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CCR2-V64IPolymorphism in Multidrug-Resistant TuberculosisPatients in Dr. Moewardi General Hospital in Surakarta Windhy Monica; Afiono Agung Prasetyo; Marwoto .
Nexus Biomedika Vol 4, No 3 (2015): Nexus Biomedika
Publisher : Nexus Biomedika

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Background: Genetic variants of CCR2 (CC chemokine receptor type 2) are associated with susceptibility to tuberculosis (TB), however its association with Multidrug-Resistant Tuberculosis (MDR-TB) is still unknown. The aim of the present study was to find out the status of CCR2-V64I polymorphisms among MDR-TB patients in Dr. Moewardi General Hospital in Surakarta. Methods: Blood samples from 36 MDR-TB patients in Dr. Moewardi General Hospital in Surakarta were subjected to DNA isolation. The DNA was genotyped for CCR2-V64I polymorphisms by a polymerase chain reaction with sequence-specific primers (PCR-SSP). Results: The wild type (GG) was found in 21/36 (58%) samples. The heterozygous genotype (GA), homozygous genotype (AA), and A allele frequencies in the population respectively were 39%, 3%, and 22%. Conclusion: The frequency of mutant type (GA and AA) was found lower than the wild type (GG) in the population of MDR-TB patients. Keywords: CCR2-V64I, MDR-TB, Surakarta

Analisis Molekuler Regio Core Promoter dan Precore/CoreIsolat Virus Hepatitis B 09IDSKAB-3 Ibnu Yudistiro; Afiono Agung Prasetyo; Yulia Sari
Nexus Biomedika Vol 2, No 1 (2013): Nexus Biomedika
Publisher : Nexus Biomedika

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Background: HBV replicates its DNA genome through reverse transcription from RNA intermediate. It is vulnerable to a high number of mutations during such reverse transcription which are frequently found in core promoter and precore/core regions. This study was aimed to identify genetic variation of HBV core promoter and precore/core regions of 09IDSKAB-3 isolate. Methods: DNA extraction was performed on 09IDSKAB-3 blood sample that was taken from Man Sex with Man Community. Core promoter and precore/core regions were determined by PCR using KL-28 and KL-6 primers and direct sequencing of the corresponding region. Molecular analysis was performed using MEGA 4.0. Results: Based on BLAST result, 09IDSKAB-3 HBV isolate had the highest similarity to isolate AP011085 from DKI Jakarta. Genetic variations A1726C in core promoter, and T1860C, C1877T, G1957C in precore/core region were found in 09IDSKAB-3 isolate. Conclusions: 09IDSKAB-3 HBV isolate was classified into genotype B and subgenotype B3 based on core promoter and precore/core region. The genetic variations found in this isolate may have influence to the replication efficiency and HBeAg/HBcAg production, therefore need further study. Keywords: hepatitis B virus, molecular analysis, core promoter region, precore/core region

Analisis Molekuler Regio Pre-S1, Pre-S2, dan S Isolat Virus Hepatitis B 09IDSKAB-3 Angga Dwi Prasetyo; Afiono Agung Prasetyo; Yulia Sari
Nexus Biomedika Vol 2, No 1 (2013): Nexus Biomedika
Publisher : Nexus Biomedika

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Background: The Hepatitis B Virus (HBV) pre-S1, pre-S2, and S region are essentially known for virus infection and replication. Eight genotypes (A to H) and nine subtypes (adw2, adw4, ayw1, ayw2, ayw3, ayw4, adrq+, adrq-, and ayr) of HBV have been identified worldwide. The aim of this study was to analyze HBV genetic variation in pre-S1, pre-S2, and S region, and to determine genotype and subtype of 09IDSKAB-3 HBV isolate from Men Who Have Sex With Men community in Surakarta. Methods: 09IDSAKAB-3 HBV DNA extraction was used as a template for amplication of pre-S1, pre-S2, and S region. The sequence results were then aligned by Clustal W with all of reference sequences reported in GenBank/DDBJ/EMNL. Genetic variation in pre-S1, pre-S2, and S region were identified using MEGA 4.0. HBV genotype and subgenotype were identified by phylogenetic analysis. HBV subtype was deduced on the basis of the predicted amino acid sequences of HBsAg. Results: Based on BLAST search in GenBank, 09IDSKAB-3 isolate was classified into genotype B3. D27E variation was found in pre-S1 region, and there were not genetic variation in pre-S2 and S region. Phylogenetic tree showed that 09IDSKAB-3 isolate was classified into genotype B3. Based on the basis of predicted amino acid sequences of HBsAg, 09IDSKAB-3 isolate was classified into subtype adw2. Conclusions: Overall, only D27E variation was found in this study. 09IDSKAB-3 isolate was classified into genoytpe B3 and subtype adw2. The amino acid variations found in the present report need further study. Keywords: HBV, pre-S1 region, pre-S2 region, S region

Antiviral Effect of Ethanolic Extract of Red Ginger Rhizome (Zingiber officinale Linn var. rubrum) Against Dengue Virus In Vitro Natasha Ninda Pramalista; Afiono Agung Prasetyo; Ratih Dewi Yudhani
Nexus Biomedika Vol 6, No 1 (2017): Nexus Biomedika
Publisher : Nexus Biomedika

