Study on BcII/St14 RFLPs in Chinese for DNA diagnosis for hemophilia A

The BcII polymorphism within DXS52 (St14) was reported. It was composed of 4 allelic fragments, 4.0 kb, 3.3 kb, 3.0 kb and 2.3 kb. The frequency of these fragment were 0.09, 0.12, 0.44 and 0.35 respectively in the Chinese. The polymorphism provided the PIC of 0.66. DNA analysis of families with hemophilia A showed that the confidence of the RFLPs was the same as the TaqI/St14 RFLPs and for carrier detection the former is much better than that of the TaqI/St14 RFLPs.     

AFLP marking and polymorphism among progenies of Gymnema sylvestre: an important medicinal plant of India

The level of polymorphism among twelve selected progenies of Gymnema sylvestre was investigated through AFLP markers by multiplexing PCR reactions using 64 (8x8) primer combinations. Fourteen primer combinations were selected as the most suitable combination for G. sylvestre. Analysis of the 12 progenies with these 14 primer pairs produced 1689 fragments of which 972 (57.5%) were polymorphic and 485 (28.7%) were unique to a particular genotype. The number of fragments produced by individual primer pairs was in the range of 55 to 225. Out of these, polymorphic fragments were in the range of 34 (E-ACC/M-CAC) to 157 (E-AGG/M-CAG) and unique bands observed were 8 (E-ACC / M-CAC) to 69 (E-AGG/M-CAC). Different primer combinations detected different levels of polymorphism, ranging from 33% (E-AGG/ M-CAC) to 69.8% (E-AGG/ M-CAC). From the observations, it appears that the primer combinations E-AGG/M-CAC, E-AGG/CTG, E-AGG/CAG and E-ACA/CAT were the most informative for the detection of polymorphism among the progenies compared with others, since they produced a high number of unique fragments. The similarity coefficient ranged from 0.212 to 0.731. High similarity was observed between progeny S8 and S9 (73%) and high divergence between progenies S3 and S11. Among the selected progeny, S9 was found to be the most similar to the parent (63%), while genotype S11 was the most distant (36.9%).     

A single-strand conformation polymorphism method for the large-scale analysis of mutations/polymorphisms using capillary array electrophoresis

We present a high-throughput single-strand conformation polymorphism (SSCP) method, performed on a commercially available capillary array DNA sequencer. We tested various sieving matrices and electrophoretic conditions, using 51 DNA fragments which included 45 fragments carrying only one single nucleotide polymorphism (SNP), 4 fragments having two SNPs and 2 fragments with insertion or deletion. Resolution of alleles was improved by increasing concentrations of both sieving matrices and buffers, and all examined polymorphisms of DNA fragments were detected, most of them (45 fragments) as clearly split allele peaks in heterozygotes. Allele frequencies of SNPs can be estimated accurately by determining the relative amounts of alleles in pooled DNA. In this method, the turn-around time for the analysis of 96 samples is less than 3 h. These results demonstrate that capillary array-based SSCP is an efficient and accurate technique for the large-scale quantitative analysis of mutations/polymorphisms.     

Detection of apolipoprotein E genotypes by capillary electrophoresis

The apolipoprotein E (apo-E) genotype of an individual is of significant relevance in the associated risk of developing cardiovascular disease and late-onset Alzheimer's disease. Detection of the six common apo-E genotypes is based on the restriction fragment length polymorphisms (RFLPs) arising from the abolition or creation of HhaI restriction sites within an amplified target DNA sequence of the apo-E gene. Genomic DNA was extracted from leukocytes, a 230 bp target sequence within the apo-E gene was amplified by polymerase chain reaction (PCR) and digested with HhaI, and the restricted DNA fragments separated by capillary electrophoresis (CE). This was performed on the BioFocustrade mark 3000 automated CE system equipped with an experimental laser-induced fluorescence (LIF) detector (Bio-Rad Laboratories, Hercules, CA), using capillaries (27 cm length, 75 mum i.d.) coated internally with polyaminoacryloylethoxyethanol. The analysis buffer (2xTris borate-EDTA, pH 8.3) was supplemented with a proprietary sieving polymer and 0.05 muM thiazole orange six. Samples were injected electrophoretically. Separations were carried out at 40 degrees C under constant voltage, and the emitted fluorescence detected at 515 nm. Restriction fragment lengths of the cleaved PCR products were estimated from the migration times, with a 20/100 bp ladder (Bio-Rad Laboratories 20/100 bp molecular ruler) serving as reference. Six different reproducible patterns were obtained for the six common apo-E genotypes, with good resolution of the component restriction fragments. The calculated sizes of the separated peaks closely corresponded with the predicted restricted fragment lengths for each specific genotype. We believe this is the first published report demonstrating the feasibility of automating the post-PCR detection of the apo-E RFLPs(2). This methodology overcomes the most labour-intensive step in apo-E genotyping, thus making it amenable to routine clinical application.     

