Detection of the weak-secretor rs1047781 (385A>T) single nucleotide polymorphism using an unlabeled probe high-resolution melting-based method

FUT2 encodes galactoside 2-α-l -fucosyltransferase 2 which determines the secretor status of ABO(H) blood group antigens. Secretors have at least one functional FUT2 allele (Se), while nonsecretors or weak secretors are homozygous for nonfunctional (non- or weak secretor) FUT2 alleles (se or Se^w). The Se^w having the 385A>T missense SNP (rs1047781) is the prevalent nonfunctional allele in East and Southeast Asians. In this study, we developed an unlabeled-probe high-resolution melting (HRM) analysis for genotyping of 385A>T and validated the method by analyzing 72 Japanese whose 385A>T genotypes were confirmed by DNA sequencing. The unlabeled-probe HRM analysis clearly discriminated three genotypes of 385A>T. In addition, the results obtained for the 72 Japanese by this method were fully concordant with previous ones. Estimation of secretor status using this cost-effective method may be useful in East and Southeast Asian populations.     

The crystal polymorphs of metazachlor

Five crystal polymorphs of the herbicide metazachlor (MTZC) were characterized by means of hot stage microscopy, differential scanning calorimetry, IR- and Raman spectroscopy as well as X-ray powder diffractometry. Modification (mod.) I, II and III° can be crystallized from solvents and the melt, respectively, whereas the unstable mod. IV and V crystallize exclusively from the super-cooled melt. Based on the results of thermal analysis and solvent mediated transformation studies, the thermodynamic relationships among the polymorphic phases of metazachlor were evaluated and displayed in a semi-schematic energy/temperature-diagram. At room temperature, mod. III° (T _fus =76°C, Δ_fus H _III =26.6 kJ mol^-1) is the thermodynamically stable form, followed by mod. II (T _fus =80°C, Δ_fus H _II =23.0 kJ mol^-1) and mod. I (T _fus =83°C, Δ_fus H _II=19.7 kJ mol^-1). These forms are enantiotropically related showing thermodynamic transition points at ~55°C (T _{trs, III/II}), ~60°C (T _{trs, III/I}) and ~63°C (T _{trs, II/I}). Thus mod. I is the thermodynamically stable form above 63°C, mod. III° below 55°C and mod. II in a small window between these temperatures. Mod. IV (T _fus =72-74°C, Δ_fus H _II =18.7 kJ mol^-1) and mod. V (T _fus =65°C) are monotropically related to each other as well as to all other forms. The metastable mod. I and II show a high kinetic stability. They crystallize from solvents, and thus these forms can be present in commercial samples. Since metazachlor is used as an aqueous suspension, the use of the metastable forms is not advisable because of a potential transformation to mod. III°. This may result in problematic formulations, due to caking and aggregation. This revised version was published online in July 2006 with corrections to the Cover Date.     

Rubidium and lithium butanoates binary phase diagram

The temperature and enthalpy vs. composition diagrams of the binary system [xC₃H₇CO₂Li+(1–x)C₃H₇CO₂Rb], where x=mole fraction, were determined by differential scanning calorimetry (DSC). This binary systems displays the formation of two mixed salts with a composition 1:1 and 1:2, which melt incongruently at T _fus=590.5 K, with Δ_fus H _m=11.6 kJ mol^–1, and congruently at T _fus=614.5 K, with Δ_fus H _m=20.2 kJ mol^–1, respectively. The phase diagram also presents an ionic liquid-crystalline phase in a wide temperature range: 95 K.     

Quantitative analysis of single‐nucleotide polymorphisms by pyrosequencing with di‐base addition

We have developed and validated a novel method for quantitative detection of SNPs by using pyrosequencing with di‐base addition (PDBA). Based on the principle that the signal intensity is proportional to the template concentration within a linear concentration range, linear formula (Y = AX + B ) for each genotype is established, and the relationship between two genotypes of a single SNP can be resolved by corresponding linear formulas. Here, PDBA assays were developed to detect variants rs6717546 and rs4148324, and the linear formulas for each genotype of rs6717546 and rs4148324 were established. The method allowed to quantitatively determine each genotype and showed 100% accordant results against a panel of defined mixtures. A set of 24 template fragments containing variants rs6717546 or rs4148324 was tested to evaluate the method. Our results showed that allele frequency of each genotype was accurately quantified, with results comparable to those of conventional pyrosequencing. Furthermore, this method was capable of detecting alleles with frequencies as low as 3%, which was more sensitive than ∼5 to ∼7% level detected by conventional pyrosequencing. This method offers high sensitivity, reproducibility, and relatively low costs, and thus could provide a much‐needed approach for quantitative analysis of SNPs in clinical samples.     

