Bioinformatics and Biomedical Research Journal
type: channel
description: Bioinformatics and Biomedical Research Journal is peer-reviewed online journal. We publish original research papers, review articles, and commentaries in the area of Bioinformatics and Basic or Translational Biomedical Sciences, including Molecular and Cellular biology, Cancer biology, Bioinformatics, Microbiology, Immunology, Pharmacology, Genetics, Biochemistry, Nanobiotechnology, Medical toxicology, and Occupational health. The aim of the journal is to provide a platform which allow researchers and academics to access and discuss relevant information that advances our understanding on biomedical problems. BBR Journal welcomes submissions of experimental research findings related to medicine and medical issue, including molecular mechanism of specific disease, gene regulation in normal and pathologic cells, design and delivery of therapeutic drugs, discovery of potential drug targets, and innovative techniques for diagnosis. This journal is published two times per year, June and December. Accepted manuscript is subject to peer-review to ensure the quality before it is published. All articles published are made freely and permanently accessible online immediately upon publication.
publisher: Future Science
language: en
publication name: Bioinformatics and Biomedical Research Journal
issn: 2620-3324
copyright: The copyright to this article is transferred to Galaxy Sciences (including without limitation, the right to publish the work in whole or in part in any and all forms of media, now or hereafter known) effective if and when the article is accepted for publication thus granting Galaxy Sciences all rights for the work so that both parties may be protected from the consequences of unauthorized use. The copyright transfer covers the exclusive right to reproduce and distribute the article, including reprints, translations, photographic reproductions, microform, electronic form (offline,online) or any other reproductions of similar nature. The authors warrant that their contribution is an original work not published elsewhere, that they have the full power to make this grant and that the article contains no matter unlawful or which invades the right to privacy or infringes any proprietary right. Reproducing Published Material from other Publishers It is absolutely essential that authors obtain permission to reproduce any published material (figures, schemes, tables or any extract of a text) which does not fall into the public domain, or for which they do not hold the copyright. Permission should be requested by the authors from the copyright holder (usually the Publisher, please refer to the imprint of the individual publications to identify the copyright holder). Permission is required for: Your own works published by other Publishers and for which you did not retain copyright. Substantial extracts from anyones’ works or a series of works. Use of Tables, Graphs, Charts, Schemes and Artworks if they are unaltered or slightly modified. Photographs for which you do not hold copyright. Permission is not required for: Reconstruction of your own table with data already published elsewhere. Please notice that in this case you must cite the source of the data in the form of either “Data from…” or “Adapted from…”. Reasonably short quotes are considered fair use and therefore do not…
items: Environmental Epigenetics: Effects of Endocrine Disruptors on Development of Obesity – Statistical Analysis
items: Identification Microorganism which have most stable ?-galactosidase Enzyme Based on Conformational Stability
items: Interaction Between Receptor TIR1 and Auxin Plant Hormone in Arabidopsis thaliana
items: Inter-species Agouti Signaling Protein (ASIP) Polymorphism Using Phylogeny Analysis
items: 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
items: Prediction of Novel Bioactive Compound fromZingiber officinale as Non-Nucleoside ReverseTranscriptase Inhibitors (NNRTIs) of HIV-1 through Computational Study
items: In Silico Study of Avocado (Persea Americana Mill.) Seed Compounds Against PBP2a Receptor onStaphylococcus aureus
items: Molecular Docking Study of Lycopene on Reducing the DNA-methyltransfer in Prostate Cancer
items: In Silico Analysis and Identification of Possible Inhibitor of H5N1 Virus
items: Medication Error Factors, Safety Guideline System, Flow of Drug Usage, and Code of Conduct toPrevent Medication Error
items: Incidence Rate of Myocardial Infarction in HIV–Infected Individuals: A System-atic Review and Meta–Analysis
items: 43 Years Old Female with Acquired Hemophilia Presented with Pseudotumor
items: Cytotoxicity Test on Breast Cancer Cell Lines T-47D treatedwith Pisang Kepok Peel Extract (Musa balbisiana)
items: The Mutation Effect of Neuraminidase and Screening Bioactive Compound toInhibiting Neuraminidase in H5N1
items: Arrangement of Burn Status for Emergency Management, Monitoring, and Evaluation of Burns in Saiful Anwar General Hospital in Malang, East Java, Indonesia
items: Can Cinnamaldehyde Increased the Innate Immune System on Medaka Larvae?
items: The Binding Prediction Model of the Iron-responsive Element Binding Protein and Iron-responsive Elements
items: The Connection of Distribution Location with Primate Kinship in Indonesia Based on Cytochrome B In Silico Analysis
items: Phylogenetic Analysis and Time Divergence of Genus Musa spp. Using S16 Protein Genes (Rps16) Intron Chloroplast
items: Bioactive Peptides from Tempeh Using Peptidecutter’s Cleavage
items: Identification of Significant Proteins in Coronavirus Disease 2019 Protein-Protein Interaction Using Principal Component Analysis and ClusterONE
items: The Art of Mesenchymal Stem Cells in Liver Fibrosis Management
items: The Role of Phytochelatin Synthase in Phytoremediation Agent: Structural Conservation of Phytochelatin (PC) Synthase to Maintain Its Activity as Heavy Metal Detoxification in Plant
items: https://journal.futuresciencepress.com/index.php/bbrj/article/view/30
items: Antimicrobial Activity of Stenochlaena palustris and Sauropus androgynus in Staphylococcus aureus, Escherichia coli and Candidia albicans
items: The Correlation of Use of Depo Medroxy Progesterone Acetate (DMPA) In-jections with Lipid Profile Levels in Rats
items: Phenol Coefficient Test Combination Infusion of Cananga odorata – Averrhoa bilimbi L. Against Staphylococcus aureus and Salmonella typhi in Vitro
items: Isolation of Arbutin from Leaves and Fruits of Buni (Antidesma Bunius L. Spreng) As Tyrosinase Enzym Inhibitor
items: Prediction of Drug-Target Interaction Using Random Forest in Coronavirus 2019 Case
items: FUNDAMENTALS OF PROTEIN-PROTEIN INTERACTIONS AND THEIR METHODS OF CHARACTERIZATION

