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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 4 Documents
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Search results for , issue "Vol. 2 No. 1 (2019): Volume 2 Issue 1" : 4 Documents clear
Phylogenetic Analysis and Time Divergence of Genus Musa spp. Using S16 Protein Genes (Rps16) Intron Chloroplast Noor, Farah Nahdia; Sholichah, Lailatus
Bioinformatics and Biomedical Research Journal Vol. 2 No. 1 (2019): Volume 2 Issue 1
Publisher : Future Science

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Abstract

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
Can Cinnamaldehyde Increased the Innate Immune System on Medaka Larvae? Puspitasari, Asthervina Widyastami; Arfiati, Diana; Hu, Shao-Yang
Bioinformatics and Biomedical Research Journal Vol. 2 No. 1 (2019): Volume 2 Issue 1
Publisher : Future Science

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Abstract

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.
The Binding Prediction Model of The Iron-responsive Element Binding Protein and Iron-responsive Elements Parikesit, Arli Aditya; Ramanto, Kevin Nathanael
Bioinformatics and Biomedical Research Journal Vol. 2 No. 1 (2019): Volume 2 Issue 1
Publisher : Future Science

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Abstract

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.
The Connection of Distribution Location with Primate Kinship in Indonesia Based on Cytochrome B In Silico Analysis Hernanda, Raden Mochammad Irvan; Ramadhanty, Asmara Nabila; Haryanti, Annisa; Prakasaditya, Yudhistira; Camin, Yeremiah Rubin
Bioinformatics and Biomedical Research Journal Vol. 2 No. 1 (2019): Volume 2 Issue 1
Publisher : Future Science

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Abstract

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.

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