the risk of hepatocellular carcinoma is different between subgenotype C1 and C2. Thus, we studied the distribution of subgenotypes of HBV in Korean chronic hepatitis B (CHB) patients., Methods: Specimens of 421 patients, who were diagnosed as CHB and underwent antiviral treatment, were used. After sequence analysis for HBV S gene, subgenotype was identified through phylogenetic analysis. Utilizing the same sequence data, the distribution of serotypes was also investigated., Results: Among 421 patient specimens, genotype C was found in 419 (99.5%) and genotype B in 2 (0.5%). Among the genotype C strains, 417 strains were C2 subgenotype and 2 strains were mixed subgenotypes. However, C2 was evidently found even in the mixed sequences. Serotypes of 419 HBV with genotype C were classified as follows: adr, 385 (91.9%), adw, 22 (5.3%), ayr, 2 (0.4%) and mixed serotype, 10 (2.3%). Serotype of both HBV with genotype B was adw., Conclusions: It was found that HBV detected in Korean CHB patients under treatment almost all belong to the C2 (Ce) genotype.

Influenza epidemics arise through the acquisition of viral genetic changes to overcome immunity from previous infections. An increasing number of complete genomes of influenza viruses have been sequenced in Asia in recent years. Knowledge about the genomes of the seasonal influenza viruses from different countries in Asia is valuable for monitoring and understanding of the emergence, migration and evolution of strains. In order to make full use of the wealth of information from such data, we have developed an integrated user friendly relational database, Influenza Sequence and Epitope Database (ISED), that catalogs the influenza sequence and epitope information obtained in Asia. ISED currently hosts a total of 13,020 influenza A and 2984 influenza B virus sequence data collected in 17 countries including 9 Asian countries, and a total of approximately 545 amantadine-resistant influenza virus sequences collected in Korea. ISED provides users with prebuilt application tools to analyze sequence alignment and different patterns and allows users to visualize epitope-matching structures, which is freely accessible at http://influenza.korea.ac.kr and http://influenza.cdc.go.kr.

New allele B*4617 showed one nucleotide difference with B*460101 at codon 167 (TGG-->TCG).

Microarray technology makes high-throughput genotyping possible by permitting the simultaneous analysis of large sets of genes on a small reaction slide. Human leukocyte antigen (HLA) loci showing high polymorphisms are suitable targets for microarray. In this study, we developed a microarray kit with newly designed oligonucleotide probes for the genotyping of HLA-A and -DRB1. In total, 42 probes were designed to hybridize to polymorphic sites for HLA-A and 36 for HLA-DRB1. Asymmetric polymerase chain reaction (PCR) using four primers was performed to amplify exon 2 of HLA-DRB1, whereas symmetric PCR was performed to amplify both exons 2 and 3 of HLA-A. Evaluation of performance using samples from 138 Koreans disclosed consistent microarray results with all sequence-based typing at the low-resolution level. Despite the occurrence of ambiguities in 35 HLA-A (25.4%) and 5 HLA-DRB1 (3.6%) cases, correct genotypes were assigned with high certainty by referring to allele distribution in Koreans. These data clearly indicate that our newly developed microarray kit is optimal in determining correct genotypes at the low-resolution level in Koreans.

Background: Panel reactive antibody (PRA) is to screen and identify HLA antibody. Majority of antibody specificities in high-PRA are directed against cross reactive group (CREG). Thus, this study was to know the advantage of identifying CREG specificity and whether antibody specificities are changed according to CREG classification., Methods: HLA class I antibodies were identified from 159 sera from 108 patients in Asan Medical Center, who had shown more than 5% PRA by anti-human globulin (AHG)-complement-dependent cytotoxicity (CDC). Tail analysis-based computer program was developed to identify specificities, applying both Rodey (R-ABC) and Takemoto (T-ABC) classification. The results were also compared with those obtained when without CREG application (ABC)., Results: Among 151 cases in which HLA specificities was identified, the frequency of CREG specificity was 22.5% in R-ABC and 27.2% in T-ABC. Eleven cases showed CREG specificities only in one classification. However, the individual antigen specificities in one hand were all included in the CREG identified in the other hand. CREG specificities in samples with PRA >50% (60%) were more frequently identified than those in samples with PRA < or =50% (9%) (in R-ABC, P<0.0001). Without applying CREG to interpretation, specificity was not identified in 9 cases., Conclusions: Application of CREG enhanced the rate of antibody identification. Antibody specificities of those cases where CREG specificities were different between Rodey and Takemoto classifications were almost the same when compared at the individual antigen level. Therefore, it was thought that it makes no difference to use any one of these two classifications in interpreting PRA.

