桉树杂交种与其亲本的近红外光谱判别

研究桉树控制授粉后目标性状的基因作用方式是探索其基因重组规律的重要内容。常规的数量统计分析精度往往不高,而DNA分析的专业要求高,且费时费力。该研究利用近红外光谱(NIRs)研究不同基因型桉树杂交种、亲本及杂交种与亲本间近红外光谱信息的关系,探索NIRs用于桉树杂交种与其亲本判别的可行性和准确性。以控制授粉的桉树亲本及其杂交F1代材料为对象,每种基因型从各自田间试验分别选取10个单株,采集树冠中上部新鲜健康叶片。用手持式近红外仪Phazir Rx(1624)采集桉树杂交种与其亲本叶片的NIRs信息。每单株选10片完全生理成熟的健康叶片,避开叶脉扫描其正面光谱5次,以50条NIRs信息的均值代表单个叶片的NIRs信息,最终每个基因型获得10条NIRs信息。对原始NIRs采用二阶多项式S.G一阶导数预处理。预处理后的NIRs用于多元统计分析,首先对桉树杂交亲本和子代样本进行主成分分析(PCA),直观展示不同基因型的分类情况。然后运用簇类独立软模式(SIMCA)和偏最小二乘判别分析(PLS-DA)两种有监督的判别模式验证NIRs用于桉树杂交种与其亲本树种的分类判别效果。PCA结果显示,不同的亲本间、杂交种间及杂交种与亲本间样本的主因子得分可以清晰地将各基因型分开。SIMCA模式判别分析中,桉树杂交种样本到亲本PCA模型的样本距离显示,待判别样本能够形成单独的聚类,且能直观反映两者的遗传相似。PLS-DA判别结果显示,桉树杂交亲本的PLS模型能通过预测其杂交子代的响应变量将其与亲本准确分开。结果表明,桉树叶片的NIRs信息可以准确地反映桉树杂交子代遗传信息的传递规律,NIRs判别模型可以准确地将各种基因型予以区分。因此,NIRs信息不仅可用于桉树杂交种和纯种的定性判别,还可以分析桉树基因重组过程中加性遗传效应的大小,从而为桉树遗传基础分析及其育种改良研究提供理论支撑。     

What is the form of muscimol from fly agaric mushroom (Amanita muscaria) in water? An insight from NMR experiment supported by molecular modeling

The biologically active alkaloid muscimol is present in fly agaric mushroom (Amanita muscaria), and its structure and action is related to human neurotransmitter _γ-aminobutyric acid (GABA). The current study reports on determination of muscimol form present in water solution using multinuclear ¹H and ¹³C nuclear magnetic resonance (NMR) experiments supported by density functional theory molecular modeling. The structures of three forms of free muscimol molecule both in the gas phase and in the presence of water solvent, modeled by polarized continuous model, and nuclear magnetic isotropic shieldings, the corresponding chemical shifts, and indirect spin–spin coupling constants were calculated. Several J-couplings observed in proton and carbon NMR spectra, not available before, are reported. The obtained experimental spectra, supported by theoretical calculations, favor the zwitterion form of muscimol in water. This structure differs from NH isomer, previously determined in dimethyl sulfoxide (DMSO) solution. In addition, positions of signals C3 and C5 are reversed in both solvents.     

Study of Endogen Substrates,Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.     

Characterization of new Pt(IV)–thiazole complexes: Analytical,spectral, molecular modeling and molecular docking studies and applications in two opposing pathways

New thiazole derivatives were synthesized and fully characterized, then coordinated with PtCl₄ salt. Also, the newly synthesized Pt(IV) complexes were investigated analytically (elemental and thermogravimetric analyses), spectrally (infrared, UV–visible, mass, ¹H NMR, ¹³C NMR, X‐ray diffraction) as well as theoretically (kinetics, modeling and docking). The data extracted led to the establishment of the best chemical and structural forms. Octahedral geometry was the only formula proposed for all complexes, which is favorable for d⁶ systems. The molecular ion peaks from mass spectral analysis coincide with all analytical data, confirming the molecular formula proposed. X‐ray diffraction (XRD) and scanning electron microscopy (SEM) allowed discrimination of features between crystalline particles and other amorphous morphology. By applying Gaussian09 as well as HyperChem 8.2 programs, the best structural forms were obtained, as well as computed significant parameters. Computed parameters such as softness, hardness, surface area and reactivity led us towards application in two opposing pathways: tumor inhibition and oxidation activation. The catalytic oxidation for CO was conducted over PtO₂, which was yielded from calcination of the most reactive complex. The success of catalytic role for synthesized PtO₂ was due to its particulate size and surface morphology, which were estimated from XRD patterns and SEM images, respectively. The antitumor activity was tested versus HCT‐116 and HepG‐2 cell lines. Mild toxicity was recorded for two of the derivatives and their corresponding complexes. This degree of toxicity is more favorable in most cases, due to exclusion of serious side effects, which is coherently attached with known antitumor drugs.     

