Bioautomation

Volume 19, Issue 4
Bioinformatics
In silico Analysis for Laccase-mediated Bioremediation of the Emerging Pharmaceutical Pollutants	423-432
Anjali Singh, Shweta Kumari, Tapan Kumar Pal [ +/- abstract ][ full text ]
Laccases, a copper oxidase enzyme, has been employed for bioremediation of anthropogenic pollutants in the recent past. Laccase has a broad range of substrate specificity which offers the prospect for screening in numerable xenobiotics. The present study was aimed to use protein-ligand docking as a tool for prediction of biodegradation of selected pharmaceutical pollutants. A comparative study was also done to determine the binding efficacy of bacterial and fungal laccase for those selected pollutants. The laccase-pollutant docking was carried out using HEX software. The docking scores of bacterial and fungal laccase for predefined pollutants were comparable to ABTS, a substrate for laccase, which suggested that laccase might be able to degrade emerging pharmaceutical pollutants. The docking analysis approach can be useful in prediction of binding competence of pharmaceutical pollutants with laccase for in situ laccase-mediated bioremediation.
A Molecular Dynamics Study on RAGE-Aβ42 Interaction and the Influence of G82S RAGE Polymorphism on Aβ Interaction	433-446
Sreeram Krishnan, Srinidhi Ravi, Sivabaakiyam Ponmalai, P. Rani [ +/- abstract ][ full text ]
Interaction of amyloid peptides (Aβ) with receptor for advanced glycation end products (RAGE) elicits an inflammatory response and augments Alzheimer's disease (AD) pathology. The present study was aimed to analyse the interactions of different forms of Aβ42 peptide with ligand binding domain of normal and G82S RAGE and their possible consequences in AD pathology. The structures of RAGE ectodomain (3CJJ), monomeric forms of Aβ42 - 1IYT (apolar) and 1Z0Q (polar) and fibrillar (2BEG) were obtained from PDB. The structure of G82 and S82 RAGE was generated using SWISS MODEL. SIFT and PolyPhen analysis was performed to predict the phenotypic and functional effect of the amino acid substitution. The G82 and S82 variant structures were simulated in GROMACS and the 10 lowest energy structures were docked with different forms of Aβ42 using CLUSPRO in antibody mode. The lowest energy docked structure was further simulated for 5 ns. The structures corresponding to 0-5 ns were taken and the amino acid interactions were generated using PDBSUM. SIFT analysis indicated that G82S SNP had a tolerating effect on the structure of protein but polyphen predicted a probable damaging effect. Highest binding score was obtained with 2BEG docked with both G82 RAGE (-375.84 ± 7.425 Kcal/mol) and G82S variant (-391.09 ± 13.391 Kcal/mol) indicating that the fibrillar form showed better interaction. Compared to G82 RAGE, the S82 variant showed better interaction to all three forms of Aβ42. The results of study indicate that RAGE interacted better with fibrillar form of Aβ42 peptide and G82S mutation enhanced the binding affinity of RAGE towards amyloid peptides leading to enhanced inflammatory response.
Comparative Transcriptome Analysis of Hot Pepper (Capsicum annuum L.) Leaf Heterosis by RNA-seq	447-458
Tao Li, Heng-ming Wang, Zhi-liang Li, Xiao-wang Xu [ +/- abstract ][ full text ]
Heterosis has been mostly used in hot pepper breeding and production, but the molecular basis of heterosis has not been extensively studied. In this study, comparative transcriptomes analysis of parental lines (D6, D7) and F₁ hybrids (D6×D7 and D7×D6) was performed. A total of 0.6 billion raw reads, and 0.44 billion high-quality reads were obtained after the filtering process. Statistical analysis of genes with presence/deletion variations showed that, there were 1068 (6.20%) and 780 (4.56%) genes in the "single parent express consistent type" in the direct (D6×D7) and reciprocal (D7×D6) F₁ hybrids, respectively. More genes fit into the non-additive expression type in two F₁ hybrids compared to the parents, and less than 8% of the genes belong to the additive expression type. 66.08% in direct and 62.96% in reciprocal F₁ hybrids belong to the epistatic dominance expression pattern. There were more differentially expressed genes (DEGs) between the two parental lines (351) than between the two hybrids (17). The results of gene ontology (GO) analysis showed that there were obvious differences in electron transmission and photorespiration between two F₁ hybrids. GO terms for regulating plant hypersensitive responses, and MAPK pathways were only enriched in the direct hybrid (D6×D7).
