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Optimization of Real-Time PCR Conditions for COVID-19 Diagnosis with Logix Smart Reagent™ Anisa Febriyanti; Seprianto Seprianto; Titta Novianti; Febriana Dwi Wahyuni; Oktaviani Naulita Turnip; Roselein Putri; Henny Saraswati
BIOEDUKASI Vol 20 No 1 (2022)
Publisher : PROGRAM STUDI PENDIDIKAN BIOLOGI FAKULTAS KEGURUAN DAN ILMU PENDIDIKAN UNIVERSITAS JEMBER

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19184/bioedu.v20i1.28356

Corona Virus Disease 2019 or COVID-19 is a new type of virus that attacks the respiratory tract and can cause death. Laboratory examinations play an essential role in diagnosing COVID-19 with a set of reagents or kits. Sampiand sampling is carried out with a nasopharyngeal swab or oropharyngeal swab. Positive samples of COVID-19 patients used in this study were converted into RNA at the COVID-19 Referral Clinic in Bekasi, after which volume optimization was carried out with a total volume of 5 µl, 8 µl, and 10 µl with the Logix Smart™ kit. The method in this study uses One-Step Real-time PCR. This method is the best method for carrying out several bear tests because it can reduce the possibility of sample contamination. The procedure is fast and has high sensitivity. The fluorescence detection used in this study was FAM with a specific target of COVID-19 RNA and ROX with a particular DNA target of RNase-P. This research was conducted to obtain optimal volume conditions under the manufacturer's standards in detecting the SARS-CoV-2 virus. The results of this study indicate that a total volume of 5 l is the optimal total volume for detecting the presence of the SARS- CoV-2 virus in samples taken from patients.

Optimasi Volume Kit Da An Gene Untuk Deteksi SARS-CoV-2 dengan Real Time RT-PCR Seprianto; Muhammad Arreza; Titta Novianti; Febriana Dwi Wahyuni; Oktaviani Naulita Turnip; Roaslein Putri; Henny Saraswati
BIOEDUSCIENCE Vol 6 No 2 (2022): BIOEDUSCIENCE
Publisher : Universitas Muhammadiyah Prof. Dr. Hamka

Background: SARS-CoV-2 is a new type of coronavirus of the genus Betacoronavirus and the family Coronaviridae that causes a respiratory disease called COVID-19. The virus has a sheath and genetic material in the form of single-chain RNA. The genome structure of this virus is divided into two types, namely genes that encode non-structural proteins consisting of the ORF1a / ORF1b gene and genes that encode structural proteins consisting of spike glycoprotein (S), envelope (E), membrane glycoprotein (M), and nucleocapsid protein (N). Methods: The method of detecting SARS-CoV-2 with real time RT-PCR is the most recommended method because it has high specificity and accuracy. The specificity of a method is necessary to be able to specifically recognize the pathogen that causes the disease. Real time RT-PCR requires sampling with a swab on the oropharynx or nasopharynx to be examined in the laboratory which later the presence of viral RNA becomes a molecule that is assessed for diagnosis results. In this study, volume optimization was carried out on the Da An Gene kit used for the detection of SARS-CoV-2 with Reverse Transcription Polymerase Chain Reaction (Real time RT-PCR) with the aim of saving the use of reagents from available kits but with amplification results remaining optimal and accurate. Results: There were three SARS-CoV-2 RNA samples used consisting of N62, N63, and N79 samples and three types of total volume used were 20 Î¼l, 15 Î¼l, and 10 Î¼l. The results of this study showed that the three positive samples contained SARS-CoV-2 with a Cq value of < 40. Conclusion: A volume of 20 Î¼l is the optimal volume, which is more efficient than the manufacturer's recommended volume of 25 ul.

