Oligonucleotide ligation assay-based DNA chip for multiplex detection of single nucleotide polymorphism

An oligonucleotide ligation assay-based DNA chip has been developed to detect single nucleotide polymorphism. Synthesized nonamers, complementary to the flanking sequences of the mutation sites in target DNA, were immobilized onto glass slides through disulfide bonds on their 5' terminus. Allele-specific pentamers annealed adjacent to the nonamers on the complementary target DNA, containing 5'-phosphate groups and biotin labeled 3'-ends, were mixed with the target DNA in tube. Ligation reactions between nonamers and pentamers were carried out on chips in the presence of T4 DNA ligase. Ligation products were directly visualized on chips through enzyme-linked assay. The effect of G:T mismatch at different positions of pentamers on the ligation were evaluated. The results showed that any mismatch between pentamer and the target DNA could lead to the decrease of ligation, which can be detected easily. The established approach was further used for multiplex detection of mutations in rpoB gene of rifampin-resistant Mycobacterium tuberculosis clinical isolates. (C) 2003 Elsevier B.V. All rights reserved.

A single-strand conformation polymorphism method by capillary electrophoresis with laser-induced fluorescence for detection of the T1151A mutation in hMLH1 gene

Mutation of hMLH1 gene plays an important role in human tumorigenesis. A highly sensitive single-strand conformation polymorphism (SSCP) method for detection of the T1151A mutation in exon 12 of the hMLH1 gene was for the first time developed employing laser-induced fluorescence capillary electrophoresis (LIF-CE). Effects of the concentration of linear polyacrylamide solution, running temperature, running voltage and the addition of glycerol on SSCP analysis were investigated, and the optimum separation conditions were defined. Thirty colorectal cancer patients and eight lung cancer patients were screened and the T1151A mutation was found in four of them. Based on CE-sequencing the mutation was further confirmed. To our knowledge, this is for the first time that the T1151A mutation is found in lung cancer. Our method is simple, rapid, and highly sensitive and is well suited to the analysis of large numbers of clinical samples.

Crystal structure and drawing-induced polymorphism in poly(aryl ether ether ketone). IV

A new crystal modification induced by strain and denoted as form II exists alongside the dominant form I structure in the uniaxially oriented poly(ether ether ketone) (PEEK) and the related polymers. The crystal structure of form II for PEEK is also found to possess a two-chain orthorhombic packing with unit cell parameters of a equal to 0.475 nm, b equal to 1.060 nm, and c equal to 1.086 nm. More extended and flattened chain conformation of form II relative to that of form I is expected to account for an 8% increase in c-axis dimension, which is attributed to the extensional deformation fixed in situ through strain-induced crystallization during uniaxial drawing. Annealing experiments suggest that form II is thermodynamically metastable and can be transformed into more stable form I by chain relaxation and reorganization at elevated temperature without external tension. This strain-induced polymorphism exists universally in the poly(aryl ether ketone) family. (C) 1999 John Wiley & Sons, Inc.

The crystal structure and drawing-induced polymorphism in poly(aryl ether ketone)s .2. Poly(ether ether ketone ketone), PEEKK

The crystal structure, morphology and polymorphism induced by uniaxial drawing of poly(ether ether ketone ketone) [PEEKK] have been studied by transmission electron microscopy (TEM), electron diffraction (ED) and wide angle X-ray diffraction (WAXD). On the basis of WAXD and ED patterns,the crystal structure of unoriented PEEKK is determined to have two-chain orthorhombic packing with unit cell parameters of a 0.772 nm, b = 0.600 nm, c = 1.004 nm (form I), A stress-induced crystal modification (form II) is identified and found to possess a two-chain orthorhombic lattice with unit cell dimensions of a = 0.461 nm, b = 1.074 nm, c = 1.080 nm. The 7.5% increase in c-axis dimension for form II is attributed to an overextended chain conformation, arising from extensional deformation during uniaxial drawing and fixed ''in-situ'' through strain-induced crystallization. The average ether-ketone bridge bond angles in form II crystal are determined to be 148.9 degrees by using standard bond lengths. The crystal morphology of PEEKK bears a great similarity to that of PEEK. The crystals grow in the form of spherulites and have the b-axis of unit cell radial. The effects of draw rate on strain-induced crystallization and induction of form II structure are also discussed.

