Bioautomation

Volume 18, Issue 4
Editorial
New Books
Bioinformatics
In silico Characterization of Retinal S-antigen and Retinol Binding Protein-3: Target against Eales' Disease	287-296
Anshul Tiwari, Monika Sharma, Sandeep Saxena, A. B. Pant, Prachi Srivastava [ +/- abstract ][ full text ]
In current study two important proteins of Eales' disease, i.e. Retinal S-antigen (RSAG) (P10523) and Retinol binding protein-3 (RBP-3) (P10745), retrieved from Swiss prot database, are analysed and characterized through in silico tools. Characterization is carried out in terms of molecular weight, atomic composition, isoelectric point, extinction coefficient, aliphatic index and instability index. Primary structure analysis of target proteins showed that most of the amino acids are hydrophobic in nature which was evident due to the high content of non-polar residues. Thermal stability, which is a notification regarding the flexibility in the structure of protein, is higher here, i.e. 88.27 for RSAG and 100.31 of RBP-3 suggesting their stability in a wide range of temperature. Secondary structure analysis of RBP-3 and RSAG reveals that RBP-3 mostly have alpha helices while RSAG have mixed secondary structures, i.e. the alpha helices, extended strands and random coils which is suggestive about the high structural conservity of protein. This evolutionary conservity makes RSAG a better target against Eales' disorder. Determination of phosphorylation as well as signal peptide cleavage sites is another integral part of in silico characterization, as these determinations confirms about the functional aspect of protein.
Comparative Modeling and Electronic Molecular Investigation for Designing Potential Inhibitor for Schizencephaly	297-304
Muhammad Aqeel, Zaheen Zakir, Seemab Amjad Fateh Khan, Sajjad Ahmad Larra [ +/- abstract ][ full text ]
Schizencephaly (SCH) is congenital brain malformation whose hallmark is the presence of one or more cleft spanning the pial surface and ependymal of one or both cerebral hemispheres associated with Homeobox protein EMX2. In current study, hybrid approach of comparative modeling and molecular docking were followed. An inhibitor (C₁₂H₁₅N₃O₂S) scrutinized from PubChem showed maximum binding affinity against EMX2. Docking studies revealed that Asn-66, Phe-71, Ala-72, Glu-73, Leu-108, Phe-109, Ala-110, Ser-111, Gln-112, Gln-113 and Tyr-127 are critical residues for receptor-ligand interaction. Comparative modeling approach coupled with docking energies and drug likeness rules illustrated that selected inhibitor protein kinase are potential inhibitor compound for targeting EMX2. This study suggests that selected inhibitor might be potent molecule based on the binding energy values and drug score. Further analysis of this inhibitor could be helpful for exploring the details of binding sites. Overall, findings of current effort may be helpful in designing the novel therapeutic targets to cure SCH.
A Double-weighted Normalization Method for Identifying Differential Expression of RNA-seq Data	305-314
Xiaohui Wu, Chuang Zhao, Yaru Su [ +/- abstract ][ full text ]
The normalization of high-throughput sequencing data from different sequencing conditions is a critical step of the entire high-throughput data analysis and processing. Normalization is important for the identification of gene structures and differentially expressed genes, which has great impact on the accuracy and reliability of downstream analysis procedures. Here, we propose a double-weighted normalization method for high-throughput sequencing data generated by RNA-seq, and present a p-value weighted method to detect differential expression from normalized data. This normalization method not only considers the overall expression level of all genes in a library, but also considers the impact of each individual gene. Experimental results show that our method can effectively normalize high-throughput data under different conditions to provide highly confident data for the downstream analysis of differential expression.