Environmental Epigenetics: Effects of Endocrine Disruptors on Development of Obesity – Statistical Analysis
type: item
description: Specific epigenetic alternation occurs by direct exposure to toxicants or abnormal nutrition, which influence disease development or physiological phenotypes. Previous study has demonstrated that exposure to endocrine disrupting compounds (EDCs) may contribute to excess adiposity and other features of dysmetabolism, accordingly, EDCs exposure may contribute to development of obesity, and insulin resistance, common precursors of type 2 diabetes and cardiovascular diseases. However, at this time, there is limited human data about contribution of environmental chemicals to the obesity epidemic. As obesity is a major public health problem in Indonesia, it is important to identify common environmental risk factors that may have a role in the development of obesity. Therefore, the objective of this study is to proof whether environmental factors/EDCs affect the development of obesity by using top-down approaches. Use two datasets, expression profile and methylation profile, from NCBI GEO database and apply statistical analysis to investigate the differentially expressed gene, analysis was conducted in R software and GEO2R web tool. Environmental epigenetics help to better understand how endocrine disruptors influences human health and disease, and there are two genes are found to be contribute to the weight gain. Further research is needed to have more confidence result of the analysis.
subject: Articles
  topic: section
subject: Epigenetics
  topic: keywords
subject: obesitas
  topic: keywords
subject: endocrine disruptor
  topic: keywords
subject: environmental factor
  topic: keywords
subject: statatistical analysis
  topic: keywords
creator: Mika Kuno
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2018-02-27
publication date: 2018-02-27
starting page: 22
ending page: 27
doi: 10.11594/

Identification Microorganism which have most stable ?-galactosidase Enzyme Based on Conformational Stability
type: item
description: 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.
subject: Articles
  topic: section
subject: β-galactosidase
  topic: keywords
subject: Homology Modeling
  topic: keywords
subject: Microorganism
  topic: keywords
subject: Stability Protein
  topic: keywords
creator: Sheilla W. Karina
creator: Didin W. Agustina
creator: Elzafa Y. Mu’jizah
creator: Aprila K. Sari
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2018-02-27
publication date: 2018-02-27
starting page: 17
ending page: 21
doi: 10.11594/

Interaction Between Receptor TIR1 and Auxin Plant Hormone in Arabidopsis thaliana
type: item
description: Auxins in gene transcription have influence that primarily mediated by TIR1 receptors, which can change the conformation of receptors and thereby promotes their interaction with auxin proteins. Recent research findings provide an increased understanding of the auxins that usually used in Arabidopsis thaliana was IAA and IBA in plant culture. The objectives of this to know the most potential auxin for inducing TIR1 receptor. Ligand (IAA, IBA, 2,4D, IPA, NAA, and Indole acetamid) and receptor (TIR1) collected from PDB, structure visualization using Pymol[10], docking between them using PyRx, and analysis of the interation using LigPlot+. Each ligand dock with receptor TIR1 in the same binding site. Docking result show IAA and IBA have highets binding affinity than other ligands. Binding analysis result show each ligand bind with different amino acid on receptor TIR1. 2,4D bind with Ser438; IAA with Leu439, Ser438, and Arg403; IBA with Leu439, Ser462, Arg436, and Arg403; Indole acetamid with Leu439, Ser438, and Arg403; IPA Leu439, Arg403, and Ser438; also NAA with Leu439.
subject: Articles
  topic: section
subject: Auxins
  topic: keywords
subject: Docking
  topic: keywords
subject: In silico
  topic: keywords
subject: TIR 1
  topic: keywords
creator: Anisa Nofita Sari
creator: Nindyawati, D. L
creator: Aqmarina, A
creator: Widhiya, E. W
creator: Lestari, N. D
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2018-02-27
publication date: 2018-02-27
starting page: 11
ending page: 16
doi: 10.11594/

Inter-species Agouti Signaling Protein (ASIP) Polymorphism Using Phylogeny Analysis
type: item
description: Variability of colour phenotypes in animal have encoded by agouty signaling protein (ASIP) and melanocortin 1 receptor (MC1R) gene polymorphisms and the pigmentation is afected by extension and agouti loci affect. Mutation in ASIP have been reported to completely eliminate the function or expression of the ASIP protein, this caused by a complete or several absence of alternative switch between eumelanin or pheomelanin syntesis and result only one of their to produce pigment. We collected nucleotide and protein sequence ASIP CDS from 7 specieses in gene bank and use a phylogenetic tree to know the distance of genes. The conserved regions lies on position 602-617 bp with consensus of 602 TGAACAAGAAATCCAA 617 which is the evidence of close taxonomic relation. Variation analyze show polimorfic white colour (G/T) black colour, white colour in Equus caballus (T/A). We found a polymorphic regions that explain the corelation to coat colour sgnaling in animal.
subject: Articles
  topic: section
subject: ASIP
  topic: keywords
subject: coloring
  topic: keywords
subject: mutation
  topic: keywords
subject: phenotype
  topic: keywords
subject: polymorphism
  topic: keywords
creator: Dewi Ratih Tirtosari
creator: Anggi Suci Febriani
creator: Wardhani, E. E
creator: Siwi, P. J
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2018-02-27
publication date: 2018-02-27
starting page: 7
ending page: 10
doi: 10.11594/

