Bioautomation

Volume 20, Issue 1
Bioinformatics
Structure Prediction of Outer Membrane Protease Protein of Salmonella typhimurium Using Computational Techniques	5-18
Rozina Tabassum, Muhammad Haseeb, Sahar Fazal [ +/- abstract ][ full text ]
Salmonella typhimurium, a facultative gram-negative intracellular pathogen belonging to family Enterobacteriaceae, is the most frequent cause of human gastroenteritis worldwide. PgtE gene product, outer membrane protease emerges important in the intracellular phases of salmonellosis. The pgtE gene product of S. typhimurium was predicted to be capable of proteolyzing T7 RNA polymerase and localize in the outer membrane of these gram negative bacteria. PgtE product of S. enterica and OmpT of E. coli, having high sequence similarity have been revealed to degrade macrophages, causing salmonellosis and other diseases. The three-dimensional structure of the protein was not available through Protein Data Bank (PDB) creating lack of structural information about E protein. In our study, by performing Comparative model building, the three dimensional structure of outer membrane protease protein was generated using the backbone of the crystal structure of Pla of Yersinia pestis, retrieved from PDB, with MODELLER (9v8). Quality of the model was assessed by validation tool PROCHECK, web servers like ERRAT and ProSA are used to certify the reliability of the predicted model. This information might offer clues for better understanding of E protein and consequently for developmet of better therapeutic treatment against pathogenic role of this protein in salmonellosis and other diseases.
Structural and Function Prediction of Musa acuminata subsp. Malaccensis Protein	19-30
Anum Munir, Azhar Mehmood, Shumaila Azam [ +/- abstract ][ full text ]
Hypothetical proteins (HPs) are the proteins whose presence has been anticipated, yet in vivo function has not been built up. Illustrating the structural and functional privileged insights of these HPs might likewise prompt a superior comprehension of the protein-protein associations or networks in diverse types of life. Bananas (Musa acuminata spp.), including sweet and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister grouped to the all-around considered Poales, which incorporate oats. Bananas are crucial for nourishment security in numerous tropical and subtropical nations and the most prominent organic product in industrialized nations. In the present study, the hypothetical protein of M. acuminata (Banana) was chosen for analysis and modeling by distinctive bioinformatics apparatuses and databases. As indicated by primary and secondary structure analysis, XP_009393594.1 is a stable hydrophobic protein containing a noteworthy extent of α-helices; Homology modeling was done utilizing SWISS-MODEL server where the templates identity with XP_009393594.1 protein was less which demonstrated novelty of our protein. Ab initio strategy was conducted to produce its 3D structure. A few evaluations of quality assessment and validation parameters determined the generated protein model as stable with genuinely great quality. Functional analysis was completed by ProtFun 2.2, and KEGG (KAAS), recommended that the hypothetical protein is a transcription factor with cytoplasmic domain as zinc finger. The protein was observed to be vital for translation process, involved in metabolism, signaling and cellular processes, genetic information processing and Zinc ion binding. It is suggested that further test approval would help to anticipate the structures and functions of other uncharacterized proteins of different plants and living being.
An in silico Approach for Structural and Functional Annotation of Salmonella enterica serovar typhimurium Hypothetical Protein R_27	31-42
Arif Khan, Hossain Ahmed, Nasreen Jahan, Syed Raju Ali, Al Amin, Mohammad Neaz Morshed [ +/- abstract ][ full text ]
Typhoid fever is a major cause of illness in most developing countries, including Bangladesh. In quest of new potential drug against Typhoid fever, the current study was designed to elucidate structural and functional details of S. typhi hypothetical protein (HP) R_27. HP R_27 has the primary amino acid sequences available only. The structural annotation was determined by ProtParam, SOPMA, and CELLO. The three-dimensional (3D) structure of HP R_27 predicted through homology modeling by using Phyre2. The 3D structure then refined and verified by ModRefiner, PROCHECK, ERRAT, QMEAN. The functional annotation was also performed by InterProScan, SMART, Pfam, NCBI-CDD and found Phospholipase D-like and DNA repair activity. Multiple sequence alignment also supported the existence of PLD-like domain and DNA repair protein domain in the selected hypothetical protein sequences. Finally, the cavity of drug binding was also identified to assist further molecular docking study and potent inhibitor identification. This in silico approach can be further utilized in molecular drug design for other clinically significant pathogens.
