Brownian dynamics simulation of knot diffusion along a stretched DNA molecule

Manipulation of individual DNA molecules by optical tweezers has made it possible to tie these molecules into knots. After stretching the DNA molecules the knots become highly localized. In their recent study, Quake and co-authors investigated diffusion of such knots along stretched DNA molecules. We used these data to test the accuracy of a Brownian dynamics simulation of DNA bending motion. We simulated stretched DNA molecules with knots 3(1), 4(1), and 7(1), and determined their diffusion coefficients. Comparison of the simulated and experimental results shows that Brownian dynamics simulation is capable of predicting the rates of large-scale DNA rearrangements within a factor of 2.     

Construction of intragenic synthetic riboswitches for detection of a small molecule

Bacterial sensors, based on ligand-mediated genetic control systems, are promising for on-site chemical detection because sensing targets and generating signals do not require costly instrumentation. Here, we have constructed intragenic synthetic riboswitches without relying on high-throughput screening and demonstrated that the riboswitches can be harnessed to develop bacterial sensors displaying readily visible reporter signals in response to theophylline. In vivo imaging using the riboswitch showed target-specific changes in the expression of a green fluorescence protein reporter, which was visible even to the naked eye.     

Highly efficient single molecule detection in microstructures

For DNA single molecule sequencing, the complete detection of all dye-labeled monomers which are cleaved off during the sequencing reaction is an essential requirement. In this work we address the feasibility of single molecule detection in microstructures with a confocal multi element set-up. We present statistical data on single molecule recognition and explain a refined data evaluation technique for single molecule burst analysis. From these data the signal-to-noise ratio in microstructures is evaluated as well as the overall detection efficiency. So far, detection efficiencies of single molecule events of up to 60% have been shown in microstructures.     

Gene expression analysis using single molecule detection

Recent developments of single molecule detection techniques and in particular the introduction of fluorescence correlation spectroscopy (FCS) led to a number of important applications in biological research. We present a unique approach for the gene expression analysis using dual-color cross-correlation. The expression assay is based on gene-specific hybridization of two dye-labeled DNA probes to a selected target gene. The counting of the dual-labeled molecules within the solution allows the quantification of the expressed gene copies in absolute numbers. As detection and analysis by FCS can be performed at the level of single molecules, there is no need for any type of amplification. We describe the gene expression assay and present data demonstrating the capacity of this novel technology. In order to prove the gene specificity, we performed experiments with gene-depleted total cDNA. The biological application was demonstrated by quantifying selected high, medium and low abundant genes in cDNA prepared from HL-60 cells.     

Rapid DNA mapping by fluorescent single molecule detection

DNA mapping is an important analytical tool in genomic sequencing, medical diagnostics and pathogen identification. Here we report an optical DNA mapping strategy based on direct imaging of individual DNA molecules and localization of multiple sequence motifs on the molecules. Individual genomic DNA molecules were labeled with fluorescent dyes at specific sequence motifs by the action of nicking endonuclease followed by the incorporation of dye terminators with DNA polymerase. The labeled DNA molecules were then stretched into linear form on a modified glass surface and imaged using total internal reflection fluorescence (TIRF) microscopy. By determining the positions of the fluorescent labels with respect to the DNA backbone, the distribution of the sequence motif recognized by the nicking endonuclease can be established with good accuracy, in a manner similar to reading a barcode. With this approach, we constructed a specific sequence motif map of lambda-DNA. We further demonstrated the capability of this approach to rapidly type a human adenovirus and several strains of human rhinovirus.     

Rapid DNA sequencing based upon single molecule detection

We are developing a laser-based technique for the rapid sequencing of 40-kb or larger fragments of DNA at a rate of 100 to 1000 bases per second. The approach relies on fluorescent labeling of the bases in a single fragment of DNA, attachment of this labeled DNA fragment to a support, movement of the supported DNA fragment into a flowing sample stream, and detection of individual fluorescently labeled bases as they are cleaved from the DNA fragment by an exonuclease. The ability to sequence large fragments of DNA will significantly reduce the amount of subcloning and the number of overlapping sequences required to assemble megabase segments of sequence information.     

