Complex shapes self-assembled from single-stranded DNA tiles

Programmed self-assembly of strands of nucleic acid has proved highly effective for creating a wide range of structures with desired shapes. A particularly successful implementation is DNA origami, in which a long scaffold strand is folded by hundreds of short auxiliary strands into a complex shape. Modular strategies are in principle simpler and more versatile and have been used to assemble DNA or RNA tiles into periodic and algorithmic two-dimensional lattices, extended ribbons and tubes, three-dimensional crystals, polyhedra and simple finite two-dimensional shapes. But creating finite yet complex shapes from a large number of uniquely addressable tiles remains challenging. Here we solve this problem with the simplest tile form, a 'single-stranded tile' (SST) that consists of a 42-base strand of DNA composed entirely of concatenated sticky ends and that binds to four local neighbours during self-assembly. Although ribbons and tubes with controlled circumferences have been created using the SST approach, we extend it to assemble complex two-dimensional shapes and tubes from hundreds (in some cases more than one thousand) distinct tiles. Our main design feature is a self-assembled rectangle that serves as a molecular canvas, with each of its constituent SST strands--folded into a 3 nm-by-7 nm tile and attached to four neighbouring tiles--acting as a pixel. A desired shape, drawn on the canvas, is then produced by one-pot annealing of all those strands that correspond to pixels covered by the target shape; the remaining strands are excluded. We implement the strategy with a master strand collection that corresponds to a 310-pixel canvas, and then use appropriate strand subsets to construct 107 distinct and complex two-dimensional shapes, thereby establishing SST assembly as a simple, modular and robust framework for constructing nanostructures with prescribed shapes from short synthetic DNA strands.     

Recent developments in neuropsychological endophenotypes for schizophrenia: Development of the MATRICS battery,liability syndromes and the near future

Cognitive deficits are now recognized widely as core features of schizophrenia, and as major contributors to the clinical outcome of the disorder. They are also studied widely as ‘endophenotypes’, reflecting a growing consensus that schizophrenia is a broader, more multidimensional illness than the diagnostic criteria required for its formal diagnosis. This evolving view of cognition underlies its utilization in recent initiatives for intervention and assessment in schizophrenia. Two of these initiatives ar...     

Construction of <Emphasis Type="Italic">k</Emphasis>-ary pseudorandom elliptic curve sequences

We present a method for constructing k-ary sequences over elliptic curves.Using the multiplicative character of order k of finite fields,we construct a family of k-ary pseudorandom elliptic curve sequences.The pseudorandom measures,such as the well-distribution measure,the correlation measure of order ■,and the linear complexity are estimated by using certain character sums.Such sequences share the same order of magnitude on the well-distribution measure,the correlation measure of order ■ as the ’truly’ random sequences.The method indicates that it is possible to construct ’good’ pseudorandom sequences over elliptic curves widely used in public key cryptography.     

Logical computation using algorithmic self-assembly of DNA triple-crossover molecules

Recent work has demonstrated the self-assembly of designed periodic two-dimensional arrays composed of DNA tiles, in which the intermolecular contacts are directed by 'sticky' ends. In a mathematical context, aperiodic mosaics may be formed by the self-assembly of 'Wang' tiles, a process that emulates the operation of a Turing machine. Macroscopic self-assembly has been used to perform computations; there is also a logical equivalence between DNA sticky ends and Wang tile edges. This suggests that the self-assembly of DNA-based tiles could be used to perform DNA-based computation. Algorithmic aperiodic self-assembly requires greater fidelity than periodic self-assembly, because correct tiles must compete with partially correct tiles. Here we report a one-dimensional algorithmic self-assembly of DNA triple-crossover molecules that can be used to execute four steps of a logical (cumulative XOR) operation on a string of binary bits.     

Experimental validation of inter-subspecific genetic diversity in rice represented by the differences between the DNA sequences of ＇Nipponbare＇ and ＇93-11＇

