全基因组测序技术研究及其在木本植物中的应用

基因组序列是开展遗传研究重要的信息基础,随着测序技术飞速发展至第3代长片段测序方法,测序读长历经从几十到数万个碱基的提升,对进一步提升基因组组装的完整度以及准确性提供了极大的裨益。现已完成了大量植物种全基因组测序工作,其中木本植物有40多个,还有更多树种的全基因组测序正在进行之中。针对各类测序技术的基因组组装及后续分析,研究人员也开发了大量的生物信息学工具。笔者从测序技术、基因组装技术和全基因组测序生物信息学分析等方面,罗列了目前已完成全基因组测序的木本植物,介绍了全基因组测序技术的发展与应用,以及适用于第3代数据基因组组装的生物学分析软件,为林木基因组研究者提供一定的借鉴。     

Nanopore-based sensing devices and applications to genome sequencing: a brief history and the missing pieces

A nanopore on an impermeable membrane, which separates two chambers containing electrolytic solu- tion, can be used as a nanometre-sized Coulter counter for single-molecule biological sensing. With an applied poten- tial, charged molecules are electrically dragged through the pore, and the analytical information is sequentially read out from the current blockades. Nucleic acid, which is an elec- trically charged polymer, is an ideal analyte for nanopore analysis and nanopore sequencing. With the advantages of high-speed, label-free and single-molecule resolution, a nanopore sequencer is considered to be the most promising candidate for the third-generation DNA sequencing. In this review, a brief history of nanopore sequencing to date is summarized and discussed along with future prospects. Although successfully demonstrated for known viral gen- ome sequences, the nanopore sequencing technique still requires missing pieces like improved accuracy, automation and throughput for clinical diagnosis-level applications.     

The diploid genome sequence of an Asian individual

Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics.     

A high-performance brain-computer interface

Recent studies have demonstrated that monkeys and humans can use signals from the brain to guide computer cursors. Brain-computer interfaces (BCIs) may one day assist patients suffering from neurological injury or disease, but relatively low system performance remains a major obstacle. In fact, the speed and accuracy with which keys can be selected using BCIs is still far lower than for systems relying on eye movements. This is true whether BCIs use recordings from populations of individual neurons using invasive electrode techniques or electroencephalogram recordings using less- or non-invasive techniques. Here we present the design and demonstration, using electrode arrays implanted in monkey dorsal premotor cortex, of a manyfold higher performance BCI than previously reported. These results indicate that a fast and accurate key selection system, capable of operating with a range of keyboard sizes, is possible (up to 6.5 bits per second, or approximately 15 words per minute, with 96 electrodes). The highest information throughput is achieved with unprecedentedly brief neural recordings, even as recording quality degrades over time. These performance results and their implications for system design should substantially increase the clinical viability of BCIs in humans.     

Retarding and manipulating of DNA molecules translocation through nanopores

Nanopores are emerging sensitive sensors that can detect and analyze single charged molecule. Nanopores present a promising approach for sequencing human gen- ome below US$1,000 because of its superior performance, such as high throughput and low cost. However, a dominant bottleneck, that is, the high translocation speed of DNA molecules, has to be overcome. This property decreases accuracy of nanopore sensors to the single-base level. In this review, we mainly introduce the recent research works of retarding and manipulating of DNA motion through nanopores by actively control of three forces, which are the driving force, interaction force between nanopore and molecule, and exterior drag force. Lastly, conclusion and further outlook are presented pore-based DNA sequencing on future directions of nano- technology.     

基于组合模型的厦门港集装箱吞吐量预测

为预测厦门港未来集装箱吞吐量,运用灰色Verhulst与马尔科夫组合模型建立厦门港集装箱吞吐量的预测模型,得出厦门港2018—2022年的集装箱吞吐量数据。研究结果表明,组合模型将平均绝对误差由3.74%降低至1.65%,预测精度为一级。预测结果具有较高的可信度,可为厦门港的集装箱未来发展规划提供参考依据。     

Hard-tip, soft-spring lithography

Nanofabrication strategies are becoming increasingly expensive and equipment-intensive, and consequently less accessible to researchers. As an alternative, scanning probe lithography has become a popular means of preparing nanoscale structures, in part owing to its relatively low cost and high resolution, and a registration accuracy that exceeds most existing technologies. However, increasing the throughput of cantilever-based scanning probe systems while maintaining their resolution and registration advantages has from the outset been a significant challenge. Even with impressive recent advances in cantilever array design, such arrays tend to be highly specialized for a given application, expensive, and often difficult to implement. It is therefore difficult to imagine commercially viable production methods based on scanning probe systems that rely on conventional cantilevers. Here we describe a low-cost and scalable cantilever-free tip-based nanopatterning method that uses an array of hard silicon tips mounted onto an elastomeric backing. This method-which we term hard-tip, soft-spring lithography-overcomes the throughput problems of cantilever-based scanning probe systems and the resolution limits imposed by the use of elastomeric stamps and tips: it is capable of delivering materials or energy to a surface to create arbitrary patterns of features with sub-50-nm resolution over centimetre-scale areas. We argue that hard-tip, soft-spring lithography is a versatile nanolithography strategy that should be widely adopted by academic and industrial researchers for rapid prototyping applications.     