Molecular Docking Explains Atomic Interaction between Plant-originated Ligands and Oncogenic E7 Protein of High Risk Human Papillomavirus Type 16	315-324
Satish Kumar, Lingaraja Jena, Sneha Galande, Sangeeta Daf, Ashok K. Varma [ +/- abstract ][ full text ]
Cervical cancer caused by Human papillomavirus (HPV) is one of the leading causes of cancer mortality in women worldwide, particularly in the developing countries. In the last few decades, various compounds from plant origin such as Curcumin, Epigallocatechin gallate (EGCG), Jaceosidin, Resveratrol etc. have been used as anti cancer therapeutic agents. Different studies have shown these plant-originated compounds are able to suppress HPV infection. The E6 and E7 oncoproteins of high-risk HPV play a key role in HPV related cancers. In this study, we explored these ligands from plants origin against E7 oncoprotein of high risk HPV 16, which is known to inactivate tumor suppressor pRb protein. A robust homology model of HPV 16 E7 was built to foresee the interaction mechanism of E7 oncoprotein with these ligands using structure-based drug designing approach. Docking studies demonstrate the interaction of these ligands with pRb binding site of E7 protein by residues Tyr52, Asn53, Val55, Phe57, Cys59, Ser63, Thr64, Thr72, Arg77, Glu80 and Asp81 and help restoration of pRb functioning. This in silico based atomic interaction between these ligands and E7 protein may assist in validating the plant-originated ligands as effective drugs against HPV.
Biomedical systems
The Research on Friction Characteristics of Non Smooth Bionic Mesoscopic Surface	325-336
Su Chunjian, Li Ning, Xiao Linjing [ +/- abstract ][ full text ]
The application of using friction to transmit power and prevent slippage is very widely used, many animals have very strong adhesion climbing ability, and it has important theoretical significance and wide application prospect to research and the prepare bionic surface to increase transmission friction using the bionic technology. In recent years, the research of foot structure of climbing animals shows that their surface morphology has both macro and micro scale features, and only study from the macro to the micro scale surface structure can be better elucidate the mechanism of increasing-friction of climbing animal. This paper will study bionic surface structure on mesoscopic scale from micron to millimeter level, research the influence of foot structure of climbing animal under mesoscopic scale on characteristics of increasing friction using bionic technology, prepare the bionic non-smooth surface of convex or concave using bionic manufacturing technology, establish the friction model of non-smooth surface, investigate the increasing-friction mechanism of the bionic surface morphology on mesoscopic scales, reveals the influence of surface morphology, layout, size and material properties on the friction characteristics, provide the design of bionic friction surface and calculation method of friction coefficient and provide reliable theoretical basis for engineering application.
Hand Vein Recognition Based on Improved Template Matching	337-348
Jun Wang, Guoqing Wang, Ming Li, Kairui Wang, Hao Tian [ +/- abstract ][ full text ]
An improved template-construction method for hand vein recognition is presented. The accomplishment of the new algorithm involves several steps. First, we design the power-controlled multispectral vein acquisition handset to establish high-quality hand vein database. Second, we propose an improved valley-shaped enhancement operator with NiBlack algorithm to realize vein segmentation. Third, we get a basic-shaped template after dilation and erosion operation in the four neighborhoods firstly, and then we can get the final matching template combining all the shapes after the process of filling the connected region whose threshold is smaller than the one we set according to the experiment effect. Finally we design the hand vein recognition experiments using the designed template and traditional template respectively. The recognition rate of the improved template is 96.6% under the 1:1 mode and 95.75% under the 1:N mode while the recognition rate of the traditional template is 89.2% under the 1:1 mode and 88.2% under the 1:N mode.
An Information System of Human Body Composition Based on Android Client	349-360
Bing Liu, Xiaofeng Li [ +/- abstract ][ full text ]
This paper proposes an information system of human body composition based on Android client. The system consists of the Android client, the measurement unit, the Database Server, the FTP Server, the Web Server and portable storage devices. It is able to collect, restore, synchronize, and batch import and export user profile information and human body composition information. The merits of the system are that the development cycle is shortened, the cost and energy consumption of equipment are reduced, and the portability and mobility are enhanced. The system has also optimized the communication of human body composition measurement. As a result, the client and the measurement unit are robust and capable of addressing the fault and solving deficiencies in the communication process. With a more reliable system, accurate transmission of data can be guaranteed.
