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All Journal Media Penelitian dan Pengembangan Kesehatan Jurnal Biotek Medisiana Indonesia Global Medical and Health Communication Elkawnie Paediatrica Indonesiana Narra J Indonesian Journal of Cancer Jurnal Kefarmasian Indonesia
Vivi Setiawaty
Pusat Biomedis dan Teknologi Dasar Kesehatan
Biochemistry, Genetics & Molecular Biology Chemistry Decision Sciences, Operations Research & Management Dentistry Engineering Health Professions Immunology & microbiology Medicine & Pharmacology Nursing Public Health

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The Effect of Pretreatment Temperature in The Mycobacterium tuberculosis Extraction Method on DNA Quality Setianingsih, Tri Yuli; Fitri, Safira; Wahyono, Daniel Joko; Setiawaty, Vivi
Elkawnie: Journal of Islamic Science and Technology Vol 10, No 2 (2024)
Publisher : Universitas Islam Negeri Ar-Raniry Banda Aceh

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22373/ekw.v10i2.23062

Abstract

Abstract: The existing DNA extraction process for Mycobacterium tuberculosis employs a pretreatment step that may not function at its full potential. This inefficient process led to complications in subsequent analysis; thus, it is necessary to determine the successful extraction method with or without adding a pretreatment step. This study aims to determine the effect of temperature pretreatment on the extraction method of M. tuberculosis on the quality of DNA for WGS examination. The research design was analytically descriptive with a kit-based extraction method from ExiPrepTM Dx Mycobacteria Genomic DNA Kit (K-4418), Bioneer. The results of this study were that DNA purity did not differ (p = 0.959) between the pretreatment heating at 950 °C (2.88) and no heating at 950 °C (2.46). DNA concentration did not differ (p-value = 0.111) between pretreatment heating 950C (0.416 ng/µL) and no heating 950C (0.653 ng/µL). The relatively low DNA concentration resulted in the DNA bands not being visualized on agarose gel electrophoresis (0.8%). In conclusion, our study showed that the pretreatment heating step on M. tuberculosis DNA extraction does not affect DNA purity, concentration, or integrity. This inefficiency step can be discarded from the M. tuberculosis DNA extraction process to simplify the extraction processing. However, other extraction kit approaches need to be explored in future studies.Abstrak: Proses ekstraksi DNA Mycobacterium tuberculosis yang saat ini dilakukan memerlukan pretreatment yang mungkin tidak berpengaruh secara optimal. Proses yang tidak efisiensi berpengaruh terhadap analisis selanjutnya, sehingga perlu untuk mengetahui keberhasilan metode ekstraksi dengan penambahan proses pretreatment. Tujuan penelitian ini adalah untuk mengetahui pengaruh pretreatment suhu pada metode ekstraksi M. tuberkulosis terhadap kualitas DNA untuk pemeriksaan WGS. Desain penelitian adalah deskriptif analitik dengan metode ekstraksi berbasis kit dari ExiPrepTM Dx Mycobacteria Genomic DNA Kit (K-4418), Bioneer. Hasil penelitian adalah kemurnian DNA tidak berbeda (p=0,959) antara pretreatment pemanasan 950C (2,88) dengan tanpa pemanasan 950C (2,46). Konsentrasi DNA tidak berbeda (p value = 0,111) antara pretreatment pemanasan 950C (0,416 ng/µL) dengan tanpa pemanasan 950C (0,653 ng/µL). Konsentrasi DNA yang relatif rendah mengakibatkan pita DNA tidak tervisualisasi pada elektroforesis gel agarosa (0,8%). Kesimpulan dari penelitian  ini, bahwa langkah pemanasan awal pada ekstraksi DNA M. tuberkulosis tidak berpengaruh terhadap kemurnian, konsentrasi, dan integritas DNA. Langkah ini dapat dihilangkan dari proses ekstraksi DNA M. tuberkulosis untuk menyederhanakan proses ekstraksi. Namun, pendekatan kit ekstraksi lainnya perlu dieksplorasi dalam penelitian selanjutnya
Comparison of c-MYC Expression between Patients with Germinal Center and Non-Germinal Center B-cell-like Diffuse Large B Cell Lymphoma Hanum, Sitti Fatimah; Hardjolukito, Endang Sri Roostini; Kusmardi, Kusmardi; Murtiani, Farida; Widiantari, Aninda Dinar; Setiawaty, Vivi
Indonesian Journal of Cancer Vol 19, No 2 (2025): June
Publisher : http://dharmais.co.id/