一种优化的认知无线电网络资源协同分配算法

在目前的认知无线电研究中,多用户OFDMA系统中如何实现子载波和功率的合理分配是研究的重点之一.针对认知无线电资源分配过程中出现的多认知用户资源分配不公平的问题,研究了认知无线电网络中授权用户占用子载带时,认知用户的吞吐量受限制的问题,提出了一种基于underlay频谱共享模式下的OFDMA认知无线电网络功率与子载带协同分配优化算法.该算法利用干扰门限的设置,使用原始感知信息(RSI)和信道状态信息(CSI)进行功率与子载波分配,然后分别进行功率控制和用户选择的计算,找到最优化传输功率与每个子载带最优使用用户,在保证授权用户免受有害干扰的前提下,使授权用户存在时,也可共享频谱传输,确保了系统的稳定性,提高了网络吞吐量.理论分析与仿真结果表明,相比传统的功率与子载波联合分配算法,该算法可以提高系统的平均加权吞吐量.     

An integrated semiconductor device enabling non-optical genome sequencing

The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.     

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells

Recent advances in whole-genome sequencing have brought the vision of personal genomics and genomic medicine closer to reality. However, current methods lack clinical accuracy and the ability to describe the context (haplotypes) in which genome variants co-occur in a cost-effective manner. Here we describe a low-cost DNA sequencing and haplotyping process, long fragment read (LFR) technology, which is similar to sequencing long single DNA molecules without cloning or separation of metaphase chromosomes. In this study, ten LFR libraries were made using only ～100?picograms of human DNA per sample. Up to 97% of the heterozygous single nucleotide variants were assembled into long haplotype contigs. Removal of false positive single nucleotide variants not phased by multiple LFR haplotypes resulted in a final genome error rate of 1 in 10?megabases. Cost-effective and accurate genome sequencing and haplotyping from 10-20 human cells, as demonstrated here, will enable comprehensive genetic studies and diverse clinical applications.     

Simulation of ChIP-Seq based on extra-sonication of IPed DNA fragments

The combination of chromatin immunoprecipitation with sequencing (ChIP-Seq) is an effective method for obtaining an in vivo genome-wide profile of the interaction of a protein with DNA. With the dramatic development of high-throughput short sequencing technologies, several new algorithms have been developed to process ChIP-Seq. However, the reported analytical tools for ChIP-Seq based on size selection of immunoprecipitated (IPed) DNA fragments are mainly adopted on the Solexa system. As a sequencer with the highest throughput, few studies of ChIP-Seq based on SOLiD system have been reported. The main difference of the SOLiD and Solexa systems exists in the length of DNA fragments during preparing sequencing libraries. The SOLiD system has relatively short DNA fragments if it processes a further sonication of IPed DNA fragments in order to meet the length requirement of DNA frag-ments for emulsion-PCR (ePCR). This work aims to investigate the influences of DNA fragment length on data analysis from ChIP-Seq. Previous studies show that typical bimodal peaks can be observed in Solexa ChIP-Seq data, but based on the analysis of the real SOLiD ChIP-Seq data in this study, we found that there were no double peaks with apparent reads shift in a local enriched region and the local reads distribution of peaks were tested by normal distribution. Using real and simulated ChIP-Seq data, three main ChIP-Seq algorithms (CisGenome, SISSRs and MACS) have been investigated. We found that algorithms developed for processing ChIP-Seq data generated from Solexa library protocol, cannot efficiently capture the feature of the ChIP-Seq data from SOLiD library. Misuse of those analytical tools would be a possible reason for failure of ChIP-Seq on the SOLiD system. Therefore, a new ChIP-Seq analytical strategy for an extra-sonication of IPed DNA fragments needs to be developed.     

基于视觉注意机制的眼底图像视盘快速定位与分割

视盘定位与分割对利用眼底图像进行眼科计算机辅助诊断十分重要。视觉注意机制模拟人类视觉系统从而能在复杂场景中快速定位目标。利用视盘在眼底图像中视觉显著度高这一特性,提出基于视觉注意模型实现视盘的快速定位并分割的算法。算法首先对不同眼底图像进行归一化,接着采用高斯金字塔提取图像不同尺度的颜色、亮度和方向特征图(feature map),进一步整合得到显著性图(saliency map),在显著性图中提取FOA(focus of attention)从而定位视盘。接着在视盘定位区域采用统计排序滤波器(rank-filter)抹除血管,在极坐标中采用亚像素提取图像边缘,实现视盘分割。采用国际Messidor数据库来验证算法的性能,定位精度为95%,运行时长为0.213 s,与其他算法相比,算法具有准确性高和实用性强等特点,具有良好的应用潜力。     