Seven nonsynonymous SNPs in the gene encoding human deoxyribonuclease II may serve as a functional SNP potentially implicated in autoimmune dysfunction

Many nonsynonymous SNPs in the human DNase II gene (DNASE2), potentially relevant to autoimmunity in conditions such as rheumatoid arthritis, have been identified, but only limited population data are available and no studies have evaluated whether such SNPs are functional. Genotyping of all the 15 nonsynonymous human DNase II SNPs was performed in three ethnic groups including 16 different populations using the PCR‐restriction fragment length polymorphism technique. A series of constructs corresponding to each SNP was examined. Fifteen nonsynonymous SNPs in the gene, except for p.Val206Ile in a Korean population, exhibited a mono‐allelic distribution in all of the populations. On the basis of alterations in the activity levels resulting from the corresponding amino acid substitutions, four activity‐abolishing and five activity‐reducing SNPs were confirmed to be functional. The amino acid residues in activity‐abolishing SNPs were conserved in animal DNase II. All the nonsynonymous SNPs that affected the catalytic activity of human DNase II showed extremely low genetic heterogeneity. However, a minor allele of seven SNPs producing a loss‐of‐function or extremely low activity‐harboring variant could serve as a genetic risk factor for autoimmune dysfunction. These functional SNPs in DNASE2 may have clinical implications in relation to the prevalence of autoimmune diseases.     

Detection of mosaicism for the polymorphic variants in the 5′‐UTR of hOGG1 by cloning and sequence analysis and pyrosequencing

Mosaicism refers to the presence of genetically distinct cell lines within an organism or a tissue. Somatic mosaicism exists in distinct populations of somatic cells and commonly arises as a result of somatic mutations, mainly in early embryonic development. SNPs are important markers that distinguish between different individuals in heterogeneous biological samples and contribute greatly to disease risk association studies. In this work, we investigated the relationship between the functional variants in the 5′‐UTR of the hOGG1 gene and the risk of type 2 diabetes. Upon detection of the polymorphisms c.‐53G>C, c.‐23A>G, and c.‐18G>T in the hOGG1 gene, we found that mosaicism was present in 3/28 (10.71%), 7/51 (13.73%), and 1/44 (2.27%) patients respectively, who were carriers of these single nucleotide variations, by cloning and sequence analysis and pyrosequencing. Statistical analysis showed that the frequency of the variation c.‐23A>G in the hOGG1 5′‐UTR in type 2 diabetic patients was significantly higher than that in healthy controls. However, sequencing of the mutant alleles in mosaic individuals showed weak peaks that may affect detection of the SNPs and impair association‐based investigations.     

A Ready‐to‐Use Electrochemical Kit Design for the Diagnosis of Single Nucleotide Polymorphisms

In this study, for the first time a model electrochemical kit was constructed for the detection of a functional polymorphism in catechol‐O‐methyl transferase (COMT) gene which is important for diagnosis of neuropsychiatric disorders as Alzheimer disease. The disposable pencil graphite electrode (PGE) is designed as a “kit” and the probe DNA covered PGE can detect single nucleotide polymorphisms (SNPs) from real samples based on the guanine oxidation signal even after 5 months of kit preparation (150 days durability).The detection limit (S/N=3) of the biosensor was calculated as 1.18 pmol of synthetic target sequence and 6.09×10⁵ molecules of real samples in 30 min detection time.     

