Zukang Lu

The Analysis on the Signals Denoising and Single Base Pair Resolution of DNA Sequencing

Capillary electrophoresis - Laser Induced fluorescence (CE - LIF) signals in DNA sequencing analysis are often contaminated by random noise, which has negative influence on the accuracy and detection limit of analysis. Wavelet analysis is a powerful tool for signal denoising comparing with other conventional denoising methods, but it needs more processing time in computer. Especially in some real-time embedded analysis system, it may increase hardware investment. Conventional denoising method such as Low-Pass filter, it can realize by cheap hardware, but its denoising quality is not very satisfactory. If we proper combined the low-pass and wavelet denoising method, it will enhance the denoising efficiency and lower the systems cost. In our experiment, a novel method was presented: CE - LIF signals acquired from PMT were preprocessed by Butterworth low-pass filter in hardware circuit and the wavelet denoising was executed in computer. If we properly choose the cut-off frequency and wavelet denoising method, the denoising efficiency was high and the denoising quality was satisfactory. The denoising experiment results indicate that our denoising method can enhance the signal-to-noise ratio (SNR) and meet the requirement of single base pair resolution in DNA sequencing.

Study on propagation characteristics of a high-powered multi-quantum-well (MQW) LD beam

The beam propagation properties of the high-powered Multi-Quantum-Well (MQW) laser diode (LD) are definitive elements in many application fields such as micro-processing, biomedical technique, and basic research, etc. In this study, the beam characteristics of a high-powered InGaAs/AlGaAs MQW-LD have been evaluated in both fast-axis and slow-axis. The multi-planar waveguide model and the non-paraxial second-order moment theory were used in analyses of the beam propagation features in the direction perpendicular to the active layer of a MQW-LD. The experimental results of the beam character measurement accord with those of the theoretical calculation very well for a sampled InGaAs/AlGaAs MQW-LD. The analysis approach is thought to be useful for design of the LDs and the other waveguiding optical devices.

Novel design for suspension array detection system

This paper presents a novel method for establishing a two-dimensional laminar fluidic suspension array which is analyzed by using time delay integration (TDI) CCD imaging technology in parallel. The method will make suspension array technology (SAT) bear high throughput as well as its flexibility. Basically, bioassays are conducted on the surface of fluorescent-dyed beads. With each bead set (i.e., multiple beads with the same fluorescent signature) having a slightly different fluorescent signature, probes are first attached to a particular bead set and then hybridized with labeled samples or targets. Two different kinds of encoding dyes are excited by red laser (635 nm, 20mw), their emission wave length are 660nm, 720nm, respectively. Fluorescent dye of reporter molecules was excited by green laser (532nm, 20mw), emitted at 580 nm. The liquid sample was pumped into micro-reservoir by a linear motor. As the velocity of liquid sample is so slow (10mm/s) it is easy to form a laminar fluidic field in the middle of the micro-reservoir. In the direction of laser propagation the size of reservoir is 0.1mm so the laminar liquid can be treated as a two-dimensional fluidic plane. The size of detection area depends on size of micro-sphere and CCD imaging area. The three kinds of fluorescence signals were focused by a lens and then split by mirrors. Fluorescence pass through three band-pass filters (±20nm) before collected by three TDI-CCDs respectively. With these high-quality filters the cross-talk between signals was diminished significantly. The analysis speed is about 2x103 micro-spheres per second, which is much higher than that obtained from currently cytometry method (about 102 micro-spheres to the same size micro-spheres).

Optical transfer function for an f-theta lens based confocal fluorescent microarray analyzer

Optical transfer function is widely used to evaluate the imaging performance of an optical system. Combined with confocal scanning technology, f-theta lens can increase the reading speed for microarrays greatly in guarantee of sufficient resolution and fluorescence collection efficiency, compared with micro-array analyzers that adopting mechanical scanning. In this paper, the characteristics of a confocal scanning f-theta objective lens, which was used in micro-array analyzing instrument, were analyzed by means of optical transfer function. In the whole system, laser passed through the f-theta lens, and arrived at the microarray slide where fluorophores were excited. Fluorescence emitting from the micro-array slide was collected by the same f-theta lens, and was captured by a detector. As a laser illumination system, the objective lens had a smaller stop aperture. As a fluorescence collection system, it had a bigger stop aperture. In conclusion, optical transfer function for the whole system, from source to detector, is the combination of that of the laser illumination, a coherent system, and that of the fluorescence collection system, an incoherent system. Uniformity of laser illumination at the micro-array slide was analyzed using optical transfer function during the course of scanning. The influence of aberrations on optical transfer function is given. The simulating results for above characteristics are also presented.

