DNA sequencing technology based on nanopore sensors by theoretical calculations and simulations

DNA sequencing based on nanopore sensors is a promising tool for third-generation sequencing technol- ogy because of its special properties, such as revolutionized speed and low cost. With about two decades of nanopore technology development, the pioneering work has dem- onstrated the ability of nanopores to perform single-mole- cule detection and DNA sequencing. However, the microscopic mechanisms of DNA transport dynamics through nanopores remain largely unknown. Currently, DNA microscopic transport in a nanopore is difficult to characterize and several unexpected experimental obser- vations are equivocal. This limitation can be resolved using theoretical calculations and simulations. These computa- tional methods can monitor the entire dynamic process that DNA undergoes in solution at a single-atom resolution that can accurately unveil the mystery of DNA transport dynamics and predict certain unexpected phenomena. This paper mainly reports the recent applications of computa- tional and simulation methods applied to the study of DNA transport through both biological and synthetic nanopores. We hope the theoretical calculations and simulations of DNA transport through nanopores can benefit the design of DNA sequencing devices.     

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.     

An integrated current measurement system for nanopore analysis

Nanopore-based techniques have attracted increasing attention as a unique tool for single-molecule analysis. To accurately detect individual motions of each single molecule, nanopore techniques are used to develop an ultrasensitive current measurement system. This work proposes an integrated current measurement system con- taining an amplifier system and a current signal acquisition system with a high current resolution and a high temporal resolution for nanopore analysis. The exploration and achievements in instrument and signal processing endow nanopore techniques with reliability, affordability, and portability, which make a great leap toward its real applications.     

Gold nanorod translocation through a solid-state nanopore

Recently, nanopores have been used in an essential technique for detecting single molecule with high sensitivity. The initial application of nanopores to DNA and RNA sequencing has been expanded to sensing pro- teins and nanoparticles, including Bovine serum albumin, silica nanoparticles, polystyrene beads, and others. In our study, for the first time, a positively charged gold nanorod was investigated using a solid-state nanopore device. Various gold nanorods passed through the nanopore with different current blockages and duration times, providing a measurement of the nanorod diameter, length, and charge. Our findings indicate that nanopore sensing might be a new method for characterizing the size, shape, and charge of nanoparticles.     

Detection and analysis of DNA recapture through a solid-state nanopore

Motion control of a single molecule through a solid-state nanopore offers a new perspective on detecting and analyzing single biomolecules. Repeat recapture of a single DNA molecule reveals the dynamics in DNA translocation through a nanopore and may significantly increase the signal-to-noise ratio for DNA base distin- guishing. However, the transient current at the moment of voltage reversal prevents the observation of instantly recaptured molecules and invalidates the continuous DNA ping-pong control. We performed and analyzed the DNA translocation and recapture experiment in a silicon nitride solid-state nanopore. Numerical calculation of molecular motion clearly shows the recapture dynamics with different delay times. The prohibited time when the data acquisition system is saturated by the transient current is derived by equivalent circuit analysis and finite element simulation. The COMSOL simulation reveals that the membrane capacitance plays an important role in determining the electric field distribution during the charging process. As a result of the transient charging process, a non-constant driving force pulls the DNA back to nanopores faster than theoretically predicted. The observed long time constant in the transient current trace is explained by the dielectric absorption of the membrane capacitor.     

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.     

An adaptive pipelining scheme for H.264/AVC CABAC decoder

An adaptive pipelining scheme for H.264/AVC context-based adaptive binary arithmetic coding （CABAC） decoder for high definition （HD） applications is proposed to solve data hazard problems coming from the data dependencies in CABAC decoding process.An efficiency model of CABAC decoding pipeline is derived according to the analysis of a common pipeline.Based on that,several adaptive strategies are provided.The pipelining scheme with these strategies can be adaptive to different types of syntax elements （SEs） and the pipeline will not stall during decoding process when these strategies are adopted.In addition,the decoder proposed can fully support H.264/AVC high 4 ∶ 2 ∶ 2 profile and the experimental results show that the efficiency of decoder is much higher than other architectures with one engine.Taking both performance and cost into consideration,our design makes a good tradeoff compared with other work and it is sufficient for HD real-time decoding.     

Complete quantum circuit of Haar wavelet based MRA

Wavelet analysis has applications in many areas, such as signal analysis and image processing. We propose a method for generating the complete circuit of Haar wavelet based MRA by factoring butterfly matrices and conditional perfect shuffle permutation matrices. The factorization of butterfly matrices is the essential part of the design. As a result, it is the key point to obtain the circuits of I2t＋W ＋I2^n-2t-2· In this paper, we use a simple means to develop quantum circuits for this kind of matrices. Similarly, the conditional permutation matrix is implemented entirely, combined with the scheme of Fijany and Williams. The circuits and the ideas adopted in the design are simple and intelligible.     

