Modulation Instability and Phase-Shifted Fermi-Pasta-Ulam Recurrence

Instabilities are common phenomena frequently observed in nature, sometimes leading to unexpected catastrophes and disasters in seemingly normal conditions. One prominent form of instability in a distributed system is its response to a harmonic modulation. Such instability has special names in various branches of physics and is generally known as modulation instability (MI). The MI leads to a growth-decay cycle of unstable waves and is therefore related to Fermi-Pasta-Ulam (FPU) recurrence since breather solutions of the nonlinear Schrödinger equation (NLSE) are known to accurately describe growth and decay of modulationally unstable waves in conservative systems. Here, we report theoretical, numerical and experimental evidence of the effect of dissipation on FPU cycles in a super wave tank, namely their shift in a determined order. In showing that ideal NLSE breather solutions can describe such dissipative nonlinear dynamics, our results may impact the interpretation of a wide range of new physics scenarios.

Quantitative candidate gene association studies of metabolic traits in Han Chinese type 2 diabetes patients

Recent genome-wide association studies have identified many loci associated with type 2 diabetes mellitus (T2DM), hyperuricemia, and obesity in various ethnic populations. However, quantitative traits have been less well investigated in Han Chinese T2DM populations. We investigated the association between candidate gene single nucleotide polymorphisms (SNPs) and metabolic syndrome-related quantitative traits in Han Chinese T2DM subjects. Unrelated Han Chinese T2DM patients (1975) were recruited. Eighty-six SNPs were genotyped and tested for association with quantitative traits including lipid profiles, blood pressure, body mass index (BMI), serum uric acid (SUA), glycated hemoglobin (HbA1c), plasma glucose [fasting plasma glucose (FPG)], plasma glucose 120 min post-OGTT (P2PG; OGTT = oral glucose tolerance test), and insulin resistance-related traits. We found that CAMTA1, ABI2, VHL, KAT2B, PKHD1, ESR1, TOX, SLC30A8, SFI1, and MYH9 polymorphisms were associated with HbA1c, FPG, and/or P2PG; GCK, HHEX, TCF7L2, KCNQ1, and TBX5 polymorphisms were associated with insulin resistance-related traits; ABCG2, SLC2A9, and PKHD1 polymorphisms were associated with SUA; CAMTA1, VHL, KAT2B, PON1, NUB1, SLITRK5, SMAD3, FTO, FANCA, and PCSK2 polymorphisms were associated with blood lipid traits; CAMTA1, SPAG16, TOX, KCNQ1, ACACB, and MYH9 polymorphisms were associated with blood pressure; and UBE2E3, SPAG16, SLC2A9, CDKAL1, CDKN2A/B, TCF7L2, SMAD3, and PNPLA3 polymorphisms were associated with BMI (all P values <0.05). Some of the candidate genes were associated with metabolic and anthropometric traits in T2DM in Han Chinese. Although none of these associations reached genome-wide significance (P < 5 x 10(-8)), genes and loci identified in this study are worthy of further replication and investigation.

Han Chinese patients with dopa-responsive dystonia exhibit a low frequency of exonic deletion in the GCH1 gene

We identified three novel mutations of the GTP cyclohydrolase 1 (GCH1) gene in patients with familial dopa-responsive dystonia (DRD), but were unable to identify meaningful sporadic mutations in patients with no obvious family DRD background. To investigate whether GCH1 regional deletions account for the etiology of DRD, we screened for heterozygous exonic deletions in DRD families and in patients with sporadic DRD. Multiple ligation-dependent probe amplification analysis and quantitative real-time polymerase chain reaction amplification was performed in all members of our DRD cohort and in controls to detect exonic deletions in GCH1, tyrosine hydroxylase, and the epsilon-sarcoglycan-encoding (SGCE) genes. Using these techniques, we detected a GCH1 exon 1 heterozygous deletion in 1 of 10 patients with sporadic DRD. Therefore, we concluded that exonic deletion in the GCH1 gene only accounted for the etiology in a small percentage of patients with sporadic DRD in our Han Chinese cohort.