An allelic ladder based upon reference alleles for mtDNA SNP analysis using the SNaPshot technique

The analysis of mitochondrial DNA (mtDNA) single-nucleotide polymorphisms (SNPs) using the SNaPshot technique (Applied Biosystems) is a fast and sensitive method for the reliable identification of disease-associated mtDNA SNPs, genetic ancestry mtDNA SNPs and forensically important mtDNA SNPs. The detection of many SNPs in one multiplex PCR and one subsequent multiplex minisequencing reaction is challenging for laboratories who want to establish this technique, due to the problem that there is no allelic ladder available for mtDNA SNP analysis via SNaPshot technique. Normally, the laboratory has to invent long-term testing and studies. The interpretation of false and correct alleles is up to some specialists knowing the expected and the estimated size of each allele SNP. We here present a protocol to assemble up to 84 alleles of 42 different mtDNA SNPs in an allelic ladder that is based upon reference alleles. We recommend using allelic ladders/reference alleles for SNP analysis to maintain high-quality analysis standards.     

The structure and thermochemistry of 3:4,5:6-dibenzo-2-hydroxymethylene-cyclohepta-3,5-dienenone (1) and some related compounds

Condensed and gas phase enthalpies of formation of 3:4,5:6-dibenzo-2-hydroxymethylene-cyclohepta-3,5-dienenone (1, (−199.1 ± 16.4), (−70.5 ± 20.5) kJ mol⁻¹, respectively) and 3,4,6,7-dibenzobicyclo[3.2.1]nona-3,6-dien-2-one (2, (−79.7 ± 22.9), (20.1 ± 23.1) kJ mol⁻¹) are reported. Sublimation enthalpies at T=298.15 K for these compounds were evaluated by combining the fusion enthalpies at T = 298.15 K (1, (12.5 ± 1.8); 2, (5.3 ± 1.7) kJ mol⁻¹) adjusted from DSC measurements at the melting temperature (1, (T _fus, 357.7 K, 16.9 ± 1.3 kJ mol⁻¹)); 2, (T _fus, 383.3 K, 10.9 ± 0.1) kJ mol⁻¹) with the vaporization enthalpies at T = 298.15 K (1, (116.1 ± 12.1); 2, (94.5 ± 2.2) kJ mol⁻¹) measured by correlation-gas chromatography. The vaporization enthalpies of benzoin ((98.5 ± 12.5) kJ mol⁻¹) and 7-heptadecanone ((94.5 ± 1.8) kJ mol⁻¹) at T = 298.15 K and the fusion enthalpy of phenyl salicylate (T _fus, 312.7 K, 18.4 ± 0.5) kJ mol⁻¹) were also determined for the correlations. The crystal structure of 1 was determined by X-ray crystallography. Compound 1 exists entirely in the enol form and resembles the crystal structure found for benzoylacetone.     

水合烟酸铜Cu(Nic)2•H2O(s)(Nic＝烟酸)的合成、表征及热力学性质

近几十年来,烟酸盐类化合物或配合物由于优越的吸收率高和无毒副作用等特点使其在化妆品、药品和食品等领域作为营养添加剂具有重要应用前景。然而,这类化合物的基础热力学数据极其缺乏,从而限制了这类化合物的理论研究和应用开发的深入开展。为此,本论文利用室温固相合成方法和球磨技术合成了一种新化合物Cu(Nic)2•H2O(s),利用化学分析、元素分析、FTIR和X-射线粉末衍射技术表征了它的结构和组成,利用精密自动绝热热量计准确地测量了它在78-400 K温区的摩尔热容。在热容曲线的T ＝ 326-346 K温区观察到一个明显的固-液相变过程。利用相变温区三次重复实验热容的测量结果确定了此相变过程的峰温、相变焓和相变熵分别为：Tfus＝(341.290 ±0.873) K, DfusHm＝(13.582±0.012) kJ×mol-1, DfusSm＝(39.797±0.067) J×K-1×mol-1。通过最小二乘法将相变前和相变后的热容实验值分别拟合成了热容对温度的两个多项式方程。通过热容多项式方程的数值积分,得到了这个化合物的舒平热容值和相对于298.15 K的各种热力学函数值,并且将每隔5 K的热力学函数值列成了表格。     

ESI-MS analyses of lake dissolved organic matter in light of supramolecular assembly