Biomedical systems
Electrocardiographic Changes in Certain Cardiovascular Physiological and Pathological Settings. Impact on Coronary Artery Bypass Grafting	43-68
Dimitar Simov [ +/- abstract ][ full text ]
Review on electrocardiographic changes provoked by aging, diagnostic tests, cardiac surgery, hemodialysis, diabetes, etc., is the objective of the current material. Several electrocardiographic (ECG) parameters that are well known risk markers of arrhythmias, incidental heart failure and sudden cardiac death (SCD) are discussed: QRS amplitude, QRS morphology, QRS duration, QRS alternans, T-wave amplitude, T-wave morphology, T-wave alternans, negative T-waves, 3D-spatial angle between maximal QRS and T vectors of the vectorcardiographic loops, ST-segment elevation, QT-interval dispersion, and heart rate. All reviewed parameters are compared with the results on the ECG-alterations, induced by coronary artery bypass grafting (CABG) surgery. Two parameters showed an improvement in the patients' condition: QRS-T angle and cardiac autonomic innervation while two others (T-wave alternans and heart rate) indicated deterioration. We tend to assume that the deterioration in this early post-operative period is an effect of the post-surgery trauma. We speculate that this effect will fade away in a period of a month and more after surgery, and we intend to conduct such a research in the future. The analysis of ECG's changes will help to better assess the impact of the CABG surgery.
Medical Image Watermarking in Sub-block Three-dimensional Discrete Cosine Transform Domain	69-78
Baoru Han, Jingbing Li [ +/- abstract ][ full text ]
Digital watermarking can be applied to protection of medical images privacy, hiding of patient's diagnosis information and so on. In order to improve the ability of resisting geometric attacks, a new watermarking algorithm for medical volume data in sub-block three-dimensional discrete cosine transform domain is presented. The original watermarking image is scrambled by a Chebyshev chaotic neural network so as to improve watermarking security. Sub-block three-dimensional discrete cosine transform and perceptual hashing are used to construct zero-watermarking. In this way it does not produce medical image distortion and gives the algorithm the ability to resist geometric attacks. Experimental results show that the algorithm has good security, and it has good robustness to various geometric attacks.
A Self-adaptive Dynamic Evaluation Model for Diabetes Mellitus, Based on Evolutionary Strategies	79-88
An-Jiang Lu, Li Jin, Hong-Xing Kan [ +/- abstract ][ full text ]
In order to evaluate diabetes mellitus objectively and accurately, this paper builds a self-adaptive dynamic evaluation model for diabetes mellitus, based on evolutionary strategies. First of all, on the basis of a formalized description of the evolutionary process of diabetes syndromes, using a state transition function, it judges whether a disease is evolutionary, through an excitation parameter. It then, provides evidence for the rebuilding of the evaluation index system. After that, by abstracting and rebuilding the composition of evaluation indexes, it makes use of a heuristic algorithm to determine the composition of the evolved evaluation index set of diabetes mellitus, It then, calculates the weight of each index in the evolved evaluation index set of diabetes mellitus by building a dependency matrix and realizes the self-adaptive dynamic evaluation of diabetes mellitus under an evolutionary environment. Using this evaluation model, it is possible to, quantify all kinds of diagnoses and treatment experiences of diabetes and finally to adopt ideal diagnoses and treatment measures for different patients with diabetics.
Development and Physical Control Research on Prototype Artificial Leg	89-98
Fei Li, Fuming Zhang, Hualong Xie [ +/- abstract ][ full text ]
To provide an ideal platform for research on intelligent bionic leg (IBL), this paper proposes a model of a biped robot with heterogeneous legs (BRHL). A prototype of an artificial leg is developed based on biological structure and motion principle analysis of human lower extremities. With regard to the driving sources, servomotors are chosen for the hip joint and ankle joint, while pneumatic muscle actuators (PMAs) are chosen for the knee joint. The control system of the bionic artificial leg is designed and a physical experimental platform is established. The physical control experiments are done based on proportional-integral-derivative (PID) control strategy. The experimental results show that such a system can realize the expected goals.
Analysis on Biomechanical Characteristics of Post-operational Vertebral C5-C6 Segments	99-114
Heqiang Tian, Xuanxuan Zhu, Jun Zhao, Chunjian Su [ +/- abstract ][ full text ]
Both anterior cervical decompression and fusion (ACDF) and artificial cervical disc replacement (ACDR) have obvious advantages in the treatment of cervical spondylosis. To analyze the operation results, it is absolutely necessary to study the biomechanics of the movement range of post-operational vertebral C5-C6 segments, especially the biomechanical characteristics in cervical tissues in actual movements. In this study, using the human vertebral 3D graph gained by imaging diagnosis (CT), a vertebral solid model is established by the 3D reconstruction algorithm and reverse engineering technology. After that, with cervical soft tissue structure added to the solid model and set with a joint contact mechanism, a finite element model with a complete, accurate cervical C5-C6 kinematic unit is constructed, based on relevant physiological anatomical knowledge. This model includes vertebral segments, an intervertebral disc, ligament and zygopophysis in the cervical C5-C6 kinematic unit. In the created vertebral finite element model, the model is amended, referring to ACDF and ACDR, and the load and constraint are applied to a normal group, a fusion group and a displacement group, so as to analyze the biomechanical characteristics of the cervical vertebra after ACDF and ACDR. By comparing the finite element simulation results of different surgeries, this paper is intended to evaluate the functions and biomechanical behaviors of the post-operational vertebra, and explore the influence of the operation on the biomechanical stability of the cervical vertebra. This will provide theoretical guidance for implementation and optimization of ACDF and ACDR.