Attomole DNA detection assay via rolling circle amplification and single molecule detection

A bead-based assay was developed for highly sensitive single molecule DNA detection. Rolling circle amplification (RCA), an isothermal amplification technique that creates tandem repeated sequences, was used in combination with a fluorescent complementary DNA to create dense clusters of fluorescence. These clusters, each corresponding to a single target molecule, can be detected unambiguously due to their high signal/noise ratios. The limit of detection of this assay is approximately 1 amol. This simple single molecule assay allows high detection sensitivity without the use of complex equipment.     

Stochastic processes in nano-biomachines revealed by single molecule detection

Proteins and their assemblies are in the size of nanometers and are exposed to thermal disturbances. Many molecular processes in these nano-biomachines are stochastic, reflecting the fact that the input energy level is comparable to that of thermal energy. These stochastic properties have been revealed by recently developed single molecule detection techniques. The movement of molecular motors, myosin, and kinesin, has been suggested to be thermally driven. Random thermal movement is biased using the energy of the ATP hydrolysis. Thus, the molecular motors may harness thermal energy. This unique mechanism may be important in understanding the operation of the biosystems.     

Bioelectrocatalytic application of titania nanotube array for molecule detection

A bioelectrocatalysis system based on titania nanotube electrode has been developed for the quantitative detection application. Highly ordered titania nanotube array with inner diameter of 60 nm and total length of 540 nm was formed by anodizing titanium foils. The functionalization modification was achieved by embedding glucose oxidases inside tubule channels and electropolymerizing pyrrole for interfacial immobilization. Morphology and microstructure characterization, electrochemical properties and bioelectrocatalytic reactivities of this composite were fully investigated. The direct detection of hydrogen peroxide by electrocatalytic reduction reaction was fulfilled on pure titania nanotube array with a detection limit up to 2.0 × 10⁻⁴ mM. A biosensor based on the glucose oxidase–titania/titanium electrode was constructed for amperometric detection and quantitative determination of glucose in a phosphate buffer solution (pH 6.8) under a potentiostatic condition (−0.4 V versus SCE). The resulting glucose biosensor showed an excellent performance with a response time below 5.6 s and a detection limit of 2.0 × 10⁻³ mM. The corresponding detection sensitivity was 45.5 μA mM⁻¹ cm⁻². A good operational reliability was also achieved with relative standard deviations below 3.0%. This novel biosensor exhibited quite high response sensitivity and low detection limit for potential applications.     

Targeted single molecule mutation detection with massively parallel sequencing

Next-generation sequencing (NGS) technologies have transformed genomic research and have the potential to revolutionize clinical medicine. However, the background error rates of sequencing instruments and limitations in targeted read coverage have precluded the detection of rare DNA sequence variants by NGS. Here we describe a method, termed CypherSeq, which combines double-stranded barcoding error correction and rolling circle amplification (RCA)-based target enrichment to vastly improve NGS-based rare variant detection. The CypherSeq methodology involves the ligation of sample DNA into circular vectors, which contain double-stranded barcodes for computational error correction and adapters for library preparation and sequencing. CypherSeq is capable of detecting rare mutations genome-wide as well as those within specific target genes via RCA-based enrichment. We demonstrate that CypherSeq is capable of correcting errors incurred during library preparation and sequencing to reproducibly detect mutations down to a frequency of 2.4 × 10⁻⁷ per base pair, and report the frequency and spectra of spontaneous and ethyl methanesulfonate-induced mutations across the Saccharomycescerevisiae genome.     

多信道脑部磁刺激仪的磁场有限元仿真

利用外部的交变磁场,可以对大脑神经系统进行无创刺激.用有限元分析软件--ANSYS对多信道脑部磁刺激仪在不同工作模式下产生的磁场进行了模拟,并将其与实验测量值进行了比较.结果表明,两者之间的误差小于6%,ANSYS能有效模拟多信道磁刺激仪所产生的磁场.通过对仿真结果进行分析得出：改变多信道磁刺激仪工作线圈的位置,可以调整所产生磁场的位置及形状;增加刺激靶位置邻近的工作线圈个数,可以有效改善磁刺激的深度.     