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
type: item
description: 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.
subject: Articles
  topic: section
subject: Microhyla
  topic: keywords
subject: Phylogenetic
  topic: keywords
subject: Sundaland
  topic: keywords
creator: Anggun Sausan Firdaus
creator: Nursita Ratih
creator: Is Karima
creator: Arfan Tri Kusuma
creator: Ngakan Made Suastika
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2018-02-27
publication date: 2018-02-27
starting page: 1
ending page: 6
doi: 10.11594/

Prediction of Novel Bioactive Compound fromZingiber officinale as Non-Nucleoside ReverseTranscriptase Inhibitors (NNRTIs) of HIV-1 through Computational Study
type: item
description: Human immunodeficiency virus 1 (HIV-1) is one of the viruses of that causes AIDS in humans and disease outbreaks in this modern era. Reverse transcriptase (RT) enzyme though to be the functional enzyme that play a role on the HIV-1 virus replication. Bioactive compounds contained on Ginger (Zingiber officinale) is known to inhibit viral replication. This study aims to determine the alternative bioactive compounds contained on Ginger (Zingiber officinale) as as a non-nucleoside reverse transcriptase (NNRTIs) HIV-1 inhibitors through computational study. The reverse transcriptase (RT) enzyme model was retrieved from protein sequence database (PDB) and validated with Ramachandran Plot and the compound contained on Ginger was retrieved from database. Analysis of molecular docking, performed using PyRx and the interactions between Reverse Transcriptase (RT) enzyme of HIV-1 virus and Zingiber officinale active compound was analyzed by PyMol and LigPlot+, also the drug-likeness molecule properties with The Lipinski Rule’s of Five. From 24 active compound which have been docked, ?-sitosterol proven to be the most potential bioactive compound as inhibitors of Reverse Transcriptase (RT) enzyme because it has more negative binding energy and the same amino acid residue with the control. Therefore, ?-sitosterol is predicted to be used as non-nucleoside reverse transcriptase (NNRTIs) HIV-1 inhibitors.
subject: Articles
  topic: section
subject: β- sitosterol
  topic: keywords
subject: HIV-1
  topic: keywords
subject: NNRTIs
  topic: keywords
subject: Zingiber officinale
  topic: keywords
creator: Viol Dhea Kharisma
creator: Syafrudin
creator: Luhur Septiadi
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2019-01-02
publication date: 2019-01-02
starting page: 49
ending page: 55
doi: 10.11594/

In Silico Study of Avocado (Persea Americana Mill.) Seed Compounds Against PBP2a Receptor onStaphylococcus aureus
type: item
description: The nosocomial infection causes 1,4 million mortality every day in the world. International Nosocomial Infection Control Consortium (INICC) data shows that 84,4% nosocomial infection is caused by S. aureus that can cause skin infection. Avocado (P. americana) seed has been reported as an antibacterial agent and used for dermatological applications. This research was aimed to know the potential of antibacterial activity of ethanolic extract of avocado seed in silico study. The in silico test used molecular docking method with PyRx software between PBP2a as receptor and phytochemical compounds in avocado seed as a ligand. The result showed that rutin compound had the best potential to bind PBP2a (binding affinity: -18,2 kcal/mol). Thus, phytochemical active compounds in avocado seed can be recommended as an antibacterial drug and can increase the number of fibroblast cells caused by S. aureus.
subject: Articles
  topic: section
subject: in silico
  topic: keywords
subject: avocado seed
  topic: keywords
subject: PBP2a
  topic: keywords
subject: Staphyloccus aureus
  topic: keywords
creator: Meike Tiya Kusuma
creator: Retno Susilowati
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2018-10-02
publication date: 2018-10-02
starting page: 45
ending page: 48
doi: 10.11594/

Molecular Docking Study of Lycopene on Reducing the DNA-methyltransfer in Prostate Cancer
type: item
description: Lycopene is a member of a carotenoid family and is naturally abundant in tomatoes. The consumption of lycopene is already needed for human because it acts as an antioxidant, meanwhile, our body cannot produce that naturally. Previous studies have shown that there is an inverse relationship between dietary lycopene intake and the risk of PCa. However, the studied mechanism underlying how the lycopene affects or inhibit the control of cancer growth, in this case, is DNA-methyltransferase that can regulate the cancer genes, is still limited, and even absent. Motivated by that, a series of the method including preparation docking, molecular docking, and identifying the biological activity were done to study the mechanism of lycopene in reducing the DNMT. The result of lycopene-DNMT binding was compared with other known ligands that already known to bind the DNMT in its active site, which is SFG and SAH. The docking results showed that the binding affinity of lycopene and DNMT is lower than other ligands. The biological activity analysis also showed that lycopene is proven to have antioxidant activity, however, it still needs further study or experimental work to prove its ability for apoptosis agonist or as anti-proliferative disease because it is only computationally proven.
subject: Articles
  topic: section
subject: DNMT
  topic: keywords
subject: lycopene
  topic: keywords
subject: molecular docking
  topic: keywords
subject: prostate cancer
  topic: keywords
creator: Annisa Muthiah Sukirman
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2018-09-03
publication date: 2018-09-03
starting page: 40
ending page: 44
doi: 10.11594/