Simultaneous estimation of genetic linkage and preferential pairing factor for a triploid population with unphased markers

Triploids,recognized to occur more frequently in natural and experimental populations of many species than previously appreciated,display important economic and biological values.Despite this,however,linkage analysis for triploids has not been well explored.We develop a statistical model for estimating and testing the linkage between molecular markers in a triploid population derived from a tetraploid and diploid parent.The model incorporates one important meiotic feature of tetraploids by which more homologous chromosomes pair with a greater likelihood than less homologous chromosomes.By implementing the EM algorithm within the maximum likelihood framework,the model provides a procedure for simultaneous estimation of the linkage and preferential pairing factor.The model accommodates the segregating patterns of pseudotest markers and intercross markers with different amounts of informativeness.The utility of the model was validated through a real data analysis and simulation studies.The model provides a statistical tool for linkage analysis in a triploid population by taking into account meiotic behavior of tetraploids.Results from the model will help to shed light on the genetic diversity and origin of a polyploid population.     

Cellular mechanism of cardiac alternans： an unresolved chicken or egg problem

T-wave alternans, a specific form of cardiac alternans, has been associated with the increased suscep- tibility to cardiac arrhythmias and sudden cardiac death （SCD）. Plenty of evidence has related cardiac alternans at the tissue level to the instability of voltage kinetics or Ca^2＋ handling dynamics at the cellular level. However, to date, none of the existing experiments could identify the exact cellular mechanism of cardiac alternans due to the bi-directional coupling between voltage kinetics and Ca^2＋ handling dynamics. Either of these systems could be the origin of alternans and the other follows as a secondary change, therefore making the cellular mechanism of alternans a difficult chicken or egg problem. In this context, theoretical analysis combined with experimental techniques provides a possibility to explore this problem. In this review, we will summarize the experimental and theoretical advances in understanding the cellular mechanism of alternans. We focus on the roles of action potential duration （APD） restitution and Ca^2＋ handling dynamics in the genesis of alternans and show how the theoretical analysis combined with experimental techniques has provided us a new insight into the cellular mechanism of alternans. We also discuss the possible reasons of increased propensity for alternans in heart failure （HF） and the new possible therapeutic targets. Finally, according to the level of electrophysiological recording techniques and theoretical strategies, we list some critical experimental or theoretical challenges which may help to determine the origin of alternans and to find more effective therapeutic tar- gets in the future.     

Statistical method for mapping QTLs for complex traits based on two backcross populations

Most important agronomic and quality traits of crops are quantitative in nature.The genetic variations in such traits are usually controlled by sets of genes called quantitative trait loci (QTLs),and the interactions between QTLs and the environment.It is crucial to understand the genetic architecture of complex traits to design efficient strategies for plant breeding.In the present study,a new experimental design and the corresponding statistical method are presented for QTL mapping.The proposed mapping population is composed of double backcross populations derived from backcrossing both homozygous parents to DH (double haploid) or RI (recombinant inbreeding) lines separately.Such an immortal mapping population allows for across-environment replications,and can be used to estimate dominance effects,epistatic effects,and QTL-environment interactions,remedying the drawbacks of a single backcross population.In this method,the mixed linear model approach is used to estimate the positions of QTLs and their various effects including the QTL additive,dominance,and epistatic effects,and QTL-environment interaction effects (QE).Monte Carlo simulations were conducted to investigate the performance of the proposed method and to assess the accuracy and efficiency of its estimations.The results showed that the proposed method could estimate the positions and the genetic effects of QTLs with high efficiency.     

First scanning Fabry-Perot interferometer developed in China

A scanning Fabry-Perot interferometer （SFPI） was first developed and deployed at the Langfang near Space Environment Field Scientific Observation Station （39.38°N, 116.65°E） of the National Space Science Center, CAS. The instrument is designed to measure the mesospheric and ther- mospheric wind velocities using the atomic oxygen 557.7-nm and 630.0-nm emissions. Data from February 28 to March 3 and February 28 to March 15 in 2011 were chosen for case study and mean value study, respectively. The errors of the meridional and zonal winds are 6.5 and 7.5 m/s at 557.7-nm and at 630.0-nm, they are 7.1 and 6.6 m/s, respectively. During the whole experiment, the instrument has performed in good condition and provided high-quality data. The mean neutral wind data were consistent with that predicted by HWM07. Good agreement has been found in between the SFPI and a neighbor Meridian Project Fabry-Perot interferometer （MP FPI）, with a corresponding coefficient （re） larger than 80 %. In general, the scanning FPI meets the design goal, and it is a useful ground-based instrument for measuring mesospheric and thermospheric winds at middle latitudes and is able to provide high-quality data for future scientific studies.     

