Developing a new nonbinary SNP fluorescent multiplex detection system for forensic application in China

Nonbinary single‐nucleotide polymorphisms (SNPs) are potential forensic genetic markers because their discrimination power is greater than that of normal binary SNPs, and that they can detect highly degraded samples. We previously developed a nonbinary SNP multiplex typing assay. In this study, we selected additional 20 nonbinary SNPs from the NCBI SNP database and verified them through pyrosequencing. These 20 nonbinary SNPs were analyzed using the fluorescent‐labeled SNaPshot multiplex SNP typing method. The allele frequencies and genetic parameters of these 20 nonbinary SNPs were determined among 314 unrelated individuals from Han populations from China. The total power of discrimination was 0.9999999999994, and the cumulative probability of exclusion was 0.9986. Moreover, the result of the combination of this 20 nonbinary SNP assay with the 20 nonbinary SNP assay we previously developed demonstrated that the cumulative probability of exclusion of the 40 nonbinary SNPs was 0.999991 and that no significant linkage disequilibrium was observed in all 40 nonbinary SNPs. Thus, we concluded that this new system consisting of new 20 nonbinary SNPs could provide highly informative polymorphic data which would be further used in forensic application and would serve as a potentially valuable supplement to forensic DNA analysis.     

Glucometer-based Ultra-sensitive BRAF V600E Mutation Detection Facilitated by Magnetic Nanochains and a Self-made Point-of-Care (POC) Device

We realized the user-friendly and field-based point-of-care detection on a self-made portable device with the aid of personal glucose meter (PGM) for single nucleotide polymorphisms (SNPs) of melanoma and colon cancer marker BRAF V600E with good sensitivity and selectivity by integrating the loop-mediated isothermal amplification (LAMP) reaction and the strand exchange signal transduction. The device is equipped with a rotating magnetic field as well as a heating element, under which the pre-added magnetic nanochains (MNCs) help to homogenize the reaction mixture and overcome the low diffusion efficacy of the reactant and the required temperature for different reactions can be met.     

基于磁性颗粒微阵列与双色荧光杂交的单核苷酸多态性分型方法研究

基于磁性颗粒微阵列与双色荧光杂交,建立了单核苷酸多态性(Single nucleoitide polymorphism,SNP)分型方法。将利用不对称扩增得到的含有待检测位点生物素标记的单链PCR产物固定在链亲和素修饰的金磁纳米颗粒(Gold magnetic nanoparticles,GMNPs)表面;将ssDNA-GMNPs混合物点样在底部固定有磁铁的载玻片上构建磁性颗粒微阵列,然后在基因框中与双色荧光探针杂交;杂交完全后,充分洗涤,通过扫描获得分型结果。通过优化不对称PCR的扩增条件,直接扩增出产量较高的单链DNA作为靶序列用于分型。利用本方法对24个样本MTHFR基因的C677T位点多态性进行了检测。实验证明,本方法步骤简单,易实现自动化操作、非常适用于分子诊断与法医鉴定。     

A mixed film composed of oligonucleotides and poly(2-hydroxyethyl methacrylate) brushes to enhance selectivity for detection of single nucleotide polymorphisms

Preliminary studies of mixed films composed of oligonucleotides and poly(2-hydroxyethyl methacrylate) (PHEMA) have recently been shown to enhance the selectivity for detection of 3 base-pair mismatched (3 bpm) oligonucleotide targets. Evaluation of selectivity for detection of single nucleotide polymorphisms (SNP) using such mixed films has now been completed. The selectivity was quantitatively determined by considering the sharpness of melt curves and melting temperature differences (ΔT_m) for fully complementary targets and SNPs. Stringency conditions were investigated, and it was determined that the selectivity was maximized when a moderate ionic strength was used (0.1-0.6 M). Increases of ΔT_m when using mixed films were up to 3-fold larger compared to surfaces containing only immobilized oligonucleotide probes. Concurrently, increases in sharpness of melt curves for 1 bpm targets were observed to be up to 2-fold greater for mixed films. The co-immobilization of PHEMA resulted in a more homogeneous distribution of oligonucleotide probes on surfaces. Lifetime measurements of fluorescence emission from immobilized oligonucleotide probes labeled with Cy3 dye indicated the difference in microenvironment of immobilized oligonucleotides in the presence of PHEMA.     