In Silico Analysis and Identification of Possible Inhibitor of H5N1 Virus
type: item
description: Fingerroot (Boesenbergia pandurata (Roxb.)) belongs to the family Zingiberaceae (Ginger). B. pandurata has pharmacological benefits such as neuroprotective, chemoprotective, anti-inflammatory, anti-angiogenic, antioxidant, an inhibitor of protease enzyme NS2B/NS3 dengue virus, Japanese encephalitis virus and swine flu virus (H1N1). This study aims to determine the most effective compounds from B. pandurata as neuraminidase inhibitors of H5N1 virus. The amino acid sequence for neuraminidase of avian influenza A virus subtype H5N1 of A/China/GD02/2006 was retrieved from protein sequence database at NCBI. Then, modeled by Swiss Model. Analyse of molecular docking was performed using PyRx and the interactions between neuraminidase inhibitors of H5N1 and B. pandurata active compound was analyzed by PyMol software and LigPlot+ software. From the 30 active compounds which have been docked, 4-hydroxypanduratin A, rubranine, boesenbergin B, boesenbergin A, 5,7-dimethoxyflavone, and tectochrysin had an equal or smaller free binding energy than control compound. 4-hydroxypanduratin A proved to be the most potent active compound as a neuraminidase inhibitor (NA 1) because it has the most negative binding energy and the same amino acid binding residue with the control compound. Therefore, 4-hydroxypanduratin A is predicted to be used as inhibitors of neuraminidase in the H5N1 virus.
subject: Articles
  topic: section
subject: Boesenbergia pandurata
  topic: keywords
subject: H5N1
  topic: keywords
subject: neuraminidae
  topic: keywords
subject: 4-hydroxypanduratin A
  topic: keywords
creator: Syafruddin
creator: Luhur Septiadi
creator: Nuri Thobibatus Shofia Alfaruqi
creator: Didik Wahyudi
creator: Viol Dhea Kharisma
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2018-09-03
publication date: 2018-09-03
starting page: 33
ending page: 39
doi: 10.11594/

Medication Error Factors, Safety Guideline System, Flow of Drug Usage, and Code of Conduct toPrevent Medication Error
type: item
description: Medication error is any preventable event that may lead inappropriate drug service or patient harm while the drug administration is in control of the healthcare professional or patient. This study aimed to analyze the factor that may lead the medication error and identify the medication error solution to pharmaceutical installation in research hospital, Indonesia. This study used an action research method. The research subject included doctor, pharmacist, pharmaceutical engineering personnel and nurses. Action research involves six process: diagnosis, reconnaissance, action plan, action, evaluation and monitoring the subject. Diagnosis were obtained from primary and secondary data. Primary data were obtained by interview, observation, and Focus Group Discussion (FGD). Secondary data were obtained from adverse event and near-miss events in medication error data in pharmacy installation. The results indicated that there were four major factor of medication error. First, prescribing error is an unclear written prescription, incomplete administration and unavailable prescription. Second, transcribe error is a misread of prescription drug that lead to mistreatment. Third, dispensing error is involved the misreading of prescription drug by pharmacist, wrong dose, wrong quantity of drugs, and incompetent pharmacist personnel. Fourth, administration error is an incorrect administration by hospital personnel. In conclusion, the establishment of safety guideline is important to medication error in pharmaceutical installation. The safety guidelines consist of the policy and standard operational procedure, flowchart of outpatient service, code of conduct of pharmacy safety and monitoring to ensure the quality of medical service.
subject: Articles
  topic: section
subject: Drug administration error
  topic: keywords
subject: medication error
  topic: keywords
subject: patient safety
  topic: keywords
subject: pharmaceutical installation
  topic: keywords
creator: Arvidareyna Panca
creator: Nikma Fitriasari
creator: Wiwik Supartiwi
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2018-08-20
publication date: 2018-08-20
starting page: 28
ending page: 32
doi: 10.11594/

Incidence Rate of Myocardial Infarction in HIV–Infected Individuals: A System-atic Review and Meta–Analysis
type: item
description: Background: The incidence rate of myocardial infarction has been reportedly higher in human immunodeficiency virus (HIV)–infected individuals compared to in uninfected individuals. HIV infection is suggested to have increased the risk of myocardial infarction (MI). To review the incidence rate of myocardial infarction in HIV–infected individuals compared to in uninfected individuals in its relation to HIV infection as a potential risk factor of MI incident. A literature search was performed in Google Scholar, PubMed, and Cochrane databases with keywords “HIV risk myocardial infarction” and “myocardial infarction in HIV” ranging from 2013 to 2019. Inclusion criteria wasfull-text observational studies that reported the incidence rate of myocardial infarction in HIV–infected individuals compared to in uninfected individuals. A total of 6 studies were eligible for review. We performed the meta–analysis with Review Manager 5.3 in May 2019. We reviewed several studies that discussed the association between HIV infection and myocardial infarction. The incidence rate of MI is higher in HIV–infected individuals compared to in non–infected individuals. It is suggested that Framingham Risk Score does not directly contribute to the higher incidence of MI in patients with HIV. Several studies also reported that low CD4 cell count and HIV–1 RNA levels less than 500 copies/mL contribute directly to the risk of myocardial infarction. There is a higher incidence rate of myocardial infarction among HIV–infected individuals compared to among non–infected individuals. Several suggested factors include low CD4 cell count and HIV–1 RNA levels less than 500 copies/mL. Thus, it may be suggested that HIV infection is a potential risk factor of MI. Further studies are needed to better understand the mechanism of HIV infection as a risk factor of MI incident.
subject: Articles
  topic: section
subject: human immunodeficiency virus
  topic: keywords
subject: incidence rate
  topic: keywords
subject: myocardial infarction
  topic: keywords
creator: Camoya Gersom
creator: Savannah Quila Thirza
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2019-07-20
publication date: 2019-07-20
starting page: 94
ending page: 99
doi: 10.11594/

