Volume 23, Issue 1
Editorial
Anniversary
The 80th Birthday of Professor Stoyan Tzonkov,
Honorary Chief Editor of the Int J Bioautomation
In silico Homology Modeling and Docking Studies of RecA from Campylobacter jejuni1-12
Mohammed Zaghlool Al-Khayyat
Mohammed Zaghlool Al-Khayyat (2019) In silico Homology Modeling and Docking Studies of RecA from Campylobacter jejuni, Int J Bioautomation, 23 (1), 1-12, doi: 10.7546/ijba.2019.23.1.1-12
Abstract: The RecA protein has an essential role in DNA recombination and repair which is mediated by its ability to bind ATP/ADP. SWISS-MODEL, an online automated server, was used to predict its tertiary structure of C. jejuni RecA. Four evaluation tools were used for quality assessment of the constructed model: QMEAN6, ERRAT, ANOLEA and PROCHECK. Quality assessments indicated that the model was of high quality and reliable for docking experiments. A total of forty natural products were used in docking the model by Hex 8.0.0 and ArgusLab 4.0.1 using ADP as control. Ten compounds had docking scores higher than that of ADP (-8.61 Kcal/mol) in ArgusLab 4.0.1 where quercetin had the highest docking score of -10.34 Kcal/mol. In Hex 8.0.0 docking, only cucurmin, taxifolin, isoquercitrin and vitexin had docking scores higher than that of ADP. These natural occurring compounds may be possible inhibitors of ATPase activity and, therefore, may be further analyzed to develop new antimicrobials targeting RecA in pathogenic bacteria.

Keywords: Antibiotic design, ArgusLab, Cucurmin, Homology modeling, Taxifolin, Quercetin
Treatment and Management of Hypertension by Targeting ACE Inhibitors: in silico Approach13-28
Seema Bawa, Sabina Yasmin, Vipin Saini, Tulshi Chakraborty, Shailendra S Chaudhaery, Md Yousuf Ansari
Seema Bawa, Sabina Yasmin, Vipin Saini, Tulshi Chakraborty, Shailendra S Chaudhaery, Md Yousuf Ansari (2019) Treatment and Management of Hypertension by Targeting ACE Inhibitors: in silico Approach, Int J Bioautomation, 23 (1), 13-28, doi: 10.7546/ijba.2019.23.1.13-28
Abstract: Hypertension means increase in blood pressure. There are different drugs which are available both as single dose and as combination therapy for treatment and management of hypertension. Our target is Angiotensin Converting Enzyme (ACE) inhibitors for better therapy or improved therapy of the hypertension patient. ACE in complex with inhibitor lisinopril, zinc cation and chloride ions (anions) have a similar structure to angiotensin I and bind to the active site of the ACE protein. The literature suggested that there are different classes of ACE inhibitors and describes their interaction with currently available drugs. We have also compiled the data on the proper management of hypertension with another relevant disease like diabetes. The number of available PDB three dimensional structure of ACE protein having different organism (74); Homo sapiens (49), Drosophila melanogaster (22), Severe acute respiratory (5), Paguma larvata (5), Bacillus thermoproteolyticus (3), Severe acute respiratory (3), Gloydius blomhoffii (2), Other (3). Our target is a well-known protein with high resolution in a human structure that is crystal structure of the Angiotensin-1 converting enzyme N-domain in complex with amyloid-beta 35-42 (PDB ID-5AMB) of recently submitted (2015) with high resolution (1.55 Å). The characteristic features of ACE having a zinc binding metallopeptidase consist of two domain of N and C terminal (different binding pattern). We have designed a better ligand interaction with this protein.

