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Merdekawati, Fusvita
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Journal : Current Biomedicine

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Optimasi suhu amplifikasi DNA pada quantitative polymerase chain reaction untuk identifikasi Mycobcterium tuberculosis resistan isoniazid Endarwati, Dwi Veni; Indra, Asep Iin Nur; Hardiana, Acep Tantan; Abror, Yogi Khoirul; Nurhayati, Betty; Merdekawati, Fusvita
Current Biomedicine Vol. 2 No. 2 (2024): July
Publisher : School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/currbiomed.2.2.61-70

Abstract

Background: Tuberculosis (TB) is a disease caused by Mycobacterium tuberculosis and is a serious threat to global health. The methods can be used to detect and identify the bacteria is quantitative polymerase chain reaction (qPCR). In this method, denaturation and extension temperatures are determining factors of success that needs to be optimized. Objective: This study aims to optimize denaturation and extension temperatures in M. tuberculosis DNA amplification. Methods: The research used quasi-experimental design. The denaturation temperature optimized were 93, 94, 95, 96, and 97°C, and the extension temperature optimized were 58, 59, 60, 61, and 62°C. The test sample was a 1 ml sputum sample isolated from a patient with isoniazid-resistant M. tuberculosis. Optimization was performed using seven test primers, namely S315T, S315N, S315I, S315R, S315G, S315L, and R463B with the katG gene target and data analysis using Ms Excel. Data optimization results were processed with Excel by taking the lowest Ct value. Results: The results showed that the optimization temperatures for denaturation were different for each primer used. Primers S315T, S315R, and S315G, optimal with denaturation temperature of 96°C, primer S315N optimal with 94°C, primers S315I and R463B optimal with 93°C, and for primer S315L optimal with 95°C, with the most widely used temperature is 96°C. The optimal extension temperature was 58°C for primers S315T, S315N, S315I, and R463B, at 60°C for primers S315R and S315G, and at 61°C for primer S315L. Conclusion: The optimal denaturation temperature in this study was 96°C and the optimal extension temperature was 58°C.
Konsentrasi dan kemurnian ekstraksi DNA metode sonikasi dan spin column dari sampel dahak penderita tuberkulosis Saputra, Fitrianingsih; Indra, Asep Iin Nur; Djuminar, Ai; Merdekawati, Fusvita; Nurhayati, Betty
Current Biomedicine Vol. 2 No. 2 (2024): July
Publisher : School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/currbiomed.2.2.84-92

Abstract

Background: The Polymerase Chain Reaction (PCR) method can identify Mycobacterium tuberculosis in a sputum sample of a patient with TB (TB). One crucial step to ensure accurate PCR results is the DNA extraction process. Objective: The research aims to compare the concentration and purity of DNA from the sputum of TB patients using ultrasound and spin column extraction techniques. Methods: The research uses descriptive study designs with post-only design strategies. The primary data was derived from 18 sputum specimens from TB patients. Concentration measurement and DNA purity testing using a nanodrop spectroscopic photometer. Results: DNA extraction by ultrasound method has an average concentration of 18.9 ± 8.5 ng/L, with a peak of 37.6 ng/ L. The spin column method produces an average of 55.5 ± 27.9 ng/μL; the peak is 105.0 ng/ μL. The purity value of the DNA extract is in the range of 1.8 ± 2.0 with the ultrasound method of 61% and the spin column of 78%. Conclusion: The sonication method has a lower average concentration and a higher percentage of purity than the spin column method, and there are differences in concentrations and purity values between the two methods.
In silico prediction of multi-epitope vaccine candidates against Mycobacterium leprae Shabrina, Almas; Indra, Asep Iin Nur; Rinaldi, Sonny Feisal; Merdekawati, Fusvita
Current Biomedicine Vol. 3 No. 1 (2025): January
Publisher : School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/currbiomed.3.1.22

Abstract

Background Leprosy, also known as Hansen's disease, is an infectious disease caused by Mycobacterium leprae. Despite ongoing efforts to control the disease, leprosy remains a global health concern, with Indonesia ranking third in the world for the highest number of cases. Objective This study aims to identify epitopes that can induce T and B cell immune responses through an in silico approach, to design a multi-epitope vaccine candidate against Mycobacterium leprae. Methods The study used an in silico vaccine design approach utilizing ESAT6, Ag85B, ML2028, ML2380, and ML2055 proteins from Mycobacterium leprae. The process involved sequence alignment, T cell (CTL and HTL) and B cell epitopes identification, and antigenicity, allergenicity, and toxicity assessment. Selected epitopes were constructed into a multi-epitope vaccine candidate using linkers. The tertiary structure of the vaccine was modeled with AlphaFold and evaluated via Prosa-web. The stability and interaction between the vaccine candidate and TLR4 were analyzed using molecular docking. Results The vaccine candidate demonstrated stable interactions with TLR4, with a binding free energy of -13.9 kcal/mol. The vaccine candidate was also predicted to be stable, antigenic, non-allergenic, non-toxic, and hydrophilic. Conclusion This in silico design of a multi-epitope vaccine candidate shows potential for development as a vaccine against leprosy.
Correlation of polymerase chain reaction results with hematocrit levels and platelet counts in dengue patients in Batam City Simangunsong, Kristina; Nurhayati, Betty; Hayati, Eem; Merdekawati, Fusvita
Current Biomedicine Vol. 3 No. 1 (2025): January
Publisher : School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/currbiomed.3.1.1