43 Years Old Female with Acquired Hemophilia Presented with Pseudotumor
type: item
description: Introduction: Acquired-haemophilia A in women is rare. This disorder is caused by the formation of auto-antibodies to factor VIII. Pseudo-tumor is a complication of hemophilia caused by recurrent bleeding which forms mass due to the presence of blood and necrotic tissue.A woman, 43 years old with complaints of left thigh lumps for 2 weeks before admitted to the hospital. Physical examination found a mass in the left thigh, with a thigh circumference of 34 cm, cystic. Laboratory tests showed coagulation disorders in the form of normal APTT lengthening after a mixing study, 2% factor VIII and 7.12 BU inhibitor levels. The ultrasound results of the femoral region showed heterogeneous cystic lesions with multi-inoculated internal echo and septa in the subcutaneous, the impression involved a muscular layer. Vascularity did not appear in it. The patient was improved with conservative therapy of 500mg corticosteroids and recombinant factor VIII. Pseudotumor hemophilia must be followed up immediately since it may cause further complications in the form of compartment syndrome. A biopsy is contraindicated in pseudotumor hemophilia. Simple imaging modalities are able to distinguish pseudotumor from other tumors. The patient was improved with conservative corticosteroid pulse dose 500g for inhibitor and recombinant factor VIII therapy. Due to limited costs, Recombinant activated factor VIII combined with activated prothrombin complex concentrate was not given.Acquired hemophilia A is a hemorrhagic disease with reduced coagulation factor VIII (F.VIII) activity due to the appearance of autoantibodies (inhibitors) against F.VIII. Hematoma is generally diffuse and very painful (Pseudomotor). In contrast to congenital hemophilia, where joint bleeding rarely occurs in AHA. The two strategies used for the management of AHA with pseudotumor in this patient is hemostatic therapy and immunosuppression.
subject: Articles
  topic: section
subject: Acquired hemofilia A
  topic: keywords
subject: high titer inhibitor
  topic: keywords
subject: pseudotumor
  topic: keywords
creator: Shinta O Wardhani
creator: Pandji Irani Fianza
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2019-07-20
publication date: 2019-07-20
starting page: 89
ending page: 93
doi: 10.11594/

Cytotoxicity Test on Breast Cancer Cell Lines T-47D treatedwith Pisang Kepok Peel Extract (Musa balbisiana)
type: item
description: Introduction: Utilization of natural ingredients such fruit as a breast cancer treatment agent is beginning to be widely studied by scientists. The goal is to reduce the side effects of chemotherapy agents. One of the potential natural ingredients as anticancer is Pisang Kepok peel (Musa balbisiana). This kind of banana contains various phytochemical compounds and high antioxidant activity that can induce cancer cell apoptosis. The purpose of this research is to know the IC50 value of Pisang Kepok peel extract thus can be known its potential as an anticancer agent. The lower of IC50 value is more cytotoxic. Method: This research is experimentally done by using CRD (Completely Randomized Design). The stages of this research are extraction and cytotoxic test (MTT assay). The extraction method was used maceration (ethanol 95%). The cytotoxic test was performed by giving Pisang Kepok unripe peel extract on the T-47D cell lines, then read the absorbance with ELISA reader at ? 595 nm and analyzed by SPSS Probit. Conclusions: Based on this results, it can be concluded that Pisang Kepok peel extract has moderate cytotoxic to T-47D cell lines, therefore indicate its potential as a candidate for breast cancer chemoprevention agents, especially at high concentrations (>250 ?g/mL).
subject: Articles
  topic: section
subject: breast cancer
  topic: keywords
subject: chemoprevention agents
  topic: keywords
subject: Pisang Kepok peel
  topic: keywords
subject: T-47D
  topic: keywords
creator: Fauchil Wardati
creator: Kholifah Holil
creator: Umaiyatus Syarifah
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2019-06-25
publication date: 2019-06-25
starting page: 84
ending page: 88
doi: 10.11594/

The Mutation Effect of Neuraminidase and Screening Bioactive Compound toInhibiting Neuraminidase in H5N1
type: item
description: Mutation that occur in the virus help to avoid the host's immune system and are passed on to the next generation and synthetic compounds begin to cause influenza viruses to be resistant. The purpose of this study was to determine the effect of mutations and inhibiting compounds for neuraminidase on the H5N1 virus. All DNA neuraminidase 1 (NA1) sequences from the H5N1 virus in 2016 were downloaded through NCBI and converted into protein sequences in ExPASy. Amino acids are aligned with Clustal Omega in EMBL-EBI and HOPE servers to predict mutation effects. Amino acid sequence A/chicken/Subang/08160018-002/2016 is used to represent neuraminidase in Indonesia. Protein molecular modeling is done using Swiss Model and Fugue, the results of subsequent modeling in Ramachandra. Eight natural compounds from plants and two control compounds, zanamivir and oseltamivir were used as ligands, docked using PyRx and visualized with PyMOL and LigPlot +. As many as 11 amino acid sequences used there are 30 regions in sequences that are mutated and alter the function of neuraminidase which initially as exo-alpha-sialidase activity becomes hydrolase activity. The docking results show that rosmarinic acid, rosmanol, chlogenic acid, oleonolic acid, carnosic acid, caryophyllene and capsaicin have binding affinity between zanamivir and oseltamivir. Visualization shows that rosmarinic acid, chlorogenic acid, rosmanol, and capsaicin compounds are predicted to replace zanamivir and oseltamivir. Because mutations in neuraminidase alter the function of neuraminidase from exo-alpha-sialidase activity into hydrolase activity and rosmarinic acid, chlorogenic acid, rosmanol, and capsaicin compounds are predicted to be inhibitors for NA1.
subject: Articles
  topic: section
subject: Neuraminidase (NAI)
  topic: keywords
subject: mutation
  topic: keywords
subject: bioactive compounds
  topic: keywords
subject: exo-alpha-sialidase
  topic: keywords
creator: Syafrudin
creator: Nina Ernawati
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2019-06-21
publication date: 2019-06-21
starting page: 73
ending page: 83
doi: 10.11594/