Keywords: Hypertension, ACE inhibitors, Angiotensin
Peculiarities in the Distribution of Temperature under the Influence of a Laser Beam in a Multilayered Medium29-40
Teodora Petrova, Zhivo Petrov
Teodora Petrova, Zhivo Petrov (2019) Peculiarities in the Distribution of Temperature under the Influence of a Laser Beam in a Multilayered Medium, Int J Bioautomation, 23 (1), 29-40, doi: 10.7546/ijba.2019.23.1.29-40
Abstract: The term thermal interaction refers to a large group of interaction types where the local temperature rise is an important parameter. Temperature is the main parameter for all thermal interactions between laser beam and tissues. In addition, in order to predict the thermal reaction in tissues, a model of distribution of temperature in a thermal reaction is necessary. Very often in biological tissues, several thermal effects are observed depending on the properties of the laser.

Keywords: Biomedical technologies, Lasers, Mathematical model
Effect of Semantic Priming for Wide Attention Focus on Visuomotor Decision-making Task in Young and Older Non-professional Drivers41-50
Milena Staneva, Valentina Grigorova
Milena Staneva, Valentina Grigorova (2019) Effect of Semantic Priming for Wide Attention Focus on Visuomotor Decision-making Task in Young and Older Non-professional Drivers, Int J Bioautomation, 23 (1), 41-50, doi: 10.7546/ijba.2019.23.1.41-50
Abstract: The study was aimed at estimating the semantic priming effect for wide attention focus on subjects response time (RT) in a decision-making visuomotor hand movement task (VMHT) performed in traffic scenarios for non-professional driver’s license tests. The priming was based on modified scrambled sentence task. Traffic scenarios were displayed either on whole screen or within the central 25% of the screen. VMHT was presented: 1) immediately after priming; 2) after primed in the same way adaptation of reactive visual saccade; 3) without priming and saccade adaptation. Thirty young and thirty older subjects took part in the study as they were divided equally into three groups with respect to the three conditions: 1) YP and OP (a group where the traffic test is performed before the sacccade adaptation); 2) YS and OS (after the saccade adaptation); 3) YC and OC (control group). The outcomes established that RTs of both YP and OP groups are higher while RTs of YS and OS groups are lower in comparison with the control groups. RTs of all older groups were significantly longer than those of the younger groups. Longer RTs were found with respect to large pictures than to small pictures. These results suggest that semantic priming has a rather negative effect on decision-making VMHT performance because priming with scrambled sentences also involves a decision-making process. Therefore, they both need similar cognitive resources of which probably VMHT is deprived by the preceding priming and as consequence its perceptual realization is delayed. The study suggests that priming and visuomotor performance are related and the effect of the former on the latter depends on which cognitive resources they need.

Keywords: Spatial selective attention, Reaction time, Saccade adaptation
TSHR169 Antigen Specifically Binds to the Thyroid-stimulating Autoantibody, Representing an Effective Biomarker for Graves’ Disease51-60
Zulkarnain Zulkarnain, Hidayat Sujuti, Djoko Wahono Soeatmadji, Didik Huswo Utomo, Aulanni’am Aulanni’am
Zulkarnain Zulkarnain, Hidayat Sujuti, Djoko Wahono Soeatmadji, Didik Huswo Utomo, Aulanni’am Aulanni’am (2019) TSHR169 Antigen Specifically Binds to the Thyroid-stimulating Autoantibody, Representing an Effective Biomarker for Graves’ Disease, Int J Bioautomation, 23 (1), 51-60, doi: 10.7546/ijba.2019.23.1.51-60
Abstract: The thyroid-stimulating hormone receptor (TSHR) is one of the thyroid antigens responsible for Graves’ disease and acts as a biomarker for early detection. The purpose of this study was to computationally compare the effectiveness of TSHR56 and TSHR169 fragments in binding to the thyroid-stimulating human monoclonal autoantibody (M22) at the molecular level. The 3D model of M22 was obtained from RCSB (ID 3G04), while the TSHR antigen models were submitted to homology modeling using SWISSMODEL and PhyreV2.0 server to predict the protein structures. The model was validated by generating a Ramachandran plot with the RAMPAGE server. Prediction of the molecular interaction between TSHR and M22 was performed using the HADDOCK web server (version 2.2). Analysis of the binding affinity was conducted using the PRODIGY server. Interactions within the TSHR-M22 complex were analyzed using DIMPLOT. The antigen models had reliability scores of 100% and 97.7% for TSHR56 and TSHR169, respectively. The results of the molecular docking analysis revealed a better HADDOCK score for TSHR169 (-144.7 ± 2.4) compared to TSHR56 (-53.3 ± 10.1). However, the affinity of TSHR56 (-10.1 Kcal/mol) and TSHR169 (-10.2 Kcal/mol) were not significantly different. The results of the TSHR-M22 interaction specificity analysis suggested that TSHR169 is superior to TSHR56, as the number of interacting amino acids was comparable to the control (TSHR260-M22). It can be concluded that TSHR169 represents a specific full-length TSHR antigen and can be developed as biomarker for Graves’ disease.

