Bioinformatics and Biomedical Research Journal
Bioinformatics and Biomedical Research Journal is peer-reviewed online journal. We publish original research papers, review articles, and commentaries in the area of Bioinformatics and Basic or Translational Biomedical Sciences, including Molecular and Cellular biology, Cancer biology, Bioinformatics, Microbiology, Immunology, Pharmacology, Genetics, Biochemistry, Nanobiotechnology, Medical toxicology, and Occupational health. The aim of the journal is to provide a platform which allow researchers and academics to access and discuss relevant information that advances our understanding on biomedical problems. BBR Journal welcomes submissions of experimental research findings related to medicine and medical issue, including molecular mechanism of specific disease, gene regulation in normal and pathologic cells, design and delivery of therapeutic drugs, discovery of potential drug targets, and innovative techniques for diagnosis. This journal is published two times per year, June and December. Accepted manuscript is subject to peer-review to ensure the quality before it is published. All articles published are made freely and permanently accessible online immediately upon publication.
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Nanostructured Lipid Carriers with the Eichhornia crassipes Extract as a Receptor, ErB-2 Inhibitor in Breast Cancer: An in Silico Study
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.
Copyright (c) 2024 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
Molecular Docking Study on Ciplukan Fruit (Physalis Angulata L) Using Receptor AChE for Anti-Alzheimer Agents
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.
Copyright (c) 2025 Bioinformatics and Biomedical Research Journal https://creativecommons.org/licenses/by-nc/4.0
Potential of Long-Jawed Mackerel (Rastrelliger) Oil as the Source of Cholecalciferol and Omega-3 to Minimize the Risk of Psoriasis
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.
THE ANTIBACTERIAL ACTIVITY OF BETEL (PIPER BATTLE L.) ANDBASIL (OCIMUM SANCTUM L.) LEAVES INFUSION AS ANTISEPTIC PREPARATIONS AGAINSTSOME BACTERIA IN VITRO
Betel leaves (Piper battle L.) and basil leaves (Ocimum sanctum L.) are parts of the plant that can be made as antiseptic preparations because they contain antibacterial compounds such as flavonoids, tannins, and saponins. Antiseptic activity can be observed based on inhibiting the colonization of standard test bacteria of the laboratory, namely Staphylococcus aureus, Staphylococcus epidermidis, Escherichia coli, Pseudomonas aeruginosa, and Salmonella typhi as well as the magnitude of the phenol coefficient value. The study aimed to analyze the infusion activity of betel and basil leaves as antiseptic preparations against some test bacteria. This study in vitro used a posttest-only control group design. The infusion treatment of betel and basil leaves is tested in a single preparation and a combination with concentrations of 50%, 75%, and 100% (w/v). The results showed there was a difference in the infusion activity of betel leaves and basil leaves in a single stock and a combination of the number of bacterial colonies tested. The effect of the treatment produces a small number of bacterial colonies in Gram-positive bacteria; 100% combination treatment (b/v) provides an inhibitory effect that is not significantly different from 70% alcohol control against all test bacteria except S.typhi: and obtained the phenol coefficient value from the combination treatment of betel and basil leaves infusion higher against Gram-positive bacteria. The conclusion of this study, the combination of betel and basil leaves infusion has antibacterial activity as an antiseptic preparation that can inhibit the growth of some test bacteria.
A REVIEW: ANALYSIS OF MICROBIOME DIVERSITY IN CANCER
There have been many studies linking the microbiome to disease, including cancer. The microbiome is all the genetic material in the form of bacteria, fungi, or viruses that exists in parts of the human body. The microbiome is reported to trigger cancer due to the presence of certain pathogenic microbes or the presence of dysbiosis. Therefore, it is necessary to analyze the diversity of the microbiome to see the relationship. Metagenomics is the latest technology that can be used to analyze the diversity of the microbiome in cancer. There are two approaches in metagenomic analysis, namely targeted sequencing and sequencing of the entire metagenome. This paper will discuss a targeted sequencing metagenomic approach for the identification of microbial diversity in cancer.