Arrangement of Burn Status for Emergency Management, Monitoring, and Evaluation of Burns in Saiful Anwar General Hospital in Malang, East Java, Indonesia
type: item
description: The article proposes an arrangement of burn status for the management of severe based on a review of management of burns. More than 95% of burns are associated with fatal fires and occur in low to middle income countries. A coordination between health officers within health facilities is crucial to provide proper management for severe burns. There is no standard yet for burn status in Indonesia. Burn status may provide better management of patients who are admitted with burns. In this article, the set of burn status was arranged for the management of patients with burns in the Saiful Anwar General Hospital. There are 3 types of burn status in this paper each for the respective use of emergency management, burn unit monitoring, and wound care evaluation. The purpose of this burn status is to facilitate a better coordination between health officers regarding management of burns in Saiful Anwar General Hospital. This paper can also become the basis of further studies regarding burns as a tool to collect data or as a basis to pioneer the standard of burn status in Indonesia to further improve the general quality of burn care and research in Indonesia. The system of medical record for patients is generally carried out to keep a record of the patient's disease progression, including the diagnosis and treatment plans carried out by doctors and medical personnel which are involved.
subject: Articles
  topic: section
subject: Burn status
  topic: keywords
subject: burns
  topic: keywords
subject: burn care
  topic: keywords
subject: emergency
  topic: keywords
creator: Herman Yosef Limpat Wihastyoko
creator: Wilma Agustina
creator: Camoya Gersom
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2019-05-24
publication date: 2019-05-24
starting page: 56
ending page: 72
doi: 10.11594/

Can Cinnamaldehyde Increased the Innate Immune System on Medaka Larvae?
type: item
description: Fish larvae are the early stage of the life cycle and the key to mass production of fish. Its nature which is susceptible to invade by pathogens, especially viruses, it is an important concern in increasing the innate immune system in virus invading. IFNa and Mx are inducer genes that have the most role in enhancing the innate immune system. The study was conducted in September 2017 with the experimental method. The sample used was 1-day-old medaka larvae in amount 30 fish in each tank with triplicate in each concentration. The cytotoxicity results showed that at 72 hours cinnamaldehyde immersion was 100% of medaka larvae survival rate at a concentration of 2.5 µg mL-1 and 0 µg mL-1 (control). One-Way ANOVA results, the genes expression of IFNa and Mx on 1-day-old medaka larvae showed decreasing at 2.5 µg mL-1 concentration of cinnamaldehyde immersion for 3 days with several observation periods (12h; 24h; 48h; and 72h) compared to control. The lowest expression of IFNa genes was 12h (2.54 x 10-5 ± 6.12 x 10-6) at a 2.5 µg mL-1concentration of cinnamaldehyde, and the highest expression of IFNa gene was 48h (3.95 x 10-4 ± 7.78 x 10-5)at 0 µg mL-1 (control)concentration of cinnamaldehyde. While the lowest Mx gene expression was 72h (8.96 x 10-3 ± 4.51 x 10-4) at a 2.5 µg mL-1concentration of cinnamaldehyde. And the highest Mx gene expression was 72h (0.88 ± 0.26) at 0 µg mL-1 (control)concentration of cinnamaldehyde. The immersion of cinnamaldehyde extract at a concentration of 2.5 µg mL-1 is not able to increase the innate immune system in medaka larvae. More assay is needed to determine the mechanism for the phenomenon of decreasing IFNa and Mx gene expression on fish larvae.
subject: Articles
  topic: section
subject: Cinnamaldehyde
  topic: keywords
subject: Genes Expression
  topic: keywords
subject: IFN-α
  topic: keywords
subject: Innate Immune System
  topic: keywords
subject: Medaka Larvae
  topic: keywords
subject: Mx
  topic: keywords
subject: Oryzias latipes
  topic: keywords
creator: Asthervina Widyastami Puspitasari
creator: Diana Arfiati
creator: Shao-Yang Hu
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2019-02-27
publication date: 2019-02-27
starting page: 21
ending page: 26
doi: 10.11594/

The Binding Prediction Model of the Iron-responsive Element Binding Protein and Iron-responsive Elements
type: item
description: Iron is essential to fulfilling an indispensable role in the biological process in human physiology. Various proteins were known involved in iron metabolism. One of the proteins called iron-responsive element binding protein (IRP)which acts as master iron of cellular iron homeostasis. There are two IRP known to date, which is: IRP1 and IRP2. Previous studies showed IRP bind to iron-responsive elements (IRE) located in 5’-UTR of the transferrin receptor 1. The interaction of IRP/IRE is well studied through many years to find a better treatment for the cellular disorder in iron metabolism. However, the structural differences of both IRP and the binding prediction model of IRP/IRE remain unclear. This study provides a better understanding of the IRP structure and the IRP/IRE2 binding prediction model in a healthy condition. Several bioinformatic analyses were implemented in this study, such as molecular docking simulation, domain prediction, and structural similarity analysis. Structural analysis of IRP demonstrates a low root mean square deviation score that indicates both of IRP have high similarity in structure with different characteristics, such as binding site, and metabolic pathway. Interestingly, molecular docking simulation showed IRP has a preferably binding site when targeting specific IRE. Thus, this information could be beneficial in developing a drug for an iron-related disease.
subject: Articles
  topic: section
subject: iron metabolism
  topic: keywords
subject: iron-responsive element binding protein
  topic: keywords
subject: iron-responsive element
  topic: keywords
subject: molecular docking simulation
  topic: keywords
creator: Kevin Nathanael Ramanto
creator: Arli Aditya Parikesit
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2025-07-30
publication date: 2025-07-30
starting page: 12
ending page: 20
doi: 10.11594/