Neuropeptide S Increases locomotion activity through corticotropin-releasing factor receptor 1 in substantia nigra of mice

Neuropeptide S (NPS), the endogenous ligand of NPS receptor (NPSR), was reported to be involved in the regulation of arousal, anxiety, locomotion, learning and memory. The basal ganglia play a crucial role in regulating of locomotion-related behavior. Here, we found that NPSR protein of mouse was distributed in the substantia nigra (SN) and globus pallidus (LGP) by immunohistochemical analysis. However, less is known about the direct locomotion-related effects of NPS in both SN and LGP. Therefore, we investigated the role of NPS in locomotion processes, using the open field test. The results showed that NPS infused into the SN (0.03, 0.1, 1nmol) or LGP (0.01, 0.03, 0.1nmol) dose-dependently increased the locomotor activity in mice. SHA 68 (50mg/kg), an antagonist of NPSR, blocked the locomotor stimulant effect of NPS in both nuleus. Meanwhile, these effects of NPS were also counteracted by the CRF1 receptor antagonist antalarmin (30mg/kg, i.p.). In addition, we found that the expression of c-Fos was significantly increased after NPS was delivered into SN. In conclusion, these results indicate that NPS-NPSR system may regulate locomotion together with the CRF1 system in SN.

Matrix isolation sublimation: An apparatus for producing cryogenic beams of atoms and molecules

We describe the apparatus to generate cryogenic beams of atoms and molecules based on matrix isolation sublimation. Isolation matrices of Ne and H2 are hosts for atomic and molecular species which are sublimated into vacuum at cryogenic temperatures. The resulting cryogenic beams are used for high-resolution laser spectroscopy. The technique also aims at loading atomic and molecular traps.

Meta-analysis demonstrates no association between XRCC1 Arg399Gln polymorphism and bladder cancer risk

We examined whether the X-ray repair cross-complementing group 1 (XRCC1) Arg399Gln polymorphism is a risk factor for bladder cancer by conducting a meta-analysis. We searched the Pubmed and Embase databases for study retrieval. This meta-analysis examined 16 case-control studies, including 892 prostate cancer cases and 1020 healthy controls. Meta-analysis results based on these studies showed no significant association between the XRCC1 Arg399Gln polymorphism and bladder cancer risk in comparisons of the glutamine (Gln) allele vs arginine (Arg) allele, Arg/Arg vs (Gln/Gln + Gln/Arg), Gln/Gln vs (Gln/Arg + Arg/Arg), Gln/Gln vs Arg/Arg, and Gln/Arg vs Arg/Arg [odds ratio (OR) = 0.96, 95% confidence interval (CI) = 0.80-1.16, P = 0.70; OR = 1.13, 95%CI = 0.70-1.82, P = 0.62; OR = 0.92, 95%CI = 0.79-1.07, P = 0.29; OR = 0.90, 95%CI = 0.69-1.16, P = 0.42; OR = 0.89, 95%CI = 0.75-1.05, P = 0.17, respectively]. In subgroup analysis by ethnicity, no association was observed between the XRCC1 Arg399Gln polymorphism and bladder cancer risk in Caucasian, Mongoloid, or black populations. We identified no association between the XRCC1 Arg399Gln polymorphism and bladder cancer risk.

Meta-analysis demonstrates no association between p53 codon 72 polymorphism and prostate cancer risk

We examined whether p53 codon 72 polymorphism confers prostate cancer risk by conducting a meta-analysis. Two investigators independently searched the Pubmed, Embase and CBM databases. This meta-analysis was made of seven case-control studies, that included 892 prostate cancer cases and 1020 healthy controls. Meta-analysis results based on all the studies showed no significant association between p53 codon 72 polymorphism and prostate cancer risk in the comparisons of Pro allele vs Arg allele; Pro/Pro + Pro/Arg vs Arg/Arg; Pro/Pro vs Pro/Arg + Arg/Arg; Pro/Pro vs Arg/Arg, and Pro/Arg vs Arg/Arg [odds ratio (OR) = 1.09, 95% confidence interval (CI) = 0.87-1.36, P = 0.47; OR = 1.22, 95%CI = 0.86-1.73, P = 0.27; OR = 1.03, 95%CI = 0.62-1.72, P = 0.91; OR = 1.22, 95%CI = 0.66-2.26, P = 0.52; OR = 1.25, 95%CI = 0.84-1.87, P = 0.27, respectively]. In the subgroup analysis by ethnicity, no association was found between p53 codon 72 polymorphism and prostate cancer risk both in Caucasian and Asian populations. We found no association between p53 codon 72 polymorphism and prostate cancer risk.