Growth Characteristics of Chikungunya Virus Isolate from Indonesia in Various Human Cell Lines in vitro Oktaviani Naulita Turnip; OKTAVIANI N. TURNIP; RAHMA F. HAYATI; RIZKA ALAWIYAH; BENEDIKTUS YOHAN; DIONISIUS DENIS; ANOM BOWOLAKSONO; AMIN SOEBANDRIO; R. TEDJO SASMONO
Microbiology Indonesia Vol. 13 No. 1 (2019): March 2019
Publisher : Indonesian Society for microbiology

Chikungunya (CHIK) fever, a febrile illness caused by Chikungunya virus (CHIKV) infection, is one of mosquito-borne viral diseases affecting people living in the tropical and subtropical regions in the world. The pathogenesis of the disease is yet to be completely unraveled, and research on CHIK has been conducted by employing various methods, including using cell lines to investigate the biological characteristics of CHIKV in vitro. To assess the suitability of human cell line model for CHIK study, various human cell lines including A549, Huh7, and HepG2 were infected with CHIKV and assayed for their susceptibility to infection. The MTT and plaque assay methods were performed to measure cell viability and virus growth kinetics, respectively. Fluorescence-activated Cell Sorting (FACS) and immunofluorescence assay were performed to measure the proportion of infected cells in the system and their morphological visualization. Both A549 and Huh7 human cell lines showed stable high cell viability upon infection while CHIKV growth kinetics were significantly lower in these cells compared to Vero-CCL81, a monkey cell line that is routinely used in other arboviruses research. Interestingly, we observed significantly different results in HepG2 human cell line, in which cell viability and CHIKV growth kinetics were significantly higher. FACS and immunofluorescence assay confirm the higher infection rate of CHIKV in HepG2 than A549 human cell line. We concluded herethat human hepatocytes HepG2 cell line was susceptible to Asian Genotype of CHIKV and proposed as an alternative cell for the in vitro CHIKV studies to the commonly used A549 and Vero cells.

Growth Characteristics of Chikungunya Virus Isolate from Indonesia in Various Human Cell Lines in vitro Oktaviani Naulita Turnip; OKTAVIANI N. TURNIP; RAHMA F. HAYATI; RIZKA ALAWIYAH; BENEDIKTUS YOHAN; DIONISIUS DENIS; ANOM BOWOLAKSONO; AMIN SOEBANDRIO; R. TEDJO SASMONO
Microbiology Indonesia Vol. 13 No. 1 (2019): March 2019
Publisher : Indonesian Society for microbiology

Chikungunya (CHIK) fever, a febrile illness caused by Chikungunya virus (CHIKV) infection, is one of mosquito-borne viral diseases affecting people living in the tropical and subtropical regions in the world. The pathogenesis of the disease is yet to be completely unraveled, and research on CHIK has been conducted by employing various methods, including using cell lines to investigate the biological characteristics of CHIKV in vitro. To assess the suitability of human cell line model for CHIK study, various human cell lines including A549, Huh7, and HepG2 were infected with CHIKV and assayed for their susceptibility to infection. The MTT and plaque assay methods were performed to measure cell viability and virus growth kinetics, respectively. Fluorescence-activated Cell Sorting (FACS) and immunofluorescence assay were performed to measure the proportion of infected cells in the system and their morphological visualization. Both A549 and Huh7 human cell lines showed stable high cell viability upon infection while CHIKV growth kinetics were significantly lower in these cells compared to Vero-CCL81, a monkey cell line that is routinely used in other arboviruses research. Interestingly, we observed significantly different results in HepG2 human cell line, in which cell viability and CHIKV growth kinetics were significantly higher. FACS and immunofluorescence assay confirm the higher infection rate of CHIKV in HepG2 than A549 human cell line. We concluded herethat human hepatocytes HepG2 cell line was susceptible to Asian Genotype of CHIKV and proposed as an alternative cell for the in vitro CHIKV studies to the commonly used A549 and Vero cells.

Optimasi Volume Kit Da An Gene Untuk Deteksi SARS-CoV-2 dengan Real Time RT-PCR Seprianto Seprianto; Muhammad Arreza; Titta Novianti; Febriana Dwi Wahyuni; Oktaviani Naulita Turnip; Roaslein Putri; Henny Saraswati
BIOEDUSCIENCE Vol 6 No 2 (2022): BIOEDUSCIENCE
Publisher : Universitas Muhammadiyah Prof. Dr. Hamka

