Human Y‐chromosome SNP characterization by multiplex amplified product‐length polymorphism analysis

We designed an allele‐specific amplification protocol to optimize Y‐chromosome SNP typing, which is an unavoidable step for defining the phylogenetic status of paternal lineages. It allows the simultaneous highly specific definition of up to six mutations in a single reaction by amplification fragment length polymorphism (AFLP) without the need of specialized equipment, at a considerably lower cost than that based on single‐base primer extension (SNaPshot?) technology or PCR‐RFLP systems, requiring as little as 0.5 ng DNA and compatible with the small fragments characteristic of low‐quality DNA. By designation of two primers recognizing the derived and ancestral state for each SNP, which can be differentiated by size by the addition of a noncomplementary nucleotide tail, we could define major Y clades E, F, K, R, Q, and subhaplogroups R1, R1a, R1b, R1b1b, R1b1c, J1, J2, G1, G2, I1, Q1a3, and Q1a3a1 through amplification fragments that ranged between 60 and 158bp.     

Glycosyl linkage characteristics and classifications of exo-polysaccharides of some regionally different strains of Lentinula edodes by amplified fragment length polymorphism assay and cluster analysis

We report here the first combined amplified fragment length polymorphism (AFLP) analysis of genomic DNA fingerprinting data and cluster analysis of the exo-polysaccharide glycosyl linkage data of 10 regionally different strains of Lentinula edodes to compare their genetic and structural similarities and differences. In addition, the monosaccharide compositions, molecular weights, glycosyl structural linkages were investigated for the exo-polysaccharides extracted from these different phylogenetic groups of regionally different L. edodes. All exo-polysaccharides had similar molecular weight distribution between 1 × 10⁴ and 3 × 10⁶ Da and the monosaccharide composition analysis revealed the presence of heterogeneous materials containing glucose, mannose, xylose, galactose, fucose, rhamnose and arabinose in different ratios. Among these monosaccharides, the glucose contents are the highest for all but one strain, indicating that glucose probably is the building block of the backbones of these exo-polysaccharides. The AFLP assay data helped to classify the 10 L. edodes strains into three distinct genetic groups. Gas chromatographic and mass spectrometric (GC-MS) data revealed five different glycosyl linkage types for these exo-polysaccharides. Most of the exo-polysaccharide backbone structures contain (1 → 4)-linked-d-glucopyranosyl and (1 → 6)-linked-d-glucopyranosyl moieties. Arabinose 1 → 4 linkages and mannose 1 → 2 linkages also exist in all strains. The only differences among these linkages are their monosaccharide compositions leading to different degree of backbone and branch formations. Cluster analyses of the GC-MS data of the exo-polysaccharides of the 10 strains resulted in 10 dendrograms. However, four of the 10 dendrograms were identical and were obtained using the average, Ward and weighted linkage type method of Manhattan distance and using the Ward method of Euclidean distance. The results of cluster analyses were not very much different from that of the AFLP assay and allowed the comparison of genetic and structural similarities and differences.     

聚合酶链式反应-限制性片段长度多态性和芯片生物分析技术用于台湾海峡常见石斑鱼和鲷鱼的品种鉴定

应用聚合酶链式反应-限制性片段长度多态性分析(PCR-RFLP)和芯片生物分析系统建立了台湾海峡常见石斑鱼和鲷鱼的分子生物学品种鉴定新方法。首先提取鱼的基因组脱氧核糖核酸(DNA)进行细胞色素b基因特定片段的PCR扩增,然后用DdeI、HaeIII和NlaIII 3种限制性内切酶进行酶切,在Agilent DNA 1000芯片上对酶切片段进行分离。该方法成功鉴定了台湾海峡常见的8种石斑鱼品种和5种鲷鱼品种,是一种快速、简便、有效的鱼类品种鉴定分析手段。     

Multiplex amplified product-length polymorphism analysis of 36 mitochondrial single-nucleotide polymorphisms for haplogrouping of East Asian populations

We present a reliable, rapid, and economical multiplex amplified product-length polymorphism (APLP) method for analyzing the haplogroup-diagnostic mitochondrial single-nucleotide polymorphisms (mtSNPs) in East Asian populations. By examining only 36 haplogroup-specific mtSNPs in the coding region by using four 9-multiplex polymerase chain reaction (PCR) and subsequent electrophoresis, we could safely assign 1815 individuals from 8 populations of Japanese, Korean, Chinese, and Germans to 45 relevant haplogroups. This multiplex APLP analysis of coding-region mtSNPs for haplogrouping is especially useful not only for molecular phylogenetic studies but also for large-scale association studies due to its rapid and economical nature. This is the first panel of mtSNPs in the coding region to be used for haplogrouping of East Asian populations.     