Role of loop entropy in the force induced melting of DNA hairpin

Dynamics of a single stranded DNA, which can form a hairpin have been studied in the constant force ensemble. Using Langevin dynamics simulations, we obtained the force-temperature diagram, which differs from the theoretical prediction based on the lattice model. Probability analysis of the extreme bases of the stem revealed that at high temperature, the hairpin to coil transition is entropy dominated and the loop contributes significantly in its opening. However, at low temperature, the transition is force driven and the hairpin opens from the stem side. It is shown that the elastic energy plays a crucial role at high force. As a result, the force-temperature diagram differs significantly with the theoretical prediction.

Effect of shear force on the separation of double-stranded DNA

Using the Langevin dynamics simulation, we have studied the effects of shear force on the rupture of short double-stranded DNA at different temperatures. We show that the rupture force increases linearly with chain length and approaches the asymptotic value in accordance with the experiment. The qualitative nature of these curves remains almost the same for different temperatures but with a shift in the force. We observe three different regimes in the extension of covalent bonds (backbone) under shear force.

CD4+ cell count and risk for antiretroviral drug resistance among women using peripartum nevirapine for perinatal HIV prevention

OBJECTIVE

To determine the association between the antenatal CD4(+) cell count and the development of viral drug resistance following the use of peripartum nevirapine (NVP) for perinatal HIV prevention.

DESIGN

Secondary analysis of data from a previously conducted randomised controlled trial.

SETTING

Lusaka, Zambia.

POPULATION

HIV-positive pregnant women.

METHODS

We analysed the data from a clinical trial of single-dose tenofovir/emtricitabine (TDF/FTC) to reduce viral drug resistance associated with peripartum NVP. The trial population was categorised according to antenatal CD4(+) cell count (200-350, 351-500 and >500 cells/μl).

MAIN OUTCOME MEASURES

The relative risk for acquiring drug resistance, determined by consensus sequencing and oligonucleotide ligation assay (OLA), was estimated using multivariable logistic regression.

RESULTS

Of the 397 study participants, 119 (30%) had a CD4(+) count of 200-350 cells/μl, 135 (34%) had a CD4(+) count of 351-500 cells/μl and 143 (36%) had a CD4(+) count of >500 cells/μl. Among women receiving no intervention, the risk for drug resistance appeared to increase as the CD4(+) cell count decreased. Participants with CD4(+) cell counts of 200-350 cells/μl randomised to the study arm had the lowest risk, suggesting a higher efficacy of the intervention within this stratum. These results were consistent at 2 and 6 weeks, regardless of how drug resistance was measured.

CONCLUSIONS

Women with CD4(+) cell counts of 200-350 cells/μl may be at increased risk for viral drug resistance following the use of peripartum NVP. Given the high prevalence of NVP resistance and the clear benefits of treatment, antiretroviral therapy should be initiated among pregnant women with CD4(+) cell counts of ≤350 cells/μl.

Femtosecond laser-drilling-induced HgCdTe photodiodes

Femtosecond-laser drilling may induce holes in HgCdTe with morphology similar to that induced by ion-milling in loophole technique. So-formed hole structures are proven to be pn junction diodes by the laser beam induced current characterization as well as the conductivity measurement. Transmission and photoluminescence spectral measurements on a n-type dominated hole-array structure give rise to different results from those of an ion-milled sample.

