Bioinformatics and Biomedical Research Journal
Latest articles in this journal
Bioinformatics and Biomedical Research Journal, Volume 4, pp 1-7; https://doi.org/10.11594/bbrj.04.01.01
Coronavirus disease 2019 is an infectious disease that causes severe respiratory, digestive, and systemic infections that caused a pandemic in 2019. One of the focuses of the drug development process to fight the coronavirus disease 2019 is by carrying out drug repurposing. This study uses random forest with a feature-based chemogenomics approach on the drug-target interaction data of coronavirus disease 2019. The feature extraction process is carried out on compounds and protein using PubChem fingerprint and amino acid composition respectively. Feature selection using XGBoost is done to reduce the data dimension. The random undersampling process was also carried out to solve the problem of imbalanced data in the dataset. Using the cross-validation process, the random forest model produced an average accuracy value of 0.98, recall value of 0.92, precision value of 0.95, AUROC value of 0.95, and F1 score of 0.93. The random forest model also produced an accuracy value of 0.99, recall value of 0.93, the precision value of 0.94, AUROC value of 0.99, and F-measure of 0.94 when used to predict the original dataset (dataset without random undersampling process).
Bioinformatics and Biomedical Research Journal, Volume 4, pp 8-18; https://doi.org/10.11594/bbrj.04.01.02
Several studies have shown that plant extractive substances have the potential as active compounds inhibiting the enzyme tyrosinase. Arbutin is an enzyme inhibitor of tyrosinase, known as a popular whitening agent used in cosmetics because of its effectiveness in overcoming skin hyperpigmentation. The purpose of this study was to conduct a qualitative and quantitative analysis of arbutin on Buni Leaves and Fruits (Antidesma bunius L. Spreng). The raw simplicia used are mature and young buni leaves, green, red and purple buni fruits. The extraction method is maceration using methanol as solvent. The initial screening for arbutin content was carried out using thin layer chromatography (TLC) and dichlormethan:methanol 50:50 used as mobile phase. Isolation of arbutin content was carried out using Preparative TLC with the same eluent. Qualitative and quantitative analysis were performed using High Pressured Liquid Chromatography (HPLC) with mobile phase of acetonitrile: water 60:40. The tyrosinase enzyme inhibition activity test was then carried out in vitro using 96-well microplate, l-tyrosine and l-dopa were used as substrate at a wavelength of 492 nm. The Rf values obtained ??for mature buni leaves and green buni fruits, respectively 0.61 and 0,62. The retention time of HPLC chromatogram respectively 2,784 minutes and 2,758 minutes. Arbutin levels in leaves and fruits are 7.9 mg / g and 2 mg / g. The activity of the enzyme tyrosinase of mature buni leaves on L-dopa and L-tyrosine substrate were respectively stated as IC50 values ??of 88.7191ppm and 101.33347 ppm. The activity of the enzyme tyrosinase of the green buni fruit on L-dopa and L-tyrosine substrate respectively stated IC50 values ??of 198,0293 ppm and 246,1296 ppm.
Bioinformatics and Biomedical Research Journal, Volume 4, pp 32-38; https://doi.org/10.11594/bbrj.04.01.05
Stenochlaena palustris and Sauropus androgynus are known to contains antimicrobial substances such as flavonoids, saponins and tannins compounds.The purpose of this study was to analyzes the antimicrobial activity of young and old leaf infusions of S. palustris and S. androgynus leaves against Staphylococcus aureus, Escherichia coli and Candida albicans. Analyze the antibacterial activity of a single preparations with a combination preparation of S.palustris (SP) and S.androgynus (SA) leaves infusion against S.aureus, E.coli and C.albicans. Leaves of S.palustris young part (SP1) taken 0-10 cm from shoots and old parts (SP2) 11-20 cm from shoots, while leaves of S.androgynus young part (SA1) leaves number 1 - 10 from the top and the old part (SA2) leaves number 11-20 from the top. The results showed that a single infusion of SP1 75% and SP2 75%, SA1 90% and SA2 90%, and a combination of SP1 75% and SA1 75%, SP2 75% and SA2 75% have the same activity as ampicillin in S.aureus. Single infusion of SP1 90% and SP2 90%, SA1 90% and SA2 90%, combination of SP1 75% and SA1 80% and the combination of SP2 80% and SA2 60% have the same activity as ciprofloxacin in E. coli. Single infusion of SP1 90% and SP2 90%, and a combination of SP1 80% and SA1 80%, SP2 80% and SA2 80% have the same activity as ketoconazole in C.albicans. The difference in activity due to differences in leaf parts used only occurred in E. coli, whereas in S.aureus and C.albicans (p <0.05).