Analysis and Experimental Study of the Flow Characteristics in a Micro-Channel	361-376
Xiaorong Wang, Jinxin Zhang, Genzhu Jiang, Guizhong Tian, Jingjing Shan [ +/- abstract ][ full text ]
To study the flow characteristics of low-speed fluid in a micro-channel, a model including the silk gland middle section, transition section, and forepart of a silkworm silk gland was established. The flow characteristics of silk solution therein were studied, and under the same average velocity, the flow characteristics of water were investigated for comparison with those of the silk solution. Results show that under the same average velocity, the axial velocity of the water was lower than that of the silk solution; the resistance coefficient change is the same, the resistance coefficient (both in the middle section and forepart) is constant, and in the conical channel, the resistance coefficient decreases linearly. At different average velocities, the variation of the water-related parameters was consistent; the conical channel differential pressure accounted for about 1.14% of the full differential pressure, and the straight channel pressure difference was 98.6%. With increasing outlet velocity, the shear layer of the silk solution gradually thinned, and the frictional pressure gradient decreased while the flow resistance also decreased. Later the flow characteristics of water and protein in the conical channel were studied and the changing relationship of the resistance coefficient and Reynolds number was analyzed. Finally, experimental research was undertaken on a micro-channel: the data were compared to simulated values, and the error was within 6%.
ECG Database Applicable for Development and Testing of Pace Detection Algorithms	377-388
Irena Jekova, Valentin Tsibulko, Ivo Iliev [ +/- abstract ][ full text ]
This paper presents an ECG database, named 'PacedECGdb' (available at http://biomed.bas.bg/bioautomation/2014/vol_18.4/files/PacedECGdb.zip), which contains different arrhythmias generated by HKP (Heidelberger Praxisklinik) simulator, combined with artificially superimposed pacing pulses that cover the wide ranges of rising edge (from <10 µs to 100 µs) and total pulse durations (from 100 µs to 2 ms) and correspond to various pacemaker modes. It involves a total number of 1404 recordings - 780 representing 'pure' ECG with pacing pulses and 624 that comprise paced ECGs corrupted by tremor. The signals are recorded with 9.81 µV/LSB amplitude resolution at 128 kHz sampling rate in order to preserve the steep raising and trailing edges of the pace pulses. To the best of our knowledge, 'PacedECGdb' is the first publicly available paced ECG database. It could be used for development and testing of methods for pace detection in the ECG. The existence of ECGs corrupted by tremor (the only physiological noise that could compromise the methods for pacing pulses detection) is an advantage, since such signals could be applied to define the signal-to-noise level for correct operation of the algorithm, or for improvement of the noise immunity of a method that is under development. The open access of the database makes it suitable for comparative studies including different algorithms.
Bioecological systems
Comparative Toxicity of Different Crude Oils on the Cardiac Function of Marine Medaka (Oryzias melastigma) Embryo	389-396
Zhendong Zhang, Qilun Yan [ +/- abstract ][ full text ]
The acute toxic effect of different crude oils (heavy crude oil and bonny light crude oil) on embryos of marine medaka Oryzias melastigma was measured and evaluated by exposure to the water-accommodated fraction (WAF) in the present study. The cardiac function of medaka embryos was used as target organ of ecotoxicological effect induced by oil exposure. Results showed that the developing marine medaka heart was a sensitive target organ to crude oil exposure the heavy crude oil WAF was more toxic to cardiac function of medaka embryos than bonny light cured oil one. Cardiac function of medaka embryos was clearly affected by exposure to heavy crude oil WAF after 24 hours exposure and showed a dose-dependent slowing of heart rate. Furthermore, swelled and enlarged heart morphology, lowered blood circulation and accumulation of blood cells around the heart area were found. However, the toxic effect of bonny light crude oil on cardiac function of medaka embryos was comparatively low. Statistical results showed that the cardiac function was only affected by highest bonny light crude oil WAF (9.8 mg/L) exposure treatment. These findings indicated that cardiac function of marine medaka embryo was a good toxicity model for oil pollution and could be used to compare and evaluate the toxicity of different crude oils. The heart rate was an appropriate endpoint in the acute toxicity test.

Sponsored by National Science Fund of Bulgaria, Grant No DNP 04-35