The Connection of Distribution Location with Primate Kinship in Indonesia Based on Cytochrome B In Silico Analysis
type: item
description: Primates are mammals in the animal kingdom and they are terestrial creatures. Primates in Indonesia approximately has 59 species and 79 subspecies which has different sizes and characteristics. Primates are arboreal creatures that spend most of their days hanging on trees for socializing, eating, and exploring. Those factors could be the reason why primates likes to migrate. Evolution by definition is the changes in the genes between the ancestor and its decendants in a long period of time. The cause of evolution varies from the earth geography, adaptability, natural selection, mating, dan mutation. Primates undergo progressive evolution which indicates its abilites to survive in different kinds of environment. This analysis is being used to find out the connection between area distribution and primates genetics in Indonesia based on Cytochrome B in silico analysis. Based on the Cytochrome B MEGA gene analysis and regional mapping using QGIS, the result of it is primates in Indonesia has genetic connection molecularly. Differentiation is not only caused by geographical changes but also by wide imigration activity. Primatesendemicity is not linier to the imigration activity.
subject: Articles
  topic: section
subject: Cytochrome b
  topic: keywords
subject: evolution
  topic: keywords
subject: in silico
  topic: keywords
subject: phylogenetic
  topic: keywords
subject: primate
  topic: keywords
creator: Raden Mochammad Irvan Hernanda
creator: Asmara Nabila Ramadhanty
creator: Annisa Haryanti
creator: Yudhistira Prakasaditya
creator: Yeremiah Rubin Camin
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2019-02-27
publication date: 2019-02-27
starting page: 7
ending page: 11
doi: 10.11594/

Phylogenetic Analysis and Time Divergence of Genus Musa spp. Using S16 Protein Genes (Rps16) Intron Chloroplast
type: item
description: Family Musaceae is divided into three genera, Musa, Musella, and Ensete. The genus Musa became the genus with the most species cultivated in the Southeast Asian region. While the genus Musella and Ensete are monospecific genera that can only be found in certain regions. Distribution of banana nomenclature until now is still a debate. The taxonomic system of bananas is still based on conventional methods, namely by marking the genome. But unfortunately the nomenclature system is not suitable to be applied in the Southeast Asian region. The systematic history of the genus Musa apparently still has many problems such as biogeography, the comparison of phylogenetic trees and their evolution. Therefore be approached through an m arka molecular phylogenetic alisis menggunakan g en protein S16 (Rps16) chloroplast introns with Bayesian inference method and divergence time estimates using the log-normal clock relaxed. The results show that the tree topology produced monophyletic lineage, in terms of the separation of the genus Musa from the Musella lasiocarpa and Ensete ventricosum Outgroups
subject: Articles
  topic: section
subject: musaceae
  topic: keywords
subject: Divergence
  topic: keywords
subject: Rps16
  topic: keywords
creator: Farah Nahdia Noor
creator: Lailatus Sholichah
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2019-02-27
publication date: 2019-02-27
starting page: 1
ending page: 6
doi: 10.11594/

Bioactive Peptides from Tempeh Using Peptidecutter’s Cleavage
type: item
description: Tempeh is an Indonesian traditional fermented food with rich nutrition and bioactive components. Rhizopus sp, especially Rhizopus oligosporus), lactic acid bacteria (Lactobacillus sp.), and yeast are microorganisms 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 ExPASy Bioinformatics portal (https://web.expasy.org/peptide_cutter/) to cleave soy proteins glycinin G1, G2, G3, G4, G5, b-conglycinin-a chain, and b chain using available enzymes in the application with two simulations. Simulation I was conducted using enzyme complex produced by Lactobacillus sp. and Rhizopus oligosporus, while simulation 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, while simulation 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 PeptideCutter tool were dominated with dipeptides and only three peptides were in the form of tripeptides, namely Leu-Leu-Phe (glycinin G1), Val-Val-Phe (glycinin G5), and Arg-His-Lys (b-conglycinin-a chain). Bioactive peptides with antihypertensive and antidiabetic properties were mostly found in this in silico method of soybean
subject: Articles
  topic: section
subject: bioactive peptides
  topic: keywords
subject: cleavage
  topic: keywords
subject: in silico
  topic: keywords
subject: PeptideCutter
  topic: keywords
subject: protein
  topic: keywords
creator: Badrut Tamam
creator: Dahrul Syah
creator: Hanifah Nuryani Lioe
creator: Maggy T. Suhartono
creator: Suratiah
creator: Wisnu Ananta Kusuma
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2020-12-20
publication date: 2020-12-20
starting page: 35
ending page: 40
doi: 10.11594/

Identification of Significant Proteins in Coronavirus Disease 2019 Protein-Protein Interaction Using Principal Component Analysis and ClusterONE
type: item
description: 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.
subject: Articles
  topic: section
subject: Centrality measurements
  topic: keywords
subject: ClusterONE
  topic: keywords
subject: COVID-19
  topic: keywords
subject: Overall centrality
  topic: keywords
subject: Protein-protein interaction
  topic: keywords
subject: Significant protein
  topic: keywords
creator: Hilmi Farhan Ramadhani
creator: Annisa
creator: Wisnu Ananta Kusuma
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2020-12-20
publication date: 2020-12-20
starting page: 25
ending page: 34
doi: 10.11594/

The Art of Mesenchymal Stem Cells in Liver Fibrosis Management
type: item
description: Liver fibrogenesis is chronic tissue damage characterized by an extracellular accumulation of fibrillar matrix associated with continuous degradation and remodelling. This scientific review describes current concepts on the pathophysiology of liver fibrosis, inflammation as a 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 therapy, 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
subject: Articles
  topic: section
subject: Fibrogenesis
  topic: keywords
subject: liver fibrosis
  topic: keywords
subject: mesenchymal stem cells
  topic: keywords
creator: Farid Amansyah
creator: Dito Anurogo
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2020-12-20
publication date: 2020-12-20
starting page: 15
ending page: 24
doi: 10.11594/

