A paper-based resonance energy transfer nucleic acid hybridization assay using upconversion nanoparticles as donors and quantum dots as acceptors

Monodisperse aqueous upconverting nanoparticles (UCNPs) were covalently immobilized on aldehyde modified cellulose paper via reduction amination to develop a luminescence resonance energy transfer (LRET)-based nucleic acid hybridization assay. This first account of covalent immobilization of UCNPs on paper for a bioassay reports an optically responsive method that is sensitive, reproducible and robust. The immobilized UCNPs were decorated with oligonucleotide probes to capture HPRT1 housekeeping gene fragments, which in turn brought reporter conjugated quantum dots (QDs) in close proximity to the UCNPs for LRET. This sandwich assay could detect unlabeled oligonucleotide target, and had a limit of detection of 13 fmol and a dynamic range spanning nearly 3 orders of magnitude. The use of QDs, which are excellent LRET acceptors, demonstrated improved sensitivity, limit of detection, dynamic range and selectivity compared to similar assays that have used molecular fluorophores as acceptors. The selectivity of the assay was attributed to the decoration of the QDs with polyethylene glycol to eliminate non-specific adsorption. The kinetics of hybridization were determined to be diffusion limited and full signal development occurred within 3 min.     

Energy of formation for and liquid binary alloys

We have investigated the free energy of formation for Ag_xIn_1-x and Ag_xSn_1-x liquid binary alloys at temperatures 1173 and 1250 K, respectively. A microscopic theory based on the first order perturbation has been applied. The interionic interaction and a reference liquid are the fundamental components of the theory. The interionic interaction is described by a local pseudopotential. A liquid of hard spheres (HS) of two different effective diametres and charges is used to describe the reference system. The results of the calculations for energy of formation agree very well with the available experimental data. Our calculations also reveal that a simple perturbative approach along with appropriate effective pair potentials can produce nearly quantitative results for the concerned alloys.     

Quantum Hall effect in back-gated InAs/GaSb heterostructures under a tilted magnetic field

We investigate the quantum Hall effect (QHE) in the InAs/GaSb hybridized electron–hole system grown on a conductive InAs substrate which act as a back-gate. In these samples, the electron density is constant and the hole density is controlled by the gate-voltage. Under a magnetic field perpendicular to the sample plane, the QHE appears along integer Landau-level (LL) filling factors of the net-carriers, where the net-carrier density is the difference between the electron and hole densities. In addition, longitudinal resistance maxima corresponding to the crossing of the extended states of the original electron and hole LLs make the QHE regions along integer-ν_net discontinuous. Under tilted magnetic fields, these R_xx maxima disappear in the high magnetic field region. The results show that the in-plane magnetic field component enhances the electron–hole hybridization and the formation of minigaps at LL crossings.     

Structural properties and tractability results for linear synteny

The syntenic distance between two species is the minimum number of fusions, fissions, and translocations required to transform one genome into the other. The linear syntenic distance, a restricted form of this model, has been shown to be close to the syntenic distance. Both models are computationally difficult to compute and have resisted efficient approximation algorithms with non-trivial performance guarantees. In this paper, we prove that many useful properties of syntenic distance carry over to linear syntenic distance. We also give a reduction from the general linear synteny problem to the question of whether a given instance can be solved using the maximum possible number of translocations. Our main contribution is an algorithm exactly computing linear syntenic distance in nested instances of the problem. This is the first polynomial time algorithm exactly solving linear synteny for a non-trivial class of instances. It is based on a novel connection between the syntenic distance and a scheduling problem that has been studied in the operations research literature.     

A novel phosphoramidite method for automated synthesis of oligonucleotides on glass supports for biosensor development

Two protocols for functionalization of glass supports with hexaethylene glycol (HEG)-linked oligonucleotides were developed. The first method (standard amidite protocol) made use of the 2-cyanoethyl-phosphoramidite derivative of 4,4′-dimethoxytrityl-protected HEG. This was first coupled to the support by standard solid-phase phosphoramidite chemistry followed by extension with a thymidylic acid icosanucleotide. Stepwise addition of the linker phosphoramidite graduated at 1% (relative to the total sites available) perstep at 50°C resulted in an optimal yield of immobilized oligonucleotides at a density of 2.24 × 10¹⁰ strands/mm². This observed loading maximum lies well below the theoretical maximum loading owing to nonspecific adsorption of HEG on the glass and subsequent blocking of reactive sites. Surface loadings as high as 3.73 × 10¹⁰/mm² and of excellent sequence quality were achieved with a reverse amidite protocol. The support was first modified into a 2-cyanoethyl-N,N-diisopropylphosphoramidite analog followed by coupling with 4,4′-dimethoxytrityl-protected HEG. This protocol is conveniently available when using a conventional DNA synthesizer. The reverse amidite protocol allowed for control of the surface loading at values suitable for subsequent analytical applications that make use of immobilized oligonucleotides as probes for selective hybridization of sample nucleic acids of unknown sequence and concentration.     

