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All Journal Jurnal IDAMAN (Induk Pemberdayaan Masyarakat Pedesaan) Jurnal Riset Kesehatan Poltekkes Depkes Bandung Nutriture Journal Current Biomedicine Media Penelitian dan Pengembangan Kesehatan
Indra, Asep Iin Nur
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Biochemistry, Genetics & Molecular Biology Decision Sciences, Operations Research & Management Dentistry Education Environmental Science Health Professions Immunology & microbiology Medicine & Pharmacology Nursing Public Health Social Sciences Veterinary Other

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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.
Co-Authors Abror, Yogi Khoirul Agustini, Siti Fajarwati Budiana, Lufthy Leidi Djuminar, Ai Endarwati, Dwi Veni Hardiana, Acep Tantan Makbul Paneja, Rosmini Binti Merdekawati, Fusvita Nurhayati, Betty Rinaldi, Sonny Feisal rohayati rohayati Saputra, Fitrianingsih Shabrina, Almas Sugihartina, Ganthina Yeni Wahyuni Zuri Rismiarti