Heavy metal concentrations in soils and plant accumulation in a restored manganese mineland in Guangxi, South China

Heavy metal contamination of metal-mined soils is a widespread problem in China. In the restored (over 20 years) Lipu manganese mineland, 36 plant species from 22 families were found colonizing, some of which were planted agronomic ones. Heavy metal concentrations in tailings were very high. Minesoils were basically unpolluted, but soils in the remaining mining area and in the vicinity of tailings dumps were polluted by Cd and Mn. Measurements of metal contents in dominant plants showed they were close to those of other mineland plants. Plants tended to have a higher Cd accumulation (as reflected by Biological Accumulation Coefficient) from soil, but have a higher Mn translocation (as indicated by Biological Transfer Coefficient) to aboveground parts. The Chinese chestnut and sugarcane cultivated on the reclaimed mineland were not safe for human consumption, and this agricultural restoration pattern should be carefully reconsidered.

Ecological restoration of mineland with particular reference to the metalliferous mine wasteland in China: A review of research and practice

Despite a principal contributor to the rapid economic growth, the mining industry in China produced a large amount of wasteland and caused water pollution and soil erosion as well as other environmental damages. In 2002, this industry generated 265.4 Mt tailings, 130.4 Mt gangue and 107.8 Mt smelting slags. The degraded land associated with mining is estimated to be 3.2 Mha by the end of 2004, deteriorating the land shortage of China. Restoration of mine wasteland began in late 1970s but the restoration process was sluggish. The overall restoration rate (the ratio of reclaimed land area to the total degraded land area) of mine wasteland was some 10-12% with a higher rate for coal mine spoils but a lower rate for metal-mined derelict land. From 1994 to 2004, 149 research papers were published about the restoration of China's mining wasteland, of which 70 were on metal-mined land and 61 on the non-metal-mined land. Although 37 institutions in China were involved in the restoration research, only a few remained active and productive. Metal-mined derelict land is often more metal toxic and deficient of macronutrients and is tougher for revegetation. Many substrate amelioration techniques were proposed and tolerant plant species were tested for use of reclamation of the metal-mined tailings. Five hyperaccumulator species have been reported in China for the potential use in phytoremediation. However, these accomplishments were all at laboratory or small-scale field demonstration stage and still far from the practical use in reality. To accelerate the restoration and utilization of mine wasteland, several recommendations are put forward in this review. Above these suggestions, the commitment and efficiency of the government at all levels are vital.

Grain yield responses to moisture regimes in a rice population: association among traits and genetic markers

Drought is a major constraint to rice (Oryza sativa L.) production in rainfed and poorly irrigated environments. Identifying genomic regions influencing the response of yield and its components to water deficits will aid our understanding of the genetic mechanism of drought tolerance (DT) of rice and the development of DT varieties. Grain yield (GY) and its components of a recombinant inbred population developed from a lowland rice and an upland rice were investigated under different water levels in 2003 and 2004 in a rainout DT screening facility. Correlation and path analysis indicated that spikelet fertility (SF) was particularly important for grain yield with direct effect (P=0.60) under drought stress, while spikelet number per panicle (SN) contributed the most to grain yield (P=0.41) under well-watered condition. A total of 32 quantitative trait loci (QTLs) for grain yield and its components were identified. The phenotypic variation explained by individual QTLs varied from 1.29% to 14.76%. Several main effect QTLs affecting SF, 1,000-grain weight (TGW), panicle number (PN), and SN were mapped to the same regions on chromosome 4 and 8. These QTLs were detected consistently across 2 years and under both water levels in this study. Several digenic interactions among yield components were also detected. The identification of genomic regions associated with GY and its components under stress will be useful to improve drought tolerance of rice by marker-aided approaches.

Expression and characterization of a recombinant Cry1Ac crystal protein with enhanced green fluorescent protein in acrystalliferous Bacillus thuringiensis

AIMS

To investigate fusion expression between Bacillus thuringiensis crystal protein and a foreign protein, the expression of a fusion protein comprised of Cry1Ac, and enhanced green fluorescent protein (EGFP) in B. thuringiensis Cry(-)B strain was examined.

