Analysis of the variations in IL-28RA gene and their association with allergic rhinitis

IL-28RA is one of the important candidate genes for complex trait of genetic diseases, but there is no published information of the genetic variation in this gene. We scanned the seven exons and their boundary introns sequence of IL-28RA including the promoter regions to analyze genetic variation sites, and identified eighteen single nucleotide polymorphisms (SNPs) and two variation sites. We chose seven SNPs (g.-1193 A>C, g.-30 C>T, g.17654 C>T, g.27798 A>G, g.31265 C>T, g.31911 C>T and g.32349 G>A) of them for large sample size genotyping, and assessed the association of genotype and allele frequencies of these SNPs between allergic rhinitis patients and non-allergic rhinitis controls. We also compared the genotype frequencies between Korean controls and Han Chinese control or Korean Chinese control. We investigated the frequencies of haplotype constructed by these SNPs between allergic rhinitis patients and non-allergic rhinitis controls. Our results suggested that the g.32349 G>A polymorphism of IL-28RA might be associated with susceptibility to allergic rhinitis (P=0.032), but seems to have no relationship with serum total IgE levels. The haplotype frequencies by these SNPs also show significant association between controls and allergic rhinitis patients.     

Theoretical Evidence for the Stronger Ability of Thymine to Disperse SWCNT than Cytosine and Adenine: self-stacking of DNA bases vs their cross-stacking with SWCNT

Self-stacking of four DNA bases, adenine (A), cytosine (C), guanine (G) and thymine (T), and their cross-stacking with (5,5) as well as (10,0) single walled carbon nanotubes (SWCNTs) were extensively investigated with a novel hybrid DFT method, MPWB1K/cc-pVDZ. The binding energies were further corrected with MP2/6-311++G(d,p) method in both gas phase and aqueous solution, where the solvent effects were included with conductor-like polarized continuum model (CPCM) model and UAHF radii. The strongest self-stacking of G and A takes displaced anti-parallel configuration, but un-displaced or "eclipsed" anti-parallel configuration is the most stable for C and T. In gas phase the self-stacking of nucleobases decreases in the sequence G>A>C>T, while because of quite different solvent effects their self-stacking in aqueous solution exhibits a distinct sequence A>G>T>C. For a given base, cross-stacking is stronger than self-stacking in both gas phase and aqueous solution. Binding energy for cross-stacking in gas phase varies as G>A>T>C for both (10,0) and (5,5) SWCNTs, and the binding of four nucleobases to (10,0) is slightly stronger than to (5,5) SWCNT by a range of 0.1-0.5 kcal/mol. The cross-stacking in aqueous solution varies differently from that gas phase: A>G>T>C for (10,0) SWCNT and G>A>T>C for (5,5) SWCNT. It is suggested that the ability of nucleobases to disperse SWCNT depends on relative strength [Formula: see text] of self-stacking and cross-stacking with SWCNT in aqueous solution. Of the four investigated nucleobases thymine (T) exhibits the highest [Formula: see text] which can well explain the experimental finding that T more efficiently functionalizes SWCNT than C and A.     

Diagnostic mutational analysis of MECP2 in Korean patients with Rett syndrome

Rett syndrome (RTT) is an X-linked dominant neurodevelopmental disorder affecting 1 per 10,000-15,000 female births worldwide. The disease-causing gene has been identified as MECP2 (methyl-CpG-binding protein 2). In this study, we performed diagnostic mutational analysis of the MECP2 gene in RTT patients. Four exons and a putative promoter of the MECP2 gene were analyzed from the peripheral blood of 43 Korean patients with Rett syndrome by PCR-RFLP and direct sequencing. Mutations were detected in the MECP2 gene in approximately 60.5% of patients (26 cases/43 cases). The mutations consisted of 14 different types, including 9 missense mutations, 4 nonsense mutations and 1 frameshift mutation. Of these, three mutations (G161E, T311M, p385fsX409) were newly identified and were determined to be disease-causing mutations by PCR- RFLP and direct sequencing analysis. Most of the mutations were located within MBD (42.3%) and TRD (50%). T158M, R270X, and R306C mutations were identified at a high frequency. Additionally, an intronic SNP (IVS3+23C>G) was newly identified in three of the patients. IVS3+23C>G may be a disease-related and Korea-specific SNP for RTT. L100V and A201V are apparently disease-causing mutations in Korean RTT, contrary to previous studies. Disease-causing mutations and polymorphisms are important tools for diagnosing RTT in Koreans. The experimental procedures used in this study should be considered for clinical molecular biologic diagnosis.     