The pedigrees of three sequenced rice cultivars were analyzed to show that a majority of the genetic composition of ＇Nipponbare＇ originates from japonica cultivars while the minority originates from indica cultivars. In contrast, ＇93-11＇ is derived mainly from indica cultivars with a smaller contribution from japonica cultivars. All ancestors of ＇Guang lu ai 4＇ appeared to be indica lines. A set of molecular markers （46 InDels and 53 SSRs） polymorphic between ＇Nipponbare＇ and ＇93-11＇ were examined in 46 typical indica and 47 typical japonica cultivars selected from 443 accessions according to Cheng＇s index. All cultivars were divided into indica and japonica groups without overlapping when clustered by Cheng＇s index, InDels and SSRs. Much higher InDel and SSR diversity between groups than within groups implies that the marker polymorphisms between ＇Nipponbare＇ and ＇93-11＇ represent a large proportion of inter-subspecific diversity. About 85% of indica cultivars and more than 90% of japonica cultivars were confirmed to have the same PCR banding patterns as ＇93-11＇ and ＇Nipponbare＇, respectively. Some polymorphic loci between ＇Nipponbare＇ and ＇93-11＇ cannot be validated in other indica and japonica cultivars, either as subspecies-specific but not predominant alleles, or alleles not specific between the two groups. It was concluded that molecular markers developed from sequence polymorphism between ＇Nipponbare＇ and ＇93-11＇ often represent inter-subspecific diversity, although some exceptions were sensitive to either particular marker loci or particular cultivars.     

Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra

DNA is renowned for its double helix structure and the base pairing that enables the recognition and highly selective binding of complementary DNA strands. These features, and the ability to create DNA strands with any desired sequence of bases, have led to the use of DNA rationally to design various nanostructures and even execute molecular computations. Of the wide range of self-assembled DNA nanostructures reported, most are one- or two-dimensional. Examples of three-dimensional DNA structures include cubes, truncated octahedra, octohedra and tetrahedra, which are all comprised of many different DNA strands with unique sequences. When aiming for large structures, the need to synthesize large numbers (hundreds) of unique DNA strands poses a challenging design problem. Here, we demonstrate a simple solution to this problem: the design of basic DNA building units in such a way that many copies of identical units assemble into larger three-dimensional structures. We test this hierarchical self-assembly concept with DNA molecules that form three-point-star motifs, or tiles. By controlling the flexibility and concentration of the tiles, the one-pot assembly yields tetrahedra, dodecahedra or buckyballs that are tens of nanometres in size and comprised of four, twenty or sixty individual tiles, respectively. We expect that our assembly strategy can be adapted to allow the fabrication of a range of relatively complex three-dimensional structures.     

混凝土收缩徐变和温度对外墙瓷砖性能及安全性研究

采用ANSYS Workbench软件平台的Fluid Flow(Fluent)分析系统件对夏季极端高温下外墙瓷砖温度进行模拟,并进行温度实测,相互验证模拟值与实测值准确性;提出了外墙柱混凝土收缩徐变各龄期的有效模量计算公式,选取6种不同尺寸的柱-砂浆-瓷砖模型,采用有效模量法模拟混凝土柱收缩徐变对外墙瓷砖剪应力和侧向变形的影响,计算外墙柱混凝土收缩徐变和夏季极端高温作用下瓷砖层剪应力值与侧向变形值。结果表明：外墙瓷砖层实测温度值略低于模拟值;极端高温和混凝土收缩徐变作用下的剪应力值与变形值相差较小,因此,在外墙瓷砖设计时要考虑温度及混凝土收缩徐变两大因素,砂浆层厚度和柱纵向配筋率均是影响剪应力值和侧向变形值大小的主要因素;夏季极端高温环境下外墙瓷砖极有可能发生水平漂移,房屋周边道路均在瓷砖脱落范围之内。     

最大匹配问题Tile自组装模型

Tile自组装模型凭借其自组装、可编程等特性在解决NP问题方面具有巨大优势.文中提出了一种求解最大匹配问题的Tile自组装新模型,该模型主要由初始配置子系统、选择子系统及检测子系统3大部分构成.新模型中首先设计Tile分子存储问题信息,其次通过Tile分子自组装操作生成最大匹配问题解空间,最后通过Tile检测分子筛选得到最大匹配问题的解.对模型从所需Tile分子种类、计算时间和计算空间3个方面进行性能分析,并通过实验模拟论证了模型的有效性和正确性.     

