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Bioinformatics and Biomedical Research Journal
Published by Future Science
ISSN : -     EISSN : 26203324     DOI : 10.11594/bbrj
Core Subject : Science, Education, Engineering,
Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Education Engineering
Bioinformatics and Biomedical Research Journal (BBR) serve the interests of the research-oriented and professional section in the fields of Bioinformatics and Biomedical Research. The current emphasis of the BBR Journal includes (but is not limited to) the following areas: Drugs Discovery Genomics study Proteomics study, structural bioinformatics Pharmacogenomics Epigentics Gene Mutation Polimorfism Biomarker Pharmaceutical Biotechnology Pharmaceutical biosciences and other field related to bioimedical research
Arjuna Subject : Biokimia, Genetika dan Biologi Molekuler - Bioteknologi
Articles 37 Documents
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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
Insights Into The Carcinogenic Effect of Key Skin Care Ingredients Leading To Breast Cancer: An In-Silico Study Kadam, Prerna; Sinha, Sangeeta; Puri, Akshita
Bioinformatics and Biomedical Research Journal Vol. 6 No. 1 (2023): Volume 6 Issue 1 (INPRESS)
Publisher : Future Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/bbrj.06.01.01

Abstract

Breast cancer is the most common form of cancer among all others, prevalent in terms of incidence rates. There is malignancy risk associated with many common skincare ingredients. This study elucidated possible hub genes related to breast cancer provoked by the effect of various chemicals in skin care formulations which were screened through literature. Aluminum chloride, Aluminum chlorohydrate, Dibutyl phthalate, Diethyl phthalate, Di-2- Ethylhexyl phthalate, Methylparaben, propylparaben, Triclosan, octamethylcyclotetrasiloxane (D4), and decamethylcyclopentasiloxane (D5) are the 10 chemicals investigated. Xenoestrogens mimic estrogen and interfere with the endocrine system and can disrupt natural hormone synthesis, secretion, transport, and binding. Pathway enrichment of the genes indicated key pathways that are mostly altered in Breast Cancer. One of the most significant pathways common to almost 7 chemicals is Endocrine disruption validating its xenoestrogenic effect while other 3 alter different pathways inducing carcinogenic effect. Taken together, the identification of hub genes, pathway enrichment and literature evidence helped to build a correlation between the chemicals and breast cancer. Further analysis of docking studies revealed that AKT1 for aluminum chloride, ESR1 for aluminum chlorohydrate and Dibutyl phthalate, PTGS2 and AR for diethyl phthalate, AKT1 for di-2-Ethylhexyl phthalate, PGR for methylparaben, AR and PGR for propylparaben, MMP9 for triclosan and CHEK1 for both decamethylcyclopentasiloxane and octamethylcyclotetrasiloxane has shown greater binding affinity highlighting the significance of these proteins and the potential carcinogenic effect of the skin care ingredients under investigation in this study leading to breast cancer.
Nanostructured Lipid Carriers with the Eichhornia crassipes Extract as a Receptor, ErB-2 Inhibitor in Breast Cancer: An in Silico Study Jocelyn Thanur; Alicia Carissa Hartanu; Gandawiguna, Vonny
Bioinformatics and Biomedical Research Journal Vol. 7 No. 1 (2024): Volume 7 Issue 1 (INPRESS)
Publisher : Future Science

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Abstract

In 2020, Indonesia had a total of 65.858 new breast cancer cases and the mortality rate reached 17 per 100,000 population in 2021. Human Epidermal Growth Factor Receptor 2 or Receptor, ErB-2 is a protein that is often used as a target for developing breast cancer drugs. Nowadays, an alternative drug from natural compounds has been developed to overcome the dangerous effect of the chemical drugs, for example by using Eichhornia extract. Due to its low solubility in water and bioavailability, it can be modified by a nanostructured lipid carrier as a sender. Therefore, this study aimed to determine the bioactive compounds in Eichhornia extract that can potentially act as Receptor, ErB-2 inhibitors when encapsulated in nanostructured lipid carriers. However, a nanostructured lipid carrier was constructed by encapsulating Eichhornia extract in vitro. According to the results of molecular docking simulations, luteolin, 2-hydroxy-8-(4 hydroxyphenyl)-phenalene-1-one, and 2-hydroxy-8-(3,4-dihydroxyphenyl)-phenalen-1-one have the highest bond energies and exceed the bond energy of the native ligand. The characterization test showed that the manufacturer’s nanostructured lipid carriers had an average size of 471.3 nm, a PDI of 0.507, a pH of 6.20, and a viscosity of 0.896 mPa·S. This nanostructured lipid carrier prototype has been successfully synthesized and nearly met the nanodrug characteristics. This present study could give a new insight in developing drug delivery that alleviate the harmful side effects of cancer chemotherapy.
Molecular Docking Study on Ciplukan Fruit (Physalis Angulata L) Using Receptor AChE for Anti-Alzheimer Agents Muhammad Farrel Rahadian; Ahmad Jauhari Fadilah Kusumah; Teuku Rizky Ollaf Ramadhan Syah
Bioinformatics and Biomedical Research Journal Vol. 7 No. 1 (2024): Volume 7 Issue 1 (INPRESS)
Publisher : Future Science