TRANSFORMING GENES IN DUCK HEPATIC CARCINOMA——mht(raf) AND Ha-ras

The transfection of NIH 3T3 cells was performed with DNAs from 2 duck primary hepatic carcinomas (DHC 40K, 9K) and I tumor-adjacent liver tissue (TAL, 9N). Transfectants were found from 40K, 9K and 9N DNAs. The secondary transfectants were obtained after transfection of RAT-1 cells with DNAs from primary transfectants. After hybridization with Ha-ras, Ki-ras, N-ras and mht oncogenes, it was found that duck mht (5.2 and 3.2 kb EcoRI fragments) and duck Ha-ras (3.4 kb EcoRI fragments) were present in all these transformants.This is the first report on transforming genes in duck primary hepatic cancer as well as tumoradjacent liver tissue     

Electrophoretic detection of genetic variability among Schistosoma japonicum isolates by sequence-related amplified polymorphism

In the present study, sequence‐related amplification polymorphism (SRAP) was utilized to study the genetic variability among Schistosoma japonicum isolates from different provinces in China, using Schistosoma mansoni from Puerto Rico for comparison. Five out of ten tested SRAP primer combinations displayed significant polymorphisms among S. japonicum isolates from China, namely ME2/EM1, ME4/EM1, ME4/EM6, ME5/EM4 and ME5/EM5. Analysis of the 61 S. japonicum samples from China with five SRAP primer combinations identified a total of 83 reproducible polymorphic fragments. The number of fragments using each primer combination ranged from 14 to 19, with an average of 16 polymorphic bands per primer pair, and the size of fragment ranged approximately from 100 to 1000 bp. Representative‐specific SRAP fragments were excised from the gels, and confirmed by PCR amplification of genomic DNA using primers designed and based on the sequences of these SRAP fragments. Based on SRAP profiles, unweighted pair‐group method with arithmetic averages (UPGMA) dendrogram was constructed. UPGMA clustering algorithm categorized S. japonicum isolates from China into nine clades and two lineages (representing the mountainous and lake/marshland regions). These results indicate the usefulness of the SRAP technique for revealing genetic variability among S. japonicum isolates from China, and the SRAP technique should be applicable to other living organisms.     

Radical ring‐opening copolymerization behavior of vinyloxirane: Synthesis of copolymer from 2‐isopropenyl‐3‐phenyloxirane and styrene and its functionalization

The radical ring‐opening copolymerization of 2‐isopropenyl‐3‐phenyloxirane (1) with styrene (St) was examined to obtain the copolymer [copoly(1‐St)] with a vinyl ether moiety in the main chain. The copolymers were obtained in moderate yields by copolymerization in various feed ratios of 1 and St over 120 °C; the number‐average molecular weights (M_n) were estimated to be 1800–4200 by gel permeation chromatography analysis. The ratio of the vinyl ether and St units of copoly(1‐St) was estimated with the ¹H NMR spectra and varied from 1/7 to 1/14 according to the initial feed ratio of 1 and St. The haloalkoxylation of copoly(1‐St) with ethylene glycol in the presence of N‐chlorosuccinimide produced a new copolymer with alcohol groups and chlorine atoms in the side group in a high yield. The M_n value of the haloalkoxylated polymer was almost the same as that of the starting copoly(1‐St). The incorporated halogen was determined by elemental analysis. The analytical result indicated that over 88% of the vinyl ether groups participated in the haloalkoxylation. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 3729–3735, 2000     

Morphological investigations of crosslinked polystyrene microspheres by seeded polymerization