Keywords: Graves’ disease, Molecular docking, Thyroid-stimulating antibody, TSHR56, TSHR169
Continuously Tested and Used QRS Detection Algorithm: Free Access to the MATLAB Code61-70
Ivan Dotsinsky, Todor Stoyanov
Ivan Dotsinsky, Todor Stoyanov (2019) Continuously Tested and Used QRS Detection Algorithm: Free Access to the MATLAB Code, Int J Bioautomation, 23 (1), 61-70, doi: 10.7546/ijba.2019.23.1.61-70
Abstract: Each ECG analysis begins with the detection of the QRS complex, which is the most distinguishable wave for initial investigation. Long ago we published an algorithm for ventricular beats (VB) detection in single ECG lead. The classification of normal QRS complexes is based on the slope, the amplitude and the width of the ECG waves. Other criteria recognize ventricular ectopic beats (EB) by presence of biphasic beats and separate premature EB from the already detected QRS complexes. The aim of this paper is to place the MATLAB program of our algorithm at disposal to the readers (supplementary MATLAB codes) looking forward to more successful ECG investigations.

Keywords: Ventricular beat detection, QRS detection, Ectopic beat detection
Improved Computer-oriented Method for Processing of Measurement Information on Greenhouse Microclimate71-86
Ivan S. Laktionov, Oleksandr V. Vovna, Yevhen O. Bashkov, Anatolii A. Zori, Vladyslav A. Lebediev
Ivan S. Laktionov, Oleksandr V. Vovna, Yevhen O. Bashkov, Anatolii A. Zori, Vladyslav A. Lebediev (2019) Improved Computer-oriented Method for Processing of Measurement Information on Greenhouse Microclimate, Int J Bioautomation, 23 (1), 71-86, doi: 10.7546/ijba.2019.23.1.71-86
Abstract: The article presents results of field testing and experimental studies on improvement of the computer-oriented method of aggregation and processing of measurement information on microclimate parameters of industrial greenhouses. The technology was developed and tested in the laboratory. It consists of a hardware component based on Arduino Mega 2560 and Ethernet Shield W5100 and modern sensor devices, a software module based on Simulink Support Package for Arduino Hardware® and a remote database of monitoring results on the ThingSpeak® server. The technology proposed in the article has a modular structure and is adaptive to types and periods of vegetation of cultivated crops. The obtained research results constitute scientific and practical basis for conducting further priority research on implementation of the developed technology into actual production conditions for growing protected crops.

Keywords: Computerized technology, Greenhouse, Hardware and software implementation, Monitoring, Microclimate
Computed Tomography Beam Hardening Correction Based on Non-linear Segmentation87-96
Xiaoke Zhang, Linyan Xue, Kang Yin, Tianyi Wang, Kun Yang
Xiaoke Zhang, Linyan Xue, Kang Yin, Tianyi Wang, Kun Yang (2019) Computed Tomography Beam Hardening Correction Based on Non-linear Segmentation, Int J Bioautomation, 23 (1), 87-96, doi: 10.7546/ijba.2019.23.1.87-96
Abstract: This paper aims to eliminate the hardening artifacts in computed tomography (CT) images caused by the polychromatic X-ray spectrum. To this end, a polynomial fitting correction method using non-liner segmentation method was developed through projection space optimization for single medium (water) and the mixed media (water-bone), and verified through simulation and phantom experiments. Unlike the traditional image space optimization strategies, the proposed method has low computing load and few noises, and only requires a one-off image reconstruction to remove the hardening artifacts. The experimental results show that the proposed method can remove CT hardening artifacts and improve the accuracy of image reconstruction, indicating that the project space-based correction method based on non-liner segmentation method can effectively eliminate artifacts and restore the true CT values.