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22236/j.bes/628595

Background: SARS-CoV-2 is a new type of coronavirus of the genus Betacoronavirus and the family Coronaviridae that causes a respiratory disease called COVID-19. The virus has a sheath and genetic material in the form of single-chain RNA. The genome structure of this virus is divided into two types, namely genes that encode non-structural proteins consisting of the ORF1a / ORF1b gene and genes that encode structural proteins consisting of spike glycoprotein (S), envelope (E), membrane glycoprotein (M), and nucleocapsid protein (N). Methods: The method of detecting SARS-CoV-2 with real time RT-PCR is the most recommended method because it has high specificity and accuracy. The specificity of a method is necessary to be able to specifically recognize the pathogen that causes the disease. Real time RT-PCR requires sampling with a swab on the oropharynx or nasopharynx to be examined in the laboratory which later the presence of viral RNA becomes a molecule that is assessed for diagnosis results. In this study, volume optimization was carried out on the Da An Gene kit used for the detection of SARS-CoV-2 with Reverse Transcription Polymerase Chain Reaction (Real time RT-PCR) with the aim of saving the use of reagents from available kits but with amplification results remaining optimal and accurate. Results: There were three SARS-CoV-2 RNA samples used consisting of N62, N63, and N79 samples and three types of total volume used were 20 Î¼l, 15 Î¼l, and 10 Î¼l. The results of this study showed that the three positive samples contained SARS-CoV-2 with a Cq value of < 40. Conclusion: A volume of 20 Î¼l is the optimal volume, which is more efficient than the manufacturer's recommended volume of 25 ul.

Optimasi Volume Kit Da An Gene Untuk Deteksi SARS-CoV-2 dengan Real Time RT-PCR Seprianto Seprianto; Muhammad Arreza; Titta Novianti; Febriana Dwi Wahyuni; Oktaviani Naulita Turnip; Roaslein Putri; Henny Saraswati
BIOEDUSCIENCE Vol 6 No 2 (2022): BIOEDUSCIENCE
Publisher : Universitas Muhammadiyah Prof. Dr. Hamka

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22236/j.bes/628595

Background: SARS-CoV-2 is a new type of coronavirus of the genus Betacoronavirus and the family Coronaviridae that causes a respiratory disease called COVID-19. The virus has a sheath and genetic material in the form of single-chain RNA. The genome structure of this virus is divided into two types, namely genes that encode non-structural proteins consisting of the ORF1a / ORF1b gene and genes that encode structural proteins consisting of spike glycoprotein (S), envelope (E), membrane glycoprotein (M), and nucleocapsid protein (N). Methods: The method of detecting SARS-CoV-2 with real time RT-PCR is the most recommended method because it has high specificity and accuracy. The specificity of a method is necessary to be able to specifically recognize the pathogen that causes the disease. Real time RT-PCR requires sampling with a swab on the oropharynx or nasopharynx to be examined in the laboratory which later the presence of viral RNA becomes a molecule that is assessed for diagnosis results. In this study, volume optimization was carried out on the Da An Gene kit used for the detection of SARS-CoV-2 with Reverse Transcription Polymerase Chain Reaction (Real time RT-PCR) with the aim of saving the use of reagents from available kits but with amplification results remaining optimal and accurate. Results: There were three SARS-CoV-2 RNA samples used consisting of N62, N63, and N79 samples and three types of total volume used were 20 Î¼l, 15 Î¼l, and 10 Î¼l. The results of this study showed that the three positive samples contained SARS-CoV-2 with a Cq value of < 40. Conclusion: A volume of 20 Î¼l is the optimal volume, which is more efficient than the manufacturer's recommended volume of 25 ul.

Epidemiological features and climatological effects on future malaria control in Indonesia Rovik, Anwar; Rahayu, Ayu; Turnip, Oktaviani Naulita; Daniwijaya, Edwin Widyanto
Berita Kedokteran Masyarakat Vol 41 No 11 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/bkm.v41i11.14397

Purpose: Malaria is a leading cause of death worldwide, including in Indonesia. Climate change should be considered when addressing malaria control in Indonesia. This study examined the relationship between climatological parameters (temperature, wind speed, humidity, and rainfall) and malaria cases in Indonesia from 2006 to 2015. Methods: Data on climatological parameters were obtained from Indonesia's 2022 statistics, while malaria case data were taken from the annual report of Indonesia's Ministry of Health. Results were presented using maps, diagrams, and graphs. The associations between climatological parameters and malaria cases were analyzed annually using GraphPad Prism 9 software. Results: Between 2006 and 2015, the API fluctuated each year. Papua province had the highest malaria incidence in Indonesia (25.5%). A significant decline in malaria cases was observed outside Papua province, whereas cases in Papua tended to increase annually. During this period, annual temperature ranged from 23.39°C to 28.44°C, wind speed from 1.01 m/s to 17.54 m/s, relative humidity from 70.85% to 85.84%, and rainfall from 99.74 to 3,838.2 mm3. Conclusion: From 2006 to 2015, annual temperature, rainfall, and relative humidity showed weak positive correlations with the API, whereas annual wind speed showed a negative correlation.