A high-performance size-exclusion chromatography (SEC) system was coupled on-line to an electrospray ionization (ESI) interface to detect gas-phase ions by an API 365 LC/MS/MS triple quadrupole analyzer. The SEC fractions of a strongly coloured freshwater solution containing dissolved organic matter-humic substances (DOM-HS) were screened both by UV₂₅₄ and by ESI mass spectrometry (ESI-MS) in the full-scan mode within the m/z range of 100–2,900 amu in negative and positive polarities. The ESI-MS spectra were also collected by direct infusion of the DOM-HS solution in both polarities. ESI-MS spectra did not primarily favour low mass compounds, and negative and positive total ion chromatograms were parallel to the SEC elution profile obtained by UV₂₅₄ detection from DOM-HS solution. The UV₂₅₄ detection overestimated the SEC portion of higher size/mass solutes and underestimated that of solutes of smaller sizes/masses as compared with the total ion chromatogram intensities in negative or positive polarities. The change of mass-weighted and number-weighted average sizes/masses (M _w and M _n) of different SEC fractions was fairly small, in contrast to UV₂₅₄ detection, with increasing elution volume. A reasonable explanation for the great differences between M _w and M _n values, obtained by UV₂₅₄ and ESI-MS detections for eight different SEC fractions, seems to be a supramolecular-type association of relatively small components through weak dispersive forces. M _n values obtained by vapour-pressure osmometry for different SEC fractions were to some extent analogous with those of negative and positive ESI-MS. The shapes obtained by either negative or positive polarities and calculated M _w and M _n values indicated a close structural similarity between each SEC fraction. Positive ion and negative ion spectra of different humic fractions represented quite similar components, and there was no evidence for noteworthy occurrence of multiply charged ions being able to lower mass distributions of negative ion spectra. The effect of nitrogen on the mass spectra seemed to be unimportant, and the weak ions observed at even m/z values correspond most likely to the ¹³C counterparts of the more abundant ¹²C odd ions. No uncontrolled ESI fragmentation was observable and humic solutes seemed to be quite heat-resistant. Direct infusion of the untreated DOM-HS solution and statistical calculation verified that the SEC-separated different fractions really represent distinct entities of the original DOM-HS mixture. ESI-MS results support the opinion that the structural composition of humic solutes in their original combined mixture resembles supramolecular-type associations of smaller molecular size entities possessing similar structural functionalities.     

Global genetic analysis of all single nucleotide polymorphisms in exons of the human deoxyribonuclease I-like 3 gene and their effect on its catalytic activity

Deoxyribonucleases (DNases) have been suggested to be implicated in the pathophysiology of autoimmune diseases. In the DNASE1L3 gene encoding human DNase I‐like 3 (DNase 1L3), a member of the DNase I family, only two non‐synonymous (R178 H and R206C) single nucleotide polymorphisms (SNPs) have been examined [Ueki et al., Clin. Chim. Acta 2009, 407, 20–24]. Three other non‐synonymous (G82R, K96N, and I243M) and four synonymous (S17S, T84T, R92R, and A181A) SNPs, in addition to R206C and R178H, have been identified in DNASE1L3. We investigated the distribution of all these SNPs in exons of the gene in eight Asian, three African, and three Caucasian populations worldwide using newly devised genotyping methods. SNP T84T showed polymorphism in all the populations, and R92R was polymorphic in the three African and three Caucasian populations; R206C was distributed only in Caucasian populations. In contrast, no minor allele was found in five SNPs (S17S, G82R, K96N, A181A, and I243M) in DNASE1L3. Generally, the DNase 1L3 gene shows relatively low genetic diversity with regard to exonic SNPs. When the effect of amino acid/nucleotide substitutions resulting from the SNPs on DNase 1L3 activity was examined, none of the synonymous SNPs had any effect on the DNase 1L3 activity, whereas among non‐synonymous SNPs, SNP G82R diminished the activity of the enzyme, being similar to R206C. These findings permit us to assume that, although only R206 exhibits polymorphisms in a Caucasian‐specific manner, at least SNPs G82R and R206C in DNASE1L3 might be potential risk factors for autoimmune disease.     

