一种基于模糊聚类的构造进化树方法

各种生物之间的进化史可以通过构建进化树来讨论,因此进化树的研究成了一个研究热点。提出将利用DNA序列的4D表示所得相似矩阵视为模糊矩阵,再利用最大树法来构建进化树的方法。该方法不需要多序列比对,计算简单,实验验证了该方法的有效性。     

基于改进非支配遗传算法的DNA编码序列优化方法

针对DNA计算中的编码序列设计问题,分析了DNA编码序列设计的目标和需要满足的约束条件,并建立了相应的数学模型。通过将约束条件引入非支配排序过程,提出了一种改进的NSGA-Ⅱ算法。实验结果表明,该算法具有良好的收敛特性和种群多样性,能为可控的DNA计算提供可靠的编码序列。     

Molecular modeling of tricyclic compounds with anilino substituents and their intercalation complexes with DNA sequences

Although 9-anilinoacridines are among the best studied antitumoral intercalators, there are few studies about the effect of isosteric substitution of a benzene moiety for a heterocycle ring in the acridine framework. According to these studies, this approach may lead to effective cytotoxic agents, but good cytotoxic activity depends on structural requirements in the aniline ring which differ from those in 9-anilinoacridines. The present paper deals with molecular modeling studies of some 9-anilino substituted tricyclic compounds and their intercalation complexes (in various DNA sequences) resulting from docking the compounds into various DNA sequences. As expected, the isosteric substitution in 9-anilinoacridines influences the LUMO energy values and orbital distribution, the dipole moment, electrostatic charges and the conformation of the anilino ring. Other important differences are observed during the docking studies, for example, changes in the spatial arrangement of the tricyclic nucleus and the anilino ring at the intercalation site. Semiempirical calculations of the intercalation complexes show that the isosteric replacement of a benzene ring in the acridine nucleus affects not only DNA affinity but also base pair selectivity. These findings explain, at least partially, the different structural requirements observed in several 9-anilino substituted tricyclic compounds for cytotoxic activity. Thus, the data presented here may guide the rational design of new agents with different DNA binding properties and/or a cytotoxic profile by isosteric substitution of known intercalators.     

Extraction of genomic DNA and detection of single nucleotide polymorphism genotyping utilizing an integrated magnetic bead-based microfluidic platform

This study presents a new magnetic bead-based microfluidic platform, which integrates three major modules for rapid leukocytes purification, genomic DNA (gDNA) extraction and fast analysis of genetic gene. By utilizing microfluidic technologies and magnetic beads conjugated with CD_15/45 antibodies, leukocytes in a human whole blood sample can be first purified and concentrated, followed by extraction of gDNA utilizing surface-charge switchable, DNA-specific, magnetic beads in the lysis solution. Then, specific genes associated with genetic diseases can be amplified by an on-chip polymerase chain reaction (PCR) process automatically. The whole pretreatment process including the leukocytes purification and gDNA extraction can be performed in an automatic fashion with the incorporation of the built bio-separators consisting of microcoils array within less than 20 min. The detection of single nucleotide polymorphism (SNP) genotyping of methylenetetra-hydrofolate reductase (MTHFR) C677T region associated with an increased risk of genetic diseases was further performed to demonstrate the capability of the proposed system. The extracted gDNA can be transported into a micro PCR chamber for on-chip fast nucleic acid amplification of detection genes with minimum human intervention. Hence, the developed system may provide a powerful automated platform for pretreatment of human leukocytes, gDNA extraction and fast analysis of genetic gene.     

The development of a glove-box/Vitrobot combination: air-water interface events visualized by cryo-TEM

Aqueous interfaces are of paramount importance in the study of biological systems as well as in the biomedical sciences. To study these interfaces at the nanometer level it is of interest to develop methods that allow their observation with cryogenic transmission electron microscopy (cryo-TEM). Prevention of dehydration to preserve the "native" state during sample preparation prior to vitrification is often one of the most important parameters to control in cryo-TEM experiments. For the preparation of these types of samples, we felt the need for an extended workspace with temperature and humidity control; a 'glove-box' that seamlessly connects to the vitrification instrument, the Vitrobot. In this paper we describe the use of the glove-box in the 2D and 3D cryo-TEM study of DNA adsorption and calcium carbonate mineralization to Langmuir films. The data presented illustrates the necessity of a humidity-controlled environment to preserve the original "native" state of the monolayer system.     

基于分支函数线性逼近的测试数据自动生成算法

软件测试是保证软件可靠性的一个重要手段.面向路径测试是软件测试中一种重要方法.提出了一种分支函数线性逼近的测试数据自动生成算法.结合赵瑞莲给出的谓词切片算法和程序DUC表达方式以及本文提出的算法,给出了一个基于程序执行的路径测试及测试数据自动生成新算法.由于算法采用DUC表达式,不仅可以从源端判断子路径是否可行,而且有效地降低了不可行路径对算法性能的影响.另外,与现有文献中单纯利用分支函数极小化方法的算法相比,新算法由于有机结合了分支函数线性逼近和极小化方法的长处,因此减少了测试用例的数量,提高了测试效率.     

Self-Mineralizing Dnazyme Hydrogel as a Multifaceted Bone Microenvironment Amendment for Promoting Osteogenesis in Osteoporosis

The accumulation of reactive oxygen species (ROS) and minimal osteogenic raw material in the osteoporotic bone microenvironment greatly inhibits the activity of osteoblasts. Herein, it is originally proposed to construct a biomatrix multifaceted bone microenvironment amendment -Mineralized zippered G4-Hemin DNAzyme hydrogel (MDH)-to improve osteoporotic osteogenic capacity and promote high-quality bone defect repair. The programmed design of the rolling circle amplified DNA hydrogel synthesis system allows the introduction of massive amounts of zippered G4-Hemin DNAzyme in MDH. The zippered G4-Hemin DNAzyme highly mimics the tight catalytic configuration of horseradish peroxidase and exerts excellent enzyme-like activity with considerable ROS molecule scavenging ability. In addition, the DNA amplification by-product pyrophosphate is ingeniously employed as a sufficient phosphorus source, thus constituting an autonomous mineralization system for waste reuse through the introduction of pyrophosphate hydrolase and calcium ions, which deposits in MDH as an osteogenic raw material and addresses the challenge of DNA hydrogel bio-application stability. The remarkable in vitro and in vivo outcomes demonstrate that MDH can effectively improve the oxidative stress status of osteoblasts, restore the balance of mitochondrial membrane potential, and reduce apoptosis, ultimately demonstrating superior osteogenic capacity.     

Revolving Vernier Mechanism Controls Size of Linear Homomultimer

A new kind of the Vernier mechanism that is able to control the size of linear assembly of DNA origami nanostructures is proposed. The mechanism is realized by mechanical design of DNA origami, which consists of a hollow cylinder and a rotatable shaft in it connected through the same scaffold. This nanostructure stacks with each other by the shape complementarity at its top and bottom surfaces of the cylinder, while the number of stacking is limited by twisting angle of the shaft. Experiments have shown that the size distribution of multimeric assembly of the origami depends on the twisting angle of the shaft; the average lengths of the multimer are decamer, hexamer, and tetramer for 0°, 10°, and 20° twist, respectively. In summary, it is possible to affect the number of polymerization by adjusting the precise shape and movability of a molecular structure.