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Bioinformatics and Biomedical Research Journal
Published by Future Science
ISSN : -     EISSN : 26203324     DOI : 10.11594/bbrj
Core Subject : Science, Education, Engineering,
Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Education Engineering
Bioinformatics and Biomedical Research Journal (BBR) serve the interests of the research-oriented and professional section in the fields of Bioinformatics and Biomedical Research. The current emphasis of the BBR Journal includes (but is not limited to) the following areas: Drugs Discovery Genomics study Proteomics study, structural bioinformatics Pharmacogenomics Epigentics Gene Mutation Polimorfism Biomarker Pharmaceutical Biotechnology Pharmaceutical biosciences and other field related to bioimedical research
Arjuna Subject : Biokimia, Genetika dan Biologi Molekuler - Bioteknologi
Articles 37 Documents
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The Correlation Between Education Level, Knowledge and Motivation in Volunteer Performance: a Post-Study on Action Research in Developing Educator Volunteers for COVID-19 Based on community empowerment using a tiered and online platform in Indonesia Khuzaiyah, Siti; Priyogo, Nur Izzah; Setianto, Gigih
Bioinformatics and Biomedical Research Journal Vol. 3 No. 2 (2020): Volume 3 issue 2
Publisher : Future Science

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Abstract

Coronavirus infection is spreading globally, including in Indonesia. The coronavirus 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. Full support is needed for volunteers so that they are motivated to carry out their roles as educator volunteers of covid-19.
The Role of Phytochelatin Synthase in Phytoremediation Agent: Structural Conservation of Phytochelatin (PC) Synthase to Maintain Its Activity as Heavy Metal Detoxification in Plant Vidayanti, Viky; Permatasari, Galuh Wening
Bioinformatics and Biomedical Research Journal Vol. 3 No. 2 (2020): Volume 3 issue 2
Publisher : Future Science

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Abstract

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, Brassica sp., Amaranthus sp., Noccaea sp., Arabidopsis sp., Nicotiana sp., and Pteris sp. 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 based on 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.
Identification of Significant Proteins in Coronavirus Disease 2019 Protein-Protein Interaction Using Principal Component Analysis and ClusterONE Ananta Kusuma, Wisnu; Farhan Ramadhani , Hilmi; Annisa
Bioinformatics and Biomedical Research Journal Vol. 3 No. 2 (2020): Volume 3 issue 2
Publisher : Future Science

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Abstract

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 cluster. 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.
Prediction of Drug-Target Interaction Using Random Forest in Coronavirus Disease 2019 Case Fadli , Aulia; Annisa , Annisa; Kusuma, Wisnu Ananta
Bioinformatics and Biomedical Research Journal Vol. 4 No. 1 (2021): Vol 4 No 1 (2021)
Publisher : Future Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/bbrj.04.01.01

Abstract

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).
Isolation of Arbutin from Leaves and Fruits of Buni (Antidesma Bunius L. Spreng) As Tyrosinase Enzym Inhibitor Palensina, Gea Ocktiah; Rosita, Leni; Sagala, Zuraida
Bioinformatics and Biomedical Research Journal Vol. 4 No. 1 (2021): Vol 4 No 1 (2021)
Publisher : Future Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/bbrj.04.01.02

Abstract

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.
Phenol Coefficient Test Combination Infusion of Cananga odorata – Averrhoa bilimbi L. Against Staphylococcus aureus and Salmonella typhi in Vitro Budiarti, Lia Yulia; Wydiamala, Erida; Ulfa, Najiya
Bioinformatics and Biomedical Research Journal Vol. 4 No. 1 (2021): Vol 4 No 1 (2021)
Publisher : Future Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/bbrj.04.01.03