Identification and Analysis of C. annuum microRNAs by High-throughput Sequencing and Their Association with High Temperature and High Air Humidity Stress	459-472
Xiao-wang Xu, Tao Li, Ying Li, Zhen-xing Li [ +/- abstract ][ full text ]
MicroRNAs (miRNAs) play an important role in many developmental processes and stress responses in plants. In this study, tolerant hot pepper cultivar 'R597' (CaR) and sensitive cultivar 'S590' (CaS) were used to detected differentially expressed miRNAs under high temperatures and high air humidity. The length distribution of obtained small RNAs was significantly different between libraries. There were a total of 71 miRNA families identified in two genotypes, and 24 conserved miRNA families were detected in all four sRNA libraries. MIR166, MIR156/157, MIR167, MIR168, MIR2118, and MIR5301 were highly expressed in four libraries, and 93 miRNAs had a species-specific expression. Among them, 60 miRNAs were preferentially expressed in S590 leaves and 33 miRNAs were preferentially expressed in R597 leaves. Mostly miRNAs were less-conserved miRNAs. The most abundant miRNAs with different expressions between two pepper species was miR6149b, which exhibited a high level (read count 42,443) in CaSCK but no expressed in CaRCK. We found 650 (CaRCK), 1054 (CaRHH), 914 (CaSCK), 1045 (CaSHH) potential targets for 92 (CaRCK), 124 (CaRHH), 128 (CaSCK), 117 (CaSHH) hot pepper miRNAs, respectively. These findings facilitate in better understanding of the molecular mechanism underlying high temperature and high air humidity condition in different pepper genotypes.
Bioprocess systems
Construction of Inorganic and Hybrid Biosorbents for Heavy Metal Ions Removal	473-482
Lyudmila Kabaivanova, Georgi Chernev, Juliana Ivanova [ +/- abstract ][ full text ]
Hybrid biosorbents, synthesized by the sol-gel method on the basis of Tetraethylorthosilicate (TEOS) proved to be efficient for the removal of the heavy metal ions from aqueous solutions. The potential use of immobilized in TEOS algal cells of the red microalga Porphyridium cruentum and its products - low and high molecular heteropolysaccharides to remove Cu(II), Cd(II) and Ni(II) ions was evaluated. A laboratory bioreactor was involved in this process. Sol-gel sorbent with TEOS only was used as a control system to the hybrid biosorbents. Their structural characterization was performed using different methods. The maximum adsorption capacities were registered for the biosorbents with immobilized algal biomass and for the preparations with TEOS and high molecular algal heteropolysaccharide: for Cu(II), Cd(II) and Ni(II), they were 18.771 and 21.715 mg·Cd·g^-1 adsorbent; 16.662 and 17.545 mg·Ni.g^-1 adsorbent and 40.633 and 34.431 mg·Cu·g^-1 adsorbent, respectively. The adsorption of toxic Cu(II), Zn(II) and Ni(II) ions in the four types of sorbents proved to be effective. High percent of these ions removal was obtained during the first hours of the adsorption process.