METHODS AND RESULTS

The N-terminal fusion expression of EGFP in Cry1Ac was attempted under the control of the native cry1Ac promoter. The EGFP gene was cloned into pProMu and named pProMu-EGFP. The transformant, ProMu-EGFP/CB produced parasporal inclusions that were of bipyramidal-shaped crystals in size ranging from 200 to 300 nm. The fusion protein was approximately 150 kDa and identified by the immunoblot analysis using a Cry1Ac antibody and also a GFP antibody. The LC(50) of the ProMu-EGFP/CB was twofold higher when compared with that by the ProAc/CB. However, the crystal protein produced by the ProMu-EGFP/CB was effective on Plutella xylostella larvae.

CONCLUSIONS

The ProMu-EGFP/CB produced bipyramidal shaped and insecticidal crystals comprising fusion proteins.

SIGNIFICANCE AND IMPACT OF THE STUDY

Through the N-terminal fusion expression of EGFP and Cry1Ac, expression and crystallization between the B. thuringiensis crystal protein and a foreign protein were validated.

Isolation and characterization of a strain of Bacillus thuringiensis ssp. kurstaki containing a new delta-endotoxin gene

A strain of Bacillus thuringiensis that showed significantly high toxicity to Plutella xylostella and Spodoptera exigua was isolated from a Korean soil sample and characterized. The isolate, named B. thuringiensis K1, was determined to belong to ssp. kurstaki (H3a3b3c) type by an H antisera agglutination test and produced bipyramidal inclusions. Plasmid pattern of K1 was different from that of the reference strain, ssp. kurstaki HD-1, but the parasporal inclusion protein profile of K1 had two major bands that were similar in size to those of ssp. kurstaki HD-1. To verify the delta-endotoxin gene types of K1, PCR analysis with specific cry gene primers was performed to show that K1 contained a new cry gene in addition to cry1Aa, cry1Ab, cry1Ac, cry1E and cry2 genes. PCR-amplified region of the new cry gene, cryX, showed 79% similarity to cry1Fa1 gene (GenBank Accession No. M63897). In an insect toxicity assay, K1 had higher toxicity against Plutella xylostella and S. exigua than ssp. kurstaki HD-1.

Molecular cloning of a new crystal protein gene cry1Af1 of Bacillus thuringiensis NT0423 from Korean sericultural farms

A new cry1Ab-type gene encoding the 130 kDa protein of Bacillus thuringiensis NT0423 bipyramidal crystals was cloned, sequenced, and expressed in a crystal-negative B. thuringiensis host. Hybridization experiments revealed that the crystal protein gene is located on a 44 MDa plasmid of B. thuringiensis NT0423. A strong positive signal detected on the 6.6 kb HindIII fragment from B. thuringiensis NT0423 plasmid DNA was cloned and sequenced. The cry1Ab-type gene, designated cry1Af1, consisted of open reading frame of 3453 bp, encoding a protein of 1151 amino acid residues. The polypeptide has the deduced amino acid sequences predicting molecular masses of 130,215 Da. With both Bt I and Br II promoter sequences were found, the B. thuringiensis NT0423 crystal protein gene promoter closely aligned with those of cry1A-type crystal protein gene. When compared with known sequences of other Cry and Cyt proteins, the Cry1Af1 protein showed maximum 93% sequence identity to Cry1Ab protein of B. thuringiensis subsp. kurstaki. The expressed Cry1Af1 protein in a crystal-negative B. thuringiensis host appears to have strong insecticidal activity against lepidopteran larvae (Plutella xylostella). Crystals containing Cry1Af1 were about six times more toxic than the wild-type crystals of B. thuringiensis NT0423.