ANTIBACTERIAL ACTIVITY OF EXTRACT COMBINATION OF LEAVES AND PEELS KAFFIR LIME (Citrus Hystrix DC.) AGAINST SOME TEST BACTERIA
Leaf and peel of the kaffir lime plant (Citrus hystrix DC.) can be used as herbal preparations to treat infections by opportunistic bacteria. Kaffir lime plant extract was prepared using maceration method with ethanol 96 % and then dissolved using aquadest. This study aimed to analyze the antibacterial activity of the combination of leaf and peel extract against Staphylococcus aureus, Staphylococcus epidermidis, Escherichia coli, and Pseudomonas aeruginosa bacteria isolates. This study used a posttest-only control group design, including phyto- chemical and in vitro antibacterial activity tests. The combination of leaf and peel extract of kaffir lime tested was 12.5%, 25%, 50%, and 75% (w/v). The results of phytochemical tests on the leaf extract and rind of limes were found to have antibacterial compounds, namely flavonoids, tannins, phenols, and alkaloids. The results of the antibac- terial activity test used the paper disc diffusion method showed that there were differences in the size of the inhibition zone for the four test bacteria; The combination treatment of 75% (1:1) leaf-peel ex- tract gave the greatest inhibitory zone effect on the four test bacteria and was equivalent to the positive control. The conclusion of the study, the combination of leaf and peel extract had different antibac- terial activity against Staphylococcus aureus, Staphylococcus epider- midis, Escherichia coli, and Pseudomonas aeruginosa.
FUNDAMENTALS OF PROTEIN-PROTEIN INTERACTIONS AND THEIR METHODS OF CHARACTERIZATION
Protein-protein interactions are ubiquitous biological phenomena in all types of organism and play vital roles in various metabolic processes. Therefore, it is very important to understand how protein-protein interactions take place and govern different mechanisms at cellular and molecular levels. Thus, determination of protein-protein interactions is the key in elucidating such mechanisms. In order to provide adequate knowledge and guidance in selecting appropriate methods to determine protein-protein interactions, this article will review basic principles, definitions, terminologies, parameters and classification of protein-protein interactions, obtained either from in silico or laboratory experimental works. Some examples of commonly used biochemical and biophysical methods for characterization of protein-protein interactions were also discussed.
Environmental Epigenetics: Effects of Endocrine Disruptors on Development of Obesity – Statistical Analysis
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.
Identification Microorganism which have most stable ?-galactosidase Enzyme Based on Conformational Stability
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.
Interaction Between Receptor TIR1 and Auxin Plant Hormone in Arabidopsis thaliana
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.
Inter-species Agouti Signaling Protein (ASIP) Polymorphism Using Phylogeny Analysis
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.
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
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.
Prediction of Novel Bioactive Compound fromZingiber officinale as Non-Nucleoside ReverseTranscriptase Inhibitors (NNRTIs) of HIV-1 through Computational Study
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.
In Silico Study of Avocado (Persea Americana Mill.) Seed Compounds Against PBP2a Receptor onStaphylococcus aureus
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-methyltransfer in Prostate Cancer
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.
In Silico Analysis and Identification of Possible Inhibitor of H5N1 Virus
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 Usage, and Code of Conduct toPrevent Medication Error
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.
Incidence Rate of Myocardial Infarction in HIV–Infected Individuals: A System-atic Review and Meta–Analysis
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.
43 Years Old Female with Acquired Hemophilia Presented with Pseudotumor
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.
Cytotoxicity Test on Breast Cancer Cell Lines T-47D treatedwith Pisang Kepok Peel Extract (Musa balbisiana)
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).
The Mutation Effect of Neuraminidase and Screening Bioactive Compound toInhibiting Neuraminidase in H5N1
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.
Arrangement of Burn Status for Emergency Management, Monitoring, and Evaluation of Burns in Saiful Anwar General Hospital in Malang, East Java, Indonesia
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.
Can Cinnamaldehyde Increased the Innate Immune System on Medaka Larvae?
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
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
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.