A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data

Single nucleotide polymorphism (SNP) arrays were used to detect chromosomal regions with DNA copy number alterations. Current statistical methods for microarray-based comparative genomic hybridization (array-CGH) analysis generally assume certain relationships among adjacent markers on the same chromosome, and these assumptions may be questionable. For an SNP-array-based CGH study, multiple normal reference SNP arrays were collected. In order to utilize these normal reference SNP arrays, we derived an empirical distribution of signal ratios for each SNP marker. With an assumed threshold value for the overall error rate control and the defined signal ratio ranges for chromosomal amplification and deletion, we proposed a procedure to identify chromosomal alteration regions based on several bootstrapped one-sample t-tests and the false discovery rate control. When we have multiple arrays for different individuals with the same disease, our method can also be used to detect SNP markers for chromosomal alteration regions that are common among these individuals. We applied our method to a published SNP array data set for breast carcinoma cell lines. For an individual with breast cancer, numerous chromosomal alteration regions were identified. Compared to results of previous studies, our method identified more chromosomal alteration regions, with some being implicated in the literature to harbor genes associated with breast cancer. For multiple cancer arrays, our results suggested the existence of common chromosomal alteration regions. However, a high proportion of false positives also indicated that genetic variations among different individuals with breast cancer can be present.     

玻璃载体表面脱氧核糖核酸的固定及其化学发光检测

用硅烷化偶联剂把ＤＮＡ直接共价固定在载玻片表面，将辣根过氧化物酶标记的探针与之进行核酸杂交，杂交后用增强的化学发光检测。方法的检出限为７５ｐｇ。研究了ＤＮＡ分子固定在玻璃载体表面的各种条件，并建立了在玻璃载体表面进行核酸杂交的体系，为研究光纤ＤＮＡ生物传感器打下了基础。     

New approaches in radical carbonylation chemistry: fluorous applications and designed tandem processes by species-hybridization with anions and transition metal species

New approaches in radical carbonylation chemistry are described. We have successfully integrated tin mediated radical carbonylation chemistry into modern fluorous applications and separation techniques. We revealed that radical carbonylation reactions can be performed using fluorous tin mediators, such as fluorous tin hydride and fluorous allyltin reagents. Fine tuning of the reaction conditions resulted in a good efficiency equivalent to conventional tin mediators. The tedious procedure of removing organotin byproducts can be circumvented through the use of fluorous/organic liquid-liquid extraction or fluorous liquid-solid phase extraction with fluorous reverse phase silica (FRPS). Also described are newly developed tandem carbonylation reactions that are based on species hybridization approaches. Using a radical/anionic hybrid system based on zinc-induced one-electron reduction, we achieved a three-component coupling reaction consisting of 4-alkenyl iodides, carbon monoxide, and electron-deficient alkenes. We observed two types of annulations processes, namely [4 + 1](radical)/[3 + 2](anionic) and [5 + 1](radical)/[3 + 2](anionic), which lead to the production of bicyclo[3.3.0]octanols and bicyclo[3.2.1]octanols, respectively. We found a radical/palladium hybrid system to be useful in the construction of new cyclic systems that incorporate two or three molecules of carbon monoxide.     

GABAA五种亚型受体与BZ配基的3D-QSAR研究

GABAA受体是中枢神经系统内重要的抑制性受体,有广泛的神经生理活性.由于镇静/抗惊厥药物在临床上的广泛应用,使得其中苯并二氮杂作用位点尤为重要.我们用比较分子场法(CoMFA)对一系列咪唑苯并二氮杂类化合物（BZ）与五种重组受体亚型的亲和力进行了结构活性关系研究,得到的一组模型都有较高的交叉验证系数.并在此基础上,建立了非交叉验证的一组PLS模型.用该组模型对随机选择的6个化合物组成的测试集进行了预测,都得到了相当满意的结果,表明所建立的一组模型具有良好的预测能力.本研究对于设计高亲和力的BZ受体的配基和研究GABAA受体的模型有指导意义.