Abstract

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.
Antimicrobial Activity of Stenochlaena palustris and Sauropus androgynus in Staphylococcus aureus, Escherichia coli and Candidia albicans Budiarti, Lia Yulia; Isnaini, Isnaini; Dayana, Puteri; Sari, Norma; S., Nur Almira R.
Bioinformatics and Biomedical Research Journal Vol. 4 No. 1 (2021): Vol 4 No 1 (2021)
Publisher : Future Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/bbrj.04.01.05

Abstract

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).
The Correlation of Use of Depo Medroxy Progesterone Acetate (DMPA) In-jections with Lipid Profile Levels in Rats: - Suratiah, Suratiah; Surinati, Dewa Ayu; Yasa, I Dewa Gede Putu Putra
Bioinformatics and Biomedical Research Journal Vol. 4 No. 1 (2021): Vol 4 No 1 (2021)
Publisher : Future Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/bbrj.04.01.04

Abstract

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.
Phylogenetic Relationship of Genus Microhyla (Amphibia, Anura) in Sunda Shelf including Sumatra, Java, Borneo, and Peninsular Malaysia as revealed by 16S rRNA mtDNA Gene Sequences Firdaus, Anggun; Ratih, N; Karima, I; Kusuma, A T; Suastika, N M
Bioinformatics and Biomedical Research Journal Vol. 1 No. 1 (2018): Volume 1 Issue 1
Publisher : Future Science

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Abstract

Sundaland was a single large landmass during Pliocene and Pleistocene period and consisted of Java, Borneo, Sumatra, Malay-Peninsula and others smaller island. We used 26 partial DNA sequences of the mitochondrial DNA genes 16S rRNA from taxa of Microhylidae (23 genus Microhyla and 3 outgroups) from GenBank. We aligned sequences using MEGA 5 software. Phylogenetic trees were constructed using maximum parsimony (MP) and maximum likelihood (ML) with 1000 bootstraps. Our results reveal three monophyletic clades which are not supported: clade A (all Sundaland, including M. malang, M. borneensis, M. mantheyi, M. achatina, M. berdmorei, M. superciliaris, and M. palmipes); clade B (from Borneo and Malay Penisular, including M. annectens, M. perparva, and M. petrigena); and clade C (consists of outgroup species, Metaphrynella pollicaris, Chaperina fusca, and Kalophrynus heterochirus). Clade A reveal three subclades with unresolved relationship: AI (M. malang, M. borneensis, M. mantheyi, M. achatina, and M. berdmorei), AII (M. supercilliaris), and AIII (M. palmipes). Clade B reveal two well-supported subclades: BI (M. annectens) and BII (M. perparva and M. petrigena). Our results show that phylogenetic within genus Microhyla was mostly affected by species distributions. Keywords: Microhyla, phylogenetic, Sundaland
Identification Microorganism which have most stable ?-galactosidase Enzyme Based on Conformational Stability Karina, Sheilla W; Agustina, Didin Wahyu; Mu'jizah, Elzafa Y; Sari, Aprilia K
Bioinformatics and Biomedical Research Journal Vol. 1 No. 1 (2018): Volume 1 Issue 1
Publisher : Future Science

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Abstract

Lactose intolerant is a condition which people can not hydrolyze lactose into glucose and galactoside. Recently Asia have 80% intolerant people in number. Body can hydrolyze and absorb lactose because they have ?-galactosidase enzyme in their digestive system which intolerant people did not have it. Dairy food industry such as milk, cheese, yoghurt and other low lactose usually adding ?-galactosidase enzyme using microorganism as source, but sometimes ?-galactosidase was isolated from microorganism has low stability. This project aim to find microorganisms that produce most stable ?-galactosidase and could be recommended for commercial industries to producing food with low lactose. This research use two step, Homology Modeling of ?-galactosidase enzyme from 10 microorganism by swiss model and calculates the free energy of unfolding using FoldX at Yasara software. Based on energy of protein stability the highest stability is Bacterioides thetainomicron and Eschericia coli. Keywords: ?-galactosidase, Homology modeling, Microorganism, Protein stability

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