The IL-10 gene is not involved in the predisposition to inflammatory bowel disease

Although genetic predisposition for inflammatory bowel disease (IBD) is well established, little is known about the accountable genes. The pathogenesis of IBD is characterized by an imbalanced activation of Th1- and Th2-lymphocytes. IL-10 represents an anti-inflammatory cytokine which downregulates the production of Th1-derived cytokines. To evaluate the role of the IL-10 gene in IBD, two polymorphisms in the promoter region (G/A at position -1082 and C/A at position -592) were genotyped in 142 patients with Crohn's disease (CD), 104 patients with ulcerative colitis (UC), and 400 healthy controls. Significant differences were not apparent, neither in the allele frequencies of either polymorphism, nor in the haplotype frequencies. Screening of the coding region of the IL-10 gene by polymerase chain reaction--single strand conformation polymorphism (PCR-SSCP) analysis revealed a rare sequence variation in exon 1 leading to an amino acid exchange (G-->A; G15R) in two patients with CD and five healthy controls. Therefore, polymorphisms of the IL-10 gene are not demonstrably involved in the predisposition of IBD in our cohorts of patients.     

Association between interleukin 6 promoter variants and chronic hepatitis B progression

Interleukin 6 (IL6) plays an essential role in the regulation of immune response to chronic disease. In this study, the three known single nucleotide polymorphisms (SNPs) in the IL6 promoter region were genotyped in a large chronic hepatitis B cohort to evaluate the effects of IL6 promoter variants. The single base extension method was used for this genotyping. Haplotypes were constructed by the three SNPs in IL6. Allele frequencies were compared for; i) patients with chronic hepatitis (CH) and chronic carriers vs. chronic hepatis patients with clinical evidence of liver cirrhosis (LC) (i.e., portal hypertension), ii) cirrhotic patients with hepatocellular carcinoma (HCC) vs. without HCC by logistic regression, and iii) with respect to the time intervals from the onset of infection to HCC. Results were analyzed by Cox relative hazard analysis on the assumption that all the patients were infected during early infancy. The frequencies of each SNP were 0.002 (IL6-597 G>A), 0.25 (IL6-572 C>G) and 0.002 (IL6-174 G>C), respectively, in the Korean population (n = 1,046). No significant associations were detected between IL6-572 C>G and chronic hepatitis B outcome in this study; i.e., LC occurrence on CH (OR = 0.16-1.27, P = 0.13- 0.71) and HCC occurrence on LC (OR = 1.04-1.23, P = 0.89-0.60) of heterozygotes and homozygotes for G allele in referent comparison to homozygotes for common allele (C/C genotype), and time interval to HCC (RH = 0.67-1.00; P = 0.14-0.99). In conclusion, there appeared to be no significant associations between IL6 promoter variants and disease outcome in chronic hepatitis B.     

三氟化氯和环氧丙烷反应的理论研究

应用密度泛函理论对三氟化氯和环氧丙烷反应产生C3H5O和C1F2自由基的机理进行了研究。在B3PW91/6-31+G(d,p)水平优化了12个不同反应通道上各驻点(反应物、中间体、过渡态和产物) 的几何构型,并计算了它们的振动频率和零点振动能。采用CCSD(T)/6-31+ G(d,p) // B3PW91/6-31+G(d,p)单点能计算方法求得各物种的能量,并作了零点能校正。计算结果表明,三氟化氯和环氧丙烷反应可经过不同的反应路径引发C3H5O自由基和C1F2自由基,其中,三氟化氯呈对称的F原子与环氧丙烷的C(1)上与CH3在同一侧的上的H原子结合的活化能最低,仅为16.81 kJ/mol。     

Experimental and computational studies of the phenyl radical reaction with propyne.

The kinetics for the gas-phase reaction of phenyl radical with propyne has been measured by cavity ring-down spectrometry (CRDS), and the mechanism and initial product branching have been elucidated with the help of quantum chemical calculations. Absolute rate constants measured by the CRDS technique can be expressed by the following Arrhenius equation: (k/cm(3) mol(-1) s(-1)): k(propyne)(T=301-428 K)=(3.68+/-0.92) x 10(11)exp[-(1685+/-80)/T]. The experiment is unable to distinguish between the possible reactive channels, but theory indicates that phenyl radicals preferably add to the unsaturated terminal carbon atom in propyne under our experimental conditions. Theoretical kinetic calculations, employing high-level G2M(RCC, RMP2) and G3 energetic and IRCMax(RCCSD(T)//B3LYP-DFT) molecular parameters, reproduce the total experimental rate constants within a factor of three. Calculated total and branching rate constants are provided for high-T kinetic modeling. Addition reactions of phenyl to C3H4 are estimated to be less important molecular-growth pathways in high-T conditions (T>1000 K) in comparison to the C6H5 + C2H2 reaction.     