Direct amino acid-catalyzed cascade reductive alkylation of arylacetonitriles: high-yielding synthesis of ibuprofen analogs

A novel approach for a one-pot, three-component reductive alkylation (TCRA) reaction of arylacetonitriles-containing electron-withdrawing groups with aldehydes/ketones and 1,4-dihydropyridine via iminium-catalysis has been developed. Many TCRA reaction products have direct applications in agricultural and pharmaceutical chemistry.     

Identification of the polymorphisms in IFITM3 gene and their association in a Korean population with ulcerative colitis

Interferons play critical roles in tumor pathogenesis by controlling apoptosis and through cellular anti-proliferative and differentiation activities. Interferon inducible transmembrane protein (IFITM) family genes have been implicated in several cellular processes such as the homotypic cell adhesion functions of IFN and cellular anti-proliferative activities. Expression levels of IFITM genes have been found to be up-regulated in gastric cancer cells and colorectal tumors. IFITM3 (also known as 1-8U) is a member of the IFITM family, and has been described as a key player in specification of germ cell fate. IFITM3 was first isolated from a genetic screen aimed at identifying genes involved in acquisition of germ cell competence. It has been proposed that epiblast cells have the highest expression of IFITM3 initiated germ cell specification and that homotypic association can discriminate germ cells from their somatic neighbors. In an attempt to better understand the genetic influences of IFITM3 on ulcerative colitis, we have identified possible variation sites and single nucleotide polymorphisms (SNPs) through two exons and their boundary IFITM3 intron sequences including the ~2.1 kb promoter regions. To determine whether or not these IFITM3 SNPs are associated with susceptibility to ulcerative colitis, frequencies of the genotype and allele of IFITM3 polymorphisms were analyzed on genomic DNAs isolated from patients with ulcerative colitis and from healthy controls. We also investigated the haplotype frequencies constructed by these SNPs in both groups. In this study, we also showed that expression level of IFITM3 mRNA was significantly higher in tissues of the ileum and cecum of the digestive system. We identified a total of seven SNPs and multiple variation regions in the IFITM3 gene. The genotype frequency of the g.-204T>G polymorphism in patients with ulcerative colitis was significantly different from that of the control group. Our results strongly suggest that polymorphisms of the IFITM3 gene may be associated with susceptibility to ulcerative colitis.     

Preparation and biological evaluation of key fragments and open analogs of scleritodermin A

The synthesis of key fragments of scleritodermin A, their assembly, and their biological evaluation as cytotoxic and anthelmintic were performed. Highlights of the synthetic route include formation of the α-ketoamide linkage and use of stereocontrolled reactions. Open analogs of this natural product were obtained using a convergent strategy.     

Systematic study on chemical oxidative and solid‐state polymerization of poly(3,4‐ethylenedithiathiophene)