Silica-Based Solid Phase Extraction of DNA on a Microchip

Micro total analysis systems for chemical and biological analysis have attracted much attention. However, microchips for sample preparation and especially DNA purification are still underdeveloped. This work describes a solid phase extraction chip for purifying DNA from biological samples based on the adsorption of DNA on bare silica beads prepacked in a microchannel. The chip was fabricated with polydimethylsiloxane. The silica beads were packed in the channel on the chip with a tapered microchannel to form the packed bed. Fluorescence detection was used to evaluate the DNA adsorbing efficiency of the solid phase. The polymerase chain reaction was used to evaluate the quality of the purified DNA for further use. The extraction efficiency for the DNA extraction chip is approximately 50% with a 150-nL extraction volume, Successful amplification of DNA extracted from human whole blood indicates that this method is compatible with the polymerase chain reaction.     

The Symbolic significance of the Rose in ＂A Rose for Emily＂

The short story ＂A Rose for Emily＂ draws a vivid picture of the southern descendents. It attracts readers＇ attention successfiully and makes us immersed in the whole story. And the ingenious usage of symbolism is a distinctive feature, which makes the story filled with pro- found implications. This paper intends to make a brief analysis the symbolic significance ofth erose in the short story.     

A membrane evolutionary algorithm for DNA sequence design in DNA computing

DNA sequence design has a crucial role in successful DNA computation,which has been proved to be an NP-hard(non-deterministic polynomial-time hard) problem.In this paper,a membrane evolutionary algorithm is proposed for the DNA sequence design problem.The results of computer experiments are reported,in which the new algorithm is validated and out-performs certain known evolutionary algorithms for the DNA sequence design problem.     

Prediction of a common neutralizing epitope of H5N1 avian influenza virus by in silico molecular docking

The H5N1 avian influenza virus （AIV） has widely spread in Asia, Europe and Africa, making a large amount of economic loss. Recently, our research group has screened a common neutralizing mono-clonal antibody named 8H5, which can neutralize almost all H5 subtype AIV ever isolated so far. Obviously, this monoclonal antibody would benefit for research and development of the universal AIV vac-cine and design of the drug against H5N1 AIV in high mutation rate. In this study, the homology modeling was applied to generate the 3D structure of 8H5 Fab fragment, and ＂canonical structure＂ method was used to define the specified loop conformation of CDR regions. The model was subjected to energy minimization in cvff force field with Discovery module in Insight II program. The resulting model has correct stereochemistry as gauged from the Ramachandran plot calculation and good 3D-structure compatibility as assessed by interaction energy analysis, solvent accessible surface （SAS） analysis, and Profiles-3D approach. Furthermore, the 8H5 Fab model was subjected to docking with three H5 subtype hemagglutinin （HA） structures deposited in PDB （ID No： ljsm, 2ibx and 2fk0） respectively. The result indicates that the three docked complexes share a common binding interface, but differ in binding angle related with HA structure similarity between viral subtypes. In the light of the three HA inter-faces with structural homology analysis, the common neutralizing epitope on HA recognized by 8H5 consists of 9 incontinuous amino acid residues： Asp^58, Asn^72, Glu^112, Lys^113, lie^114, Pro^118, Ser^120, Tyr^137, Tyr^252 （numbered as for ljsm sequence）. The primary purpose of the present work is to provide some insight into structure and binding details of a common neutralizing epitope of H5N1 AIV, thereby aiding in the structure-based design of universal AIV vaccines and anti-virus therapeutic drugs.     

Full-angle optical imaging of near-infrared fluorescent probes implanted in small animals

To provide a valuable experimental platform for in vivo biomedical research of small animal model with fluorescence mediated approach, we developed a whole-body near-infrared fluorescence molecular imaging system as described in this paper. This system is based on a sensitive CCD camera and has the ability to achieve 360~ full-angle source illuminations and projections capture of the targets to obtain the dense sampling by performing rotational scan. The measurement accuracy is validated from cylinder phantom experiments by the comparison between the experimental data and theoretical predictions. Finally, we also present typical in vivo images of fluorescent tube implanted into the mouse body. The results are promising and have proved the system imaging performance for macroscopic optical biomedical research.     

Research on dynamic characteristics model test scheme for middle pylon of multi pylon multi span suspension bridges

Multi-pylon multi-span suspension bridge is a new type super flexible structure system, and the rigidity design of middle pylon is one of the main difficult technical issues. Due to the requirements of longitudinal rigidity, the structural form and the corresponding foundation type of middle pylon are different from those of the ordinary steel pylon, and the complicated dynamic characteristics make the calculation quite difficult. In this article, exploration has been made in selection of similarity ratio, selection of model materials, section simulation, restriction conditions simulation, fixing of mass blocks, fabrication scheme and testing method by taking into account different construction and working conditions such as restriction conditions and working environment of a 3-pylon suspension bridge, to conduct the test experimental design of the dynamic behavior of the middle pylon, with the purpose to reveal its dynamic characteristics and make comparison and analysis with theoretical assumptions, to provide basis for anti-wind and anti-seismic design and as a reference for the design and research of 3-pylon 2-span suspension bridges in the future.