Bioautomation

Volume 19, Issue 3
Bioinformatics
In silico Analysis of the Functional and Structural Impacts of Non-synonymous Single Nucleotide Polymorphisms in the Human Paraxonase 1 Gene	275-286
Sudip Paul, Md. Solayman, Moumoni Saha, Md. Sabir Hossain [ +/- abstract ][ full text ]
Computational approaches could help in identifying deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in a disease related gene which is a difficult and laborious task through laboratory experiments. In the present study, we analyzed the impacts of nsSNPs on structure and function of Paraxonase 1 (PON1) using different bioinformatics tools. The human PON1 protein sequence and its corresponding gene's SNP information were collected from UniProt and dbSNP databases, respectively. We utilized SIFT, Polyphen, I-Mutant 2.0, MutPred, SNP and GO, PhD-SNP and PANTHER tools in order to examine the total 39 nsSNPs occurring in the PON1 coding region. We filtered the most pathological mutations by combining the scores of the aforementioned servers and found 8 SNPs (G344C, S302L, W281C, D279Y, H134R, F120S, L90P, C42R) as deleterious and disease causing. The PDB structure of PON1 protein was obtained from RCSB Protein Data Bank (PDB ID: 1V04). The deleterious SNPs in native PON1 were introduced using Swiss-PDB Viewer package and changes in free energy were observed for six out of eight mutant structures. Two SNPs, S302L (substitution of serine to leucine at 302 position in amino acid sequence) and L90P (substitution of leucine to proline at 90 position in amino acid sequence) caused the highest energy increase amongst all. The findings implicate that these nsSNPs would be analyzed further in detail to enumerate their possible association with the protein deteriorating and disease causal potentialities.
Genome-wide Identification, Phylogenetic and Expression Analysis of ABC1K Gene Family in Tomato (Solanum lycopersicum L.)	287-302
Tao Li, Xin-xin Shao, Zhi-liang Li, Xiao-wang Xu, Ying Li, Zhen-xing Li [ +/- abstract ][ full text ]
Activity of bc1 complex (ABC1K) is a protein kinase commonly found in eukaryotes and prokaryotes. It plays an important role in various developmental and physiological processes, especially critical for plant response to diverse biotic and abiotic stresses. In this study, a genome analysis was carried out and 18 genes of ABC1K family were identified in tomato. Phylogenetic results showed that these members could be classified into three groups ‒ ancestral clade, mitochondrial clade and photosynthetic-specific clade, with several subgroups based on subcellular location prediction by WoLF PSORT and all the SlABC1K proteins contained an ABC1K conserved kinase motifs-VAIK (VAVK, VAMK) and DFG (DEG). Conserved motifs analyzed by MEME program indicated that all ABC1K protein contains motif 2, 5, 6 and 8. Predictably, the SlABC1K proteins were localized in chloroplasts or mitochondria; in our analysis of expression patterns, SlABC1K genes could be detected in all tomato organs, and eight genes were specifically expressed in tomato leaf, which implied that the SlABC1Ks might be involved in energy metabolism in tomato. The expression of several genes was significantly changed under abiotic stress, implying their probability of performing various roles in abiotic stresses (NaCl, high temperature, cold, abscisic acid and salicylic acid).
Modeling the Process of Color Image Recognition Using ART2 Neural Network	303-310
Todor Petkov, Sotir Sotirov, Maciej Krawczak [ +/- abstract ][ full text ]
This paper thoroughly describes the use of unsupervised adaptive resonance theory ART2 neural network for the purposes of image color recognition of x-ray images and images taken by nuclear magnetic resonance. In order to train the network, the pixel values of RGB colors are regarded as learning vectors with three values, one for red, one for green and one for blue were used. At the end the trained network was tested by the values of pictures and determines the design, or how to visualize the converted picture. As a result we had the same pictures with colors according to the network. Here we use the generalized net to prepare a model that describes the process of the color image recognition.