Association of Paraoxonase 1 (PON1) polymorphisms with osteoporotic fracture risk in postmenopausal Korean women

There is increasing evidence of a biochemical link between lipid oxidation and bone metabolism. Paraoxonase 1 (PON1) prevents the oxidation of low-density lipoprotein (LDL) and metabolizes biologically active phospholipids in oxidized LDLs. Here, we performed association analyses of genetic variation in PON1 to ascertain its contribution to osteoporotic fractures (OFs) and bone mineral density (BMD). We directly sequenced the PON1 gene in 24 Korean individuals and identified 26 sequence variants. A large population of Korean postmenopausal women (n=1,329) was then genotyped for eight selected PON1 polymorphisms. BMD at the lumbar spine and femoral neck was measured using dual-energy X-ray absorptiometry. Lateral thoracolumbar (T4-L4) radiographs were obtained for vertebral fracture assessment, and the occurrence of non-vertebral fractures (i.e., wrist, hip, forearm, humerus, rib, and pelvis) was examined using self-reported data. Multivariate analyses showed that none of the polymorphisms was associated with BMD at either site. However, +5989A>G and +26080T>C polymorphisms were significantly associated with non-vertebral and vertebral fractures, respectively, after adjustment for covariates. Specifically, the minor allele of +5989A>G exerted a highly protective effect against non-vertebral fractures (OR=0.59, P=0.036), whereas the minor allele of +26080T>C was associated with increased susceptibility to vertebral fractures (OR=1.73, P=0.020). When the risk for any OFs (i.e., vertebral or non-vertebral) was considered, the statistical significance of both polymorphisms persisted (P=0.002-0.010). These results suggest that PON1 polymorphisms could be one of useful genetic markers for OF risk in postmenopausal women.     

四波混频过程中差频与和频的竞争研究

Tunable intense Vacuum Ultraviolet (VUV) laser was generated by two-photon resonant four wave difference frequency mixing (ω-=2ωUV-ωT) in Xenon. In the experiment some resonance attenuations of the VUV were observed at certain difference frequencies. These attenuations occur when the sum frequencies ω+=2ωUV+ωT coincide with excited ns (n=10,11) and nd (n=8~13) states. The third order linear susceptibility χ(3)（2ωUV+ωT;ωUV,ωUV+ωT） is reasonably increased by the double resonance enhancement, so the conversion efficiency of sum frequency mixing can be very high and the power of the pump laser is decreased and thus the difference frequency output is attenuated.     

CH3CH2+O(3P)反应机理的理论研究

The reaction for CH3CH2+O(3P) was studied by ab initio method. The geometries of the reactants, intermediates, transition states and products were optimized at MP2/6-311+G(d,p) level. The corresponding vibration frequencies were calculated at the same level. The single-point calculations for all the stationary points were carried out at the QCISD(T)/6-311+G(d,p) level using the MP2/6-311+G(d,p) optimized geometries. The results of the theoretical study indicate that the major products are the CH2O＋CH3, CH3CHO+H and CH2CH2+OH in the reaction. For the products CH2O＋CH3 and CH3CHO+H, the major production channels are A1: (R)→IM1→TS3→(A) and B1: (R)→IM1→TS4→(B), respectively. The majority of the products CH2CH2+OH are formed via the direct abstraction channels C1 and C2: (R)→TS1(TS2)→(C). In addition, the results suggest that the barrier heights to form the CO reaction channels are very high, so the CO is not a major product in the reaction.     

