Bioautomation

Volume 17, Issue 1
Editorial
New books
Bioinformatics
Computer Modeling of Human Delta Opioid Receptor	5-16
Tatyana Dzimbova, Fatima Sapundzhi, Nevena Pencheva, Peter Milanov [ +/- abstract ][ full text ]
The development of selective agonists of δ-opioid receptor as well as the model of interaction of ligands with this receptor is the subjects of increased interest. In the absence of crystal structures of opioid receptors, 3D homology models with different templates have been reported in the literature. The problem is that these models are not available for widespread use. The aims of our study are: (1) to choose within recently published crystallographic structures templates for homology modeling of the human δ-opioid receptor (DOR); (2) to evaluate the models with different computational tools; and (3) to precise the most reliable model basing on correlation between docking data and in vitro bioassay results. The enkephalin analogues, as ligands used in this study, were previously synthesized by our group and their biological activity was evaluated. Several models of DOR were generated using different templates. All these models were evaluated by PROCHECK and MolProbity and relationship between docking data and in vitro results was determined. The best correlations received for the tested models of DOR were found between efficacy (erel) of the compounds, calculated from in vitro experiments and Fitness scoring function from docking studies. New model of DOR was generated and evaluated by different approaches. This model has good GA341 value (0.99) from MODELLER, good values from PROCHECK (92.6% of most favored regions) and MolProbity (99.5% of favored regions). Scoring function correlates (Pearson r = -0.7368, p-value = 0.0097) with erel of a series of enkephalin analogues, calculated from in vitro experiments. So, this investigation allows suggesting a reliable model of DOR. Newly generated model of DOR receptor could be used further for in silico experiments and it will give possibility for faster and more correct design of selective and effective ligands for δ-opioid receptor.
Taxonomic Study of Campylobacter Species using hsp60 Protein	17-24
Mohammed Z. Saeed Al-khayyat [ +/- abstract ][ full text ]
hsp60 protein sequences of twenty two Campylobacter species were downloaded from NCBI (National center for biotechnology information). Alignments and phylogenetic tree were constructed using ClustalW2, and the protein sequences showed 100% similarities between C. curvus and C. concisus, and between C. lari and C. fetus subspecies. The phylogenetic tree showed that C. rectus and C. sputorum are of the same line of origin and the same applies to C. peloridis and C. volucris. Amino acid substitutions between C. helveticus and C. upsaliensis were in the positions 98 and 149 where N replaced S respectively. Only one amino acid substituted in the position 38 where N replaced A between C. peloridis and C. volucris while six substitutions between C. curvus and C. concisus in the positions 94, 98, 118, 150, 153 and 160 so E, N, A, I, V and T and V replaced Q, S, P, V, I and S respectively. Seventeen amino acid substitutions between C. rectus and C.sputorum in the amino acid positions 6, 23, 32, 34, 42, 44, 47, 66, 68, 70, 94, 118, 122, 126, 127, 150 and 153 that made the two species being divergent from each other.
Bioprocess systems
Establishment of Fed-batch Fermentation Conditions for Biocontrol Bacteria B579	25-32
Fang Chen, Min Wang, Yu Zheng, Yanchun Zhang, Deduo Han, Shangjing Guo [ +/- abstract ][ full text ]
In order to increase the cell concentration in fermentation, feeding strategy and feeding amount were optimized. The result showed that glucose feedback feeding strategy is the best one, and glucose concentration should be controlled at 6.0 g/L during the fermentation of B. subtilis B579. The final cell concentration was 9.5×10⁹ CFU/mL, which represented a 1.9-fold increase when compared with those of before optimized. Feed-batch fermentation in 7L fermenter was conducted under the following condition: temperature 37°C, pH 7.0, DO 10%, then supplemented glucose to the fermenter during the fermentation, and kept the glucose concentration at 6.0 g/L, after 35 h fermentation the final cell concentration was 3.9×10¹⁰ CFU/mL, which represented a 3.8-fold increase compared with those of before optimized.
Biosorption of BF-4B Reactive Red Dye by using Leaves of Macrophytes Eichhornia crassipes	33-44
Aparecido Nivaldo Módenes, Andreine Aline Ross, Bruna Vanessa Souza, Juliana Dotto, Claudinéia Queli Geraldi, Fernando Rodolfo Espinoza-Quiñones, Alexander Dimitrov Kroumov [ +/- abstract ][ full text ]
The removal potential on BF-4B reactive red dye by Eichhornia crassipes dried leaves has been investigated. Furthermore, the influence of process parameters such as solution pH, agitation, and particle size on the dye adsorption efficiency was assessed. Both kinetic and equilibrium experiments were performed in batch operation of the system. Kinetic results demonstrated that the equilibrium state was achieved after 45 min process time. The kinetic experimental data were best described by applying a pseudo-second order model that evaluated the value of rate constant 0.22 g/mg/min and an equilibrium dye concentration 8.20 mg/g. A set of isotherm models, taken from knowledge database, was tested in order to represent the equilibrium adsorption data. The Langmuir model performed the best when fitting experimental data where the maximum adsorption capacity of 20.38 mg/g was achieved. The results demonstrated that the E. crassipes has good potential to be used as a biosorbent in industrial treatment systems to remove reactive dyes from textile effluents.
Biomedical systems
Is there an Optimal Shape of the Defibrillation Shock: Constant Current vs. Pulsed Biphasic Waveforms	45-56
Ivan Dotsinsky, Tsvetan Mudrov, Vessela Krasteva, Jecho Kostov [ +/- abstract ][ full text ]
Three waveforms for transthoracic defibrillation are assessed and compared: the Pulsed Biphasic Waveform (PBW), the Rectilinear Biphasic Waveform (RBW), and the "lossless" constant current (LLCC) pulses. Two indices are introduced: 1) k_f = W/W₀ - the ratio between the delivered energy W and the energy W₀ of a rectangular pulse with the same duration and electric charge; 2) η_C = W/W_C0 - the level of utilizing the initially loaded capacitor energy WC0. The envisioned comparative study shows that η_C index is favorable for both PBW and LLCC, while k_f of both RBW and LLCC demonstrates advantage over the PBW in the range of small inter-electrode thoracic impedances below 80 Ω. Some design considerations are also discussed. The attractive LLCC concept needs large and heavy inductive coil to support the constant current amplitude, besides it is capable to induce strong electromagnetic influences due to the complex current control. The RBW technology controls the delivery of current through a series of internal resistors which are, however, a source of high heat losses. The PBW implements controlled duty cycle of high-frequency chopped pulses to adapt the energy delivery in respect of the patient impedance measured at the beginning of the shock. PBW technology makes use of small capacitors which allows the construction of light weight and small-size portable devices for transthoracic defibrillation.