Blood Plasma Thermograms Dataset Analysisby Means of InterCriteria and Correlation Analyses for the Case of Colorectal Cancer	115-124
Svetla Todinova, Deyan Mavrov, Sashka Krumova, Pencho Marinov, Vassia Atanassova, Krassimir Atanassov, Stefka G. Taneva [ +/- abstract ][ full text ]
The approaches of InterCriteria Analysis and Correlation Analysis are applied to a dataset of calorimetric and statistical parameters obtained from blood plasma proteome thermograms of colorectal cancer patients. The analysis was performed for four individual predefined subsets of calorimetric profiles. Specific interrelations between the studied criteria were identified that were found to differ among the different calorimetric subsets. For three of the subsets the enthalpy of the thermal profiles was in strong consonance with the excess heat capacity of the immunoglobulins assigned thermal transition. For the calorimetric subsets that differed most from the control healthy set a strong interrelation between the excess heat capacities of the main plasma proteins (albumin and immunoglobulins) was additionally evident. Our results demonstrate that these mathematical approaches can complement the analysis of calorimetric datasets generated for a variety of diseases.
Bioecological systems
Research of Wireless Sensor Monitoring Network of Melon Fly under Different Temperatures and Other Environmental Conditions	125-134
Shihao Zhou, Liang Zong [ +/- abstract ][ full text ]
In order to achieve multi-point, highly efficient and real-time wireless transmission of data about melon fly monitoring under various temperatures and other variable environmental conditions, this paper proposes and builds a model of a melon fly monitoring system with a wireless sensor network. Combined with multi-hop wireless sensor networks suitable for Adaptive Ad Hoc Transmission Control Protocol (ADTCP) algorithm, the transmission-limited congestion window is a method to reduce network congestion, simulate the aggregation node of the sensor network through a wireless transceiver platform, and finally to compile monitoring data in a central computer. The proposed scheme can effectively mitigate congestion problems of the wireless sensor network for monitoring melon flies at the aggregation node, can improve the data transmission performance of the monitoring network, and can adapt to various environmental conditions.
Research on the Relationship between Landslide of Farming Terraces and the Intensity of Rainfall and Slope Angle Based on the Indoor Rainfall Slide Slope Model	135-142
Dongqin Chen [ +/- abstract ][ full text ]
Due to the increase of geographical disaster in China, it is necessary to study the formation mechanism to make a preparation for the future prevention of geological disasters and effectively reduce the unnecessary financial loss and casualties. We found there is a powerful connection between heavy rainfall and landslide slope. Thus, this article takes the accumulation of gravel soil as the research material to set up indoor rainfall and landslide model test. By comparing the rules of pore water pressure and soil pressure responding to different rainfall intensity and slope angle, we discussed over the effects of rainfall intensity and slope angle on the sliding of accumulation gravelly soil.
Influence of Engineering Bacteria Quantitative Inspection on Diversity of Anpeng Alkali Mine Resources Exploitation	143-154
Yu Tao [ +/- abstract ][ full text ]
Cadmium (Cd) is a heavy metal pollutant seriously threatening creatures, and highly concentrated Cd in soil severely inhibits the activity of microbial populations. Soil in Anpeng Alkali Mine area in Nanyang city (Henan province) is seriously polluted by heavy metal. Both copper (Cu) and Cd content are found to be over standard, in which, Cu belongs to mild contamination while Cd is a serious contamination. To detect diversity of microbial communities in soil in the process of bioremediation, Cd polluted soil samples are collected from orefield for pot experiment, Biolog micro-plate technology is used to study the influence of applying low, medium and high amount of rice straw (5.3 t/ha, 10.2 t/ha and 23.4 t/ha) in polluted soil and combining low, medium and high amount of rice straw with surface displayed engineering bacteria (X4/pCIM) on microbial community. In the meantime, X4/pCIM is quantitatively measured by real-time polymerase chain reaction (PCR). Biolog experimental results indicate that the combination of rice straw and engineering bacteria is able to change the composition of soil microbial community, and has a difference in influencing rhizosphere and non-rhizosphere microorganisms. Through real-time PCR, it is found that the number of engineering bacteria falls to 103 after 120 days of bioremediation. Therefore, it can be concluded that combining rice straw with engineering bacteria can change the composition of soil microbial community and have diverse influences as application rate changes, without obvious rules to follow.