Bioautomation

Volume 18, Issue 1
Editorial
Anniversary
The 80th Birthday of Professor Ivan Dotsinsky
New Books
Bioinformatics
Molecular Docking Improvement: Coefficient Adaptive Genetic Algorithms for Multiple Scoring Functions	5-14
Zhengfu Li, Xicheng Wang, Keqiu Li, Junfeng Gu, Ling Kang [ +/- abstract ][ full text ]
In this paper, a coefficient adaptive scoring method of molecular docking is presented to improve the docking accuracy with multiple available scoring functions. Based on force-field scoring function, we considered hydrophobic and deformation as well in the proposed method, Instead of simple combination with fixed weights, coefficients of each factor are adaptive in searching procedure. In order to improve the docking accuracy and stability, knowledge-based scoring function is used as another scoring factor. Genetic algorithm with the multi-population evolution and entropy-based searching technique with narrowing down space is used to solve the optimization model for molecular docking. To evaluate the method, we carried out a numerical experiment with 134 protein-ligand complexes of the publicly available GOLD test set. The results validated that it improved the docking accuracy over the individual force-field scoring. In addition, analyses were given to show the disadvantage of individual scoring model. Through the comparison with other popular docking software, the proposed method showed higher accuracy. Among more than 77% of the complexes, the docked results were within 1.0 Å according to Root-Mean-Square-Deviation (RMSD) of the X-ray structure. The average computing time obtained here is 563.9 s.
Comparison of the Effects of Nanometer Titanium Dioxide with Two Crystal Forms on Rabbits Blood Routine Index and Organ Coefficient in the Instillation of Non-exposure Bronchus Toxic Contamination	15-22
Huyan An [ +/- abstract ][ full text ]
Purpose: to compare the effect of nanometer rutile TiO₂ and nanometer anatase TiO₂ with same dose and size on rabbit's important organ coefficient and blood routine. Method: divided 30 rabbits randomly into 5 groups, namely the saline control group, micron rutile TiO₂, micron anatase TiO₂, nanometer rutile TiO₂, nanometer anatase TiO₂. Dosed each rabbit with 2.5 ml·kg^-1·bw^-1 with one-time non-exposed pipe drip dye, and put them to death after 20 days. Determined the size, shape, main viscera quality, organic coefficient and blood routine (19 indicators) of nanometer TiO₂ with different crystals. Results: rabbit lung viscera coefficient in the nanometer rutile TiO₂ exposed group is obviously higher than that of micron anatase TiO₂ (p<0.05). Rabbit blood routine: nanometer rutile TiO₂ has the highest mean corpuscular-hemoglobin concentration, while the other three groups have significant differences in the mean corpuscular-hemoglobin concentration, p<0.05. For the white blood cell count (WBC), micron anatase TiO₂ group has the highest, while compared with the micron anatase TiO₂ group, the normal saline control group, micron rutile TiO₂ group and nanometer anatase TiO₂ group all have significant differences, p<0.05. Conclusion: nanometer rutile TiO₂ will increase rabbit lung viscera coefficient and mean corpuscular hemoglobin concentration. Toxic effect of nanometer rutile TiO₂ and nanometer anatase TiO₂ on rabbit are different.
In silico Sequence Analysis, Structure Prediction and Function Annotation of Human Bcl-X Beta Protein	23-30
Anjali Singh, Tapan Kumar Pal [ +/- abstract ][ full text ]
Bcl-X proteins are the one of the best categorized member of the Bcl-2 protein families which acts as primary regulators of apoptosis in mammalian cells. The Bcl-X proteins are potential anti-cancer drug targets. In this study, the tertiary structure of the beta isoform of the apoptosis regulator Bcl-X in humans (h-Bcl-Xβ) has been predicted by fold-recognition (threading) approach. In silico assessment of the h-Bcl-Xβ protein revealed the characteristic structural features of anti-apoptotic Bcl-2 protein family in h-Bcl-Xβ protein. The predicted model was comprised of BH1-BH4 domains, seven alpha-helices and a C-terminal transmembrane domain for membrane localization and sub-cellular targeting. Quality assessment of the predict model confirmed its reliability as fairly good model. Active sites of h-Bcl-Xβ protein were identified using CASTp server. The future work can be directed towards drug designing for cancer treatment by regulating the activity of h-Bcl-Xβ proteins.
Biomedical systems
Current Statement of Electrochemotherapy in Bulgaria	31-44
Biliana Nikolova, Ekaterina Peycheva, Tsvetan Mudrov, Tatiana Dobreva, Mikhail Matveev, Iana Tsoneva [ +/- abstract ][ full text ]
Electrochemotherapy is one fast, easy, effective and safe method for treatment of patients with clinical and cytological diagnosis of skin tumors as Carcinoma basocellulare, Carcinoma spinocellulare, Kaposi sarkoma and Mycosis fungoides in stage I (T1N0M0). Therapy is based on the temporary formation of pores on the surface of the cell membrane, resulting from the application of electric field with appropriate intensity and duration trough which the cytostatic drug as bleomycin is introduced into the tumor cells. This work presents data on the last version of electroporator and the treated patients by the method electrochemotherapy recently.
Bioecological systems
Method for Determining Organic Compound Concentration in Biological Systems by Permanganate Redox Titration	45-52
Оlga Suslova, Vera Govorukha, Оksana Brovarskaya, Nadezhda Matveeva, Hanna Tashyreva, Oleksandr Tashyrev [ +/- abstract ][ full text ]
An effective express method of determining organic compound concentration in biological systems (soil water extracts, culture liquid etc.) is developed. The method is based on the permanganate redox titration of carbon-containing sample in an acidic medium (pH ≈ 0) at temperature of 100°C. On the example of basic microbial metabolism of monosaccharides, alcohols, organic acids, the suitability of the method for quantitative determination of total organic carbons is shown. The method measures the rate of glucose consumption by Escherichia coli 926 (ATCC 8789) in M9 medium. We created the average calibration curve for determining carbon concentration in multi-component biological samples. The permanganate method provides high accuracy results which are comparable with the widely used phenol-sulfuric acid method. The sensitivity of the method to carbon concentration is 25 mg/l.