Multiple transgenes Populus xeuramericana ＇Guariento＇ plants obtained by biolistic bombardment

A JERF36 regulation gene, a selection marker gene （NPT-Ⅱ）, and the foreign genes levansucrase （SacB）, Vitreoscilla hemoglobin （vgb）, and Binary coleopterus insect resistance （BtCry3A＋OC-I） were co-transferred into Populus xeuramericana ＇Guariento＇ using biolistic bombardment; 25 kanamycin resistant plants were obtained, The results of PCR and Southern hybridization showed that the foreign genes had been integrated into the genome of P, xeuramericana ＇Guariento＇ and 5 genes were all transferred into 7 poplar plants, The results of a BtCry3A ELISA experiment indicated that the BtCry3A gene was expressed in the 7 transgenic poplar plants, and these plants grew well on coastal saline land,     

Exsolution microstructures in ultrahigh-pressure rocks: Progress, controversies and challenges

Exsolution microstructures in minerals of rocks from orogenic belts played an important role in recognition of ultrahigh-pressure （UHP） metamorphism in their host rocks by defining the subduction depth and improving our understanding of the dynamics during the subduction and exhumation of UHP rocks. However, it is a challenging scientific topic to distinguish the ＇exsolution microstructures＇ from the ＇non-exsolution microstructures＇ and decipher their geological implications. This paper describes the subtle differences between the ＇exsolution microstructures＇ and the ＇non-exsolution microstructures＇ and summarizes the progress in studies of exolution microstructures from UHP rocks and mantle rocks of ultra-deep origin. We emphasize distinguishing the ＇exsolution microstructures＇ from the ＇non-exsolution microstructures＇ based on their geometric topotaxy and chemistry. In order to decipher correctly the exsolution microstructures, it is crucial to understand the changes of chemistry and habits of host minerals with pressure and temperature, Therefore, it is important to combine observations of exsolution microstructure in natural rocks with experimental results at high pressure and temperature and results of micro-scale analyses. Such studies will improve our understanding of the UHP metamorphism and cast new lights on solid geoscience issues such as deep subduction of continental crusts and crust-mantle interactions.     

Synoptic-scale variation of δ18O in summer monsoon rainfall at Lijiang, China

Based on the daily δ~(18)O data in June―September 2003 at Lijiang and the daily mean NCEP/ NCAR reanalysis data, synoptic-scale variation of δ~(18)O in summer monsoon rainfall was investigated. The 'precipitation amount effect' is obvious for the daily δ~(18)O variation, whereas the 'temperature effect' is insignificant. Alternate occurrences of active phase and break phase of the southwest monsoon probably influence the synoptic-scale δ~(18)O variation prominently. Moreover, the isotopic composition in precipitation during the late monsoon months is presumably influenced significantly by recycling of monsoon precipitation. Both the above factors disturb the 'amount effect' of isotopic variation in the monsoon region. This study also indicates that the synoptic-scale rainfall δ~(18)O variation at Lijiang in summer is domi-nated by the Indian monsoon depression (low pressure) system at large scale. These results are important for further studying the 'amount effect' and reconstructing paleoclimate in the monsoon region.     

一种基于DNA自组装模型求解最大团问题的算法

基于tiles理论模型和已有DNA自组装模型,结合最大团问题给出基于DNA自组装模型的算法设计,得到具体设计初始分子、规则分子和检测分子所需的DAE块种类.在此基础上采用荧光标记和凝胶电泳生物操作提出了一种求解最大团问题算法.该算法设计tiles的种类为Θ(n2+|E|),其生物操作复杂性为Θ(1).此算法降低了实验的复杂度,而且保证了实验的易操作性和结果的准确性。     

Accurate multiplex gene synthesis from programmable DNA microchips

Testing the many hypotheses from genomics and systems biology experiments demands accurate and cost-effective gene and genome synthesis. Here we describe a microchip-based technology for multiplex gene synthesis. Pools of thousands of 'construction' oligonucleotides and tagged complementary 'selection' oligonucleotides are synthesized on photo-programmable microfluidic chips, released, amplified and selected by hybridization to reduce synthesis errors ninefold. A one-step polymerase assembly multiplexing reaction assembles these into multiple genes. This technology enabled us to synthesize all 21 genes that encode the proteins of the Escherichia coli 30S ribosomal subunit, and to optimize their translation efficiency in vitro through alteration of codon bias. This is a significant step towards the synthesis of ribosomes in vitro and should have utility for synthetic biology in general.     

基于sub-tile的对称有界DNA结构自组装及应用

使用一种基于DNA sub-tile的自组装策略,通过模块化的方式灵活构建多种刚性DNA tile,同时利用DNA tile 的对称性,创建多种有限尺寸,空间可寻址的纳米网格结构,并阐述其可能在癌症治疗中作为小分子纳米药物颗粒运载工具,实现定向给药的潜在应用.     

