| Volume 28, Issue 1 | |
| Editorial | |
| Anniversary | |
| The 85th Birthday of Professor Stoyan Tzonkov, Honorary Chief Editor of the Int J Bioautomation | |
| The 70th Birthday of Academician Krassimir Atanassov, Topic Editor of the Int J Bioautomation | |
| Genome Wide Identification, Characterization and Evolutionary Analysis of T6SS in Burkholderia cenocepacia Strains | 5-30 |
| Sardarni K. Raza, Muhammad Ibrahim, Kainaat, Afshan Farid, Sardar S. N. Khan, Aqsa Talat, Tayyaba Arzoo, Syeda I. Fatima, Abdul Waheed | |
| doi: 10.7546/ijba.2024.28.1.000905 | |
| [ +/- how to cite ][ +/- abstract ][ full text ] | |
| Sardarni K. Raza, Muhammad Ibrahim, Kainaat, Afshan Farid, Sardar S. N. Khan, Aqsa Talat, Tayyaba Arzoo, Syeda I. Fatima, Abdul Waheed (2024) Genome Wide Identification, Characterization and Evolutionary Analysis of T6SS in Burkholderia cenocepacia Strains, Int J Bioautomation, 28 (1), 31-44, doi: 10.7546/ijba.2024.28.1.000905 | |
| Abstract: Pathogens of the Burkholderia genus are causing diseases in a diverse variety of hosts. After the discovery of T6SS, it was found to play a pivotal role in virulence and other pathogenicity factors in different pathogenic Burkholderia species. For this study, three strains of Burkholderia cenocepacia were selected from different ecological niches; J2315 from humans, MC0-3 from the rhizosphere of maize, and YG-3 from the Populus tree. The sequenced genomes were retrieved from PATRIC. It was found that B. cenocepacia J2315 and MC0-3 strains had only 1 cluster of T6SS in their genomes while the YG-3 strain had 3 clusters. The circular genomic map and phylogenetic tree suggested major differences in T6SS clusters 2 and 3 of the YG-3 strain from other clusters. From the results obtained in the study and reviewing the literature, it was concluded that all 3 strains harbor T6SS-1 type cluster that is involved in causing virulence in eukaryotic organisms and several bacterial species. This factor of causing virulence in the bacteria species might be helpful for B. cenocepacia strains J2315, MC0-3 and YG-3 in survival and niche adaptation.
Keywords: Burkholderia cenocepacia, Cross-kingdom, J2315, MC0-3, T6SS, YG-3 | |
| Dynamic Model Inference of Gene Regulatory Network based on Hybrid Parallel Genetic Algorithm and Threshold Qualification Method | 31-44 |
| Xiaomei Ding, Huaibao Ding, Fei Zhou | |
| doi: 10.7546/ijba.2024.28.1.000928 | |
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| Xiaomei Ding, Huaibao Ding, Fei Zhou (2024) Dynamic Model Inference of Gene Regulatory Network based on Hybrid Parallel Genetic Algorithm and Threshold Qualification Method, Int J Bioautomation, 28 (1), 5-30, doi: 10.7546/ijba.2024.28.1.000928 | |
| Abstract: Gene regulation is the process by which various substances in cells regulate the behaviour of gene expression, thereby controlling almost all cellular activities. Therefore, studying gene regulation not only helps to uncover the internal laws governing life processes but also plays a crucial role in predicting, diagnosing, treating, and designing drugs for genetic diseases. By utilizing multi-source biological information such as gene expression profiles, transcription factor information, and protein interaction data, a network model can be developed to depict the regulatory relationships between genes, facilitating further research. To address the limitations of traditional gene regulatory network construction methods, a novel dynamic model has been created by combining hybrid genetics and threshold restriction. This model comprises two parts: solution space reduction and parameter fitting. During solution space reduction, singular value decomposition is employed to define a mathematically feasible gene regulatory network, reducing unnecessary calculations. Subsequently, the control genes of each gene are constrained within a certain range using threshold limitation, enhancing computational efficiency while adhering to bioinformatics principles. In the parameter fitting phase, parallel genetic algorithms are utilized to expediently optimize the entire solution space. The mountain climbing method is then applied to solve problems meticulously within a limited scope, improving calculation accuracy. In this study, this approach was applied to establish genetic regulatory systems for complex skin melanoma and type 2 diabetes. Through comparison with actual networks, the validity of the method was confirmed. Compared to traditional genetic and particle swarm optimization methods, the effectiveness of the proposed method was verified. This paper models the intricate mechanism of gene regulation and elucidates the regulatory process involving genes, proteins, and small biological molecules in greater detail than other models, aligning more closely with intracellular dynamics laws.