Ethanol from Cellulosic Biomass with Emphasis of Wheat Straw Utilization. Analysis of Strategies for Process Development	483-506
Alexander Dimitrov Kroumov, Maya Zaharieva, Venko Beshkov [ +/- abstract ][ full text ]
The "Green and Blue Technologies Strategies in HORIZON 2020" has increased the attention of scientific society on global utilization of renewable energy sources. Agricultural residues can be a valuable source of energy because of drastically growing human needs for food. The goal of this review is to show the current state of art on utilization of wheat straw as a substrate for ethanol production. The specifics of wheat straw composition and the chemical and thermodynamic properties of its components pre-determined the application of unit operations and engineering strategies for hydrolysis of the substrate and further its fermentation. Modeling of this two processes is crucially important for optimal overall process development and scale up. The authors gave much attention on main hydrolisis products as a glucose and xylose (C6 and C5 sugars, respectivelly) and on the specifics of their metabolization by ethanol producing microorganisms. The microbial physiology reacting on C6 and C5 sugars and mathematical aproaches describing these phenomena are discussing, as well.
Monitoring Biological Modes in a Bioreactor Process by Computer Simulation	507-520
Samia Semcheddine, Abdel Aitouche [ +/- abstract ][ full text ]
This paper deals with the general framework of fermentation system modeling and monitoring, focusing on the fermentation of Escherichia coli. Our main objective is to develop an algorithm for the online detection of acetate production during the culture of recombinant proteins. The analysis the fermentation process shows that it behaves like a hybrid dynamic system with commutation (since it can be represented by 5 nonlinear models). We present a strategy of fault detection based on residual generation for detecting the different actual biological modes. The residual generation is based on nonlinear analytical redundancy relations. The simulation results show that the several modes that are occulted during the bacteria cultivation can be detected by residuals using a nonlinear dynamic model and a reduced instrumentation.
Biomedical systems
Design and Evaluation of a Low-cost Piezoelectric Device for Remote Diagnosis of Respiratory Diseases	521-530
Rohan Palanki, Justin Poiroux, Srinivas Palanki [ +/- abstract ][ full text ]
In this research, a piezoelectric film was utilized to develop a low-cost biomedical device for diagnosis and management of breathing disorders. First, it was shown that when a commercial polyvinylidene fluoride (PVDF) film was subjected to airflow generated from human breath, the voltage generated increased with decreasing film thickness. Then, a device was fabricated that records a patient's breathing pattern and sends this data to a remote email address via the Raspberry Pi, an inexpensive computer. It was shown that the breathing patterns could be recorded in a reproducible manner with this device. Next, the efficacy of the device to detect breathing disorders was tested. A restrictive ventilatory abnormality was simulated by tying a crepe bandage around the chest. It was shown that this device could successfully distinguish between breathing in a normal patient and the breathing of a patient with a restrictive ventilatory abnormality. It is possible to fabricate this device for less than $100, thereby making it accessible to a large number of patients with chronic lung diseases.
Classification Probability Analysis for Arrhythmia and Ischemia Using Frequency Domain Features of QRS Complex	531-542
Akash Kumar Bhoi, Karma Sonam Sherpa, Bidita Khandelwal [ +/- abstract ][ full text ]
Two of the most common cardiovascular diseases are myocardial ischemia and cardiac arrhythmias. Using the frequency domain features of QRS complex (i.e., frequency of the maximum peak in power spectrum and total average power) the proposed approach analyzes classification probability for these diseases by implementing Linear Discriminant Analysis (LDA) and Decision Tree. Moreover the classification probability is visualized using Naive Bayes classification algorithm. The methodology includes the QRS complex detection technique which is mainly comprises of three stages: Stage-1 - baseline drifts and noise cancellation using Moving Average Filter (MAF) and Stationary Wavelet Transform (SWT); Stage-2 - R-peaks localization using threshold based windowed filter: Stage-3 - Q and S inflection points detection using search interval method. To perform uniform classification probability analysis, the proposed methodology is evaluated with 108 selected episodes which show 100% accuracy in QRS complex detection. The 108 episodes includes 36 lengthy ECG recordings from FANTASIA database (healthy subjects), MIT-BIH Arrhythmia database (arrhythmic subjects) and Long-Term ST database (ischemic subjects) respectively. Moreover, the energy surface distribution of segmented QRS complex is analysed with Short-Term Fourier Transform (STFT) which transforms time domain information of the complex into time-frequency domain.
