International Journal Bioautomation最新文献

{"title":"Genome Wide Identification, Characterization and Evolutionary Analysis of T6SS in Burkholderia cenocepacia Strains","authors":"Sardarni K. Raza, Muhammad Ibrahim, Kainaat, Afshan Farid, Sardar S. N. Khan, A. Talat, Tayyaba Arzoo, Syeda I. Fatima, Abdul Waheed","doi":"10.7546/ijba.2024.28.1.000905","DOIUrl":"https://doi.org/10.7546/ijba.2024.28.1.000905","url":null,"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.","PeriodicalId":38867,"journal":{"name":"International Journal Bioautomation","volume":"39 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140405395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic Model Inference of Gene Regulatory Network based on Hybrid Parallel Genetic Algorithm and Threshold Qualification Method","authors":"X. Ding, Huaibao Ding, Fei Zhou","doi":"10.7546/ijba.2024.28.1.000928","DOIUrl":"https://doi.org/10.7546/ijba.2024.28.1.000928","url":null,"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.","PeriodicalId":38867,"journal":{"name":"International Journal Bioautomation","volume":"38 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140405397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differential Effect of Novel Plant Cystatins on the Adhesive Behaviour of Normal and Cancer Breast Cells","authors":"K. Hristova-Panusheva, M. Keremidarska-Markova, Natalia Krasteva","doi":"10.7546/ijba.2024.28.1.000971","DOIUrl":"https://doi.org/10.7546/ijba.2024.28.1.000971","url":null,"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.","PeriodicalId":38867,"journal":{"name":"International Journal Bioautomation","volume":"105 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140403316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of Graphene Oxide and Ammonia-modified Graphene Oxide Particles on ATPase Activity of Rat Liver Mitochondria","authors":"Natalia Krasteva, M. Shkodrova, M. Keremidarska-Markova, Dilyana Doncheva-Stoimenova, K. Hristova-Panusheva, Milena Mishonova, M. Chichova","doi":"10.7546/ijba.2024.28.1.000957","DOIUrl":"https://doi.org/10.7546/ijba.2024.28.1.000957","url":null,"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.","PeriodicalId":38867,"journal":{"name":"International Journal Bioautomation","volume":"99 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140405727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Ecological Role of Probiotics in in vitro Culture for the Improvement of Health in the Poultry Industry","authors":"Olivier Nsenge, B. Mangata, D. Eyul’anki, Emmanuel Makaly","doi":"10.7546/ijba.2023.27.4.000925","DOIUrl":"https://doi.org/10.7546/ijba.2023.27.4.000925","url":null,"abstract":"The general objective of this work was to isolate from yoghourts cultured strains of lactobacilli with potential for use as probiotics in poultry farming. Three yoghourts were cultured to see the presence of lactobacilli in the Rogosa agar base culture medium. It was found that only one yoghourt (number 1) showed the growth of lactobacilli. This yoghourt was immediately selected for further cultivation. Afterwards, the Lactobacillus strains were isolated and fortified under CO2 and then inoculated into a solution of peptone water, which constituted inoculums to be administered to an experimental group of poultry. Another group served as controls. Pathogenic strains of Escherichia coli were also administered to both groups (experimental and control, each comprising five hens). The results showed significant weight gain from the experimental group (positive effect on immunity) and freedom from disease after an incubation period (inhibitory effect of the lactobacillus strains on the Escherichia coli strains), whereas the control group showed less weight gain than the experimental group and development of colibacillosis after an incubation period. The positive effects of the Lactobacillus strains observed on the poultry of the experimental group proved the ecological role of these microorganisms in improving the health of the poultry by inhibiting the effects of pathogenic Escherichia coli strains. This suggests reassuring prospects for the reduction of antibiotic use in both human and animal care.","PeriodicalId":38867,"journal":{"name":"International Journal Bioautomation","volume":"144 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139014463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterizing Morphometric and Nanomechanical Malignant Cell Features in a Rare Paediatric γδ T-acute Lymphoblastic Leukaemia: Insights from a Single Case Study Using Atomic Force Microscopy","authors":"Konstantin Bachvarov, Velichka Strijkova, B. Antonova, Maya Jordanova, Yoan Dimitrov, S. Todinova","doi":"10.7546/ijba.2023.27.4.000949","DOIUrl":"https://doi.org/10.7546/ijba.2023.27.4.000949","url":null,"abstract":"The most common cancer in paediatric age is acute lymphoblastic leukaemia (ALL) which accounts for nearly a quarter of all cases of paediatric cancer. ALL cases are classified as B-cell or T-cell precursor ALL, based on their immunophenotypical features. Patients with T-cell ALL (T-ALL) comprise 10–15% of all newly diagnosed cases and are more prevalent in boys and in older age compared to the overall incidence peak age of ALL. In this case report, we present the morphometric and nanomechanical features of T-lymphoblasts derived from an 11-month-old infant with a rare subtype of γδ T-ALL with aggressive biological behavior. To investigate these features, we employed atomic force microscopy (AFM) and compared the blast cell deviations found in their nanostructure and elasticity to those of normal lymphocytes from a healthy child. The malignant T-lymphoblasts exhibited reduced roughness and Young’s modulus values. This single case analysis demonstrates the potential of the AFM method to provide additional information regarding the characteristics of malignant cells and suggests its potential as a complementary approach for distinguishing neoplastic cells from normal cells. The application of AFM could potentially facilitate the introduction of in vitro tests to determine the efficacy of anti-leukemic treatments.","PeriodicalId":38867,"journal":{"name":"International Journal Bioautomation","volume":"21 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139024481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Physical