Keywords: Hybrid parallel genetic algorithm, Threshold limit method, Singular value decomposition, Gene regulatory network | |
| Effect of Graphene Oxide and Ammonia-modified Graphene Oxide Particles on ATPase Activity of Rat Liver Mitochondria | 45-58 |
| Natalia Krasteva, Milena Shkodrova, Milena Keremidarska-Markova, Dilyana Doncheva-Stoimenova, Kamelia Hristova-Panusheva, Milena Mishonova, Mariela Chichova | |
| doi: 10.7546/ijba.2024.28.1.000957 | |
| [ +/- how to cite ][ +/- abstract ][ full text ] | |
| Natalia Krasteva, Milena Shkodrova, Milena Keremidarska-Markova, Dilyana Doncheva-Stoimenova, Kamelia Hristova-Panusheva, Milena Mishonova, Mariela Chichova (2024) Effect of Graphene Oxide and Ammonia-modified Graphene Oxide Particles on ATPase Activity of Rat Liver Mitochondria, Int J Bioautomation, 28 (1), 45-58, doi: 10.7546/ijba.2024.28.1.000957 | |
| Abstract: Graphene and its derivatives have become promising materials for biomedical applications in the last decade. Before their widespread application, however, evaluating their toxicity and mechanisms underlying interactions with cellular components is imperative. Aims: Assessment of the effect of two graphene derivatives, pristine graphene oxide (GO) and ammonia-modified GO (GO-NH2) particles, on the ATPase activity of rat liver mitochondria and ROS production. Methods: Liver mitochondria were isolated from male albino rats and treated with different concentrations of GO and GO-NH2 particles (4, 10, 25, and 50 μg/ml). ATPase activity of both, intact and uncoupled by freezing/thawing mitochondria was determined by the measurement of inorganic phosphate (Pi) released from ATP. The generation of hydrogen peroxide (H2O2) after exposure of mitochondria to GO and GO-NH2 particles was determined by a DCFH-D assay. Results: GO and GO-NH2 particles applied at concentrations of 4 and 50 μg/ml did not affect the ATPase activity of intact mitochondria. In contrast, in uncoupled mitochondria, they demonstrated a stimulating effect on ATPase activity. The impact of GO-NH2 was more substantial and concentration-dependent. ROS production was also higher in GO-NH2-treated mitochondria. Conclusion: The present study demonstrated that GO and GO-NH2 particles can exert a cytotoxic effect on mitochondria even after a short-time of exposure to both types of particles.
Keywords: Graphene-based flakes, Cytotoxicity, ATP production, Nanoparticle-induced mitochondrial toxicity | |
| Differential Effect of Novel Plant Cystatins on the Adhesive Behaviour of Normal and Cancer Breast Cells | 59-67 |
| Kamelia Hristova-Panusheva, Milena Keremidarska-Markova, Natalia Krasteva | |
| doi: 10.7546/ijba.2024.28.1.000971 | |
| [ +/- how to cite ][ +/- abstract ][ full text ] | |
| Kamelia Hristova-Panusheva, Milena Keremidarska-Markova, Natalia Krasteva (2024) Differential Effect of Novel Plant Cystatins on the Adhesive Behaviour of Normal and Cancer Breast Cells, Int J Bioautomation, 28 (1), 59-67, doi: 10.7546/ijba.2024.28.1.000971 | |
| Abstract: In the present work, we have investigated a novel recombinant cystatin dgECP1 and its mutant form, dgECP1m1, focused on their impact on the adhesive behaviour of two breast cell lines: the cancerous, MDA-MB-231, and the normal, MCF-10A. DgECP1 cystatin is intriguing with its RGD motif, responsible for cell adhesion and typical for mammalian extracellular matrix proteins but uncommon for plant cystatins. The presence of the RGD sequence suggests the potential of the dgECP1 to influence the adhesion of cancer cells and, respectively, cancer metastasis. A mutant form of the dgECP1cystatin, dgECP1m1, where RGD is replaced with HGD tripeptide, was also investigated. We found that both phytocystatins exerted differential effects on the adhesion behaviour of normal and cancer cells. In the case of dgECP1 cystatins, the effect on cancer cell adhesion also depends on the mode of administration of the cystatin to cells. When dgECP1 is pre-adsorbed on a substrate, it improves the attachment of breast cancer cells and induces cell aggregation, which is more typical for normal breast cells, and oppositely suppressed adhesion of cancer cells when added to the medium. The mutant form, dgECP1m1, inhibited cancer cell adhesion independently on the way of administration. On the other hand, both plant cystatins only slightly reduced the adhesion of normal mammary cells pointing to the higher sensitivity of cancer cells to both cystatins. These preliminary results open the possibility of considering the plant cystatin dgECP1 for anti-cancer strategies.
Keywords: Phytoprotease inhibitors, Phytocystatins, RGD motif, Metastasis, Cell attachment |
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