Phylogenetic Analysis of H1N1 Proteins for Understanding Its Allocation	311-324
Shruti Ambhore, Sneha Galande, Lingaraja Jena, Satish Kumar [ +/- abstract ][ full text ]
A serious Influenza pandemic infection has rapidly spread across the world since 2009 causing nearly 300,000 deaths globally within the first year of the pandemic. In 2014 and 2015, the swine flu pandemic hits again with increased rate of reported cases. H1N1, a swine influenza virus is a known causative agent of swine flu. This outbreak caused by subtype H1N1 in humans is due to transfer of swine influenza virus from pig to human. The entire Influenza A virus genome contained eight RNA segments such as Matrix protein, Hemagglutinin, Neuraminidase, Nucleocapsid protein, Polymerase PB1, Polymerase PA, Polymerase PB2 and Non-structural protein. In this study, phylogenetic analysis of protein sequences of human H1N1 viruses was carried out using MEGA 6 software to demonstrate the route map of its infection. Phylogenetic analysis of the sequences from Asian and other foreign countries, available at NCBI protein database were retrieved and analyzed. The result shows that many proteins of Indian entries were clustered within India while few with close Asian and foreign countries and very few remained non-clustered as evidenced in all sequences. The study helps understood the distribution and flow pattern of H1N1 virus across the world and Phylogenetic tools predicted the defined phyletic clusters available in that population.
Bioprocess systems
Efficient Improving the Activity and Enantioselectivity of Candida rugosa Lipase for the Resolution of Naproxen by Enzyme Immobilization on MCM-41 Mesoporous Molecular Sieve	325-334
Ying Chen, Yi Xu, Xiao-mei Wu [ +/- abstract ][ full text ]
Lipase from Candida rogusa was immobilized on MCM-41 mesoporous molecular sieves in a trapped aqueous-organic biphase system for the resolution of racemic naproxen methyl ester. It was interesting that the activity and enantioselectivity of the immobilized lipase were improved significantly relative to the free enzyme. The proportion of water (ml)/support (g) has a dramatic influence on the activity and enantioselectivity of lipase immobilized onto MCM-41 molecular sieves. It was also found that the activity of immobilized lipase was more sensitive to pH value and temperature than the free one. Higher pH value will increase the activity but decrease the enantioselectivity of the immobilized lipase. The enantioselectivity of the immobilized lipase was not altered significantly within the range of tested temperature. The immobilized lipase can be reused for at least 8 batches without significant lose of activity with the aid of methanotrophic bacteria to eliminate the methanol produced during the resolution process.
Biomedical systems
Simulation and Analysis of ACDR-oriented Vertebral Endplate Cutting Process	335-350
Heqiang Tian, Peng Yang, Jun Zhao, Chunjian Su [ +/- abstract ][ full text ]
In the artificial cervical disc replacement (ACDR), the polishing quality of fitting surface between vertebral endplate and artificial intervertebral disc has a direct relation with operation result. For this reason, an in-depth study is necessary on the vertebral endplate cutting process. This paper is intended to simulate and analyze the cutting process of vertebral endplate using numerical computation method. Firstly, a plane cutting model is established through an analysis on the cutting process to simulate the single-edge cutting process, and the temperature distribution calculation is carried out using the mean heat flux of continuous cutting. Secondly, a vertebral endplate material constitutive model is established on the basis of the endplate anatomy and mechanical property, so that some problems are analyzed about simulation algorithm, frictional contact and chip separation in the vertebral endplate cutting finite element (FE) simulation. Finally, stress distribution, cutting force, endplate deformation and residual stress and cutting temperature, as well as simulation results, are analyzed in vertebral endplate cutting process. The FE simulation may simplify vertebral endplate cutting, improve analytical precision, avoid plenty of repetitive cutting experiments, and reduce research cost greatly. Moreover, it gives full and fine description to the whole continuous, dynamic cutting process. All of this lay solid theoretical basis for an in-depth study of influence of different cutting parameters on endplate cutting as well as improvement of operation effect.
Multidimensional Analytical Study of Heart Sounds: A Review	351-376
Akash Kumar Bhoi, Karma Sonam Sherpa, Bidita Khandelwal [ +/- abstract ][ full text ]
Heart diagnosis by phonocardiography and auscultation is highly dependent on experience and there is a considerable inter-observer variation. The complex structure of the Phonocardiogram (PCG) and the variations due to cardiac contractility can generate additional difficulties for auscultation. This review paper focuses on such critical problem solving issues with a variant of analysis. However, different methods and techniques are also described for detection and analysis of PCG signal and it will certainly aid findings in novel computational tools in biosignal processing.