The crystal structure and drawing induced polymorphism in poly(aryl ether ketone)s .3. Crystallization during hot-drawing of poly(ether ether ketone ketone)

The evolution of crystallinity and polymorphism during hot-drawing of amorphous poly(ether ether ketone ketone) (PEEKK) as a function of strain rate, draw ratio, and temperature was investigated. In modification I, the competition of chain extension and molecular alignment is responsible for the strain rate and temperature dependence. Modification II crystallization is basically controlled by chain extension during stretching. The former can be transformed into the latter via relaxation during stretching or annealing at elevated temperature.

The crystal structure and drawing-induced polymorphism in poly(aryl ether ketone)s .1. Poly(oxybiphenyl-4-4'-diyloxy-1,4-phenylenecarbonyl-1,3-phenylenecarbonyl-1,4-phenylene)

Crystal structure and polymorphism induced by uniaxial drawing of a poly(aryl ether ketone) [PEDEKmK] prepared from 1,3-bis(4-fluorobenzoyl)benzene and biphenyl-4,4'-diol have been investigated by means of transmission electron microscopy (TEM), electron diffraction (ED), wide-angle X-ray diffraction (WAXD), and differential scanning calorimetry (DSC) techniques. The melting and recrystallization process in the temperature range of 250-260 degrees C, far below the next melting temperature (306 degrees C), was identified and found to be responsible for the remarkable changes in lamellar morphology. Based on WAXD and ED patterns, it was found that crystal structure of isotropic-crystalline PEDEKmK obtained under different crystallization conditions (melt-crystallization, cold-crystallization, solvent-induced crystallization, melting-recrystallization, and crystallization from solution) keeps the same mode of packing, i.e., a two-chain orthorhombic unit cell with the dimensions a = 0.784 nm, b = 0.600 nm, and c = 4.745 nm (form I). A second crystal modification (form II) can be induced by uniaxial drawing above the glass transition temperature, and always coexists with form I. This form also possesses an orthorhombic unit cell but with different dimensions, i.e., a = 0.470 nm, b = 1.054 nm, c = 5.064 nm. The 0.32 nm longer c-axis of form II as compared with form I is attributed to an overextended chain conformation due to the expansion of ether and ketone bridge bond angles during uniaxial drawing. The temperature dependence of WAXD patterns for the drawn PEDEKmK suggests that form II can be transformed into the more stable form I by relaxation of overextended chains and relief of internal stress at elevated temperature in absence of external tension.

Effect of lanthanum ions on the lipid polymorphism of phosphatidylethanolamines

The influence of lanthanum ions on the polymorphic phase of egg phosphatidylethanolamine and dielaidoylphosphatidylethanolamine (PE and DEPE) has been investigated by means of P-31-nuclear magnetic resonance (P-31-NMR) and high sensitivity differential scanning calorimetry (DSC) techniques. P-31-NMR experiments show that lanthanum ions promote the formation of the hexagonal II phase at temperatures lower than those of the pure egg PE, DSC results also show that lanthanum ions induce the formation of hexagonal II phase in DEPE liposomes even al very low ion concentration, The effect of lanthanum ions on the polymorphism of PE liposomes is much greater than that of calcium.

GENETIC MAPPING OF THE LAMINARIA JAPONICA (LAMINARALES, PHAEOPHYTA) USING AMPLIFIED FRAGMENT LENGTH POLYMORPHISM MARKERS

To establish a molecular-marker-assisted system of breeding and genetic study for Laminaria japonica Aresch., amplified fragment length polymorphism (AFLP) was used to construct a genetic linkage map of L. japonica featuring 230 progeny of F-2 cross population. Eighteen primer combinations produced 370 polymorphic loci and 215 polymorphic loci segregated in a 3:1 Mendelian segregation ratio (P <= 0.05). Of the 215 segregated loci, 142 were ordered into 27 linkage groups. The length of the linkage groups ranged from 6.7 to 90.3 centimorgans (cM) with an average length of 49.6 cM, and the total length was 1,085.8 cM, which covered 68.4% of the estimated 1,586.9 cM genome. The number of mapped markers on each linkage group ranged from 2 to 12, averaging 5.3 markers per group. The average density of the markers was 1 per 9.4 cM. Based on the marker density and the resolution of the map, the constructed linkage map can satisfy the need for quantitative trait locus (QTL) location and molecular-marker-assisted breeding for Laminaria.

