Volume 16, number 4
Editorial
New books
Bioinformatics
In silico Characterization of Plant and Microbial Antifreeze Proteins225-238
Md. Musharaf Hossain, Abu Taher Mohammad Jannatul Mosnaz, Abdul Mohin Sajib, Jewel Halder, Raihan Mahmud, Khairul Alam Mohammad Nayeem, Nabangshu Shekhar Das, Muzahidul Islam Sarkar, Janmajoy Dey, Akhikun Nahar
[ +/- abstract ][ full text ]
Antifreeze proteins (AFPs) are class of proteins that protect organisms from the damage caused by freezing through their ability to inhibit ice growth and effectively lower the temperature at which water freezes. In this study, a total of 25 antifreeze proteins were selected from four different sources (plant, bacteria and fungus) where they represent distinct physicochemical and structural features. Several Physico-chemical properties such as grand average hydropathy (GRAVY), aliphatic index (AI), extinction coefficient (EC), isolelectric point (pI), and instability index (II) were computed. S-S bridges and secondary structures were analyzed using CYS_REC and SOPMA programs respectively. The three dimensional structure of Antifreeze proteins is predicted by using three homology modelling server Geno3D, Swiss-model and CPHmodels. These models were evaluated with PROCHECK, What If, and ProSA programs. Model visualization and analysis was done with Pymol. These structures will provide a good foundation for functional analysis of experimentally derived crystal structures.
Rational Drug Designing Strategies and Inhibitor Optimization: Anthrax Lethal Toxin Factor239-250
Pawan Kumar Jayaswal, Ganesh Chandra Sahoo, Pradeep Das
[ +/- abstract ][ full text ]
Anthrax toxin protein protective antigen, edema factor and lethal factor are secreted by Bacillus anthracis bacteria causes several adverse effects on human as well as on ruminant animals and considered as serious biological weapons. Lethal toxin protein (combination of lethal factor and protective antigen) is highly lethal to the host and responsible for the disruption of signalling pathways, cell destruction, and circulatory shock. 1YQY is one of the crystal structures of lethal toxin protein. It has two domains - Anthrax_M_tox and ATLF where the hydroxymate as well as Zn cofactor are attached. Known inhibitor of the protein 1YQY was identified and downloaded from pubchem. Interaction of the inhibitors with the protein was examined through in silico docking approach with AutoDock 3.0.5 and Hex. Some of the inhibitors apparently interact with several-conserved residue in the cofactor-binding site. The docking work suggests virtual derivatives of the predicted inhibitor that can improve hydrogen bond interaction between inhibitor and protein. From structural and docking analyses, it is hypothesized that 1YQY protein interacts with azelastine molecule shows the lowest docking energy in AutoDock software.
In silico Prediction of MicroRNAs in Plant Mitochondria251-262
Banu Pradheepa Kamarajan, Jaiashre Sridhar, Selvi Subramanian
[ +/- abstract ][ full text ]
MicroRNAs are endogenous, short (ca. 21 base), non-coding, post transcriptional, regulatory RNA molecules. These microRNAs (miRNAs) are complementary to their target messenger RNAs, and bind principally to its 3' UTR. The conserved nature of miRNAs, and their high sequence complementarities of miRNA and its targets in plants, provides the basis for the easy identification of miRNA and its targets. Presence of miRNA in plant mitochondria is scantily studied. Identification of miRNA targets in plant mitochondria might indicate the involvement of miRNA in mitochondrial gene regulation and nuclear mitochondrial interactions. In this study, we used a computational approach to predict miRNA targets in plant mitochondria. The mitochondrial gene targets identified for miRNAs are located both in mitochondrial and nuclear compartments. This observation points to a fairly early origin of miRNAs. Besides, most of the targets identified can have copies in two compartments and suggest the possibility of miRNA mediated regulation. This study unfurls the possibility of regulating the plant mitochondrial genes by amending the miRNA genes in the nuclear compartment.
Bioprocess systems
Ultrasound Beam Focusing Considering the Cutaneous Fat Layer Effects263-272
A.B.M. Aowlad Hossain, Laehoon H. Kang
[ +/- abstract ][ full text ]
Commercial medical ultrasound scanners assume average sound velocity of 1540 m/s while sound speed varies at different tissues. This assumption limits focusing quality and degrades contrast and resolution, particularly for patients with fatty abdominal wall. This paper presents a simple two layer model to demonstrate the effect of ultrasound beam focusing quality in inhomogeneous medium based on Huygens's principle. A time delay function for ultrasonic phase array has been derived using in vivo information of fat layer and considering refraction in the interface of two layers. Simulated beam pattern and corresponding beam profiles at the focal depth using conventional delay time and that for proposed two layer model are compared. An experimental setup was designed to assess the image quality using a commercial ultrasound scanner and a phantom of two layers with different sound velocity. Simulated and experimental results indicate that obtained images using time delays for two layer model show better contrast resolution.
Biomedical systems
Ventricular Beat Detection and Classification in Long Term ECG Recordings273-290
Stoyan Tanev
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The QRS detection is key component of each automated ECG analysis. For this purpose a lot of QRS algorithms have been already developed. In the same time the number of new published methods continues to grow up. This implicitly proves the impossibility of building such detector that could totally cover the variety of all shapes of ventricular beats encountered in practice. Generally, limited studies on discrimination between normal (sinus) and ectopic beats are available. The paper describes very fast procedure for accurate QRS detection in long term ECG Holter recordings, followed by classification of the complexes in normal and ectopic. The algorithm was tested with the widely accepted AHA and MIT-BIH databases. The obtained sensitivity and specificity are comparable to other published results.
Digital Operation of Microelectronic Circuits Analogous to Protein Hydrogen Bonding Networks291-308
Elitsa Gieva, Rostislav Rusev, George Angelov, Marin Hristov, Tihomir Takov
[ +/- abstract ][ full text ]
Two hydrogen bonding networks with water molecules and branching residues extracted from β-lactamase protein are investigated and their proton transfer characteristics are studied by creating analogous electrical circuits consisting of block-elements. The block-elements and their proton transfer are described by polynomials that are coded in Matlab and in Verilog-A for use in the Spectre simulator of Cadence IC design system. DC and digital pulse analyses are performed to demonstrate that some circuit outputs behave as repeaters while other - behave as inverters. The results also showed that the HBN circuits might behave as a D-latch and a demultiplexer.

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