Abstract

Background Dengue hemorrhagic fever (DHF) is a viral disease transmitted by Aedes aegypti mosquitoes, posing global public health challenge. The Riau Islands Province has the highest incidence of DHF in Indonesia. Objective This study aimed to investigate the relationship between hematocrit and platelet levels with the cycle threshold (Ct) values of polymerase chain reaction (PCR) results in DHF cases in Batam City, Riau Islands Province. Methods A descriptive correlation study was conducted using data from 102 patients infected with the dengue virus. Hematocrit and platelet counts were measured using a hematology analyzer, while Ct values for DENV1, DENV2, DENV3, and DENV4 were obtained through real-time qRT-PCR. Pearson's correlation test was employed to analyze the relationship between these variables. Results The study found no significant gender difference in DHF incidence (males: 50%, females: 50%). The highest prevalence was observed in the 6–11 years age group (44.1%), followed by the 12–18 years group (25.5%), the >18 years group (24.5%), and the 1–5 years group (11.8%). DENV3 was identified as the dominant serotype. No statistically significant correlation was found between Ct values and hematocrit (p = 0.607) or platelet counts (p = 0.323). Conclusion DHF cases in this study showed no gender disparity, with the most affected group being children aged 6–11 years, and DENV3 was the prevalent serotype. Ct values did not show a statistically significant correlation with hematocrit levels or platelet counts, suggesting that these hematological parameters may not predict viral load in DHF cases.
Sensitivity and specificity of the lipoarabinomannan test compared to GeneXpert in urine samples for tuberculosis diagnosis Irawan, Danni; Rismiarti, Zuri; Tantan, Acep; Merdekawati, Fusvita
Current Biomedicine Vol. 3 No. 1 (2025): January
Publisher : School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/currbiomed.3.1.7

Abstract

Background Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB), primarily affecting lung tissue but also capable of infecting pleura, lymph nodes, bones, and other extrapulmonary sites. Lipoarabinomannan (LAM) is a critical lipopolysaccharide in the outer wall of mycobacterial cells and can be detected in the urine of TB patients as an antigen. Objective This study aimed to assess the sensitivity and specificity of the LAM test compared to GeneXpert in urine samples from suspected TB patients. Methods A quasi-experimental design was employed, where urine samples were collected from patients diagnosed with TB at Sidawangi Lung Hospital, West Java Province. The LAM test was performed on 40 samples by applying 60 µL of urine onto LAM test strips, while MTB presence in urine was examined using GeneXpert. Results LAM test results showed 32.5% positivity, while 67.5% were negative. GeneXpert results indicated 20% positivity and 80% negativity. The LAM test demonstrated a sensitivity of 100% and specificity of 79.4% compared to GeneXpert, with an area under the curve (AUC) value of 0.897. Conclusion The LAM test showed high sensitivity and moderate specificity compared to GeneXpert in urine samples of suspected TB patients.
Co-Authors Abror, Yogi Khoirul Adrian Prasetya, Rifky Anhar, Citra Amaniah Dewi Nurhayati Djuminar, Ai Dzulhizza, Zaskia Puteri Endarwati, Dwi Veni Endrique Putri, Salmanda Ernawati Ernawati Febriyanti, Intan Hardiana, Acep Tantan Hasan, Zulfikar Ali Hayati, Eem Heri Setiyo Bekti I Gusti Agung Ayu Dharmawati Iin Nur Indra, Asep Iis Kurniati Indra , Asep Iin Nur Indra, Asep Iin Nur Irawan, Danni Juliastuti, Aditya Khairunnisa, Syirin Nisrina Khoirul Abror, Yogi Kurnaeni, Nani Lesiani, Bunga Rossa Maynar, Larasati Putri Nina Marliana, Nina Noviar, Ganjar nur amani putri, afifah Nur Habibah Nurhayati, Betty Nurhayati, Nuli Pratama, Resta Ratna Juwita Rahayu, Ira Gustira Rahmawati, Tia Rinaldi, Sonny Faisal Rinaldi, Sonny Feisal Rohayati rohayati rohayati Saputra, Fitrianingsih Shabrina, Almas Simangunsong, Kristina Solihat, M. Firman Sufa, Hafizah Ilmi Sulaeman, Rizal Pratama Sundara Mulia, Yuliansyah Suryawan, Muhammad Raihan Syafitri, Andita Izmi Tantan, Acep Trimulyani, Annisa Zahrani, Azka Hasbia Zanuba, Haifanisya Zahra Zuri Rismiarti