Bioinformatics and Biomedical Research Journal, Volume 4, pp 27-31; https://doi.org/10.11594/bbrj.04.01.04
Introduction: Family Planning is a national strategy of Indonesia government to manage the population growth. Depo Medroxyprogesterone Acetate (DMPA) is one of injectable contraceptives most widely used because it is simple and easy to obtain. However, it has various side effects causing imbalance of hormone estrogen, in turns to result in a decrease in HDL (High Density Lipoprotein) and an increase in LDL (Low Density Lipoprotein) which will result in an increase in total cholesterol. It will also affect changes in fat metabolism in human body due to hormonal influences. This results in dyslipidemia and atherosclerosis. Method: The method in this study is an experimental study with a pretest-posttest control group design. Results: The purpose of this study was to determine the relationship between duration of use of DMPA injections with lipid profile levels in mice. The data were analyzed by using the Paired t-test parametric test to compare between treatment groups. This study found that there were significant differences in HDL levels and total cholesterol levels between before and after administration of DMPA injections on the 14th and 35th days. There is a significant relationship between the duration of administration of DMPA injections with HDL levels and total cholesterol levels in mice. However, there was no difference in LDL levels and triglyceride levels between before and after administration of DMPA injection on day of 14 and day of 35, while, there was a significant difference between before and after the 35th day. There is no relationship between duration of administration of DMPA injections with LDL levels, while there is a relationship among mice triglycerides. Conclusions: Administration of DMPA injections for a long time lowers HDL.
Bioinformatics and Biomedical Research Journal, Volume 4, pp 19-26; https://doi.org/10.11594/bbrj.04.01.03
Cananga odorata (kenanga) flowers and Averrhoa bilimbi L. (belimbing wuluh) fruit are plant parts that contain relatively the same antibacterial compounds, namely flavonoids, saponins, and tannins. Both of these plants can be developed as an alternative natural antiseptic preparation, which is made in the form of a combination infusion. The effectiveness of an antiseptic preparation is measured by the coefficient value of the phenol antiseptic substance compared to 5% phenol against several standard test bacteria. This study aims to determine the antibacterial activity of the combination infusion of Cananga odorata flower - Averrhoa bilimbi L. fruit against Staphylococcus aureus ATCC 25923 and Salmonella typhi ATCC 19430 based on the in vitro phenol coefficient test. The phenol coefficient test method was carried out conventionally. The coefficient value close to 1 can be said that the antiseptic preparation has good activity and is equivalent to the phenol coefficient value as a comparison. The results showed that the mean coefficient of the phenol coefficient of the combination infusion of Cananga odorata flower - Averrhoa bilimbi L. fruit was 0.91 against S. aureus and 0.83 against S. typhi. The conclusion of this study, the antibacterial activity of the combination infusion of Cananga odorata flower - Averrhoa bilimbi L. fruit against Staphylococcus aureus obtained a higher phenol coefficient value than Salmonella typhi.
Bioinformatics and Biomedical Research Journal, Volume 3, pp 25-34; https://doi.org/10.11594/bbrj.03.02.04
Coronavirus Disease 2019 (COVID-19) will cause disease complications and organ damage due to excessive inflammatory reactions if left untreated. Computational analysis of protein-protein interactions can be carried out in various ways, including topological analysis and clustering of protein-protein interaction networks. Topological analysis can identify significant proteins by measuring the most important nodes with centrality measurements. By using Principal Component Analysis (PCA), the types of centrality measures were extracted into the overall centrality value. The study aimed to found significant proteins in COVID-19 protein-protein interactions using PCA and ClusterONE. This study used 57 proteins associated with COVID-19 to obtain protein networks. All of these proteins are homo sapiens organism. The number of proteins and the number of interactions from 57 proteins were 357 proteins and 1686 interactions. The results of this study consisted of two clusters; the best cluster was the first cluster with a lower p-value but had an average overall centrality value that closed to the second clus-ter. There are twenty important proteins in that cluster, and all of these proteins are related to COVID-19. These proteins are expected to be used in the process of discovering medicinal compounds in COVID-19
Bioinformatics and Biomedical Research Journal, Volume 3, pp 35-40; https://doi.org/10.11594/bbrj.03.02.05