一种高精度的非平稳随机信号实时建模算法研究

针对传统的非平稳随机信号时变参数筹分模型算法的不足,论文把非平稳随机信号时变参数差分模型与一种带自适应遗忘因子的RLS算法结合起来,形成一种有效的非平稳随机信号实时建模算法,仿真分析表明该算法不仅能获得快的收敛速度而且能获得高的建模精度。     

Range Assignment for Biconnectivity and k-Edge Connectivity in Wireless Ad Hoc Networks

Depending on whether bidirectional links or unidirectional links are used for communications, the network topology under a given range assignment is either an undirected graph referred to as the bidirectional topology, or a directed graph referred to as the unidirectional topology. The Min-Power Bidirectional (resp., Unidirectional) k-Node Connectivity problem seeks a range assignment of minimum total power subject to the constraint that the produced bidirectional (resp. unidirectional) topology is k-vertex connected. Similarly, the Min-Power Bidirectional (resp., Unidirectional) k-Edge Connectivity problem seeks a range assignment of minimum total power subject to the constraint the produced bidirectional (resp., unidirectional) topology is k-edge connected. The Min-Power Bidirectional Biconnectivity problem and the Min-Power Bidirectional Edge-Biconnectivity problem have been studied by Lloyd et al. [23]. They show that range assignment based the approximation algorithm of Khuller and Raghavachari [18], which we refer to as Algorithm KR, has an approximation ratio of at most 2(2 – 2/n)(2 + 1/n) for Min-Power Bidirectional Biconnectivity, and range assignment based on the approximation algorithm of Khuller and Vishkin [19], which we refer to as Algorithm KV, has an approximation ratio of at most 8(1 – 1/n) for Min-Power Bidirectional Edge-Biconnectivity. In this paper, we first establish the NP-hardness of Min-Power Bidirectional (Edge-) Biconnectivity. Then we show that Algorithm KR has an approximation ratio of at most 4 for both Min-Power Bidirectional Biconnectivity and Min-Power Unidirectional Biconnectivity, and Algorithm KV has an approximation ratio of at most 2k for both Min-Power Bidirectional k-Edge Connectivity and Min-Power Unidirectional k-Edge Connectivity. We also propose a new simple constant-approximation algorithm for both Min-Power Bidirectional Biconnectivity and Min-Power Unidirectional Biconnectivity. This new algorithm applies only to Euclidean instances, but is best suited for distributed implementation. A preliminary version of this work appeared in the proceedings of the 2nd International Conference on AD-HOC Network and Wireless (Adhoc-Now 2003). Research performed in part while visiting the Max-Plank-Institut fur Informatik. Gruia Calinescu is an Assistant Professor of Computer Science at the Illinois Institute of Technology since 2000. He held postdoc or visiting researcher positions at DIMACS, University of Waterloo, and Max-Plank Institut fur Informatik. Gruia has a Diploma from University of Bucharest and a Ph.D. from Georgia Insitute of Technology. His research interests are in the area of algorithms. Peng-Jun Wan has joined the Computer Science Department at Illinois Institute of Technology in 1997 and has been an Associate Professor since 2004. He received his Ph.D. in Computer Science from University of Minnesota in 1997, M.S. in Operations Research and Control Theory from Chinese Academy of Science in 1993, and B.S. in Applied Mathematics from Tsinghua University in 1990. His research interests include optical networks and wireless networks.     

A Bluetooth Based Sensor Network for Civil Infrastructure Health Monitoring

Communicating with sensors has long been limited either to wired connections or to proprietary wireless communication protocols. Using a ubiquitous and inexpensive wireless communication technology to create Sensor Area Networks (SANs) will accelerate the extensive deployment of sensor technology. Bluetooth, an emerging, worldwide standard for inexpensive, local wireless communication is a viable choice for SANs because of its inherent support for some of the important requirements – low power, small form factor, low cost and sufficient communication range. In this paper we outline an approach, centered on the Bluetooth technology, to support a sensor network composed of fixed wireless sensors for health monitoring of highways, bridges and other civil infrastructures. We present a topology formation scheme that not only takes into account the traffic generated by different sensors but also the associated link strengths, buffer capacities and energy availability. The algorithm makes no particular assumptions as to the placement of nodes, and not all nodes need to be in radio proximity of each other. The output is a tree shaped scatternet rooted at the sensor hub (data logger) that is balanced in terms of traffic carried on each of the links. We also analyze the scheduling, routing and healing aspects of the resulting sensor-net topology.     

A Multilayer Optical Packet Switching Network Based on the Kautz Graph and Optical Passive Star Couplers

The multihop optical network is the most appropriate solution to satisfy the increasing applications of Internet services. This paper extends the regular Kautz graph to one with multiple layers in order to produce more architectural variations. The connectivity between adjacent layers utilizes the systematic connection patterns of a regular Kautz graph. A routing algorithm based on its property is presented. Optical passive star (OPS) couplers are adopted to implement our new topologies. Three scheduling criteria that can solve the contention problem in the intermediate nodes are evaluated and compared in terms of their capability to improve the accessibility.