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Abstract

Neurodegenerative diseases, especially Alzheimer's, have become a global problem with an ever-increasing number of patients, as many as 46 million people worldwide. Alzheimer's is a multifactorial disease, so it has several treatment approaches, such as controlling acetylcholine levels with acetylcholinesterase enzyme inhibitors. The application of chemical drugs is used for healing therapy but can cause side effects. Therefore, using active constituents derived from plants is tested as a potential drug in neurodegenerative disease therapy. The reasons for choosing herbal medicines are the availability of materials, more economical prices, and low toxic effects. Ciplukan fruit (Physalis angulata L) contains polyphenolic compounds from the flavonoid class, which can reduce oxidative stress and have the potential to prevent or treat Alzheimer's disease. Molecular docking simulation was performed with AChE (PDB ID: 4EY7) and receptors based on target proteins for Alzheimer's treatment. The in silico testing phase begins with receptor preparation using the Molegro Molecular Viewer 2.5 application, method validation using the AutoDockTools 1.5.6 application, ligand preparation using the Marvin Sketch application and Lipinski screening, ligand binding to the receptor using the AutoDockTools 1.5.6 application, analysis and visualization of docking results using the BIOVIA Discovery Studio Visualizer. The results showed that the compounds Ergost-5-en-3-ol with a value of -12.85 kcal mol and 1-dehydrohydrocortisone with a value of -10.23 kcal/mol from Ciplukan Fruits (Physalis angulata L) have potential as drug candidates with AChE enzyme inhibition mechanism.
Potential of Long-Jawed Mackerel (Rastrelliger) Oil as the Source of Cholecalciferol and Omega-3 to Minimize the Risk of Psoriasis Fatima Amentha Kenya; Nayla Fauziah; Pipit Fitriani
Bioinformatics and Biomedical Research Journal Vol. 7 No. 1 (2024): Volume 7 Issue 1 (INPRESS)
Publisher : Future Science

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Abstract

The impact of psoriasis extends beyond skin inflammation and can significantly impact the patients' mental health. Fish oil is considered an alternative to combat chronic dermatitis, mainly due to its omega-3 fatty acid and cholecalciferol contents. Long-jawed mackerel (Rastrelliger), an abundant fish in Indonesian waters, is recognized for its high omega-3 and cholecalciferol that competes with commercial and other local fish species. This study aims to analyze the nutritional content in Rastrelliger fish oil as an alternative for controlling psoriasis. This study also used the wet rendering method to compare fish oil from silver catfish and skipjack tuna. The three samples were analyzed using Fourier Transformed Infrared Spectroscopy (FTIR) spectroscopy to identify their Omega-3 and cholecalciferol contents. This process yielded 51 grams of oil from 292 grams of Rastrelliger fish. Rastrelliger's fat content was 1.83±0.03%, with a water content of 70.06±1.87%. FTIR spectrum indicated the presence of alkenes, carboxyl, methyl, and methylene groups, which are functional groups of Omega-3 fatty acids. The content in 100 grams of Rastrelliger fish was 2.2 grams of Omega-3 and 2.04 mcg of cholecalciferol. There is potential for controlling psoriasis, as the need for Omega-3 and cholecalciferol can be met. In conclusion, Rastrelliger fish oil demonstrates promising potential as a treatment measure for the autoimmune disease psoriasis.

Page 4 of 4 | Total Record : 37

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