Framework for Testing and Evaluating of a Mechatronic Shunting System","authors":"A. Alkharabsheh, L. Momani, Yousef Qawaqzeh, A. Alsakarneh","doi":"10.7546/ijba.2023.27.4.000938","DOIUrl":"https://doi.org/10.7546/ijba.2023.27.4.000938","url":null,"abstract":"Shunt is a flexible tube called a catheter implanted inside the brain where cerebrospinal fluid (CSF) is produced. Existing treatments rely on passive implantable shunts with differential pressure valves. The authors defined, designed, and programmed an intelligent wireless hydrocephalus shunting system. The shunting system was designed, simulated, and tested to carry out many tasks such as regulating the mechatronic valve, collecting Injection Control Pressure (ICP) readings, analyzing these readings, responding to all emergency cases, and diagnosing the whole shunting system. Nowadays, many challenges face clinical trials for new medical devices. Clinical trials are complex and require following several rules and regulations to ensure compliance with different standards. Due to the difficulty of using medical trials, an urgent need for a physical framework for implementing a virtual model of intracranial pressure and cerebrospinal fluid dynamics in hydrocephalus mechatronic shunt testing. Such a physical framework will play a vital role in assessing the functioning of the whole mechatronic shunting system. A framework of a mechatronic shunting system (implanted and external) is illustrated and integrated with embedded management and diagnosis software. Such a framework will help assess, test, and evaluate the main functions of the proposed shunting system.","PeriodicalId":38867,"journal":{"name":"International Journal Bioautomation","volume":"153 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139015356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Semi-synthetic EEG Data for the Evaluation of Linear EEG Cleaning Methods","authors":"Wadda Benjamin du Toit, Martin Venter, David Vandenheever","doi":"10.7546/ijba.2023.27.4.000907","DOIUrl":"https://doi.org/10.7546/ijba.2023.27.4.000907","url":null,"abstract":"Electroencephalography (EEG) data recordings can be contaminated by artefacts that reduce the quality and make analysis difficult, and therefore cleaning methods are essential for accurate analysis of EEG data. It is not yet well established how to measure performance based on measured contaminated data since there is no established benchmark for comparison. Here we use “clean” EEG data synthetically contaminated by electrocardiography (ECG), electrooculography (EOG) and electromyography (EMG). This introduces fewer assumptions to the comparison between various cleaning methods, providing a clear datum for comparison. Further contamination is controlled, adding artefacts individually and also as a combination of artefacts. The results show that signal to noise ratio (SNR) of the simulated artefacts was within the same ranges as found with measured artefacts from literature. Popular linear cleaning methods were evaluated on the dataset, showing similar results to those in the literature, further validating the usefulness and accuracy of the semi-synthetic dataset. The semi-synthetic dataset showed comparable characteristics to real measured EEG data and proved useful in the assessment of EEG cleaning methods. The cleaning methods showed varied results when performance was evaluated on individual artefacts.","PeriodicalId":38867,"journal":{"name":"International Journal Bioautomation","volume":"339 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139023686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Effects of Mountain Hiking on Physical Condition of Youth Basketball Players during the Preparatory Phase","authors":"V. Jordanov, Simeon Ribagin","doi":"10.7546/ijba.2023.27.4.000967","DOIUrl":"https://doi.org/10.7546/ijba.2023.27.4.000967","url":null,"abstract":"In team sports, according to perform variety of motor skills, development of special abilities and overall physical fitness it is of great importance to optimize the training programs which involves progressive cycling of various aspects during a specific periods of time. Most coaches and athletes change the intensity, volume, and exercises in their workouts to improve performance. Little is known about the effects of mountain hiking on physical condition and preparation of youth basketball players and implementation of such activities in the training programs. Therefore, this study aims to analyze the effects of a mountain hiking on the physical condition of youth basketball players during the preparatory phase and to compare the results with the results of a control group of players performing standard training sessions in the same training period.","PeriodicalId":38867,"journal":{"name":"International Journal Bioautomation","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139024234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico Analysis Predicts that Mir-6770-5p Can Target the X Gene of All Hepatitis B Virus Genotypes","authors":"Amrizal Muchtar, Ramdhani M. Natsir, Minarty M. Natsir, Andi Sitti Fahirah Arsal, Hisashi Iizasa, Hironori Yoshiyama","doi":"10.7546/ijba.2023.27.3.000915","DOIUrl":"https://doi.org/10.7546/ijba.2023.27.3.000915","url":null,"abstract":"To date, effective medication against hepatitis B virus (HBV) has not been developed. MicroRNAs (miRNAs) comprise a promising therapeutic approach to inhibit the virus. In this study, 1917 miRNAs in the miRBase database were screened using bioinformatics software to obtain candidates that can target HBV genotype B. Two parameters, namely pairing pattern and minimum free energy were used to select the qualifying miRNAs. Three miRNAs targeting the X gene and one miRNA targeting the C gene were identified out of 39 initial candidates. Uniquely, miR-6770-5p was the only candidate that could target the X gene of all HBV genotypes, with a higher potency of inhibition compared to other candidates. The three other candidates also showed good potency for some genotypes; thus, the identified candidates show promise as therapeutics for hepatitis infection.","PeriodicalId":38867,"journal":{"name":"International Journal Bioautomation","volume":"47 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135589081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}