ApiIa抗菌肽基因的化学合成,克隆及其在酵母中的表达

用固相亚磷酰胺法合成了ＡｐｉＩａ抗菌肽基因,全长为８０个核苷酸。它被分成４个寡核苷酸片段,分别在ＤＮＡ合成仪上的合成经分离纯化后的寡核苷酸片段经酶促连接,然后被克隆到分泌型载体质粒ｐＡＦＤ１０１上,经限制酶酶切,ＰＣＲ模板检测以及双链ＤＮＡ序列分析检测,证明合成的ａｐｉＩａ基因和设计的完全一致。     

超大地形分块建模算法的研究

研究了虚拟现实领域中超大规模地形快速、实时渲染的问题,提出一种新的地形建模方法.该方法将现实中所要表现的整块超大规模的地形分割成若干块小的地形分片,由这些小地形分片按照一定规则进行拼接,从而还原出原有的超大地形.在实际进行虚拟漫游时,只需要根据用户摄像机所在的具体位置,动态地载入进入用户视野范围的小地形分片的数据,同时...     

不同污水处理厂脱水污泥烧制建筑瓷砖的初步研究

对取自福州3个污水处理厂的脱水污泥进行含水率、挥发性固体含量、灰分、pH值等理化性能的测试,应用X-射线粉末衍射(XRD)、X-射线荧光分析(XRF)、热重分析(TG)、扫描电镜(SEM)等手段对样品的成分、结构进行详细表征,并以污泥作为添加原料进行烧制建筑瓷砖的初步研究.实验结果表明,污水处理厂污泥可被用于陶瓷等建筑材料的生产;将污泥以一定配比量与生产原料掺杂后,按相应的工艺烧制得到的瓷砖能满足制品的指标要求,这一成果可望为污泥在建筑材料方面的应用提供一定的理论依据.     

Cloning, construction of prokaryotic expression vector and expression ofEscherichia coli cytosine deaminase gene

Cytosine deaminase gene ofEscherichia coli strain H-30 was cloned, and its initiation codon of ‘GTG’ was mutated to ‘ATG’ by PCR. Prokaryotic recombinant expression vector pBV220-CD was constructed. Clone with high enzyme activity were selected by detecting their specific activity of cytosine deaminase. 5-FC(5-FC, 5-fluorocytosine) could induce the lethal toxicity to cells containing active CD gene. DNA sequence analysis indicated that there were 16 altered bases and 5 of them resulted in the alteration of amino acids in predicted peptide by comparing DNA sequence of the clone H-30-CD-11 with high enzyme activity with CD gene reported in Gene Bank.     

Genetic insight of the H5N1 hemagglutinin cleavage site

The cleavability of the hemagglutinin (HA) plays a major role in virulence of avian influenza viruses. Detailed analyses of the cleavage sequences and their evolution would give insights into the high pathogenicity of the H5N1 virus. HA segments were visually identifiable in the cellular automata (CA) image, and a feature gene segment (FGS) was only found in H5N1 rather than any other subtype. This FGS is a 30-bp gene segment mainly consisting of ‘A’ and ‘G’. When translated into amino acids the FGS converted into a sequence of mainly basic amino acids with positive charges. This feature amino acid segment (FAAS) was located in the cleavage site loop of HA which was potentially cleavable by various proteases. The 3D structure of H5N1 HA was reconstructed using homology modelling. It was found that the cleavage site loop was well exposed to potential proteases. The molecular surfaces were reconstructed to study how mutation and deletion of some amino acids in the FAAS affected the charge distribution. It was found that some mutations had severely changed the landscape of the charge dis- tribution. Statistical analyses of FAAS were made with respect to when and where the H5N1 viruses were found. In 2005, there were less un-mutated FAAS than the other years according to temporal evolution, and more mutated FAAS appeared in China than other regions according to geographic dis- tribution. These results are helpful for exploring the evolution of virus high pathogenicity.     

三维DNA自组装在多维背包问题中的应用研究

利用DNA自组装执行计算的思想已从实验上被证明了其可行性．已有多种理论模型被提出用以解决各种NP问题．基于DNA Tile自组装模型理论在二维下的扩展,本文设计了可以实现这一算法的三维DNA Tile组装系统,提出了一种用于解决多维背包问题的三维DNA自组装模型．该模型可以非确定性的输出可行性解决方案．分析表明系统可以在线性组装步骤内完成计算,所需的Tile种类数与问题维数无关．为探索三维DNA自组装的计算能力进行了一次有意义的尝试．