基于大规模天线阵的多长度导频机制研究

在基于时分双工的大规模天线阵系统中,导频污染是阻碍实现高频谱效率、高吞吐率的最主要瓶颈之一.传统的单长度导频机制使得用户受到所有相邻小区非正交导频序列用户的干扰,进而加重导频污染问题.因此,提出一种新的多长度导频机制(MLPS),使得目标小区各用户的导频长度可以更加接近其最优导频长度,从而减弱导频污染对系统的影响进而提升吞吐率的目的.首先,利用Monte-Carlo仿真观察出系统内各用户最优导频长度的分布情况.然后,基于多长度导频机制带来的不同长度导频间干扰与导频-数据干扰,给出一种可行的导频设计准则和两种时分双工时序策略,分别用于消除以上两类干扰.实验结果表明,相比于传统单长度导频机制,多长度导频机制在上行、下行吞吐率上分别有18%与20%的提升.     

Characterization of the common genetic defect in humans deficient in debrisoquine metabolism

In population studies of individuals given the antihypertensive drug debrisoquine, two distinct phenotypes have been described: extensive metabolizers excrete 10-200 times more of the urinary metabolite 4-hydroxydebrisoquine than poor metabolizers. In family studies the poor-metabolizer phenotype behaves as an autosomal recessive trait with an incidence between 5% and 10% in the white population of Europe and North America, and extends to the deficient metabolism of more than 20 commonly prescribed drugs. Clinical studies have shown that such individuals are at high risk for the development of adverse side effects from these and probably many other drugs. Here we show that poor metabolizers have negligible amounts of the cytochrome P450 enzyme P450db1. We have cloned the human P450db1 complementary DNA and expressed it in mammalian cell culture. Furthermore, by directly cloning and sequencing cDNAs from several poor-metabolizer livers, we have identified three variant messenger RNAs that are products of mutant genes producing incorrectly spliced db1 pre-mRNA, providing a molecular explanation for one of man's most commonly defective genes (frequency of mutant alleles 35-43%).     

直角坐标采样时单一基准径向圆跳动误差的最小二乘评定法与仿真分析

用传统的测量方法不能得到单一基准径向圆跳动误差的准确值·根据单一基准径向圆跳动误差的定义,建立了在直角坐标采样时该项误差的最小二乘评定法数学模型,并用计算机进行仿真分析·结果表明,所建立的数学模型具有编程简单,计算精度较高等特点·所建立的数学模型为研制形位误差虚拟测量系统提供了理论基础·     

DataMatrix码的嵌入式识别算法

为从复杂的实际应用环境中分割DataMatrix 码图像, 提高解码准确率与速度, 采用互相关图像匹配算法进行条码的初定位, 并利用“金字塔分层冶思想降低其运算量。利用改进后的Hough 变换对定位后的图像进行“L冶边界线段坐标的精确测定, 从而完成解码前的准备工作。整个算法及解码流程在ARM9 内核的S3C2440 芯
片搭载Linux 系统下进行, 结果显示, 采用该算法流程的扫码终端能使解码精度从85% 提升至近100%, 并且可将平均解码时间由2. 3 s 缩减在500 ms 以内, 可满足实际解码需要。     

Biomechanics: independent evolution of running in vampire bats

Most tetrapods have retained terrestrial locomotion since it evolved in the Palaeozoic era, but bats have become so specialized for flight that they have almost lost the ability to manoeuvre on land at all. Vampire bats, which sneak up on their prey along the ground, are an important exception. Here we show that common vampire bats can also run by using a unique bounding gait, in which the forelimbs instead of the hindlimbs are recruited for force production as the wings are much more powerful than the legs. This ability to run seems to have evolved independently within the bat lineage.     

反算管道传热系数影响因素的敏感性分析

采用系统单因素敏感性分析方法,结合苏霍夫温降公式和现场测试数据,对反算管道传热系数K的进出站温度、管道周围介质温度、含水率和输量,五个因素进行敏感性分析。研究表明:进出站温度对反算管道总传热系数的影响最敏感,其次为含水率和输量,管道周围介质温度最不敏感;因此应尽量减小现场采集进出站温度、含水率和输量的误差,以提高K反算的精度。     

双概率检测无线传感器网络MAC协议分析

提出了一种新的随机多址无线传感器网络MAC协议,通过划分分组发送时间为1+a,采用1时间内p1概率检测与a时间内p2概率检测控制策略,对多通道随机多址无线传感器网络MAC协议进行了理论分析.在可控性增加的基础上,得出了系统的吞吐量、多业务优先级的吞吐量和信息分组发送时延等重要系统参数.此外,还通过传感器网络实验和计算机仿真实验验证了理论分析的正确性.新的控制协议,其节点接入控制更加精细,更适于无线传感器网络的MAC接入控制.