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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 28 Documents
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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
Interaction Between Receptor TIR1 and Auxin Plant Hormone in Arabidopsis thaliana Sari, Annisa N; Nindyawati, Dwi L; Aqmarina, Ananda; Widhiya, Eva W; Lestari, N D
Bioinformatics and Biomedical Research Journal Vol. 1 No. 1 (2018): Volume 1 Issue 1
Publisher : Future Science

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Abstract

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. Keywords: Auxins, docking, in silico, TIR1
Inter-species Agouti Signaling Protein (ASIP) Polymorphism Using Phylogeny Analysis Tirtosari, D R; Febriani, A S; Wardhani, Erintha E; Siwi, Putih J
Bioinformatics and Biomedical Research Journal Vol. 1 No. 1 (2018): Volume 1 Issue 1
Publisher : Future Science

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Abstract

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. Keywords: ASIP, Coloring, Mutation, Phenotype, Polymorphism.
Environmental Epigenetics: Effects of Endocrine Disruptors on Development of Obesity – Statistical Analysis Kuno, Mika
Bioinformatics and Biomedical Research Journal Vol. 1 No. 1 (2018): Volume 1 Issue 1
Publisher : Future Science

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Abstract

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. Keywords: Epigenetics, obesitas, endocrine disruptor, environmental factor, statatistical analysis
The In Silico Analysis and Identification of Possible Inhibitor of H5N1 Virus: Compounds Analysis and Identification of Possible Neuraminidase Inhibitors Syafrudin, Syafrudin; Septiadi, Luhur; Alfaruqi, Nuri Thobibatus Shofia; Wahyudi, Didik; Kharisma, Viol Dhea
Bioinformatics and Biomedical Research Journal Vol. 1 No. 2 (2018): Volume 1 Issue 2
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Abstract

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.
Medication Error Factors, Safety Guideline System, Flow of Drug Use, and Code of Conduct to Prevent Medication Error Panca, Arvidareyna; Fitriasari, Nikma; Supartiwi, Wiwik
Bioinformatics and Biomedical Research Journal Vol. 1 No. 2 (2018): Volume 1 Issue 2
Publisher : Future Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/bbrj.01.02.01

Abstract

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.
In Silico Study of Avocado (Persea americana Mill.) Seed Compounds Against PBP2a Receptor on Staphylococcus aureus Kusuma, Meike Tyas; Susilowati, Retno
Bioinformatics and Biomedical Research Journal Vol. 1 No. 2 (2018): Volume 1 Issue 2
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Abstract

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.
Molecular Docking Study of Lycopene on Reducing the DNA-methyltransferase in Prostate Cancer Sukirman, Annisa Muthiah
Bioinformatics and Biomedical Research Journal Vol. 1 No. 2 (2018): Volume 1 Issue 2
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Abstract

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.
Prediction of Novel Bioactive Compound from Zingiber officinale as Non-nucleoside Reverse Transcriptase Inhibitors (NNRTIs) of HIV-1 through Computational Study Kharisma, Viol Dhea; Septiadi, Luhur; Syafrudin, Syafrudin
Bioinformatics and Biomedical Research Journal Vol. 1 No. 2 (2018): Volume 1 Issue 2
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Abstract

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.

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