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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 10 Documents
 1 
Search results for , issue "Vol. 1 No. 1 (2018): Volume 1 Issue 1" : 10 Documents clear
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

Show Abstract | Download Original | Original Source | Check in Google Scholar

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

Show Abstract | Download Original | Original Source | Check in Google Scholar

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

Show Abstract | Download Original | Original Source | Check in Google Scholar

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

Show Abstract | Download Original | Original Source | Check in Google Scholar

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

Show Abstract | Download Original | Original Source | Check in Google Scholar

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
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

Show Abstract | Download Original | Original Source | Check in Google Scholar

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

Show Abstract | Download Original | Original Source | Check in Google Scholar

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

Show Abstract | Download Original | Original Source | Check in Google Scholar

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

Show Abstract | Download Original | Original Source | Check in Google Scholar

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

Show Abstract | Download Original | Original Source | Check in Google Scholar

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

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