Systematic research on the synthesis, chemical oxidative polymerization of 3,4‐ethylenedithiathiophene (EDTT) in the presence of surfactants or not, and solid‐state polymerization of 2,5‐dibromo‐3,4‐ethylenedithiathiophene (DBEDTT) and 2,5‐diiodo‐3,4‐ethylenedithiathiophene (DIEDTT) under solventless and oxidant‐free conditions has been investigated. Effects of oxidants (Fe³⁺ salts, persulfate salts, peroxides, and Ce⁴⁺ salts), solvents (H₂O, CH₃CN/H₂O, and CH₃CN), surfactants, and so forth on polymerization reactions and properties of poly(3,4‐ethylenedithiathiophene) (PEDTT) were discussed. Characterizations indicated that FeCl₃ was more suitable oxidant for oxidative polymerization of EDTT, while CH₃CN was a better solvent to form PEDTT powders with higher yields and electrical conductivities. Dispersing these powders in aqueous polystyrene sulfonic acid (PSSH) solution showed better stability and film‐forming property than sodium dodecylsulfate and sodium dodecyl benzene sulfonate. Oxidative polymerization of EDTT in aqueous PSSH solutions formed the solution processable PEDTT dispersions with good storing stability and film‐forming performance. Solvent treatment showed indistinctive effect on electrical conductivity of free‐standing PEDTT films. As‐formed PEDTT synthesized from solid‐state polymerization showed similar electrical conductivity, poorer stability, but better thermoelectric property than oxidative polymerization. Contrastingly, PEDTT synthesized from DIEDTT showed higher electrical conductivity (0.18 S cm^?1) than DBEDTT which showed better thermoelectric property with higher power factor value (6.7 × 10^?9 W m^?1 K^?2). © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Geometry of lidocaine-like molecules: 2. Crystal structures of 2-benzyl-2-(1-piperidinyl)-N-(2,6-dimethylphenyl) acetamide and its hydrochloride hemihydrate

The title compounds both crystallize in the monoclinic space group P2₁ (Z = 4), with a = 12.574(1), b = 9.653(1) c = 16.483(1) Å, and = 91.84(1)° for the free base and a = 10.991(2), b = 16.864(3), c = 12.030(2) Å, = 99.35(3)° for the hydrochloride. The most important factors affecting conformation of the molecules are: ortho-substitution of the benzene ring in the acetanilide system and substitution of the C atom. Surprisingly, the conformation does not depend on the protonation state of the amine nitrogen atom, which greatly affects packing and hydrogen bonding patterns in the crystalline state. The conformation in which the H atom of the charged amine group is in a trans position to the main backbone of the molecule, is probably responsible for the antiarrhythmic activity, while a gauche conformation promotes local anaesthetic action. The separation of the lipophilic (xylidine) and amine groups, being two important pharmacophores, equals about 4.7 Å in the studied compounds and other structures comprising the amino-2,6-dimethyl-acetanilide system.     

Structure of 1,4-dihydro-1-ethyl-4-iminecinnoline-3-carboxylic acids, classical isosters of quinolone antibacterials: Crystal structures of hydrochlorides of 7-chloro and 7-methyl derivatives

Crystal structures of hydrochlorides of 7-chloro- and 7-methyl-4-iminecinnoline analogs of antibacterial quinolones have been determined by X-ray diffraction methods. The cell parameters for the 7-chloro (1) analog in the space group P2₁/c are a = 9.061(1), b = 19.062(1), c = 7.310(1)Å, = 104.92(1)°, Z = 4, and D _calc = 1.569 g/cm³ and for the 7-methyl (2) analog in the space group P are a = 7.277(5), b = 9.080(5), c = 10.058(5) Å, = 106.10(1), = 102.38(1), = 90.18(1)°, Z = 2, and D _calc = 1.429 g/cm³. Despite geometrical equivalency of methyl and chlorine and some resemblance of their packings, the crystal structures are not isostructural. Each compound forms a strong intramolecular hydrogen bond between protonated 4-imine (a donor) and 3-carboxylic (an acceptor) groups. Compounds with a similar bond, but with reversed functionality and orientation of the 3-carboxylic group, form common quinolones, being mostly 4-oxoquinoline-3-carboxylic acids. The difference should exclude chemical affinity of 4-imine analogs to the guanine base of a bacterial DNA in DNA-gyrase complex, as proposed by Shen et al. ² for 4-oxoquinoline-3-carboxylic acids showing antibacterial activity. Also the free acidic function of a carboxyl group may significantly lower permeability of 4-imine-3-carboxylic analogs of quinolones. Surprisingly, they have demonstrated antibacterial activity comparable with that of nalidixic acid.