Previous surveys of the prevalence of hepatitis C virus (HCV) in Korea have identified types 1 and 2, but little has been said of other genotypes and viral subtypes. In this study, HCV genotypes in Korea were investigated using Restriction Fragment Mass Polymorphism (RFMP) assay, a sensitive and specific method for genotyping based on MALDI-TOF mass spectrometry. A total of 1,043 independent serum samples from HCV-infected patients were analyzed. Of interest, 15 subjects (1.4%) were determined to contain HCV genotype 6 and 46 subjects (4.4%) contained mixed genotypes with the most prevalent genotypes being HCV 1b and 2a/c (45.0% and 35.4%, respectively). The 15 subjects with HCV genotype 6 comprised eight cases of subtype 6c, including one case of mixed infection with 1b, three cases of HCV 6a, and six cases of unassigned subtypes. Sequencing corroborated the identity of genotype 6 from 13 subjects, while the line probe assay (LiPA) mis-identified them as genotype 1b. The majority (7/9) of the genotype 6 patients enrolled for interferon/ribavirin therapy, achieved a sustained virologic response. The ability of the RFMP assay to differentiate various HCV genotypes should enable better analysis of the relationship between HCV genotype and disease prognosis.

Neisseria gonorrhoeae is an obligate human pathogen that is the etiological agent of gonorrhea. We explored variations in the genes of a multidrug-resistant N. gonorrhoeae isolate from a Korean patient in an effort to understand the prevalence, antibiotic resistance, and importance of horizontal gene transfer within this important, naturally competent organism. Here, we report the complete annotated genome sequence of N. gonorrhoeae strain NCCP11945.

Background: Human bocavirus (HBoV) is a parvovirus that has been recently detected in patients with respiratory illness., Objectives: We developed a sensitive, specific, and quantitative real-time PCR assay based on the TaqMan method for HBoV detection and quantification in respiratory specimens., Study Design: Three individual real-time PCR assays were designed to amplify HBoV NS1, NP-1, and VP1 genes. For clinical evaluation, 506 nasal aspirates obtained from patients with acute respiratory tract infections during December 2006 to May 2007 were tested., Results: Each assay had a broad dynamic range (50 x 10(7) to 5 x 10(7)copies of plasmid DNA) and high inter- and intra-assay reproducibility. The detection limit of each assay was 10 genome copies per reaction, and no crossreactivity with other major respiratory viruses or bacteria was detected. Clinical evaluation revealed that 11 (2.1%) of 506 patients diagnosed with upper respiratory tract infections, pneumonia, bronchitis, pharyngitis, or sinusitis had HBoV detected by all three assays, with viral loads ranging from 8.2 x 10(4) to 8.1 x 10(9)copies/ml of specimen., Conclusions: The three assays for HBoV diagnosis and quantification are highly sensitive, specific real-time tools for the reliable epidemiological and pathogenetic study of HBoV infection.

Background: We describe the development of a novel matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)-based single nucleotide polymorphism (SNP) scoring strategy, termed Restriction Fragment Mass Polymorphism (RFMP) that is suitable for genotyping variations in a simple, accurate, and high-throughput manner. The assay is based on polymerase chain reaction (PCR) amplification and mass measurement of oligonucleotides containing a polymorphic base, to which a typeIIS restriction endonuclease recognition was introduced by PCR amplification. Enzymatic cleavage of the products leads to excision of oligonucleotide fragments representing base variation of the polymorphic site whose masses were determined by MALDI-TOF MS., Results: The assay represents an improvement over previous methods because it relies on the direct mass determination of PCR products rather than on an indirect analysis, where a base-extended or fluorescent report tag is interpreted. The RFMP strategy is simple and straightforward, requiring one restriction digestion reaction following target amplification in a single vessel. With this technology, genotypes are generated with a high call rate (99.6%) and high accuracy (99.8%) as determined by independent sequencing., Conclusion: The simplicity, accuracy and amenability to high-throughput screening analysis should make the RFMP assay suitable for large-scale genotype association study as well as clinical genotyping in laboratories.

