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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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The The Mutation Effect of Neuraminidase and Screening Bioactive Compound to Inhibiting Neuraminidase in H5N1 Ruslan, Syafrudin; Ernawati, Nina
Bioinformatics and Biomedical Research Journal Vol. 1 No. 3 (2018): Volume 1 Issue 3
Publisher : Future Science

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Abstract

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.
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
Cytotoxicity Test on Breast Cancer Cell Lines T-47D treated with Pisang Kepok Peel Extract (Musa balbisiana) Wardati, Fauchil; Holil, Kholifah; Syarifah, Umaiyatus
Bioinformatics and Biomedical Research Journal Vol. 1 No. 3 (2018): Volume 1 Issue 3
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Abstract

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).
Arrangement of Burn Status for Emergency Management, Monitoring, and Evaluation of Burns in Saiful Anwar General Hospital in Malang, East Java, Indonesia Wihastyoko, Herman Yosef Limpat; Agustina, Wilma; Gersom, Camoya
Bioinformatics and Biomedical Research Journal Vol. 1 No. 3 (2018): Volume 1 Issue 3
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Abstract

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.
43 Years Old Female with Acquired Hemophilia Presented with Pseudotumor Ward, Shinta Oktya; Fianza, Pandji Irani
Bioinformatics and Biomedical Research Journal Vol. 1 No. 3 (2018): Volume 1 Issue 3
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Abstract

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.
Incidence Rate of Myocardial Infarction in HIV–Infected Individuals: A System-atic Review and Meta–Analysis Gersom, Camoya; Thirza, Savannah Quila
Bioinformatics and Biomedical Research Journal Vol. 1 No. 3 (2018): Volume 1 Issue 3
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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.
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
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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
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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
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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.
The Art of Mesenchymal Stem Cells in Liver Fibrosis Management Anurogo, Dito; Amansyah, Farid
Bioinformatics and Biomedical Research Journal Vol. 3 No. 2 (2020): Volume 3 issue 2
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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

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