 Crosslinked polystyrene microspheres with novel surface and inner morphologies were synthesized by seeded polymerization following a seed-swelling method, using uncrosslinked polystyrene microspheres as seeds and a mixture of toluene, styrene (St), and divinylbenzene (DVB) as the swelling agent. With the increasing toluene/ (St+DVB) ratio, the crosslinked particles changed from smooth-surfaced spheres to deformed spheres with dimples or heavy dents at the surface. A single hole inside the spherical particles was produced at low St/DVB ratio, while higher St/DVB ratios gave irregular dented or dimpled particles. Ultrathin cross-section observation by TEM revealed a non-uniformly crosslinked inner structure. Received: 20 January 1998 Accepted: 14 April 1998     

A new silent mutation found in the Chinese PAH locus and its role in the prenatal diagnosis of phenylketonuria

A silent mutation or sequence polymorphism. A to T substitution at codon 399 in exon 11 of the PAH gene from a Chinese PKU patient, was found by sequence analysis. The frequencies of this new mutation in normal and abnormal (PKU) genes were 0.005 and 0.09, respectively, based on the analyses of 100 normal individuals and 39 PKU patients using DNA amplification with polymerase chain reaction (PCR) and oligonucleotide hybridization methods. This silent mutation can be used as a "genetic marker" for PKU prenatal diagnosis. Recently, a fetus at risk for PKU, who could not be completely predicted by RFLPs linkage analysis, was prenatally diagnosed with this genetic marker.     

1,3-二烯基-1,1,3,3-四甲基二硅氧烷/苯乙烯共聚合的环化率与竞聚率

对１３０℃下１，３ 二烯基 １，１，３，３ 四甲基二硅氧烷（ＤＶＤＳ）／苯乙烯（Ｓｔ）的溶液环化共聚合动力学进行了研究．根据低转化率（＜１０％）的共聚物组成及环状结构比例，通过参数估计方法，求得环化率与竞聚率，分别为ｒ１＝０１０２、ｒ２＝３４８、ｒｃ＝００２１０、Ｋｃ＝３８１ｍｏｌ／Ｌ、Ｋ′ｃ＝０３８９ｍｏｌ／Ｌ，同时得到它们９５％置信概率的联合置信区间及其交互影响的联合置信区间．表明ＤＶＤＳ的反应活性较Ｓｔ低，其非环状结构自由基具有较强的分子内环化反应能力；环的位阻效应使环状结构ＤＶＤＳ自由基的活性低于其非环状结构自由基．     

Emulsion copolymerization of styrene with acrylic or methacrylic acids – distribution of the carboxylic group

Studies on batch emulsion copolymeization of styrene with acrylic acid (AA) or methacrylic acid (MAA) were carried out. The effect of AA or MAA on the total conversion of the monomers was studied by a gravimetric method. The distribution of the carboxylic group in the copolymer microspheres was investigated by X-ray photoelectron spectroscopy and elemental analysis. The surface content of the carboxylic groups of styrene (St)/AA copolymer microspheres was found to be higher than that of St/MAA copolymer microspheres. The effects of partial neutralization of MAA in emulsifier-free emulsion copolymerization and seeded emulsion copolymerization on the distribution of the carboxylic group was also investigated. Received: 14 December 1999/Accepted: 23 August 2000     

A NEW SILENT MUTATION FOUND IN THE CHINESE PAH LOCUS AND ITS ROLE IN THE PRENATAL DIAGNOSIS OF PHENYLKETONURIA

A silent mutation or sequence polymorphism, A to T substitution at codon 399 in exon11 of the PAH gene from a Chinese PKU patient, was found by sequence analysis. The fre-quencies of this new mutation in normal and abnormal (PKU) genes were 0.005 and 0.09,respectively, based on the analyses of 100 normal individuals and 39 PKU patients usingDNA amplification with polymerase chain reaction (PCR) and oligonucleotide hybridizationmethods. This silent mutation can be used as a "genetic marker" for PKU prenatal diagno-sis. Recently, a fetus at risk for PKU, who could not be completely predicted by RFLPslinkage analysis, was prenatally diagnosed with this genetic marker.     