Identification of shrimp species in raw and processed food products by means of a polymerase chain reaction-restriction fragment length polymorphism method targeted to cytochrome b mitochondrial sequences

A novel PCR-RFLP method has been developed for the identification of six commercially relevant penaeid shrimp species in raw and processed food products. The method can be completed within 8 h. To implement the method, PCR amplification with the crustF/crustR primers, targeted to the amplification of a ca. 181 bp region of the cytochrome b (cytb) mitochondrial gene in penaeid shrimps, was coupled to restriction analysis with CviJI, DdeI and NlaIV. The method was also applied successfully to the identification of shrimp species in complex processed foods, including this type of shellfish as an added-value food ingredient. The small size of this molecular target facilitates amplification from fresh, frozen, or precooked samples, where DNA fragmentation may be relevant and fragment size critical. We also report the first cytb mitochondrial sequences described to date for the species Farfantepenaeus notialis, Parapenaeus longirostris and Pleoticus muelleri, and these nearly triplicate current knowledge of reference nucleotide sequences in this mitochondrial region for this group of species. The cytb mitochondrial gene may also be considered as a molecular marker for identification and phylogenetic purposes in penaeid shrimp species.     

聚合酶链式反应-限制性片段长度多态性和芯片生物分析技术用于渤海地区鱼种鉴定

以渤海湾具有重要商业价值的9种海鱼(小黄鱼、花鲈、蓝点马鲛、鲐、钝吻黄盖鲽、棘头梅童鱼、许氏平鲉、高眼鲽和长蛇鲻)为研究对象,利用聚合酶链式反应(PCR)-限制性片段长度多态性(RFLP)和芯片生物分析技术对其进行鱼种鉴定。首先提取其基因组脱氧核糖核酸(DNA),对其细胞色素b的特定片段(464 bp)进行扩增,然后选择DdeI、HaeIII和NlaIII3种限制性内切酶进行酶切,并利用芯片生物分析技术得到酶切产物的特异图谱和确切的片段大小,从而有效区分了9种海鱼。研究结果表明,PCR-RFLP和芯片生物分析技术在鱼种鉴定上具有精确、鉴别和快速三大优势,可为鱼类食品检测提供科学依据。     

Genetic evidence of an Asian background in heteroplasmic Iberian cattle (Bos taurus): effect on food authentication studies based on polymerase chain reaction-restriction fragment length polymorphism analysis

This work was aimed at identifying nucleotide polymorphic sites in a 359 bp region of the cytochrome b (cytb) mitochondrial gene of Iberian cattle (Bos taurus). This region is widely used as target in polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) species identification studies in foodstuffs destined for human and animal consumption. Two different coexisting restriction patterns were observed in four of the six animals studied when the 359 bp DNA fragment was cleaved with PalI, HinfI, MvaI, RsaI, or MboI. The amplification of both genotypes with the mitochondrial-specific primers L14735 and H15149 revealed the absence of nuclear pseudo-cytb genes, confirming the existence of mitochondrial heteroplasmy. The two coexisting mtDNA fragments were selectively sequenced in PCR extracts in which one genotype predominated over the other, both exhibiting a sequence variation of 10.4%. From the 37 nucleotide mismatches observed between genotypes, 32 were transitions and five were transversions. While 31 of the nucleotide mismatches between genotypes resulted to be conservative at the amino acid level, six changes implied amino acid substitutions, five of them being located in the variable transmembrane region. Genetic analysis suggests the presence of an Asian background in the mitochondria of Iberian cattle: while one of the genotypes matched the published sequence for Bos taurus, the other genotype clustered with a B. primigenius indicus animal and close to an Asian Bos taurus animal. These results also suggest that a number of current PCR-RFLP species identification methods based on cytb sequences may not be reliable for the accurate detection and identification of bovine material: an alternative battery of enzymes consisting of MmeI, NlaIV, and AluI is proposed.     