Influence of the yihE gene of Shigella flexneri on global gene expression: on analysis using DNA arrays

Inactivation of dsbA (disulfide bond formation), either by an insertion (Sh4, dsbA::kan) or by alteration of the active site (Sh42, dsbA33G), renders Shigella flexneri avirulent. However, Sh4 and Sh42 behave differently in many ways in vitro and in vivo. A gene of unknown function, yihE, up-stream and cotranscribed with dsbA, is thought to differentiate Sh4 and Sh42 as the kan insertion may result in a truncated unstable yihE-dsbA mRNA in Sh4. To gain insight into the function of yihE, DNA array hybridization was performed to study the genomic expression in Sh4, Sh42, and a newly constructed yihE mutant (Sh54). Compared to the wild-type, M90TS, Sh4, and Sh54 demonstrated significantly changed transcription levels of about 100 genes, of which many involved in energy metabolism and stress response were down- and up-regulated, respectively. In contrast, Sh42 showed altered transcription levels of only 20 genes. The results argue that yihE is principally responsible for the changed genomic expression in Sh4 and Sh54. Given the fact that the transcription of yihE-dsbA is regulated by the CpxRA two-component signal transduction system, yihE is probably involved in the extracytoplasmic stress response in a manor deserving further studies.

Fluorescent microsphere-based readout technology for multiplexed human single nucleotide polymorphism analysis and bacterial identification

Large-scale human genotyping requires technologies with a minimal number of steps, high accuracy, and the ability to automate at a reasonable cost. In this regard, we have developed a rapid, cost-effective readout method for single nucleotide polymorphism (SNP) genotyping that combines an easily automatable single-tube allele-specific primer extension (ASPE) with an efficient high throughput flow cytometric analysis performed on a Luminex 100 flow cytometer. This robust technique employs an ASPE reaction using PCR-derived target DNA containing the SNP and a pair of synthetic complementary capture probes that differ at their 3' end-nucleotide defining the alleles. Each capture probe has been synthesized to contain a unique 25-nucleotide identifying sequence (ZipCode) at its 5' end. An array of fluorescent microspheres, covalently coupled with complementary ZipCode sequences (cZipCodes), was hybridized to biotin-labeled ASPE reaction products, sequestering them for flow cytometric analysis. ASPE offers both an advantage of streamlining the SNP analysis protocol and an ability to perform multiplex SNP analysis on any mixture of allelic variants. All steps of the assay are simple additions of the solutions, incubations, and washes. This technique was used to assay 15 multiplexed SNPs on human chromosome 12 from 96 patients. Comparison of the microsphere-based ASPE assay results to gel-based oligonucleotide ligation assay (OLA) results showed 99.2% agreement in genotype assignments. In addition, the microsphere-based multiplex SNPs assay system was adapted for the identification of bacterial samples by both ASPE and single base chain extension (SBCE) assays. A series of probes designed for different variable sites of bacterial 16S rDNA permitted multiplex analysis and generated species- or genus-specific patterns. Seventeen bacterial species representing a broad range of gram-negative and gram-positive bacteria were analyzed within 16 variable sites of 16S rDNA sequence. The results were consistent with the published sequences and confirmed by direct DNA sequencing.

Flow cytometric platform for high-throughput single nucleotide polymorphism analysis

We have developed a rapid, cost-effective, high-throughput readout for single nucleotide polymorphism (SNP) genotyping using flow cytometric analysis performed on a Luminex 100 flow cytometer. This robust technique employs a PCR-derived target DNA containing the SNP, a synthetic SNP-complementary ZipCode-bearing capture probe, a fluorescent reporter molecule, and a thermophilic DNA polymerase. An array of fluorescent microspheres, covalently coupled with complementary ZipCode sequences (cZipCodes), was hybridized to the reaction products and sequestered them for flow cytometric analysis. The single base chain extension (SBCE) reaction was used to assay 20 multiplexed SNPs for 633 patients in 96-well format. Comparison of the microsphere-based SBCE assay results to gel-based oligonucleotide ligation assay (OLA) results showed 99.3% agreement in genotype assignments. Substitution of direct-labeled R6G dideoxynucleotide with indirect-labeled phycoerythrin dideoxynucleotide enhanced signal five- to tenfold while maintaining low noise levels. A new assay based on allele-specific primer extension (ASPE) was validated on a set of 15 multiplexed SNPs for 96 patients. ASPE offers both the advantage of streamlining the SNP analysis protocol and the ability to perform multiplex SNP analysis on any mixture of allelic variants.