Bioinformatics Analysis of Quercetin and Morin Bioactivity from Morinda citrifolia L. Targeting Streptococcus mutans Virulence Factors In Dental Caries Cases Astrid Ekklesia Saputri; Rian Ka Praja; Agnes Frethernety; Oktaviani Naulita Turnip; Ysrafil Ysrafil
Biology, Medicine, & Natural Product Chemistry Vol 15, No 1 (2026)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2026.151.535-553

Dental caries remains one of the most neglected oral diseases, particularly among populations living far from healthcare services. Its pathogenesis is largely triggered by poor oral hygiene and the activity of Streptococcus mutans. The use of synthetic antimicrobial agents often leads to prolonged side effects and a higher risk of antibiotic resistance. As an alternative, Morinda citrifolia L. extract shows high potential due to its good public acceptance, minimal side effects, and proven in vitro efficacy in inhibiting S. mutans growth. This study aimed to investigate the bioactivity factors of S. mutans in relation to specific components of Morinda citrifolia L. as an alternative therapeutic agent for dental caries using a bioinformatics-based approach. A descriptive-exploratory bioinformatics method was employed using computational analysis. The bacterial FASTA sequence of Streptococcus mutans UA159 was retrieved from the National Center for Biotechnology Information (NCBI) database and analyzed using several software tools, including STITCH v5.0, VICMPred, VirulentPred, BepiPred v1.0, MHC I and MHC II BindingPred, and PSORTb v3.0. The analysis revealed notable interactions in bioactivity between S. mutans proteins and the phytocompounds quercetin and morin. Seven virulent proteins PknB, SMU_1806, SMU_1213c, SMU_922, SMU_906, SMU_525, and SMU_1078c, contribute to cellular process, metabolism, virulence factors, and information & storage. Five proteins were identified in the cytoplasmic membrane, one in cell wall, and also cytoplasm. Quercetin and morin demonstrated strong antibacterial potential against S. mutans through interactions with virulent proteins. PknB, SMU_906, and SMU_1078c stand out in epitope T cell analysis with high affinity, demonstrating the ability to provoke an adaptive immune system response. Location complexity of 5’-nucleotide enzyme targeted by strategic antimicrobials leads to bacterial mortality.

Development of siRNA-Based Therapeutic Strategy Targeting Virulence Factor lpfA of Zoonotic Escherichia coli O157:H7 Rian Ka Praja; Oktaviani Naulita Turnip; Hanasia Hanasia; Reny Rosalina
Biology, Medicine, & Natural Product Chemistry Vol 15, No 1 (2026)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2026.151.159-165

This study aimed to identify potential small interfering RNA (siRNA) molecules capable of silencing the lpfA virulence gene of Escherichia coli O157:H7, a zoonotic pathogen responsible for severe gastrointestinal disease. The nucleotide sequence of lpfA from E. coli O157:H7 strain Sakai was analyzed, and candidate siRNAs were designed using multiple bioinformatics tools, including siPRED, siRNA Scales, MaxExpect, and DuplexFold. Top ten selected siRNA candidates demonstrated high predicted inhibitory activity, with silencing efficiencies ranging from 93.73% to 94.66%. Secondary structure predictions indicated stable folding without inhibitory intramolecular structures, while binding energy analysis showed strong siRNA–mRNA duplex stability, with the best candidate exhibiting -26.5 kcal/mol. These findings suggest that the identified siRNAs possess strong theoretical potential to suppress lpfA expression and may serve as candidates for future experimental validation. Overall, this study provides a foundational step toward developing siRNA-based therapeutic strategies targeting key virulence factors of E. coli O157:H7.

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