A simple and precise diagnostic method for spinal muscular atrophy using a quantitative SNP analysis system

A simple and precise diagnostic method for spinal muscular atrophy (SMA) using high‐resolution CE‐based single‐strand conformation polymorphism (CE‐SSCP) was developed in this study. SMA is a common genetic disorder caused by an abnormality in the relative copy numbers of SMN1 and its centromeric copy SMN2, which differ only in two nucleotides, namely at exons 7 and 8. Therefore, the precise discrimination of the differences in sequence as well as their relative quantities is crucial for the diagnosis of SMA. Multiplex ligation‐dependent probe amplification and sequence‐sensitive DNA separation using hydroxyethyl cellulose and hydroxypropyl cellulose blended polymer matrix are currently the available methods used in the diagnosis of SMA. However, these methods are limited by their extended hybridization step and low resolution. In this study, the simultaneous discrimination of SMN exons 7 and 8 was successfully demonstrated using high‐resolution CE‐SSCP. Unlike the previously reported alternative method, single base differing amplicons were baseline‐separated because of its extraordinary resolution, thus providing accurate and precise quantification of each paralog.     

Capillary electrophoresis with dual laser detection in separation of amplified fragment length polymorphism fragments

We are presenting the application of CE technique with dual‐channel LIF detection for the simultaneous separation of DNA fragments labeled with two different fluorescence dyes. The optimal conditions of the analysis were determined for the separation of amplified fragment length polymorphism (AFLP) fragments labeled with 5′‐6‐carboxyfluorescein (6‐FAM) and the DNA size standard labeled with sulfoindocyanine succinimidyl ester (Cy‐5). CE equipped with both argon ion and diode lasers is a good alternative for sequencers and might be applied in analyses of PCR products generated by various fingerprinting methods.     

A novel method developed for acetylcholine detection in royal jelly by using capillary electrophoresis coupled with electrogenerated chemiluminescence based on a simple reaction

A novel method for highly sensitive detection of acetylcholine in royal jelly was proposed by using CE coupled with electrogenerated chemiluminescence (ECL). Acetylcholine, which could not react with Tris(2,2′‐bipyridine)ruthenium(II) to strengthen its ECL signals, decomposed into trimethylamine and strengthened the ECL signals sharply when it was heated to its melting point. This reaction needed no additional reagent and it was mild, simple, stable and rapid, without any side reaction. By combining the above process with CE separation technique, trimethylamine in royal jelly was completely separated from interfering substances and was successfully detected within 4 min. The limit of detection for acetylcholine was found to be 6.3×10^?8 g/mL with a signal‐to‐noise ratio of 3:1. Acetylcholine in the royal jelly was detected to be 912±58 μg/g. The recoveries of acetylcholine chloride in the sample were in the ranges of 92–106%. The coefficients of variation for intra‐day and inter‐day reproducibility were equal to or less than 4.9 and 6.8%, respectively.     

Effect of temperature gradients on single-strand conformation polymorphism analysis in a capillary electrophoresis system using Pluronic polymer matrix

Capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) analysis is a prominent bioseparation method based on the mobility diversity caused by sequence-induced conformational differences of single-stranded DNA. The use of Pluronic polymer matrix has opened up new opportunities for CE-SSCP, because it improved the resolution for various genetic analyses. However, there still exists a challenge in optimizing Pluronic-based CE-SSCP, because the physical properties of Pluronic solutions are sensitive to temperature, particularly near the gelation temperature, where the viscoelasticity of Pluronic F108 solutions sharply changes from that of a Newtonian fluid to a hydrogel upon heating. We have focused on a set of experiments to control the ambient temperature of the CE system with the aim of enhancing the reliability of the CE-SSCP analysis by using the Applied Biosystems ABI 3130xl genetic analyzer with Pluronic F108 solution matrix. The ambient temperature control allowed us to vary the inlet and outlet portion of the capillary column, while the temperature of the column was kept at 35 °C. The resolution to separate 2 single-base-pair-differing DNA fragments was significantly enhanced by changing the temperature from 19 to 30 °C. The viscoelastic properties of the F108 solution matrix upon heating were also investigated by ex situ rheological experiments with an effort to reveal how the development of gels in Pluronic solutions affects the resolution of CE-SSCP. We found that the column inlet and outlet temperatures of the capillary column have to be controlled to optimize the resolution in CE-SSCP by using the Pluronic matrix.     