Aging effect in ceramic superconductors

A three-dimensional lattice of the Josephson junctions with a finite self-conductance is employed to model ceramic superconductors. By using Monte Carlo simulations it is shown that the aging disappears in the strong screening limit. In the weak screening regime, aging is present even at low temperatures. For intermediate values of the self-inductance, aging occurs in an intermediate temperature interval but is suppressed entirely at high and low temperatures. Our results are in good agreement with experiments.

Dynamical chaos and power spectra in toy models of heteropolymers and proteins

The dynamical chaos in Lennard-Jones toy models of heteropolymers is studied by molecular dynamics simulations. It is shown that two nearby trajectories quickly diverge from each other if the heteropolymer corresponds to a random sequence. For good folders, on the other hand, two nearby trajectories may initially move apart but eventually they come together. Thus good folders are intrinsically nonchaotic. A choice of a distance of the initial conformation from the native state affects the way in which a separation between the twin trajectories behaves in time. This observation allows one to determine the size of a folding funnel in good folders. We study the energy landscapes of the toy models by determining the power spectra and fractal characteristics of the dependence of the potential energy on time. For good folders, folding and unfolding trajectories have distinctly different correlated behaviors at low frequencies.

A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension

A rapid, high throughput readout for single-nucleotide polymorphism (SNP) analysis was developed employing single base chain extension and cytometric analysis of an array of fluorescent microspheres. An array of fluorescent microspheres was coupled with uniquely identifying sequences, termed complementary ZipCodes (cZipCodes), which allowed for multiplexing possibilities. For a given assay, querying a polymorphic base involved extending an oligonucleotide containing both a ZipCode and a SNP-specific sequence with a DNA polymerase and a pair of fluoresceinated dideoxynucleotides. To capture the reaction products for analysis, the ZipCode portion of the oligonucleotide was hybridized with its cZipCodes on the microsphere. Flow cytometry was used for microsphere decoding and SNP typing by detecting the fluorescein label captured on the microspheres. In addition to multiplexing capability, the ZipCode system allows multiple sets of SNPs to be analyzed by a limited set of cZipCode-attached microspheres. A standard set of non-cross reactive ZipCodes was established experimentally and the accuracy of the system was validated by comparison with genotypes determined by other technologies. From a total of 58 SNPs, 55 SNPs were successfully analyzed in the first pass using this assay format and all 181 genotypes across the 55 SNPs were correct. These data demonstrate that the microsphere-based single base chain extension (SBCE) method is a sensitive and reliable assay. It can be readily adapted to an automated, high-throughput genotyping system. [Primer sequences used in this study are available as online supplementary materials at www.genome.org.]

Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry

BACKGROUND

We have developed a rapid, high throughput method for single nucleotide polymorphism (SNP) genotyping that employs an oligonucleotide ligation assay (OLA) and flow cytometric analysis of fluorescent microspheres.

METHODS

A fluoresceinated oligonucleotide reporter sequence is added to a "capture" probe by OLA. Capture probes are designed to hybridize both to genomic "targets" amplified by polymerase chain reaction and to a separate complementary DNA sequence that has been coupled to a microsphere. These sequences on the capture probes are called "ZipCodes". The OLA-modified capture probes are hybridized to ZipCode complement-coupled microspheres. The use of microspheres with different ratios of red and orange fluorescence makes a multiplexed format possible where many SNPs may be analyzed in a single tube. Flow cytometric analysis of the microspheres simultaneously identifies both the microsphere type and the fluorescent green signal associated with the SNP genotype.

RESULTS

Application of this methodology is demonstrated by the multiplexed genotyping of seven CEPH DNA samples for nine SNP markers located near the ApoE locus on chromosome 19. The microsphere-based SNP analysis agreed with genotyping by sequencing in all cases.

CONCLUSIONS

Multiplexed SNP genotyping by OLA with flow cytometric analysis of fluorescent microspheres is an accurate and rapid method for the analysis of SNPs.