The Role of Phytochelatin Synthase in Phytoremediation Agent: Structural Conservation of Phytochelatin (PC) Synthase to Maintain Its Activity as Heavy Metal Detoxification in Plant
type: item
description: 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.
subject: Articles
  topic: section
subject: alignment
  topic: keywords
subject: phytochelatin
  topic: keywords
subject: structure comparison
  topic: keywords
creator: Viky Vidayanti
creator: Galuh Wening Permatasari
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2020-12-20
publication date: 2020-12-20
starting page: 9
ending page: 14
doi: 10.11594/

https://journal.futuresciencepress.com/index.php/bbrj/article/view/30
type: item
title: 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
description: 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.
subject: Articles
  topic: section
subject: education
  topic: keywords
subject: knowledge
  topic: keywords
subject: motivation
  topic: keywords
subject: performance
  topic: keywords
subject: covid-19
  topic: keywords
subject: educator volunteers
  topic: keywords
creator: Siti Khuzaiyah
creator: Nur Izzah Priyogo
creator: Gigih Setianto
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2025-07-25
publication date: 2025-07-25
starting page: 1
ending page: 8
doi: 10.11594/

Antimicrobial Activity of Stenochlaena palustris and Sauropus androgynus in Staphylococcus aureus, Escherichia coli and Candidia albicans
type: item
description: 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).
subject: Articles
  topic: section
subject: Stenochlaena palustris
  topic: keywords
subject: Sauropus androgynus
  topic: keywords
subject: Staphylococcus aureus
  topic: keywords
subject: Escherichia coli
  topic: keywords
subject: Candida albicans
  topic: keywords
creator: Lia Yulia Budiarti
creator: Isnaini
creator: Puteri Dayana
creator: Nur Almira R. S.
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2025-07-25
publication date: 2025-07-25
starting page: 32
ending page: 38
doi: 10.11594/

The Correlation of Use of Depo Medroxy Progesterone Acetate (DMPA) In-jections with Lipid Profile Levels in Rats
type: item
description: 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.
subject: Articles
  topic: section
subject: DepoMedroxy Progesterone Acetate
  topic: keywords
subject: Hypercholesterolemia
  topic: keywords
subject: Hyperlipidemia
  topic: keywords
subject: Lipid Profiles
  topic: keywords
creator: Suratiah
creator: Dewa Ayu Surinati
creator: I Dewa Gede Putu Putra Yasa
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2025-07-25
publication date: 2025-07-25
doi: 10.11594/

Phenol Coefficient Test Combination Infusion of Cananga odorata – Averrhoa bilimbi L. Against Staphylococcus aureus and Salmonella typhi in Vitro
type: item
description: 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.
subject: Articles
  topic: section
subject: phenol coefficient
  topic: keywords
subject: combination infusion
  topic: keywords
subject: Cananga odorata
  topic: keywords
subject: Averrhoa bilimbi L.
  topic: keywords
subject: Staphylococcus aureus
  topic: keywords
subject: Salmonella typhi
  topic: keywords
creator: Lia Yulia Budiarti
creator: Erida Wydiamala
creator: Najiya Ulfa
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2025-07-25
publication date: 2025-07-25
starting page: 19
ending page: 26
doi: 10.11594/

Isolation of Arbutin from Leaves and Fruits of Buni (Antidesma Bunius L. Spreng) As Tyrosinase Enzym Inhibitor
type: item
description: 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.
subject: Articles
  topic: section
subject: Arbutin
  topic: keywords
subject: Buni Leaves
  topic: keywords
subject: Buni fruits
  topic: keywords
subject: TLC
  topic: keywords
subject: HPLC
  topic: keywords
subject: Tyrosinase enzyme inhibitor
  topic: keywords
creator: Gea Ocktiah Palensina
creator: Leni Rosita
creator: Zuraida Sagala
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2021-06-30
publication date: 2021-06-30
starting page: 8
ending page: 18
doi: 10.11594/

Prediction of Drug-Target Interaction Using Random Forest in Coronavirus 2019 Case
type: item
description: 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).
subject: Articles
  topic: section
subject: Coronavirus disease 2019
  topic: keywords
subject: drug-target interaction
  topic: keywords
subject: random forest
  topic: keywords
subject: random undersampling
  topic: keywords
subject: XGBoost
  topic: keywords
creator: Aulia Fadli
creator: Annisa
creator: Wisnu Ananta Kusuma
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2025-07-25
publication date: 2025-07-25
starting page: 1
ending page: 7
doi: 10.11594/

FUNDAMENTALS OF PROTEIN-PROTEIN INTERACTIONS AND THEIR METHODS OF CHARACTERIZATION
type: item
description: Protein-protein interactions are ubiquitous biological phenomena in all types of organism and play vital roles in various metabolic processes. Therefore, it is very important to understand how protein-protein interactions take place and govern different mechanisms at cellular and molecular levels. Thus, determination of protein-protein interactions is the key in elucidating such mechanisms. In order to provide adequate knowledge and guidance in selecting appropriate methods to determine protein-protein interactions, this article will review basic principles, definitions, terminologies, parameters and classification of protein-protein interactions, obtained either from in silico or laboratory experimental works. Some examples of commonly used biochemical and biophysical methods for characterization of protein-protein interactions were also discussed.
subject: Review Article
  topic: section
subject: contacting residues
  topic: keywords
subject: hot spots
  topic: keywords
subject: interacting residues
  topic: keywords
subject: protein-protein interfaces
  topic: keywords
subject: residue interface propensities
  topic: keywords
creator: Kholis A. Audah
rights: Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
date: 2021-12-31
publication date: 2021-12-31
starting page: 70
ending page: 82
doi: 10.11594/bbrj.04.02.04