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33371/ijoc.v19i2.1277

Abstract

Background: c-MYC expression has been used as a prognostic marker to predict prognosis and determine therapeutic strategies in both Diffuse Large B Cell Lymphoma (DLBCL) subtypes. No study on c-MYC expression associated with DLBCL has ever been conducted in Indonesia. Our study aimed to evaluate differences in c-MYC expression in both DLBCL subtypes and assess the immunophenotype profile.Method: We selected 40 DLBCL cases and divided them into Germinal Center B-cell (GCB) and non-GCB subtypes using Hans Criteria. We evaluated c-MYC expression, and a cut-off value of 60.4% was determined using Receiver Operating Characteristic (ROC) curve analysis.Results: We found that c-MYC expression was significantly higher in GCB subtypes compared to non-GCB subtypes (n = 17 (42.5%) vs n = 20 (7.5%), p 0.000 and mostly had an immunophenotype of CD10+/BCL6+/MUM1+.Conclusion: Higher c-MYC expression is found more frequently in GCB subtypes. These findings suggest that c-MYC may play a subtype-specific role in DLBCL pathogenesis, potentially influencing therapeutic decisions for Indonesian patients. Future studies should validate these results in larger, multi-center cohorts and explore the mechanistic link between c-MYC and the GCB subtype and its clinical implications for targeted therapies.
Biomarkers for predicting COVID-19 mortality: A study at Sulianti Saroso Infectious Disease Hospital, Indonesia Maemun, Siti; Widiantari, Aninda D.; Murtiani, Farida; Herlina, Herlina; Tanjungsari, Dian W.; Wijiarti, Kunti; Pratiwi, Tiara Z.; Matondang, Faisal; Rusli, Adria; Rivaldiansyah, Rivaldiansyah; Tampubolon, Maria L.; Mariana, Nina; Setiawaty, Vivi; Purnama, Tri B.
Narra J Vol. 5 No. 2 (2025): August 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v5i2.1936

Abstract

The high transmissibility and mortality rates of the COVID-19 pandemic pose significant challenges. Patients can deteriorate rapidly, making it crucial to identify laboratory biomarkers for high-risk individuals. The aim of this study was to evaluate the predictive value of various laboratory parameters, including C-reactive protein (CRP), D-dimer, ferritin, neutrophil-to-lymphocyte ratio (NLR), prothrombin time (PT), and procalcitonin (PCT), in predicting COVID-19 mortality. A retrospective cohort study was conducted at Sulianti Saroso Infectious Disease Hospital, where COVID-19 patients were categorized into survivors and non-survivors. The Mann-Whitney test was used to assess group differences, while receiver operating characteristic (ROC) curve analysis was performed to evaluate the predictive performance of each biomarker, with Youden's index (J) determining optimal cut-off values. Kaplan-Meier analysis was used to compare median survival times, and Cox regression assessed hazard rates and the relationship between biomarkers and mortality. A total of 1,598 patients were analyzed, the majority of whom were admitted with oxygen saturation levels >95% and classified as having mild to moderate disease severity. Among them, 216 patients died, resulting in a mortality rate of 13.52%. Significant variations in mortality rates were observed along the survival functions for NLR, ferritin, D-dimer, CRP, and PCT (p<0.001). The survival curves for these biomarkers demonstrated distinct trends across tertiles over time. Among hematological markers, NLR was significantly associated with mortality (p<0.001), with a 1.5–2.2% increased risk per unit increase. Biochemical markers (complete blood count) proved to be more effective than hematological parameters (NLR, ferritin, PT, D-dimer, CRP, PCT) when evaluating individual prognostic performance. Bivariate analysis of CRP, D-dimer, ferritin, NLR, PT, and PCT between survivors and non-survivors showed significant differences. Notably, NLR and PCT were highly relevant for predicting disease prognosis and mortality, with sensitivity and specificity values exceeding 80%.
Optimization of DNA Extraction and Whole Genome Sequencing for Neisseria gonorrhoeae Isolates and Clinical Samples Using Oxford Nanopore Technology Wahyono, Daniel Joko; Nastiti, Swasti Arum; Sulaiman, Verawati; Pratama, Wahyu Agung; Setiawaty, Vivi
Elkawnie Vol. 12 No. 1 (2026)
Publisher : Faculty of Science and Technology Universitas Islam Negeri Ar-Raniry