Prediction of Negative Conversion Days of Childhood Nephrotic Syndrome Based on the Improved Backpropagation Neural Network with Momentum	543-554
Yi-jun Liu, Bei-hong Wang, Jiali Tang, Ming-fang Zhu, Dan Chen, Hong-fen Jiang, Xiang-jun Chen [ +/- abstract ][ full text ]
Childhood nephrotic syndrome is a chronic disease harmful to growth of children. Scientific and accurate prediction of negative conversion days for children with nephrotic syndrome offers potential benefits for treatment of patients and helps achieve better cure effect. In this study, the improved backpropagation neural network with momentum is used for prediction. Momentum speeds up convergence and maintains the generalization performance of the neural network, and therefore overcomes weaknesses of the standard backpropagation algorithm. The three-tier network structure is constructed. Eight indicators including age, lgG, lgA and lgM, etc. are selected for network inputs. The scientific computing software of MATLAB and its neural network tools are used to create model and predict. The training sample of twenty-eight cases is used to train the neural network. The test sample of six typical cases belonging to six different age groups respectively is used to test the predictive model. The low mean absolute error of predictive results is achieved at 0.83. The experimental results of the small-size sample show that the proposed approach is to some degree applicable for the prediction of negative conversion days of childhood nephrotic syndrome.
Bioecological systems
Biodegradation of Gallic Acid in Chinese Nutgall Processing Wastewater with a Sequencing Batch Reactor	555-562
Hui-long Fang, Jun-jie Wang [ +/- abstract ][ full text ]
The degradation of gallic acid in the Chinese nutgall processing wastewater was carried out in a sequencing batch reactor (SBR). The biodegradability of gallic acid was monitored, and the effect of initial concentration, temperature, pH, and salinity on the degradation of gallic acid was studied. The result showed that the biodegradability of gallic acid was poor, but enough to meet the requirement of SBR process by further pre-treatment which would improve the biodegradability. A first-order Monod kinetic model was used to describe the degradation process of gallic acid. The removal efficiency decreased with the increase of the initial gallic acid concentration. The raise of temperature and pH were not conducive for the removal of gallic acid. When the salinity was 2 g·L^-1 or less, the increase of the salinity content would improve the gallic acid removal efficiency, and the removal efficiency was higher than 75% when the salinity content was less than 10 g·L^-1.
Study on Constitutive Model for Root System of Korshinsk peashrub in Axial Tension	563-574
Guo-jian Feng, Jun Du, Wei-wei Zhu, Zhi-gang Qiu [ +/- abstract ][ full text ]
Constitutive model for root system of Korshinsk peashrub (Caragana korshinskii Kom.) in axial tension is an important tool for analyzing the mechanism of soil reinforcement of root system. This model enables a mechanical analysis on strength and deformation of root system and root-soil complex. We carried out axial tension test of root system of Korshinsk peashrub in this paper and discussed the stress-strain relation. Based on the experimental results, the constitutive model for root system of Korshinsk peashrub in axial tension was established. Results showed that: (1) When the strain was smaller than 4%, the stress-strain relation was linear for single root, corresponding to linear elastic deformation; when the strain was larger than 4%, the single root underwent plastic deformation; (2) Elastic modulus of the root system was related to root diameter by a power function. The smaller the root diameter, the higher the elastic modulus was; (3) Root diameter was related to the ultimate tensile strength of root also by a power function. The smaller the root diameter, the higher the ultimate tensile strength of root was; (4) The tensile stress-strain curve of the root system divided into ascending segment and descending segment, which was fitted by parabola and curvilinear model, respectively.