Empeh is an Indonesian traditional fermented food with rich nutrition and bioactive components. Rhizopus sp,especially Rhizopus oligosporus), lactic acid bacteria (Lactobacillus sp.), and yeast aremicroorganisms involved in Tempeh fermentation. An interesting offer of Bioinformatics (in silico method) as a supporting tool in molecular biology studies has emerged, such as in protein cleavage. This study utilized PeptideCutter application on ExPASyBioinformatics portal (https://web.expasy.org/peptide_cutter/) to cleave soy proteins glycinin G1, G2, G3, G4,G5,-conglycinin-chain,andchainusingavailable enzymes in the applicationwith twosimulations. Simulation I was conducted using enzyme complex produced by Lactobacillus sp.and Rhizopus oligosporus, whilesimulation II was used enzyme complex produced by Lactobacillus sp., Rhizopus oligosporus, and Klebsiella pneumonia. Simulation I was conducted using enzyme complex produced by Lactobacillus sp. and Rhizopus oligosporus, whilesimulation II was used enzyme complex produced by Lactobacillus sp., Rhizopus oligosporus, and Klebsiella pneumoniae. A total of 58 peptides was found from the simulation I and higher than simulation I (41 peptides). The bioactive peptides by the cleavages using PeptideCuttertool were dominated with dipeptides and only three peptides were in the form of tripeptides, namely Leu-Leu-Phe(glycininG1), Val-Val-Phe(glycininG5), and Arg-His-Lys(-conglycinin-chain). Bioactive peptides with antihypertensive and antidiabetic properties were mostly found in this in silicomethod of soybean cleavage.
Bioinformatics and Biomedical Research Journal, Volume 3, pp 15-24; https://doi.org/10.11594/bbrj.03.02.03
Liver fibrogenesisis chronic tissue damage characterized by an extracellular ac-cumulation of fibrillar matrix associated with continuous degradation and remod-elling. This scientific review describes current concepts on the pathophysiology of liver fibrosis, inflammation asa fundamental concept of liver fibrosis, mechanistic concepts of liver fibrosis, the role of mesenchymal stem cells (MSC) in liver injury, the functional effects of MSC secretome, the advantages of secretome ther-apy, and the latest research developments on MSC. The role of MSCs has been proven in many liver fibrosis studies involving experimental animals. However, it still requires further research for safety and efficacy aspects.
Bioinformatics and Biomedical Research Journal, Volume 3, pp 9-14; https://doi.org/10.11594/bbrj.03.02.02
Phytochelatin (PC) Enzyme has crucial role in heavy metal detoxification and homeostasis in plants. This study aimed to evaluate the genetic variation of PC synthase related to its activity based on structural comparison. We evaluated PC genes and protein sequences from 6 plants namely, Brassicasp., Amaranthussp., Noccaeasp., Arabidopsissp., Nicotianasp., and Pterissp. All sequences were aligned based on CLUSTALW matrix for DN sequences and MUSCLE algorithm for protein sequences. Data were clustered using MEGA Software for similarity clustering. Selected data were further modeled using SWISSMODEL to evaluate the 3D-structural analysis based on homology modeling. Thus, all protein models were superimposed and evaluated the structure comparison based on RMSD data. The result showed that genetic variation of PC gene is high among species. But it is clustered for the same species has similar sequence. In addition, protein sequences also showed the high diversity among species and it is still clustered basedon their genus. RMSD data showed that PC synthase from 6 plant has similar structure and tend to conserved even there is genetic variation or amino acid modification. We concluded that structural of PC gene is more conserved than its sequences. It is important to keep its function among species.
Bioinformatics and Biomedical Research Journal, Volume 3, pp 1-8; https://doi.org/10.11594/bbrj.03.02.01
COVID-19 infection is spreading globally, including in Indonesia. The corona-virus transmits so quickly; there is panic in the community to avoid transmission. Stakeholders could develop educator volunteers based on community empowerment to increase public knowledge so that they can prevent transmission of the Corona Virus. Aims. This study aimed to determine the correlation between education level, knowledge and motivation in volunteer performance after training on developing educator volunteers of COVID-19. Methods. This study was action research with a post-test evaluation approach The population in this study were 250 educator volunteers of COVID-19. The sampling technique used a Slovin formula with the total sample was 50 people. The data were analyzed using the Pearson chi-square test and Spearman rank. Results. There was a significant correlation between motivation for volunteer performance (p-value 0.014). Meanwhile, the education and knowledge variables did not have a substantial correlation on volunteer performance with p-value 0.917 and 0.243, respectively. Conclusions. Mental and material support from Muhammadiyah Board (as the leader) are needed for volunteers so that they are motivated to carry out their roles as educator volunteers of COVID-19.