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22373/ekw.v12i1.32066

Abstract

Abstract: Gonorrhea is a sexually transmitted infection caused by Neisseria gonorrhoeae. Whole-genome sequencing (WGS) is essential for genomic studies of this bacterium to understand its epidemiology and mechanisms of antibiotic resistance. The success of WGS depends on obtaining high-quality genomic DNA. This study aimed to determine optimal DNA concentration and purity from optimized extraction of two isolates from two clinical samples and to achieve optimized genomic data analysis from WGS of both sample types. DNA extraction was performed using the Qiagen DNeasy Blood and Tissue Kit, and WGS was conducted on the GridION platform (Oxford Nanopore Technologies) with Epi2Me software for metagenomic analysis. The results showed that isolates produced higher DNA concentrations with A260/280 ratios of 1.8–2.0, whereas some clinical samples exhibited contamination. Metagenomic analysis revealed Neisseria gonorrhoeae dominance in isolates but low proportions in clinical samples, where other bacteria predominated. In conclusion, optimizing DNA extraction improved DNA quality and enabled valid WGS analysis. Metagenomic analysis revealed that N. gonorrhoeae dominated cultured isolates (~60–72% of reads) but was present at very low levels (<6%) in clinical samples, which were predominantly composed of E. coli, Klebsiella spp., and host DNA. These findings provide practical guidance for optimizing DNA extraction strategies in WGS-based studies of Neisseria gonorrhoeae, particularly for low-biomass clinical samples. They may support more accurate genomic surveillance and antibiotic resistance profiling to inform targeted treatment strategies. Abstrak: Gonore merupakan Infeksi Menular Seksual (IMS) yang disebabkan oleh Neisseria gonorrhoeae. Whole Genome Sequencing (WGS) merupakan metode penting dalam studi genomik bakteri untuk memahami epidemiologi dan mekanisme resistensi antibiotik. Keberhasilan WGS sangat bergantung pada kualitas DNA genomik yang diperoleh. Penelitian ini bertujuan untuk memperoleh nilai optimal konsentrasi dan kemurnian DNA hasil optimasi ekstraksi dari dua isolat pada dua sampel klinis, serta memperoleh hasil optimasi analisis data genomik WGS dari kedua jenis sampel tersebut. Ekstraksi DNA dilakukan menggunakan Qiagen DNeasy Blood and Tissue Kit, sedangkan WGS dilakukan pada platform GridIon (Oxford Nanopore Technologies) dengan perangkat lunak Epi2Me untuk analisis metagenomik. Hasil menunjukkan isolat menghasilkan konsentrasi DNA yang lebih tinggi dengan rasio A260/280 mendekati 1,8–2,0, sementara beberapa sampel klinis menunjukkan adanya kontaminasi. Analisis metagenomik menunjukkan dominasi Neisseria gonorrhoeae pada isolat, namun rendah pada sampel klinis yang didominasi oleh bakteri lain. Berdasarkan hasil tersebut, dapat disimpulkan bahwa optimasi ekstraksi DNA berhasil meningkatkan kualitas DNA dan memungkinkan analisis WGS yang valid. Analisis metagenomik memperlihatkan bahwa N. gonorrhoeae mendominasi isolat (~60–72% bacaan), namun sangat sedikit (<6%) pada sampel klinis, yang didominasi oleh E. coli, Klebsiella, dan DNA inang. Temuan ini memberikan panduan praktis untuk mengoptimalkan strategi ekstraksi DNA dalam studi berbasis WGS pada Neisseria gonorrhoeae, khususnya untuk sampel klinis dengan biomassa rendah, serta dapat mendukung pengawasan genomik yang lebih akurat dan profil resistensi antibiotik untuk memberikan informasi bagi strategi pengobatan yang lebih tepat sasaran.
Co-Authors Adria Rusli, Adria Agus Kosasih, Agus Agustiningsih -, Agustiningsih Agustiningsih Agustiningsih Anita Juniatiningsih Arie Ardiansyah Nugraha, Arie Ardiansyah Daniel Joko Wahyono Darmawan B Setyanto, Darmawan B Darmawan B. Setyanto, Darmawan B. David H Sidabutar, David H Dewi Lokida Eka Pratiwi Endang R Sedyaningsih Endang R. Sedyaningsih Endang Sri Roostini Hardjolukito Fera Ibrahim Fitri, Safira Hana Apsari Pawestri, Hana Apsari Hanum, Sitti Fatimah Herlina Herlina Herna -, Herna Holy A. Wibowo Jahiroh, Jahiroh Kartika D. Puspa Kartika Dewi Puspa Krisna N.A. Pangesti Krisna Nur Andriana Pangesti Kunti Wijiarti, Kunti Kusmardi , Maemun, Siti Matondang, Faisal Mirna Robert D.R. van Beest Holle Murtiani, Farida Nastiti, Swasti Arum Ni Ketut Susilarini Nike Susanti, Nike Nina Mariana, Nina PERTIWI, INTAN Pratama, Wahyu Agung Pratiwi, Tiara Z. Purnama, Tri B. Rahyussalim Rahyussalim, Rahyussalim Reni Herman Renti Mahkota Ririn Ramadhany Rivaldiansyah, Rivaldiansyah rosamarlina, rosamarlina Saptuti Chunaeni, Saptuti Setianingsih, Tri Yuli Sheila Kadir, Sheila Sinta Purnamawati Sulaiman, Verawati Tampubolon, Maria L. Tanjungsari, Dian W. Titi Sundari Tjahyani M. Sudiro Tri Kurniawati, Tri Widiantari, Aninda D. Widiantari, Aninda Dinar Wignjadiputro, Ira Yuyun SM Soedarmono, Yuyun SM