Keywords: Computed tomography, Beam hardening correction, Projection space
Experimental Study on Relation between Whole-salt Quantity and Electric Conductivity97-104
Yu Zhang, Xichun Jia, Xuemei Lai, Yinhua Huang
Yu Zhang, Xichun Jia, Xuemei Lai, Yinhua Huang (2019) Experimental Study on Relation between Whole-salt Quantity and Electric Conductivity, Int J Bioautomation, 23 (1), 97-104, doi: 10.7546/ijba.2019.23.1.97-104
Abstract: Through different water-soil ratio, oscillation time, ion contents and soil salt quantity, the correlation and regression between the whole soil salinity in oasis-desert ecotones in Tarim basin and electro conductivity of soil soak-out-liquid have been studied by electric conductivity methods. The results indicated: when water-soil ratio was 1:1-6:1, there was significantly correlation between electro conductibility and whole-salt quantity. But the 5:1 water-soil ratio is better according to the soil characteristic in this locality. After the oscillation time of soil samples was 10 minutes under the 5:1 water-soil ratio, the electro conductibility of soak-out-liquid there was not marked difference. The correlation between ion of comparative large contents and the electro conductibility soak-out liquid was very marked. When soil salinity is large, linear functions can be used to better measure the whole salt quantity of this local by subsection analysis.

Keywords: Soak-out liquid, Electrical conductivity, Whole-salt quantity, Oasis-desert ecotones
Operon Prediction Model Based on Markov Clustering Algorithm105-116
Zhenmei Zhang, Yongquan Liang
Zhenmei Zhang, Yongquan Liang (2019) Operon Prediction Model Based on Markov Clustering Algorithm, Int J Bioautomation, 23 (1), 105-116, doi: 10.7546/ijba.2019.23.1.105-116
Abstract: There are many operon prediction models, but few methods can be applied to the operon prediction of new sequencing species effectively. In this paper, an operon prediction model based on Markov clustering algorithm is proposed. The model uses some generic attribute information of genomes and graph clustering algorithm instead of classifier to predict operon. Similarly to most operon prediction models, E. coli K12 and B. subtilis str. 168 were used to assess the prediction capability of the proposed model, the experiment results show that the proposed model has better capability of operon prediction than some other classical operon prediction methods.

Keywords: Operon Prediction, Markov Clustering Algorithm, Generic Attribute, Graph Clustering
An Improved Smith-Waterman Algorithm Based on Spark Parallelization117-129
Yanfeng Liu, Leixiao Li, Jing Gao
Yanfeng Liu, Leixiao Li, Jing Gao (2019) An Improved Smith-Waterman Algorithm Based on Spark Parallelization, Int J Bioautomation, 23 (1), 117-129, doi: 10.7546/ijba.2019.23.1.117-129
Abstract: This paper proposes the design and the implementation of a Spark parallelization plan for improving the Smith-Waterman (SW) algorithm, named the Spark-OSW algorithm. Then, the Spark-OSW was verified through accuracy, performance and acceleration tests. The results show that the proposed algorithm achieved 100% accuracy, ran much faster than the SW, and performed well in cluster environment. The research findings shed important new light on the database search for gene sequences.

Keywords: Sequence alignment, Smith-Waterman algorithm, Spark parallelization, Spark-OSW algorithm

Sponsored by National Science Fund of Bulgaria, Grant No KP-06-NP/9/2018

© 2019, BAS, Institute of Biophysics and Biomedical Engineering