Assessing genetic identity of sporophytic offspring of the brown alga Undaria pinnatifida derived from mono-crossing of gametophyte clones by use of amplified fragment length polymorphism and microsatellite markers

The haploid stage of gametophytes of the subtidal brown alga Undaria pinnatifida can be vegetatively propagated under favorable conditions. This unique characteristic makes it possible to establish independent gametophyte cell lines that are zoospore-derived. Sporophytic offspring can be generated through hybridizing the male and female gametophytes, which are derived from different cell lines. Accumulated experiences in this and other species in Laminariales demonstrated the applicability of this novel way to breed desired strains for open-sea cultivation. Sporophytic offspring originated from mono-crossing of male and female gametophyte clones were shown to have similar morphological characteristics under identical ambient conditions. However, there has been no report to relate this similarity on molecular levels. In this report, amplified fragment length polymorphism (AFLP) and microsatellite markers were used to analyze the genetic identity of sporophytic offspring of U. pinnatifida originated from two mono-crossing lines (M1 and M2), two self-breeding lines (S1 and S2) and one wild population (W). Totally 318 AFLP loci were revealed by use of 11 primer sets, of which 4.7%, 0.3%, 17.9%, 16.4% and 36.5% were polymorphic in M1, M2, S1, S2 and W, respectively. The pairwise genetic identity among the individuals of the same line was assessed. It was shown that offspring from mono-crossing lines had a higher degree of identity (95.6-100%) than self-breeding lines (87.7-98.4%) and the wild population (81.5-92.1%). Analysis by use of six microsatellite loci also revealed a higher genetic identity among individuals of the mono-crossing line, further confirming the results of AFLP analysis. Results from this investigation support, on molecular levels, the novel way to produce and maintain strains in U. pinnatifida by use of different gametophyte cell lines.

The polymorphism of lysozyme gene in Zhikong scallop (Chlamys farreri) and its association with susceptibility/resistance to Listonella anguillarum

Lysozyme functions as a crucial biodefence effector against the infection of bacterial pathogens in innate immunity. The nucleotide sequence polymorphisms in promoter region of a nuclear goose type lysozyme gene from Zhikong scallop Chlamys farreri (designated as CFLysG) were investigated to explore their association with susceptibility/resistance to Listonella anguillarum infection. Eight sites of single nucleotide polymorphisms (SNPs) and two sites of insert-deletion (ins-del) polymorphisms were identified in the promoter region of CFLysG. Two of them, -753 TATCTCGATCAGG ins-del polymorphism and -391 A-G SNP were selected to analyze their distribution in the susceptible and resistant stocks, which were identified according to the survival time after L. anguillarum challenge. Using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), two genotypes were found at each site, which were ins/del and ins/ins at locus -753, and A/A and A/G at locus -391, respectively. The -753 ins/del genotype was more prevalent in the resistant stock than that in the susceptible stock, 30% vs 16.67% in frequency, but there was no significant difference in the frequency distribution between these two stocks (P=0.15). In contrast, the frequency of -391A/G genotype in the resistant stock was significantly higher (30%) than that in the susceptible stock (7.14%) (P=0.007), indicating a significant association with the resistance of Zhikong scallop to L anguillarum. To confirm the presumption, another independent challenge experiment was performed, in which the cumulative mortality of scallops with -391 A/A genotype (96.8%) was significantly higher than those with -391 A/G genotype (64.5%) (P=0.001), which further validate the association between -391 A/G genotype and the resistance of Zhikong scallop to L anguillarum. These results suggested that the -391 A/G could be a potential marker applied in future selection of Zhikong scallop with enhanced resistance to L anguillarum. (C) 2008 Elsevier Ltd. All rights reserved.