腈菌唑的热容和热力学性质

通过小样品精密自动绝热热量计测定了自己合成并提纯的腈菌唑 (C₁₅H₁₇ClN₄) 在78 ～ 368K温区的低温摩尔热容。量热实验发现, 该化合物在363 ~ 372 K温区, 有一固-液熔化相变过程, 其熔化温度为 (348.800±0.06)K, 摩尔熔化焓、摩尔熔化熵及化合物的纯度分别为：(30931±11) J•mol^-1、(88.47±0.02) J•mol^-1•K^-1和0.9941(摩尔分数)。用差示扫描量热(DSC) 技术对该物质的固-液熔化过程作了进一步研究，结果与绝热量热法一致。     

Calorimetric study and thermal analysis of crystalline nicotinic acid

As one primary component of Vitamin B₃, nicotinic acid [pyridine 3-carboxylic acid] was synthesized, and calorimetric study and thermal analysis for this compound were performed. The low-temperature heat capacity of nicotinic acid was measured with a precise automated adiabatic calorimeter over the temperature rang from 79 to 368 K. No thermal anomaly or phase transition was observed in this temperature range. A solid-to-solid transition at T _trs=451.4 K, a solid-to-liquid transition at T _fus=509.1 K and a thermal decomposition at T _d=538.8 K were found through the DSC and TG-DTG techniques. The molar enthalpies of these transitions were determined to be Δ_trs H _m=0.81 kJ mol^-1, Δ_fus H _m=27.57 kJ mol^-1 and Δ_d H _m=62.38 kJ mol^-1, respectively, by the integrals of the peak areas of the DSC curves. This revised version was published online in August 2006 with corrections to the Cover Date.     

Heat capacities and thermodynamic properties of 2-benzoylpyridine (C12H9NO)

The heat capacities of 2-benzoylpyridine were measured with an automated adiabatic calorimeter over the temperature range from 80 to 340 K. The melting point, molar enthalpy, Δ_fusH^m, and entropy, Δ_fusS^m, of fusion of this compound were determined to be 316.49±0.04 K, 20.91±0.03 kJ mol^–1 and 66.07±0.05 J mol^–1 K^–1, respectively. The purity of the compound was calculated to be 99.60 mol% by using the fractional melting technique. The thermodynamic functions (H_T–H_298.15) and (S_T–S_298.15) were calculated based on the heat capacity measurements in the temperature range of 80–340 K with an interval of 5 K. The thermal properties of the compound were further investigated by differential scanning calorimetry (DSC). From the DSC curve, the temperature corresponding to the maximum evaporation rate, the molar enthalpy and entropy of evaporation were determined to be 556.3±0.1 K, 51.3±0.2 kJ mol^–1 and 92.2±0.4 J K^–1 mol^–1, respectively, under the experimental conditions.     

Characterisation of regioselectively functionalized 2,3-O-carboxymethyl cellulose by enzymatic and chemical methods

The determination of the molecular structure of 2,3-O-carboxymethyl cellulose (2,3-O-CMC), prepared via 6-O-(4-monomethoxy)triphenylmethyl cellulose, was carried out in detail by means of enzymatic and chemical methods. The 2,3-O-CMCs had degrees of substitution (DS) in the range of 0.5–1.2 showing a narrow molar mass distribution as revealed by SEC. As a result of an endoglucanase treatment, an intensive depolymerization of the samples occurred which was more pronounced for 2,3-O-CMC with comparatively low DS. All degraded samples could be separated into 18 fractions by preparative SEC and the proportion of each individual repeat unit was analysed by anion exchange chromatography (AEC) following complete hydrolytic chain degradation. The results indicated a homogeneous distribution of the functional groups within the polymer chain. Moreover, it became obvious that a preferred carboxymethylation of O-2 compared with O-3 occurred and that a preferred functionalization of already carboxymethylated units occurred as the reaction progressed. AEC with pulsed amperometric detection, which was used to separate and analyse the differently functionalized repeating units as well as glucose, had to be calibrated. Therefore, a method to determine the response factors of the individual carboxymethylated glucose units was developed using ¹³C NMR spectroscopic measurements (inverse gated decoupling) of depolymerised 2,3-O-CMC.     