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Introduction: Dengue virus is a type of virus that causes various reactions, from asymptomatic infection to harmful manifestations, such as dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). Currently, the treatments of DHF cases have been limited to symptomatic and supportive therapies only. Therefore, it is necessary to develop new strategies in facing these cases. One of them is by using natural ingredients with antiviral potential. The aim of this study is to understand the antiviral effects of the ethanol extract of red ginger rhizome (Zingiber officinale Linn var. rubrum) against dengue virus in vitro. Methods : The subject of this research was Dengue virus serotype 2 strain New guinea C (DENV-2 NGC) which was infected into Huh-7 cell line. The research was divided into 2 parts. The first was inhibition test of the extract against DENV-2 which was assessed by average of infectivity percentage with Focus Forming Unit assay method. The second was toxicity test of the extract in Huh 7 cells which was assessed by average of viability percentage by MTT assay method. The herb extract effective as a Dengue antivirus was defined by average infectivity percentage of ? 20% and average viability percentage of > 50%. Results: Ethanolic extract of Red Ginger rhizome (Zingiber officinale Linn var. Rubrum) with concentration 80, 40, 20, 10, 5, 2.5 g/ml had average percentage of infectivity respectively: 9.2% ; 25.3% ; 32.3% ;47.5% ; 66.6% ; 73.4%. While the average percentage of viability were: 92.2% ; 94.3% ; 96.7 % ; 99.6% ; 102.7% ; 105.9%. Conclusions: Ethanolic extract of rhizome Red Ginger (Zingiber officinale Linn var. Rubrum) is not effective in inhibiting the replication of dengue virus serotype DENV-2 in vitro because it has the average infectivity percentage ? 20 and has no toxic effects on cells Huh-7 because it has the average viability percentage > 50. Key Words: Zingiber officinale Linn var. rubrum, Dengue virus, DENV-2, Huh-7 cell line.

Delesi Gen APOBEC3B pada Pasien Human Immunodeficiency Virus di RSUD Dr. Moewardi Surakarta Ekkim Al Kindi; Afiono Agung Prasetyo; Yulia Sari
Nexus Biomedika Vol 3, No 1 (2014): Nexus Biomedika
Publisher : Nexus Biomedika

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Background:HIV infection on human can get inhibition from intrinsic factor. Human can produce antivirus protein which is encoded by APOBEC3 gene. APOBEC3B (A3B) is one of APOBEC3 protein, which cannot be degradated by HIV vif protein. Therefore A3B protein is a potent inhibitor of HIV replication. But, A3B gene can get a deletion, which can decrease its effect in inhibiting HIV infection.The aim of this study was to find correlation between CD4 cells count in A3B gene deletion-positive respondents and A3B gene deletion-negative respondents. Methods: There were 51 HIV patients in Dr. Moewardi General Hospital Surakarta on November 2011, which were included as our respondents. We take respondentss blood and were isolated their DNA. Then, we run in PCR with deletion primer (Deletion_F dan Deletion_R) to detect if there was a deletion in A3B gene sequence. We run electrophoresis in 1% agarose gel with Loading Quick ?X174/HaeIII 72-1353bp as a marker. Then, we visualized the gel on Gel Documentation and was interpreted. Data of A3B gene deletion, respondentss description, HIV RNA detection, and CD4 cell count were analysed with Chi Square. Results:About 36 respondents (70.6%) were positive for deletion in A3B gene. Four of them were positive for HIV RNA detection. The average of CD4 cells count in respondents, who were positive for A3B gene deletion, was 426.86 407.4 cells/l and the others were 496.93 573.0 cells/l (p = 0.782). There were no correlation (p > 0.050) between A3B gene deletion in female respondents and CD4 cells count. A3B gene deletion was more likely to be found in female respondents (OR = 2.286; 95% CI : 0.669 7.808). Conclusions:There were no differences between the average of CD4 cell counts in A3B gene deletion-positive respondents and A3B gene deletion-negative respondents. Keywords:Polymorphism, Deletion, APOBEC3B, HIV

APOBEC3B Gene Deletion Status inMultidrug-Resistant Tuberculosis(MDR-TB) Patients in Dr. MoewardiGeneral Hospital in Surakarta Fitri Ika Suryani; Afiono Agung Prasetyo; Hudiyono .
Nexus Biomedika Vol 4, No 3 (2015): Nexus Biomedika
Publisher : Nexus Biomedika

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Background: Data of APOBEC3B gene deletion status in Indonesia are limited. Moreover, information aboutAPOBEC3B gene deletion status in Multidrug-Resistant Tuberculosis (MDR-TB) patients in Dr. Moewardi General Hospital in Surakarta was unknown. This study was aimed to know the APOBEC3B gene deletion status in MDR-TB patients in Dr. Moewardi General Hospital in Surakarta. In the future, this research was expected can be used as asupporting examination in chronic tuberculosis patients which tend to progressively become MDR-TB. Methods: Blood samples from 43 MDR-TB patients in Dr. Moewardi General Hospital in Surakarta were collected, DNA isolation was performed for all samples, followed by a single Polymerase Chain Reaction (PCR)to detectthe presentation of APOBEC3B gene deletion genotype. Results: APOBEC3B gene deletion genotype was detected in81.4%(35/43) samples. Conclusions: The APOBEC3B gene deletion genotype was frequently found in MDR-TB patients in Dr. Moewardi General Hospital in Surakarta. Keywords: APOBEC3B, deletion, MDR-TB

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