Mutations in the YMDD motif of the hepatitis B virus (HBV) polymerase gene increase lamivudine resistance of HBV, highlighting the clinical importance of accurate and sensitive detection of HBV mutants. Using dual-priming oligonucleotide primer technology, an assay that can detect mutations at codons 180 (L528M) and 204 (YVDD, YIDD, and YSDD) by a single-step multiplex PCR was developed. This Seeplex Lami-DR assay was sufficiently sensitive to detect 10(3)HBV/ml and was able to detect minor mutants comprising as little as 2% of the viral population. Mutants were detected in 57 of 65 serum samples (88%) from patients with chronic hepatitis B who had been treated with lamivudine (median, 32 months; range, 1-83 months). The agreement with direct sequencing was only 38.5% (25/65). Discrepancies between these methods resulted from detection of additional mutants by the Seeplex Lami-DR assay, as confirmed by a novel verification analysis. This assay is not only highly accurate and sensitive, but is also simple and cost-effective, requiring no expensive probes, laborious sequencing procedures, or digestion with restriction enzymes. Accordingly, the Seeplex HBV Lami-DR assay should be considered as a first-line, cost-effective tool for detecting viral mutations in patients with chronic hepatitis B receiving lamivudine therapy.

Background: Although hepatitis B surface antigen (HBsAg) rapid test based on immunochromatographic assay (ICA) is now widely used, the test has not been evaluated sufficiently enough to validate its performance. Thus, it is important to summarize the clinical performance of the test kits. In this study, we performed meta-analysis for the performance of the HBsAg rapid tests., Methods: PubMed database was searched using keywords about the accuracy of diagnostic tests for hepatitis B virus (HBV) infection. Two investigators assessed methodological quality utilizing standards for reporting of diagnostic accuracy studies (STARD) checklist. After performing a heterogeneity test, we obtained pooled sensitivity and specificity. Positive and negative predictive values (PPV and NPV) were simulated according to HBV prevalence., Results: A total of 38 studies was selected from 10 papers. The quality scores ranged from 3 to 13 (median, 8). Kappa value was good (0.85). The performance of the 38 studies was heterogeneous. When 33 studies with better quality from 7 papers were re-selected, the pooled sensitivity and specificity were 98.07% (95% confidence interval, CI: 97.67-98.47%) and 99.56% (95% CI: 99.21-99.91%), respectively. With an HBV prevalence of 5%, PPV and NPV were predicted to be 92.14% and 99.90%, respectively., Conclusions: In view of high HBV prevalence in Korea, it is thought that the HBsAg rapid test can be used for HBV screening in small-sized laboratories or for epidemiologic studies. This study should be helpful in establishing a guideline for the proper performance evaluation of the HBsAg rapid tests.

Background: Hepatitis B virus (HBV) DNA quantification is necessary for starting and monitoring of antiviral therapy in patients with chronic hepatitis B. This study was intended to assess the clinical performance of Abbott RealTime HBV Quantification kit (Abbott Laboratories, USA)., Methods: The performance was evaluated in terms of precision, linearity, detection sensitivity, cross-reactivity, and carry-over. A correlation with the Real-Q HBV Quantification kit (BioSewoom Inc., Korea) was also examined using serum samples from 64 patients diagnosed with chronic hepatitis B and underwent lamivudine therapy in Asan Medical Center. We verified the trueness of the system by comparing the outputs with the assigned values of the BBI panel (BBI Diagnostics, USA)., Results: Within-run and between-run coefficients of variation (CV) were 3.56-4.71% and 3.03-4.98%, respectively. Linearity was manifested ranging from 53 to 10(9)copies/mL and the detection sensitivity was verified to be 51 copies/mL. None of hepatitis C virus showed cross-reactivity. No cross-contamination occurred when negative and positive samples were alternatively placed in a row. It showed a good correlation with the Real-Q HBV (r(2)=0.9609) and the test results for the BBI panel were also well agreed to the assigned values (r(2)=0.9933)., Conclusions: The performance of Abbott RealTime HBV Quantification kit was excellent; thus, it should be widely used in starting and monitoring of antiviral therapy in Korean patients with chronic hepatitis B.