Determination of alcohols in gasoline blends using a multi-dimensional switching system

Methanol, 2-Me-propanol-2, propanol-2, benzene, toluene and xylenes in gasoline blends were determined using a valveless multi-dimensional switching system (MDSS) with two packed columns and temperature programming. Compounds of interest, interfering with paraffins and naphthenes, were in a sequence of four heart cuts transferred onto the second column. The resulting baseline separation enabled precise quantitative measurement within a short analysis time. Instrument settings, times of switching and integration parameters were stored in an instrument memory file (user table) and thus high precision in the measurements was achieved.     

A theoretical NMR study of polymorphism in crystal structures of azoles and benzazoles

The NMR chemical shifts of two azoles and one benzazole whose crystal structures present polymorphism have been computed using the GIPAW approach. ¹⁵N and ¹³C nuclei have been studied. Statistical analysis of the computed ¹³C and ¹⁵N chemical shifts indicates that the GIPAW chemical shifts reproduce with a high degree of accuracy those experimentally reported. This methodology can be used to identify other polymorphic crystal structures.     

A kinetic and spectroscopic study of the interaction between a M(CO)5 (M=Cr, W) fragment and ethyl diazoacetate

The reaction between Cr(CO)₅[C₆H₆] and ethyl diazoacetate (EDA) has been studied using the technique of laser flash photolysis. Results indicate that the Cr(CO)₅ fragment reacts very rapidly with the EDA ligand. Low temperature spectroscopic studies suggest that in the case of W(CO)₅, and by analogy also in the case of Cr(CO)₅, the initial adduct between the pentacarbonyl fragment and EDA is one where the oxygen atom of the diazocarbonyl ligand is bound to the metal center. This kinetic product is then converted to a thermodynamically favored complex which is tentatively assigned as the nitrogen bound W(CO)₅-EDA complex that appears to be stable at r.t.     

Identification of FAMEs using ECL values and a three-dimensional Kováts retention index system

n-Alkanes and fatty acid methyl esters have been chromatographed on four capillary columns of different polarity (LM-1 (100% polydimethylsiloxane), CB-225 (25% cyanopropyl, 25% phenyl polysiloxane), LM-100 (immobilized polyethylene glycol), and BPX-70 (70% cyanopropyl polysiloxane)) with the goal of identifying the major fatty acid methyl esters obtained by derivatization of vegetable oils. Chromatographic retention data were employed for the construction of a three-dimensional Kováts retention index system and for the elaboration of a table of equivalent chain length values.     

C-H bond activation of methane in aqueous solution: a hybrid quantum mechanical/effective fragment potential study

In this study, we investigated the C? H bond activation of methane catalyzed by the complex [PtCl₄]^2?, using the hybrid quantum mechanical/effective fragment potential (EFP) approach. We analyzed the structures, energetic properties, and reaction mechanism involved in the elementary steps that compose the catalytic cycle of the Shilov reaction. Our B3LYP/SBKJC/cc‐pVDZ/EFP results show that the methane activation may proceed through two pathways: (i) electrophilic addition or (ii) direct oxidative addition of the C? H bond of the alkane. The electrophilic addition pathway proceeds in two steps with formation of a σ‐methane complex, with a Gibbs free energy barrier of 24.6 kcal mol^?1, followed by the cleavage of the C? H bond, with an energy barrier of 4.3 kcal mol^?1. The activation Gibbs free energy, calculated for the methane uptake step was 24.6 kcal mol^?1, which is in good agreement with experimental value of 23.1 kcal mol^?1 obtained for a related system. The results shows that the activation of the C? H bond promoted by the [PtCl₄]^2? catalyst in aqueous solution occurs through a direct oxidative addition of the C? H bond, in a single step, with an activation free energy of 25.2 kcal mol^?1, as the electrophilic addition pathway leads to the formation of a σ‐methane intermediate that rapidly undergoes decomposition. The inclusion of long‐range solvent effects with polarizable continuum model does not change the activation energies computed at the B3LYP/SBKJC/cc‐pVDZ/EFP level of theory significantly, indicating that the large EFP water cluster used, obtained from Monte Carlo simulations and analysis of the center‐of‐mass radial pair distribution function, captures the most important solvent effects. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Inverse gas chromatography in the study of polymer degradation. Part 4: A study of model systems for reinforced vulcanizates

Summary Inverse gas chromatography with olefinic stationary phases, impregnated with silica gel or carbon black, and air as carrier gas has been found to yield characteristic shifts of retention data and concomitant changes in peak shape. The plots of retention index versus oxygen flow obtained indicate carbon black to have significant antioxidant properties, which are not altogether lost on solvent extraction. On the other hand, silica gel yields results consistence with the existence of a novel chain scission repair process.     