Preparation of Quaternary Amphiphilic Block Copolymer PMA-b-P (NVP/MAH/St) and Its Application in Surface Modification of Aluminum Nitride Powders

Poly(methyl acrylate)-b-poly(N-vinyl pyrrolidone/maleic anhydride/styrene) (PMA-b-P (NVP/MAH/St)) quaternary amphiphilic block copolymer prepared by reversible addition-fragmentation chain transfer (RAFT) was used to improve the anti-hydrolysis and dispersion properties of aluminum nitride (AIN) powders that were modified by copolymers. Its structure was characterized by Fourier transform infrared spectroscopy (FT-IR) and Hydrogen nuclear magnetic spectroscopy (¹H-NMR). The results demonstrate that the molecular weight distribution of the quaternary amphiphilic block copolymers is 1.35–1.60, which is characteristic of controlled molecular weight and narrow molecular weight distribution. Through charge transfer complexes, NVP/MAH/St produces a regular alternating arrangement structure. After being treated with micro-crosslinking, AlN powder modified by copolymer PMA-b-P(NVP/MAH/St) exhibits outstanding resistance to hydrolysis and can be stabilized in hot water at 50 °C for more than 14 h, and the agglomeration of powder particles was improved remarkably.     

交联苯乙烯/丙烯酰胺共聚微球的制备及其C_(60)功能化初探

以二乙烯基苯 (DVB)为交联剂 ,利用一次投料分散共聚合的方法合成了交联的苯乙烯 (St) /丙烯酰胺 (Am )共聚微球 .实验发现 ,共聚单体Am的投料量和介质的极性对微球的形态有着显著的影响 .在反应过程中交联PS链段和PAm链段发生相分离 ,使粒子产生异形 .随后 ,通过微球上的酰胺基团与C60 的反应 ,将C60 引入微球表面 .初步的光电导性能测试表明 ,带有C60 的微球具有较好的光电导性能     

A study of comparability in amplified fragment length polymorphism profiling using a simple model system

A simple amplified fragment length polymorphism (AFLP) model, using the bacteriophage lambda genome, was developed to test the reproducibility of this technique in an international comparative study. Using either non-selective or selective primers, nine fragments or subsets of two or three fragments, respectively, were predicted using in silico software. Under optimized conditions, all predicted fragments were experimentally generated. The reproducibility of the AFLP model was tested by submitting both "unknown" DNA template that had been restricted and ligated with AFLP linkers (R/L mixture) and corresponding primer pairs to nine laboratories participating in the study. Participants completed the final PCR step and then used either slab gel electrophoresis or CE to detect the AFLP fragments. The predicted fragments were identified by the majority of participants with size estimates consistently up to 3 base pair (bp) larger for slab gel electrophoresis than for CE. Shadow fragments, 3 bp larger than the predicted fragments, were often observed by study participants and organizers. The nine AFLP fragments exhibited relative intensities ranging from less than 3% to 22% and, apart from the two weakest fragments, with a % CV of 16 to 25. Fragments containing the highest guanine-cytosine (GC) content of 50-56% showed the greatest stability in the AFLP profiles.     

Emulsifier-free emulsion copolymerization of styrene and acrylamide using an amphoteric initiator

Emulsifier-free emulsion copolymerization of styrene (St) and acrylamide (AAm) has been investigated in the presence of an amphoteric water-soluble initiator, 2,2′-azobis[N-(2-carboxyethyl)-2-2-methylpropionamidine]hydrate (VA057). The kinetics of polymerization and the colloidal properties of the resulting latices were studied and compared with the cases using ionic initiators. When adopting the amphoteric initiator at pHs lower than 10, stable amphoteric poly (St/AAm) latices, evidenced by the electrophoretic mobility, were prepared directly. Meanwhile, almost the same conversion versus time curves appeared and there were no apparent differences in the final particle sizes for those polymerizations, whereas in the polymerization at pH 10, a much lower rate of copolymerization and a larger size of particles were observed. The surface charge density and the growth rate of latex particles produced with VA057 at pH<10 were comparable to those of the particles with a cationic initiator, 2,2′-azobis(2-amidinopropane)dihydrochloride, but were apparently lower than those with an anionic initiator, potassium persulfate, when the polymerizations were carried out under corresponding conditions. The number of initiator fragments incorporated onto the particle surfaces was independent of polymerization pH, except for pH 10. The abnormal performance of VA057 at pH 10 was attributed to its degradation due to hydrolysis. Received: 14 December 1999 Accepted: 22 February 2000     

Inverse-flow derivatization for capillary electrophoresis of DNA fragments with laser-induced fluorescence detection

A novel method is presented to detect DNA fragments separated by capillary electrophoresis (CE) with laser-induced fluorescence (LIF) detection using inverse-flow derivatization. In electrophoresis, the intercalating dye, thiazol orange was only added to the separation buffer at the positive polarity. The negatively charged DNA fragments migrated from the negative polarity to the positive polarity, while the positively charged dye migrated in the opposite direction. When DNA fragments met with dye ions, the DNA–dye complexes were formed. The complexes continued migrating to the positive end, due to their net negative charges. When the complexes passed through the detection window, the fluorescent signals were generated. Importantly, DNA fragments migrated as their native state before DNA–dye complexes were formed. This procedure was used to detect double stranded DNA (dsDNA) and single stranded DNA (ssDNA) fragments, and polymerase chain reaction (PCR) products. The excellent resolution and good reproducibility of DNA fragments were achieved in non-gel sieving medium. This procedure may be useful in genetic mutation/polymorphism detections.     