Background: Since the human genome project was completed in 2003, there have been numerous reports on cancer and related markers. This study was aimed to develop a system to extract automatically information regarding the relationship between cancer and tumor markers from biomedical literatures., Methods: Named entities of tumor markers were recognized by both a dictionary-based method and machine learning technology of the support vector machine. Named entities of cancers were recognized by the MeSH dictionary., Results: Relational and filtering keywords were selected after annotating 160 abstracts from PubMed. Relational information was extracted only when one of the relational keywords was in an appropriate position along the parse tree of a sentence with both tumor marker and disease entities. The performance of the system developed in this study was evaluated with another set of 77 abstracts. With the relational and filtering keyword used in the system, precision was 94.38% and recall was 66.14%, while without the expert knowledge precision was 49.16% and recall was 69.29%., Conclusions: We developed a system that can extract relational information between a tumor and its markers by incorporating expert knowledge into the system. The system exploiting expert knowledge would serve as a reference when developing another information extraction system in various medical fields.

Several machine learning algorithms have recently been applied to modeling the specificity of HIV-1 protease. The problem is challenging because of the three issues as follows: (1) datasets with high dimensionality and small number of samples could misguide classification modeling and its interpretation; (2) symbolic interpretation is desirable because it provides us insight to the specificity in the form of human-understandable rules, and thus helps us to design effective HIV inhibitors; (3) the interpretation should take into account complexity or dependency between positions in sequences. Therefore, it is necessary to investigate multivariate and feature-selective methods to model the specificity and to extract rules from the model. We have tested extensively various machine learning methods, and we have found that the combination of neural networks and decompositional approach can generate a set of effective rules. By validation to experimental results for the HIV-1 protease, the specificity rules outperform the ones generated by frequency-based, univariate or black-box methods.

Background & Aims: Although autoimmune pancreatitis (AIP) responds well to corticosteroid therapy, relapse during maintenance corticosteroid therapy or after the withdrawal of corticosteroid treatment is not uncommon. To date, the factors related to relapse of AIP have not been fully explored., Methods: To determine the clinical and genetic predictors relating to the relapse of AIP, we evaluated clinical factors, HLA polymorphisms, and the amino acid sequences in 40 patients with AIP., Results: At a median follow-up period of 40 months (range, 12-67 months), relapse developed in 13 of 40 patients with AIP (33%), in whom complete remission was achieved with oral corticosteroid therapy. Among demographics, clinical characteristics in the initial diagnosis of AIP, we could not find any clinical predictor for relapse of AIP; however, in amino acid sequence analysis for relapse of AIP, the substitution of aspartic acid to nonaspartic acid at residue 57 of DQbeta1 showed a significant association with relapse of AIP (nonrelapse group, 29.6%; relapse group, 100%; P = .00003; odds ratio, 3.38; 95% confidence interval, 1.9-6.0). There was a significant difference in the timing of relapse of AIP, according to density of the nonaspartic acid residue at DQbeta1 57 (nonaspartic acid homozygosity: mean +/- SD, 6.7 +/- 4.2 months; nonaspartic acid heterozygosity: mean +/- SD, 33 +/- 11 months; P < .001)., Conclusions: Substitution of aspartic acid to nonaspartic acid at DQbeta1 57 appears to represent a key genetic factor for relapse of AIP (ClinicalTrials.gov number, NCT00444444).

Background/aims: The risk of developing autoimmune hepatitis (AIH) has been suggested to be associated with the presence of HLA-DRB1 alleles encoding the 'shared epitope' at amino acid positions 67-72 in the third hypervariable region (HVR3) of DRbeta. We aimed to identify the specific HLA alleles that are susceptible to type 1 AIH in Koreans, and to validate the shared epitope hypothesis in this single ethnic group., Methods: Sixty-two adult patients with definite type 1 AIH and 154 healthy controls were enrolled. Alleles of HLA class I and II genes were genotyped using sequence-based typing., Results: By high-resolution analysis, the frequencies of DRB1 *0405 and DQB1 *0401 were significantly increased in patients with AIH (P = 0.0001, OR = 3.74; P = 0.00006, OR = 3.95, respectively). The six amino acid motif represented by the single letter code LLEQRR or LLEQKR at positions 67-72 of the DRbeta polypeptide was not sufficient to show an increased risk for the disease. Interestingly, the QRRAA motif at positions 70-74 was significantly increased in Korean patients (P=0.04, OR=1.84)., Conclusions: The shared epitope hypothesis may be extended to the amino acid motif at positions 70-74 of HLA-DRbeta in order to better predict the susceptibility to type 1 AIH.