Molar heat capacity and thermodynamic properties of 1,2-cyclohexane dicarboxylic anhydride [C8H10O3]

The molar heat capacity C _p,m of 1,2-cyclohexane dicarboxylic anhydride was measured in the temperature range from T=80 to 390 K with a small sample automated adiabatic calorimeter. The melting point T _m, the molar enthalpy Δ_fus H _m and the entropy Δ_fus S _m of fusion for the compound were determined to be 303.80 K, 14.71 kJ mol⁻¹ and 48.43 J K⁻¹ mol⁻¹, respectively. The thermodynamic functions [H _T-H _273.15] and [S _T-S _273.15] were derived in the temperature range from T=80 to 385 K with temperature interval of 5 K. The thermal stability of the compound was investigated by differential scanning calorimeter (DSC) and thermogravimetry (TG), when the process of the mass-loss was due to the evaporation, instead of its thermal decomposition.     

Genetic and expression analysis of SNPs in the human deoxyribonuclease II: SNPs in the promoter region reduce its in vivo activity through decreased promoter activity

Five SNPs in the human DNase II gene have been reported to be associated with rheumatoid arthritis (RA). Genotype and haplotype analysis of 14 SNPs, nine SNPs of which reported in the NCBI dbSNP database in addition to these five SNPs, was performed in healthy subjects. The enzymatic activities of the amino acid substituted DNase II corresponding to each SNP and serum DNase II in healthy Japanese, and promoter activities derived from each haplotype of the RA‐related SNPs were measured. Significant correlations between genotype in each RA‐related SNP and enzymatic activity levels were found; alleles associated with RA exhibited a reduction in serum DNase II activity. Furthermore, the promoter activities of each reporter construct corresponding to predominant haplotypes in three SNPs in the promoter region of the gene exhibited significant correlation with levels of serum DNase II activity. These findings indicate these three SNPs could alter the promoter activity of DNASE2, leading to a decline in DNase II activity in the serum through gene expression. Since the three SNPs in the promoter region of the DNase II gene could affect in vivo DNase II activity through reduction of the promoter activity, it is feasible to identify these SNPs susceptible to RA.     

Densely crosslinked polycarbosiloxanes. I. Synthesis

Novel densely crosslinked polycarbosiloxanes were obtained by using functional branched prepolymers. Two types of soluble prepolymers were prepared from di- and trifunctional alkoxysilane monomers via cohydrolysis/condensation and for both final crosslinking occurred via hydrosilylation. The prepolymers having only vinyl functionalities (poly[phenylmethylvinyl]siloxanes, system A) were crosslinked by using a crosslinking agent with reactive silicon–hydrogen bonds. In the prepolymers having both silicon–vinyl and silicon–hydrogen functionalities (poly[phenylmethyl-vinylhydro]siloxanes, system B) crosslinking took place intermolecularly. For the characterization of the prepolymers ¹H-NMR, ²⁹Si–NMR, FT–IR spectroscopy, analytical SEC and VPO were employed. The prepolymers were fractionated with preparative SEC and the fractions analyzed with ¹H-NMR and analytical SEC. The crosslinking reaction was followed by FT–IR spectroscopy. The polymer networks were fully transparent homogeneous materials and are promising for future optical applications. © 1997 John Wiley & Sons, Inc.     

Online Coupling of Size‐Exclusion Chromatography and IR Spectroscopy to Correlate Molecular Weight with Chemical Composition

The determination of molecular weight and correlated chemical composition is of major interest for the advanced analysis of copolymers, blends, or unknown samples. In this work, we present a new way of online coupling IR spectroscopy and SEC to achieve a chemically sensitive, universally applicable SEC detector. Our method overcomes the limitations of existing spectroscopy–SEC combinations. We solved the major problems, like huge intensity of solvent signals (polymer concentration in detector <1 g L⁻¹) and short measuring time (<30 s), by recording the IR spectra with fully optimized sensitivity and by following mathematical solvent suppression. The measuring time for a certain S/N was reduced in several optimization steps by a factor of more than 70 000. The resulting sensitivity allows online coupled IR–SEC measurements.