Infrared Spectrum Visualizing Human Acupoints and Meridian-like Structure

This study investigates the infrared radiant characteristics of human acupoints and meridian-like structure by use of infrared thermal imaging. Thirty healthy youth volunteers are studied in our experiment. We find that human acupoints and meridian-like structure can be visualized or revealed in the infrared spectrum range in some of them under natural condition. The infrared radiant tracks of meridian courses over body surface coincide or basically coincide with that of human meridians described by the traditional Chinese medicine textbook. The facts show evidence for the objective existence of acupuncture meridians structure in human body. The results suggest that infrared radiant track along human meridian courses is a normal vital and physiological phenomenon appearing in human being.

Detecting system based on framing camera for suspension array

High speed imaging technology has been applied on biomedical research for a long history. Suspension array technology is a new generation of biochip, which was widely used in fields of life science and analytical chemistry, and was developed quickly. This study present a detecting system based on framing camera for suspension array. In suspension array microspheres were used as the carrier of bio-probes and microchannels were used as analyzing platform. By pre-dyeing of fluorophores in microbeads, the addressing of microbeads was implemented by optical coden. Bio-probes attached to microbeads were distinguished by intensity of fluorescence. Suspension array was usually detected with flow cytometry serially, which was slow relatively. Then a 2D parallel measurement system based on framing camera for suspension array was established in order to increase the measurement speed. Liquid sample containing microsphere was injected into microchannel by a 100ul syringe connected by a capillary. Microspheres flowing in the microchannel form a 2D layer, which was illuminated freezingly by a pulsed Xenon lamp and imaged by a microscopy objective in parallel. The microfluidic channel was designed and fabricated, which was a rectangle microchannel of 1mm×50um in cross-section. The image was captured by CCD and transmitted into computer by frame grabber. Image was processed to distinguish microspheres extract information from the background. Thus area measurement of suspension array in microchannel was realized. Compared with flow cytometry, this technology increased analyzing rate greatly, which could be thousands of microspheres per second.

Research on the technology of fluorescence separation from exciting light for LIF detection

Laser-induced fluorescence (LIF) is widely used in biological detection system in characteristic of high sensitivity and selectivity, especially for microarray biochip readout and capillary electrophoresis detection. In these systems, fluorescence separation from background noise is necessary. In this paper, two methods of fluorescence separation were investigated. One adopts a total reflection mirror with a hole at the center; the other uses a dichroic mirror. For dichroic mirror system, fluorescence could transmit through the filter or be reflected by it. Signal to noise ratio depends on dichroic mirror transmitting spectra and reflecting spectra. For center hole mirror system, partial fluorescence loses during propagating through the center hole directly. Detected fluorescence is the part that reflected by the mirror outside the center hole. Size of the hole in the mirror must be changed in different systems. Performance of system with an f-theta lens as scanning lens for laser focus and fluorescence collecting was simulated. Collinear systems with above-mentioned two methods were set up and compared. Simulated results were verified by experiments.

Investigation of the Optical Properties of Human Meridian by Reflectance Measurement

This study investigates the light propagation along the human meridian line and non-meridian line by diffuse reflectance measurement. Laser irradiates on the acupuncture points on the meridian line and the reference points on the nonmeridian line, and the diffuse light signals are detected on the meridian line and nonmeridian line respectively. Nineteen subjects are tested in this study. The medical statistical analysis software SPSS13.0 is used to analyze the results. Our study shows that the light propagates better along the meridian line than nonmeridian line (P<0.01).

Limitation of detection of microarray analyzer based on CCD

The most successful biochip technologies today are flat microarray and suspension microarray. Usually probes are fluorescence labeled. The fluorophores are excited by laser with a special wavelength. Because the fluorescence signal is very weak, it is hard to detect. The limitation of detection (LOD) is an important index of microarray analyzer. The dependence of LOD of flat and suspension microarray analyzer based on CCD and the fluorescent intensity on characters of excitation light optical system and fluorescence collection optical system as well as the parameters of elements system has been analyzed in detail based on the system configuration. A formula of LOD and fluorescence signal intensity depending on those parameters has been established. The study analyzed system limitation of detection (LOD). Also present a formula of minimal detectable fluorescent molecule numbers as the function of each parameter of microarray analyzer based on CCD. Estimated LOD of our suspension microarray detection system is about 7.9 fluorophores/μm2 at exposure time 1s.

Novel confocal microarray scanner for fluorescence detection

A novel confocal microarray scanner was introduced, which employed a 532nm laser and a 635nm laser to excite Cy3 and Cy5 fluorophores respectively. The fluorescent signal was detected using a photomultiplier tube (PMT) sequentially. One dimension scanning of the microarray slide was performed by a telecentric objective with a moving coil optical scanner; the other dimension was scanned by a stepping motor driving the precise guidance. Experimental results show that scanning resolution of the presented microarray scanner can reach 5 microns, its dynamic range is near 4 orders of magnitude and the limit of detection is 1.12 about fluors per square micron. The cross-talk error is eliminated almost completely by its sequential scanning mode.