Biomarkers enable early diagnosis, guide molecularly targeted therapy and monitor the activity and therapeutic responses across a variety of diseases. Despite intensified interest and research, however, the overall rate of development of novel biomarkers has been falling. Moreover, no solution is yet available that efficiently retrieves and processes biomarker information pertaining to infectious diseases. Infectious Disease Biomarker Database (IDBD) is one of the first efforts to build an easily accessible and comprehensive literature-derived database covering known infectious disease biomarkers. IDBD is a community annotation database, utilizing collaborative Web 2.0 features, providing a convenient user interface to input and revise data online. It allows users to link infectious diseases or pathogens to protein, gene or carbohydrate biomarkers through the use of search tools. It supports various types of data searches and application tools to analyze sequence and structure features of potential and validated biomarkers. Currently, IDBD integrates 611 biomarkers for 66 infectious diseases and 70 pathogens. It is publicly accessible at http://biomarker.cdc.go.kr and http://biomarker.korea.ac.kr.

An enrichment semi-nested PCR procedure was developed for detection of Clostridium botulinum types A, B, E, and F. It was applied to sediment samples to examine the prevalence of C. botulinum in the Korean environment. The first pair of primers for the semi-nested PCR was designed using a region shared by the types A, B, E, and F neurotoxin gene sequences, and the second round employed four nested primers complementary to the BoNT/A, /B, /E, and /F encoding genes for simultaneous detection of the four serotypes. Positive results were obtained from the PCR analysis of five of 44 sediments (11%) collected from Yeong-am Lake in Korea; all were identified as deriving from type B neurotoxin (bontb) genes. Two of the C. botulinum type B organisms were isolated, and their bontb genes sequenced. The deduced amino acid sequences of BoNT/B showed 99.5 and 99.8% identity with the amino acid sequence of accession no. AB084152. Our data suggest that semi-nested PCR is a useful tool for detecting C. botulinum in sediments, and renders it practicable to conduct environmental surveys.

Interactions involved in the formation of gas-phase proton-bonded molecular complexes of cytosine (C) and guanine (G) were theoretically investigated for the case of C(+)G and C(+)GC using B3LYP density functional theory. In this study, particular focus was on the dimeric interaction of proton-bonded C(+)G, where a proton bond and a hydrogen bond are cooperatively involved. The dimer interaction energy in terms of dissociation energy (D(e)) was predicted to be 41.8 kcal/mol. The lowest (frozen) energy structure for the C(+)G dimeric complex was found to be CH(+)...G rather than C...H(+)G in spite of the lower proton affinity of the cytosine moiety, which was more stable by 3.3 kcal/mol. The predicted harmonic vibrational frequencies and bond lengths suggest that the combined contributions of proton and hydrogen bonding may determine the resultant stability of each complex structure. In contrast to the dimer case, in the case of the isolated C(+)GC triplet, the two minimum energy structures of CH(+)...GC and C...H(+)GC were predicted to be almost equivalent in total energy. The dissociation energy (D(e)) for the C(+)G pairing in the C(+)GC triplet was 43.7 kcal/mol. Other energetics are also reported. As for the proton-transfer reaction in the proton-bond axis, the forward proton-transfer barriers for the dimer and trimer complexes were also predicted to be very low, 3.6 and 1.5 kcal/mol (DeltaE(e)(PT)), respectively.

The aims of this study were to summarize results on the association of HLA-DRB1 with rheumatoid arthritis (RA) in Asians and to determine if the shared epitope (SE) hypothesis could explain the meta-analysis results. Among the papers published between January 1987 and July 2006 on RA susceptibility in Asian-Mongoloid populations (Korean, Japanese, Chinese, and Thai), 12 were selected for the metaanalysis. Mongoloid-Asian patients with RA had significantly higher frequencies of HLA-DRB1*0101, *0401, *0410, and *1001 than controls (OR 1.5-2.1, p<0.05 for association). When analyses were restricted to more ethnically homogeneous populations, HLA-DRB1*0405 showed a significant susceptibility to RA in Koreans (OR 5.65, 95% CI 4.32-7.39), whereas the HLA-DRB1*0301, *0403, *0406, *0701, *1301, and *1405 alleles showed protective association with RA (OR 0.32-0.70, p<0.05 for association). In conclusion, it was found that HLA-DRB1 *0101, *0401, *0405, *0410, and *1001 are susceptible, while HLA-DRB1* 0301, *0403, *0406, *0701, *1301, and *1405 are protective in Asian-Mongoloids. All the RA-associated alleles except DRB1*0301 could be explained by the structural model supporting the SE hypothesis that RA susceptibility is determined by the combination of amino acid residues at HLA-DR beta71 and beta74, not by beta71 alone.