A novel high-resolution chipCE assay for rapid detection of EGFR gene mutations and amplifications in lung cancer therapy by a combination of fragment analysis, denaturing CE and MLPA

There is a growing interest in evaluating molecular markers as predictors of response to new generation of targeted cancer therapies. One of such areas is biological therapy targeting epidermal growth factor receptor gene (EGFR) in lung cancer. The testing of tumor tissue is focused on specific EGFR mutations and EGFR gene amplification, since tumors exhibiting positivity of either of the two marker types are highly sensitive towards the treatment. Although traditional methods of DNA sequencing and fluorescence in situ hybridization are still in use for the detection of EGFR mutations and gene amplification, respectively, there is a need for new dedicated techniques with the primary emphasis on simplicity, sensitivity, speed and cost effectiveness. The main purpose of this work was to integrate diverse assays for both EGFR tests onto a single platform to eliminate the need for different instruments and separate processing. We demonstrate a chip capillary electrophoresis (chipCE) application for EGFR mutation detection by a combination of fragment analysis and denaturing CE along with multiplex ligation-dependent probe amplification (MLPA) for evaluation of EGFR amplification. All separations are carried out in denaturing sieving polymer on a modified Bioanalyzer 2100 chipCE instrument running at temperatures of up to 65°C. The main strength of the resulting high-resolution chipCE application is in its simplicity, speed of analysis and minimal amount of sample required for complete testing of EGFR status. Such an approach could potentially fit medium throughput laboratories providing molecular pathology services for clinical oncologists with fast turnaround times and limited consumption of tissue material.     

A capillary electrophoretic system based on a novel microemulsion for the analysis of coenzyme Q10 in human plasma by electrokinetic chromatography

A new analytical method for determination of coenzyme Q10 (2,3‐dimethoxy‐5‐methyl‐6‐decaprenyl‐1,4‐benzoquinone, CoQ10) in human plasma was developed based on CE using a double tensioactive microemulsion. CoQ10 was quantitatively extracted into 1‐propanol/hexane and quantified by MEEKC. The microemulsion was prepared by mixing 1.4% w/w sodium bis(2‐ethylhexyl) sulfosuccinate, 4% w/w cholic acid, 1% w/w octane, 8.5% w/w butanol, 0.1% w/w PVA and 85% w/w 10 mM Tris buffer at pH 9.0. The optimized electrophoretic conditions included the use of an uncoated silica capillary of 60 cm total length and 75 μm id, an applied voltage of 20 kV, room temperature and 214 nm ultraviolet detection. Selectivity, linearity, LOD, LOQ, precision and accuracy were evaluated as the parameters of validation. Owing to its simplicity and reliability, the proposed method can be an advantageous alternative to the traditional methodology for the quantitation of CoQ10 in human plasma with good accuracy and precision.     

Metabolic profiling of serum in patients with cartilage tumours using 1H-NMR spectroscopy: A pilot study

Cartilage-forming lesions include tumours that can vary in severity from benign enchondromas to high-grade malignant chondrosarcomas. Chondrosarcoma is the second most frequent malignant bone tumour, accounting for 20–30% of all malignant bone neoplasms. Surgery is the standard treatment for cartilage tumours (CTs); however, their incidental diagnosis and the difficult differentiation of low-grade lesions like chondrosarcoma grade I from benign entities like enchondroma are challenges for clinical management. In this sense, the search for circulating biomarkers for early detection and prognosis is an ongoing interest. Targeted metabolomics is a powerful tool that can propose potential biomarkers in biological fluids as well as help to discover disturbed metabolic pathways to reveal tumour pathogenesis. In this context, the aim of this study was to investigate the ¹H nuclear magnetic resonance metabolomic serum profile of patients with CTs contrasted with healthy controls. Forty-one metabolites were identified and quantified; the multivariate statistical methods principal component analysis and partial least squares discriminant analysis reveal a clear separation of the CT group, that is, the differential metabolites that were involved in two main metabolic pathways: the taurine and hypotaurine metabolism and synthesis and degradation of ketone bodies. Our results represent preliminary work for emergent serum-based diagnostics or prognostic methods for patients with chondrogenic tumours.