Phylogenetic Analysis and Time Divergence of Genus Musa spp. Using S16 Protein Genes (Rps16) Intron Chloroplast
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
Bioactive Peptides from Tempeh Using Peptidecutter’s Cleavage
Tempeh is an Indonesian traditional fermented food with rich nutrition and bioactive components. Rhizopus sp, especially Rhizopus oligosporus), lactic acid bacteria (Lactobacillus sp.), and yeast are microorganisms involved in Tempeh fermentation. An interesting offer of Bioinformatics (in silico method) as a supporting tool in molecular biology studies has emerged, such as in protein cleavage. This study utilized PeptideCutter application on ExPASy Bioinformatics portal (https://web.expasy.org/peptide_cutter/) to cleave soy proteins glycinin G1, G2, G3, G4, G5, b-conglycinin-a chain, and b chain using available enzymes in the application with two simulations. Simulation I was conducted using enzyme complex produced by Lactobacillus sp. and Rhizopus oligosporus, while simulation II was used enzyme complex produced by Lactobacillus sp., Rhizopus oligosporus, and Klebsiella pneumonia. Simulation I was conducted using enzyme complex produced by Lactobacillus sp. and Rhizopus oligosporus, while simulation II was used enzyme complex produced by Lactobacillus sp., Rhizopus oligosporus, and Klebsiella pneumoniae. A total of 58 peptides was found from the simulation I and higher than simulation I (41 peptides). The bioactive peptides by the cleavages using PeptideCutter tool were dominated with dipeptides and only three peptides were in the form of tripeptides, namely Leu-Leu-Phe (glycinin G1), Val-Val-Phe (glycinin G5), and Arg-His-Lys (b-conglycinin-a chain). Bioactive peptides with antihypertensive and antidiabetic properties were mostly found in this in silico method of soybean
Identification of Significant Proteins in Coronavirus Disease 2019 Protein-Protein Interaction Using Principal Component Analysis and ClusterONE
Coronavirus Disease 2019 (COVID-19) will cause disease complications and organ damage due to excessive inflammatory reactions if left untreated. Computational analysis of protein-protein interactions can be carried out in various ways, including topological analysis and clustering of protein-protein interaction networks. Topological analysis can identify significant proteins by measuring the most important nodes with centrality measurements. By using Principal Component Analysis (PCA), the types of centrality measures were extracted into the overall centrality value. The study aimed to found significant proteins in COVID-19 protein-protein interactions using PCA and ClusterONE. This study used 57 proteins associated with COVID-19 to obtain protein networks. All of these proteins are homo sapiens organism. The number of proteins and the number of interactions from 57 proteins were 357 proteins and 1686 interactions. The results of this study consisted of two clusters; the best cluster was the first cluster with a lower p-value but had an average overall centrality value that closed to the second cluster. There are twenty important proteins in that cluster, and all of these proteins are related to COVID-19. These proteins are expected to be used in the process of discovering medicinal compounds in COVID-19.
The Art of Mesenchymal Stem Cells in Liver Fibrosis Management
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
The Role of Phytochelatin Synthase in Phytoremediation Agent: Structural Conservation of Phytochelatin (PC) Synthase to Maintain Its Activity as Heavy Metal Detoxification in Plant
Phytochelatin (PC) Enzyme has crucial role in heavy metal detoxification and homeostasis in plants. This study aimed to evaluate the genetic variation of PC synthase related to its activity based on structural comparison. We evaluated PC genes and protein sequences from 6 plants namely, Brassica sp., Amaranthus sp., Noccaea sp., Arabidopsis sp., Nicotiana sp., and Pteris sp. All sequences were aligned based on CLUSTALW matrix for DN sequences and MUSCLE algorithm for protein sequences. Data were clustered using MEGA Software for similarity clustering. Selected data were further modeled using SWISSMODEL to evaluate the 3D-structural analysis based on homology modeling. Thus, all protein models were superimposed and evaluated the structure comparison based on RMSD data. The result showed that genetic variation of PC gene is high among species. But it is clustered for the same species has similar sequence. In addition, protein sequences also showed the high diversity among species and it is still clustered based on their genus. RMSD data showed that PC synthase from 6 plant has similar structure and tend to conserved even there is genetic variation or amino acid modification. We concluded that structural of PC gene is more conserved than its sequences. It is important to keep its function among species.