Volume 16, number 3
Editorial
New books
Bioinformatics
In silico Comparative Modeling of PapA1 and PapA2 Proteins Involved in Mycobacterium Tuberculosis Sulfolipid-1 Biosynthesis Pathway155-164
Rana Adnan Tahir, Sheikh Arslan Sehgal, Ambreen Ijaz
[ +/- abstract ][ full text ]
Tuberculosis is one of the most serious health problems, as globally; around 2 billion or one third of the world's total population has been infected with Mycobacterium tuberculosis. Mycobacterium tuberculosis is a unique among bacterial pathogens in that it displays a wide array of complex lipids and lipoglycans on its cell surface. One such glycolipid, sulfolipid-1 (SL-1), is the most sulfatide, consists of a trehalose core, four fatty acyl groups, and a sulfate ester. Several proteins involved in SL-1 biosynthesis have been identified, the enzymes that acylate the T2S core to form SL1278 and SL-1, and the biosynthetic order of these acylation reactions, are unknown. Here we studied the in silico identification of PapA2 and PapA1, proteins responsible for the sequential acylation of T2S to form SL1278 and are essential for SL-1 biosynthesis, by applying different bioinformatics tools. Benchmark, of 3 different homology modeling programs Modeller, Swiss-Model (Deep View), and ESyPred3D, has been performed used to transform the alignment to a 3D model. The 3D structures of targeted proteins were evaluated by evaluation tools, ANOLEA and Verify3D. It is concluded that in SL-1 biosynthesis pathway, PapA1 and PapA2 proteins could be used as drug target, drug lead design and to find out the other proteins involved in this pathway that not yet have been identified and may be used to the cure of tuberculosis infection.
Phylogenetic and Chronological Analysis of Proteins Causing Alzheimer's, Parkinson's and Huntington's Diseases165-178
Bilal Hussain, Hina Khalid, Shahid Nadeem, Tayyaba Sultana, Saima Aslam
[ +/- abstract ][ full text ]
It is evident that Neurodegenerative diseases (Alzheimer's, Parkinson's and Huntington's) have many similarities at cellular and molecular level as they carry parallel mechanisms including protein aggregation and inclusion body formation caused by protein mis-folding. The main objective of this study was to have detailed insight on variation and resemblance among these proteins. One hundred and four protein sequences, both directly and indirectly involved in disease mechanism to perform phylogenetic analysis revealing insight on evolutionary relationship among these proteins, were selected. The percentage of replicate trees, in which the associated taxa clustered together in the bootstrap test, was 1000 replicates. Various statistical tests were performed for the confirmation of results e.g., Tajma's Neutrality Test showed D > 6, nucleotide diversity π > 0.6 and ps value as greater than 1. Phylogenetic analysis showed that the protein sequences of neurodegenerative diseases had high sequence similarity and identity to each other as depicted by the evolutionary tree. It showed the similar mechanism of evolving from each other and had similar mechanism of generating mis-folding leading towards symptoms of disease.
Controlling B-Spline Snake Behavior using Particle Swarm Optimization179-186
Habibullah Akbar, Nanna Suryana, Shahrin Sahib
[ +/- abstract ][ full text ]
Traditional active contour models are hardly convergence to object boundaries where subjective contour and complex background appear. One of the main reasons is because the weighted combination of image energy functions can produce totally different B-Spline snake behaviors. Some efforts have been focused to improve the external energy forces but also lead to higher computational cost. In this research, an approach based on the particle swarm optimization is utilized to control the snake behavior without the necessity of computing the additional information. In the proposed approach, the weighted parameters are optimized using particle swarm optimization by evaluating control points of B-Spline snake in the image energy terms. This method enables the snake to initialize the image energy coefficient automatically and in more convenient way. Experimental results demonstrate that the proposed method can improve the snake behavior.
Bioprocess systems
Pilot-scale Biogas Plant for the Research and Development of New Technologies187-202
Ivan Simeonov, Boyko Kalchev, Snezhanka Mihaylova, Venelin Hubenov, Anatoliy Aleksandrov, Rashko Georgiev, Nicolai Christov
[ +/- abstract ][ full text ]
Тhe paper describes a new pilot-scale biogas plant of the Institute of Microbiology - Bulgarian Academy of Sciences. The equipment includes: a 100 L pilot bioreactor, a 200 L metal gasholder, sensors, actuators, a two-level automatic process monitoring and control system, a fire and explosion protection system and two web cameras. The monitoring and control system is composed on the lower level of a controller Beckhoff, and on the higher level - of a PC with specialized software (under development). The pilot biogas plant is designed to work out and scale up various anaerobic digestion (AD) technologies based on different types of feedstock. All the data will be stored on the PC for quick reference and possibly data mining, parameter identification and verification of different AD mathematical models.
Biomedical systems
Study of Transthoracic Impedance Cardiogram for Assessment of Cardiac Hemodynamics in Atrial Fibrillation Patents203-210
Vessela Krasteva, Irena Jekova, Elina Trendafilova, Sarah Ménétré, Tsvetan Mudrov, Jean-Philippe Didon
[ +/- abstract ][ full text ]
This study aims to test the usability of the transthoracic impedance cardiogram (ICG) for assessment of the quality of myocardial contractions in atrial fibrillation (AFIB) vs. sinus rhythm (SR), using signals recorded via defibrillation pads during external cardioversion (ECV). Data from 88 patients with persistent AFIB who received planned ECV are processed. AFIB is treated with cardioverter/defibrillator DG4000 (Schiller Médical, France) using a non-escalating protocol 200J/200J/200J. Successful ECV is defined as restoration of SR for >1min. The electrocardiogram (ECG), thoracic baseline impedance (Z) and dynamic impedance components dZ, dZ/dt captured via self-adhesive pads in antero- apical position are processed. Heartbeat contractions are evaluated by several measures extracted from the mean ICG patterns during systole: from dZ pattern - ICG (peak amplitude, range, area); from dZ/dt pattern - ICG velocity (peak, range, area) and left ventricular ejection time (LVET). The hemodynamical indices measured before and after ECV are: mean heart rate over 2 minutes (HR), standard deviation of HR (HRV), systolic (SysBP) and diastolic (DiaBP) blood pressure. When the rhythm converts from AFIB to SR (74 patients), all measures on dZ, dZ/dt patterns significantly increase: dZ (64-102%), dZ/dt (31-67%), LVET (18%), p < 0.05. Significant decrease of HR (-36%), HRV (-53%), SysBP (-11%) and DiaBP (-19%) are also observed. Unsuccessful ECVs without conversion to SR (14 patients) are, however, associated with non-significant increase of dZ (10-21%), dZ/dt (0.3-29%), LVET (9%), p > 0.05 when comparing pre-shock AFIB vs. post-shock AFIB. No clear change in HR (-9%) and HRV (6%), and slight decrease of SysBP (-10%) and DiaBP (-8%) are observed. The level of improvement of cardiac output quality in post-shock SR vs. pre-shock AFIB as estimated by ICG is related to a set of more than 60 clinical and hemodynamical parameters. Significant correlation coefficients are found to: Beta-Blocker (-0.25), Number of anti-arrhythmic drugs (-0.29), ΔST (0.37), pre-shock HR (0.43), ΔHR (-0.40), pre-shock HRV (0.30), ALT (0.46), ΔCK-MB (-0.32), ΔHR (-0.26), pre-shock DiaBP (0.24).

Sponsored by National Science Fund of Bulgaria, Grant No DNP 03/32

© 2012, BAS, Institute of Biophysics and Biomedical Engineering