Interaction and protection mechanism between Li@C(60) and nucleic acid bases (NABs): performance of PM6-DH2 on noncovalent interaction of NABs-Li@C60

To discuss the protection mechanism of DNA from radiation as well as assess the performance of PM6-DH2 on noncovalent interactions, the interaction of four nucleic acid bases (NABs) such as adenine (A), cytosine (C), guanine (G), and thymine (T), with Li@C(60) was extensively investigated with the-state-of-art theoretical methods describing noncovalent systems, like M06-2x, PBE-D, and PM6-DH2 methods. In the gas phase, the binding strength of NABs to Li@C(60) from M06-2x decreases in the sequence, G>C>A>T. As dispersion was explicitly included, PBE-D relatively enhances the binding of A and T and corrects the sequence to, G>A>C～T. PM6-DH2 predicted similar binding energies to those from PBE-D within 0.5 kcal/mol and the same binding sequence, suggesting that the PM6-DH2 method is promising for nano-scale systems. In the aqueous solution, binding of NABs-Li@C(60) is considerably decreased, and the M06-2X and PM6-D methods yield a different sequence from the gas phase, G>A>T>C. The encapsulation of Li atom results in a lower IP for Li@C(60) than those of NABs, and the dominant localization of single-occupied molecular orbital on Li@C(60) moiety of the complexes NABs-Li@C(60) further indicates that an electron would be ejected from Li@C(60) upon radiation and Li@C(60) is therefore able to protect DNA bases from radiation. In addition, it was revealed that Li prefers coordination with the hexagonal ring at Li@C(60) , which clarifies the existing controversy in this respect. Finally, Yang's reduced density gradient approach clearly shows that the weak and strong noncovalent interaction regions in the complexes, NABs-Li@C(60) and (NABs-Li@C(60) )(+).     

A nucleotide composition constraint of genome sequences

Let a, c, g and t denote the occurrence frequencies of A, C, G and T, respectively, in a genome. We calculated the statistical quantity S = a2 + c2 + g2 + t2 for each of 809 genomes (11 archaea, 42 bacteria, 3 eukaryota, 90 phages, 36 viroids and 627 viruses) and 236 plasmids. We found that S < 1/3 is strictly valid for almost all of the above genomes or plasmids. As a direct deduction of the above observation, it is shown that (i) the statistical quantity S is a kind of genome order index, which is negatively correlated with the Shannon H function; (ii) S < 1/3 suggests that a minimal value of the Shannon H function is required for each genome; (iii) S defined above would be a new biological statistical quantity, useful to describe the composition features of genomes; (iv) By jointly considering the Chargaff Parity Rule 2, it is shown that the genomic G + C content should be in between 0.211 and 0.789.     

Molecular characterization and first report of Cryptosporidium genotypes in human population in the Slovak Republic

In our study, we examined 91 fecal samples from five different groups of people containing HIV patients, hemodialysis patients, kidney transplant recipients, immunocompetent humans without clinical signs, and humans with suspected cryptosporidiosis. The purpose of our study was to determine species and genotype composition of representatives of Cryptosporidium spp. using PCR analysis of small subunit ribosomal RNA gene and 60‐kDa glycoprotein gene and examine their phylogenetic relationship. In HIV‐positive/AIDS‐infected group of patients and in hemodialysis patients, no presence of Cryptosporidium species was detected. In two kidney transplant recipients, we detected species/genotypes Cryptosporidium parvum IIaA13G1T1R1 (KT355488) and Cryptosporidium hominis IaA11G2R8 (KT355489) and in two immunocompetent patients with clinical symptoms, we identified Cryptosporidium muris and C. hominis IbA10G2T1 (KT355490). In the group of healthy immunocompetent individuals without clinical signs, we identified species/genotype C. hominis IbA11G2 (KT355491) in one sample.     

Angiotensin converting enzyme I/D, angiotensinogen T174M-M235T and angiotensin II type 1 receptor A1166C gene polymorphisms in Turkish hypertensive patients

Essential hypertension is a multifactorial disease in which genetic and enviromental factors play an important role. These factors differ in each population. As there are no existing data for the Turkish population, we investigated four Renin Angiotensin System (RAS) gene polymorphisms, the angiotensin converting enzyme (ACE), angiotensinogen (AGN) M235T/T174M and angiotensin II type 1 receptor A1166C polymorphism in 109 hypertensive and 86 normotensive Turkish subjects. Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism (RFLP), and agarose gel electrophoresis tecniques were used to determine these polymorphism. The frequencies of person that carry ACE D allel (DD+ID) was significantly higher in hypertensive group (99.1%) than controls (80%) (P 0.000). M235T TT genotype was also found significantly higher in hypertensives than control group (20% vs 2.7%; P 0.001). The frequency of AGN 174M allele was higher in the hypertensive group than control subjects (8.76% vs 4.81%). Frequency of ATR1 C allele (AC+CC genotypes) was found higher hypertensives than controls (39.4% vs 25.9%; P = 0.054). Our results suggest that an interaction exists between the RAS genes and hypertension in Turkish population.     