2-Aminopurine flipped into the active site of the adenine-specific DNA methyltransferase M.TaqI: crystal structures and time-resolved fluorescence

We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA helix and occupying virtually the same position in the active site as the natural target adenine. Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this state: base flipping is accompanied by the loss of the very short ( approximately 50 ps) lifetime component associated with fully base-stacked 2-aminopurine in DNA, and 2-aminopurine is subject to considerable quenching by pi-stacking interactions with Tyr108 in the catalytic motif IV (NPPY). This proves 2-aminopurine to be an excellent probe for studying base flipping by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same distinctive fluorescence response confirms complete destacking from DNA and is also observed when the proposed key residue for base flipping by M.TaqI, the target base partner thymine, is substituted by an abasic site analog. The corresponding cocrystal structure shows 2-aminopurine in the active site of M.TaqI, demonstrating that the partner thymine is not essential for base flipping. However, in this structure, a shift of the 3' neighbor of the target base into the vacancy left after base flipping is observed, apparently replicating a stabilizing role of the missing partner thymine. Time-resolved fluorescence and acrylamide quenching measurements of M.TaqI complexes in solution provide evidence for an alternative binding site for the extra-helical target base within M.TaqI and suggest that the partner thymine assists in delivering the target base into the active site.     

A clustering algorithm based on two distance functions for MEC model

Haplotype reconstruction, based on aligned single nucleotide polymorphism (SNP) fragments, is to infer a pair of haplotypes from localized polymorphism data gathered through short genome fragment assembly. This paper first presents two distance functions, which are used to measure the difference degree and similarity degree between SNP fragments. Based on the two distance functions, a clustering algorithm is proposed in order to solve MEC model. The algorithm involves two sections. One is to determine the initial haplotype pair, the other concerns with inferring true haplotype pair by re-clustering. The comparison results prove that our algorithm utilizing two distance functions is effective and feasible.     

Single-strand conformation polymorphism analysis of candidate genes for reliable identification of alleles by capillary array electrophoresis

We investigated the reliability of capillary array electrophoresis-single strand conformation polymorphism (CAE-SSCP) to determine if it can be used to identify novel alleles of candidate genes in a germplasm collection. Both strands of three different size fragments (160, 245 and 437 bp) that differed by one or more nucleotides in sequence were analyzed at four different temperatures (18 degrees C, 25 degrees C, 30 degrees C, and 35 degrees C). Mixtures of amplified fragments of either the intron interrupting the C-terminal WRKY domain of the Tc10 locus or the NBS domain of the TcRGH1 locus of Theobroma cacao were electroinjected into all 16 capillaries of an ABI 3100 Genetic Analyzer and analyzed three times at each temperature. Multiplexing of samples of different size range is possible, as intermediate and large fragments were analyzed simultaneously in these experiments. A statistical analysis of the means of the fragment mobilities demonstrated that single-stranded conformers of the fragments could be reliably identified by their mobility at all temperatures and size classes. The order of elution of fragments was not consistent over strands or temperatures for the intermediate and large fragments. If samples are only run once at a single temperature, small fragments could be identified from a single strand at a single temperature. A combination of data from both strands of a single run was needed to identify correctly all four of the intermediate fragments and no combination of data from strands or temperatures would allow the correct identification of two large fragments that differed by only a single single-nucleotide polymorphism (SNP) from a single run. Thus, to adequately assess alleles at a candidate gene locus using SSCP on a capillary array, fragments should be < or =250 bp, samples should be analyzed at two different temperatures between 18 degrees C and 30 degrees C to reduce the variability introduced by the capillaries, data should be combined from both strands and both temperatures, and undenatured double-stranded (ds)DNA molecular weight standards, such as ROX 2500, should be included as internal standards.