Change in Performance of BALB/c Mouse Pulmonary Macrophage Surface Receptor after Exercise and its Influence on Phagocytic Activity	377-384
Ming Zhang [ +/- abstract ][ full text ]
Objective: To study the effect of exercise on phagocytosis by pulmonary bronchoalveolar macrophages (BAMs). Methods: A total of 120 seven- to nine-week-old male BALB/c mice were randomly assigned into the following groups based on exercise intensity on a treadmill: control exercise (CE) group, acute moderate exercise (ME) group, and strenuous exercise group. Lung lavage was conducted to collect BAMs from the mice. Phagocytic behavior and surface receptor expression on BALB/c mouse BAMs were analyzed through fluorescence microscopy and flow cytometry. Results: In the SE group, expression levels of macrophage scavenger receptors (surface receptor [SR-A] type I/II and macrophage receptor [MARCO], complement receptor3 (CR3), and intercellular adhesion molecule 1 (ICAM-1) were upregulated; by contrast, expression level of extensive G-type immune globulin receptor (Fc Rs) was not upregulated. The promoting percentage of phagocytosis in the CE group was 100%; the highest promoting percentage of phagocytosis was 161% observed in MARCO, followed by 116% detected in CR3; the promoting percentage of phagocytosis found in SR-A type I/II and ICAM-1 increased by approximately 65%. Indeed, these scavenger receptors were involved in phagocytosis induced by macrophages. MARCO was also necessary to elicit a stimulatory effect on macrophage phagocytic activity. Conclusions: The phagocytosis of unopsonized particles was possibly mediated by MARCO expression.
Study on Compression Induced Contrast in X-ray Mammograms Using Breast Mimicking Phantoms	385-396
A. B. M. Aowlad Hossain, Min Hyoung Cho, Soo Yeol Lee [ +/- abstract ][ full text ]
X-ray mammography is commonly used to scan cancer or tumors in breast using low dose x-rays. But mammograms suffer from low contrast problem. The breast is compressed in mammography to reduce x-ray scattering effects. As tumors are stiffer than normal tissues, they undergo smaller deformation under compression. Therefore, image intensity at tumor region may change less than the background tissues. In this study, we try to find out compression induced contrast from multiple mammographic images of tumorous breast phantoms taken with different compressions. This is an extended work of our previous simulation study with experiment and more analysis. We have used FEM models for synthetic phantom and constructed a phantom using agar and n-propanol for simulation and experiment. The x-ray images of deformed phantoms have been obtained under three compression steps and a non-rigid registration technique has been applied to register these images. It is noticeably observed that the image intensity changes at tumor are less than those at surrounding which induce a detectable contrast. Addition of this compression induced contrast to the simulated and experimental images has improved their original contrast by a factor of about 1.4
A Novel Medical Image Watermarking in Three-dimensional Fourier Compressed Domain	397-408
Baoru Han, Jingbing Li, Mengxing Huang [ +/- abstract ][ full text ]
Digital watermarking is a research hotspot in the field of image security, which is protected digital image copyright. In order to ensure medical image information security, a novel medical image digital watermarking algorithm in three-dimensional Fourier compressed domain is proposed. The novel medical image digital watermarking algorithm takes advantage of three-dimensional Fourier compressed domain characteristics, Legendre chaotic neural network encryption features and robust characteristics of differences hashing, which is a robust zero-watermarking algorithm. On one hand, the original watermarking image is encrypted in order to enhance security. It makes use of Legendre chaotic neural network implementation. On the other hand, the construction of zero-watermarking adopts differences hashing in three-dimensional Fourier compressed domain. The novel watermarking algorithm does not need to select a region of interest, can solve the problem of medical image content affected. The specific implementation of the algorithm and the experimental results are given in the paper. The simulation results testify that the novel algorithm possesses a desirable robustness to common attack and geometric attack.
Bioecological systems
Comparative Research on EPS Extraction from Mechanical Dewatered Sludge with Different Methods	409-418
Weiyun Wang, Wanyu Liu, Lingyun Wang [ +/- abstract ][ full text ]
In order to find a suitable extracellular polymer substance (EPS) extraction method for mechanical dewatered sludge, four different methods including EDTA extraction, alkali extraction, acid extraction, ultrasonic extraction method have been used in extracting EPS from belt filter dewatered sludge. The contents of polysaccharide and proteins extracted from the dewatered sludge by different extraction methods are also analyzed. The results indicated that EDTA method and alkali extraction method are more suitable for dewatered sludge with more EPS content and less cell damage, while sulfuric acid extraction and ultrasonic extraction were poorer with obvious cell lysis shown by higher DNA content in extracted EPS. Contents of proteins and polysaccharide in EPS extracted from mechanical dewatered sludge, is at the contents between that in EPS extracted from activated sludge and anaerobic digestion sludge.