Biogenic magnetite as a basis for magnetic field detection in animals

Bacteria, sharks, honey bees, and homing pigeons as well as other organisms seem to detect the direction of the earth's magnetic field. Indirect but reproducible evidence suggests that the bees and birds can also respond to very minute changes in its intensity. The mechanisms behind this sensitivity are not known. Naturally magnetic, biologically precipitated magnetite (Fe₃O₄) has been found in chitons, magnetotactic bacteria, honey bees, homing pigeons, and dolphins. Its mineralization in localized areas may be associated with the ability of these animals to respond to the direction and intensity of the earth's magnetic field. The presence of large numbers (～10⁸) of superparamagnetic magnetite crystals in honey bees and similar numbers of single-domain magnetite grains in pigeons suggests that there may be at least two basic types of ferrimagnetic magnetoreceptive organelles. Theoretical calculations show that ferrimagnetic organs using either type of grain when integrated by the nervous system are capable of accounting for even the most extreme magnetic field sensitivities reported. Indirect evidence suggests that organic magnetite may be a common biological component, and may account for the results of numerous high field and electromagnetic experiments on animals.     

Synthesis and simulation of a two-level magnetic control system for tokamak-reactor plasma

Synthesis and simulation of a hierarchical (two-level) magnetic system for controlling a tokamakreactor plasma throughout the entire divertor discharge stage, including the plasma current ramp-up phase, are carried out. The plasma vertical velocity is stabilized about zero by using a proportional controller in a scalar control loop. The gain of the controller—the coefficient that ensures the required stability margins—is found by using a second-order linear model constructed by solving the identification problem on the basis of numerical experiments carried out with the DINA plasmophysical computer code. The internal cascade (the lower level of the system) for tracking the scenario currents in the poloidal magnetic field coils is synthesized by using the complete dynamic channel decoupling method. The external cascade (the upper level of the system) for tracking the plasma current and shape is synthesized by using the method of pseudoseparation of the control channels and the multidimensional diagonal proportional-integral controller, with proportional, integrating, and double integrating units connected in parallel in each channel. In the hierarchical control system, the lower level (the internal cascade) is subordinated to the upper level (the external cascade). The external cascade acts on the internal one by the signals that set the required currents in the coils of the central solenoid and of the poloidal magnetic field in order to ensure the required plasma current and shape in accordance with the output signals from the plant, which are transmitted through the vector feedback channel. The lower level is aimed exclusively at tracking the reference inputs by tracking the currents in the control coils. An operating mode of the system under the conditions of current saturation in the control coils is proposed and implemented. Results are presented from numerical simulations of the two-level (cascade) control system for reference scenario no. 2 of the ITER database (www.iter.org) with the DINA nonlinear code.     

Cy3-3-acylcholine: a fluorescent analogue of acetylcholine for single molecule detection

We synthesized a novel fluorescent analogue of acetylcholine, Cy3-3-acylcholine. The molecular weight of the products agreed with structural predictions. Discrete intensity changes of fluorescent spots due to a single ligand binding/unbinding to nAChR were visualized by TIRF microscopy. The agonist effect of the Cy3-3-acylcholine on nicotinic acetylcholine receptor (nAChR) was confirmed electrophysiologically. This newly synthesized fluorescent analogue will enable us to conduct more elaborate studies on single channel interaction processes between nAChR and ligands.     

A novel real-time ultrasonic method for prion protein detection using plasminogen as a capture molecule

Background  

High resolution ultrasonography (HR-US) can monitor the molecular changes and biochemical interactions between proteins in real-time. The aim of this study was to use HR-US to characterize the real-time interactions between plasminogen coated beads and PrP^Sc and to determine if this approach could be applied to the identification of animals affected by prion diseases. Plasminogen, immobilized to beads, was used as a capturing tool for PrP^Sc in brain homogenates from scrapie affected sheep and the binding reaction was monitored in real-time in an ultrasonic cell.