Applying frequency chaos game representation with perceptual image hashing to gene sequence phylogenetic analyses

As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can store rich genetic information into FCGR graphics. To each FCGR image, we construct its perceptual image hashing (PIH) matrix using the bicubic interpolation zooming. The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. The performance benchmark rankings demonstrate the effectiveness of the FCGR-PIH algorithm and its potential for large-scale genome sequence analysis.

Microfluidic separation of viruses from blood cells based on intrinsic transport processes

Clinical analysis of acute viral infection in blood requires the separation of viral particles from blood cells, since the cytoplasmic enzyme inhibits the subsequent viral detection. To facilitate this procedure in settings without access to a centrifuge, we present a microfluidic device to continuously purify bionanoparticles from cells based on their different intrinsic movements on the microscale. In this device, a biological sample is layered on top of a physiological buffer, and both fluids are transported horizontally at the same flow rate in a straight channel under laminar flow. While the micron sized particles such as cells sediment to the bottom layer with a predictable terminal velocity, the nanoparticles move vertically by diffusion. As their vertical travel distances have a different dependence on time, the micro- and nanoparticles can preferentially reside in the bottom and top layers respectively after certain residence time, yielding purified viruses. We first performed numerical analysis to predicate the particle separation and then tested the theory using suspensions of synthetic particles and biological samples. The experimental results using dilute synthetic particles closely matched the numerical analysis of a two layer flow system containing different sized particles. Similar purification was achieved using diluted blood spiked with human immunodeficiency virus. However, viral purification in whole blood is compromised due to extensive bioparticle collisions. With the parallelization and automation potential offered by microfluidics, this device has the potential to function as an upstream sample preparation module to continuously provide cell depleted bio-nanoparticles for downstream analysis.

Concentration and purification of human immunodeficiency virus type 1 virions by microfluidic separation of superparamagnetic nanoparticles

The low concentration and complex sample matrix of many clinical and environmental viral samples presents a significant challenge in the development of low cost, point-of-care viral assays. To address this problem, we investigated the use of a microfluidic passive magnetic separator combined with on-chip mixer to both purify and concentrate whole-particle human immunodeficiency virus type 1 (HIV-1) virions. Virus-containing plasma samples are first mixed to allow specific binding of the viral particles with antibody-conjugated superparamagnetic nanoparticles, and several passive mixer geometries were assessed for their mixing efficiencies. The virus-nanoparticle complexes are then separated from the plasma in a novel magnetic separation chamber, where packed micrometer-sized ferromagnetic particles serve as high magnetic gradient concentrators for an externally applied magnetic field. Thereafter, a viral lysis buffer was flowed through the chip and the released HIV proteins were assayed off-chip. Viral protein extraction efficiencies of 62% and 45% were achieved at 10 and 30 muL/min throughputs, respectively. More importantly, an 80-fold concentration was observed for an initial sample volume of 1 mL and a 44-fold concentration for an initial sample volume of 0.5 mL. The system is broadly applicable to microscale sample preparation of any viral sample and can be used for nucleic acid extraction as well as 40-80-fold enrichment of target viruses.