Homoaromaticity in carbene intermediates

Analyses of isodesmic reactions for singlet 7-carbenanorbornene (4S), 8-carbena-endo-tricyclo[3.2.1.0(2,4)]octane (5S), 3-carbenabicyclo[3.1.0]hexane (3S), 2-carbenanorbornene 6S, and 2-carbenabicyclooctadiene 7S at the B3LYP/6-311+G(3df, 2p)//B3LYP/6-31G level provide stabilization energies of 13.83, 13. 50, 3.00, -2.22, and -3.01 kcal/mol, respectively. The C7 carbene in 4S and the C8 carbene center in 5S are strongly bent toward the double bond and cyclopropane ring, respectively, in contrast to their related triplets, 4T and 5T and parent hydrocarbons. The geometric change for 3S compared to 3T or to parent bicyclo[3.1. 0]hexane is minimal. Comparison of the stability of 6S with 2-carbenanorbornane and the geometry of 6S with that of 6T and also with the singlet and triplet 2-carbenanorbornane suggests very modest bridging. The stabilization energy and geometry of 2-carbenabicyclooctadiene 7 resemble antihomoaromatic bicyclooctadienyl cation 9 rather than the related homoaromatic bicyclooctadienyl anion 8. The diamagnetic susceptibility exhaltations (Deltachi) of 3, 4, 5, and 7, calculated at the B3LYP/6-311+G(2d,p)//B3LYP/6-31G level, are -0.7, 22.7, 26.0, and -10.3 cgs-ppm, respectively. The singlet-triplet energy differences, DeltaE(TS), for carbenacyclohexane, carbenacyclopentane, 3, 4, 5, 6, 7, and 2-carbenabicyclo[3.2.1]oct-3-ene at the B3LYP/6-311+G(3df, 2p)//B3LYP/6-31G level are 3.4, 10.3, 8.8, 27.1, 25.9, 12.7, -4.0, and -0.9 kcal/mol, respectively.     

离子液体双水相技术萃取头孢呋辛酯及其机理探究

通过研究离子液体四氟硼酸1-丁基-3-甲基咪唑( [Bmim]BF4)-Na2-CO3双水相体系对头孢呋辛酯的萃取性能,建立了萃取环境水样中头孢呋辛酯的双水相法.考察了双水相体系组成及相关条件对萃取率的影响,并对其萃取作用力及萃取机制进行了探索.结果表明,Na2CO3用量为0.8～2.0 9,[Bmim]BF4用量为1～2 mL时,随着二者用量的增加,萃取率有所增加.与[Bmim]C1/Na2CO3双水相体系相比,[Bmim]BF4/Na2CO3双水相体系更适于萃取头孢呋辛酯.热力学参数AG°T＜0,AH°r＞0,△S°T＞0,说明萃取过程的主要推动力为疏水性相互作用.在最佳萃取条件下,用此方法萃取环境水样中的头孢呋辛酯,二次萃取率大于93％,重现性好.整个萃取过程快速、高效且无乳化现象.     

CH3F分子间相互作用的ab initio研究

在MP2/6-311+ +G(3d,3p)电子相关校正水平上,对CH₃F二聚体可能存在的几何构型进行全自由度能量梯度优化和频率验证,发现3种势能面上有极小点的构型.进一步在高级电子相关校正的MP4S-DTQ、CCSD(T)/6-311+ +G(3df,3pd)方法水平上,对其中总能量最小的构型进行精确计算,得到二聚体的结合能为-9.707kJ/mol.研究结果支持了由光谱实验结果推测的构型,解释了CH₃F二聚体的谐振频率的多样性.     

DFT investigation of the mechanism of CH2CO + O(3P) reaction

A detailed theoretical survey of the potential energy surface (PES) for the CH₂CO + O(³P) reaction is carried out at the QCISD(T)/6‐311+G(3df,2p)//B3LYP/6‐311+G(d,p) level. The geometries, vibrational frequencies, and energies of all stationary points involved in the reaction are calculated at the B3LYP/6‐311+G(d,p) level. More accurate energy information is provided by single‐point calculations at the QCISD(T)/6‐311+G(3df,2p) level. Relationships of the reactants, transition states, intermediates, and products are confirmed by the intrinsic reaction coordinate (IRC) calculations. The results suggest that P1(CH₂+CO₂) is the most important product. This study presents highlights of the mechanism of the title reaction. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005