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All Journal HAYATI Journal of Biosciences VALENSI Medical Journal of Indonesia Indonesian Journal of Chemistry Jurnal Riset Sains dan Kimia Terapan JSMARTech : Journal of Smart Bioprospecting and Technology Makara Journal of Science
Saamia, Vira
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Earth & Planetary Sciences Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience

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Development of Bacillus subtilis Detection Method Targeting Genes codY, narH, and ureC Using Polymerase Chain Reaction Nurjayadi, Muktiningsih; Berkahingrum, Ayu; Putri, Adinda Myra Amalia; Rahmawati, Atikah Nur; Anggraeni, Rosita Gio; Fahriza, Tiara; Declan, Jefferson Lynford; Putri, Gladys Indira; Krisdawati, Ismaya; Juliansyah, Dandy Akbar; Azzahra, Maharanianska; Maulana, Irvan; Kartika, Irma Ratna; Kurniadewi, Fera; Sukmawati, Dalia; Rahayu, Sri; Saamia, Vira; Wiranatha, I Made; Abomoelak, Bassam; El Enshasy, Hesham
JSMARTech: Journal of Smart Bioprospecting and Technology Vol. 5 No. 1 (2024): JSMARTech Volume 5, No. 1, 2024
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2024.005.01.26

Abstract

Bacillus subtilis, a causative agent of foodborne illness in bread, cakes, cereals, and cheese leading to symptoms like diarrhea and nausea, was investigated for its role in nosocomial infections, including endocarditis, bacteremia, septicemia, and meningitis. The research focused on three genes: codY, narH, and ureC, which respectively contribute to bacterial survival through biofilm and spore formation, acid resistance, and adaptation to anaerobic conditions. The objective of this study was to evaluate the codY, narH, and ureC genes using the Gradient PCR method for Bacillus subtilis detection in bread and cheese through Real-Time PCR. During the research, bacterial growth was observed with an OD600 of 1.438 in Tryptic Soy Broth (TSB), and colonies of medium size, smooth, cream-coloured, and round shape were successfully isolated on Tryptic Soy Agar (TSA). The DNA template used had a 71.5 ng/µL concentration with an A260/280 ratio of approximately 1.830. The annealing temperature for Gradient PCR used was 53-62°C. The primers successfully amplified codY (175 bp), narH (222 bp), and ureC (153 bp) gene amplicons. The optimal annealing temperature for the primers used was 60°C, as indicated by the presence of a single bright band in electrophoresis. Using these three different genes, testing can also be conducted with the Multiplex PCR method. The next step involves developing a detection kit using optimized primers and annealing temperatures for the identification of Bacillus subtilis in bread and cheese samples using Real-Time PCR.
Limit Detection of Short Tandem Repeats (STR) Analysis on Touch DNA Samples Saamia, Vira; Yudianto, Ahmad; Nurjayadi, Muktiningsih; Novitasari, Novitasari; Furqoni, Abdul Hadi
Indonesian Journal of Chemistry Vol 24, No 5 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.94081

Abstract

Forensic short tandem repeats (STR) profiling on touch DNA samples has emerged as a primary method for human identification. The stability and uniqueness of STR combination from the targeted locus in each individual make it a precision marker for human identification. Touch DNA samples can be found in traces of biological material shed from a person. This work aimed to identify the lowest concentration limit required for generating an interpretable DNA profile and the sensitivity of the STR loci applied. Touch DNA samples were collected from donors who were asked to hold a rope for 5 min. A double swab technique was used to lift the touch samples from the rope. These samples are subjected to DNA extraction and quantification. Two STR amplification cycles, 29 and 34 cycles, were used. DNA concentration greatly influences the success of amplifying the target allele at each STR locus to be interpreted into a complete DNA profile, shown by its allele peak. Touch DNA concentration >0.25 ng can produce a complete DNA profile. LCN method successfully amplified touch DNA with a concentration 0.0625–0.25 ng/µL. Limit detection of touch DNA analysis is 0.25 ng/µL. Low-copy DNA can still be analyzed within 0.0625–0.25 ng/µL.
Touch DNA viability on various substrates from different shedder levels Saamia, Vira; Yudianto, Ahmad; Nurjayadi, Muktiningsih; Novitasari
Medical Journal of Indonesia Vol. 33 No. 3 (2024): September
Publisher : Faculty of Medicine Universitas Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13181/mji.oa.247398

Abstract

BACKGROUND Touch DNA samples are frequently discovered at crime scenes, including those found at the scene, on the victim, with the suspect, or on objects related to the incident. This study aimed to investigate 3 key factors affecting touch DNA samples: the characteristics person that shed the DNA, surfaces variants where the DNA was deposited, and different sampling methods effectiveness that influence DNA quantity, quality, and detection. METHODS 9 participants grouped into high, intermediate, and low shedder levels simultaneously tied 2 types of ropes, non-porous and porous. The first person will hold a rope for 5 min then pass it to the second person to hold on the same spot for another 5 min. DNA was collected from each rope using the double swab and tape-lift method, extracted, and quantified using real-time polymerase chain reaction (PCR). Touch DNA profile at 20 short tandem repeat loci was amplified in PCR system and detected on capillary electrophoresis. RESULTS Type of substrate (p = 0.97) or sampling method (p = 0.053) used for touch DNA collection did not significantly impact the DNA yield or profiling outcomes. A notable difference (p<0.001) was found in DNA quantity between high, intermediate, and low shedders, regardless of the substrate or method used. CONCLUSIONS Individual shedder level has a greater influence on the results of touch DNA analysis regarding the DNA quantity and profiling quality than substrate type and sample procedure.
Detection of the Yersinia enterocolitica Bacteria Targeting the myfA and ystA Genes in Contaminated Vegetable Samples using Real-Time PCR to Develop Rapid Detection of Food Poisoning Bacteria Nurjayadi, Muktiningsih; Anggraeni, Rosita GIo; Putri, Gladys Indira; Declan, Jefferson Lynford; Juliansyah, Dandy Akbar; Fahriza, Tiara; Putri, Adinda Myra Amalia; Berkahingrum, Ayu; Rahmawati, Atikah Nur; Kartika, Irma Ratna; Kurniadewi, Fera; Sukmawati, Dalia; Rahayu, Sri; Saamia, Vira; Wiranatha, I Made; Abomoelak, Bassam; El-Enshasy, Hesham Ali
HAYATI Journal of Biosciences Vol. 32 No. 4 (2025): July 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.4.989-1002

Abstract

Yersinia enterocolitica is a pathogenic bacterium with the ability to survive and multiply in food in a low-temperature environment that can cause death in humans. In previous studies, the optimum annealing temperature of ymoA, ystA, and ail gene primers with amplicons of 185 bp, 123 bp, and 192 bp, respectively, was successfully found. This study aims to develop a pathogenic bacteria detection kit with confirmation, sensitivity, and specificity of myfA and ystA primers in detecting Yersinia enterocolitica bacteria quickly and accurately using the real-time Polymerase Chain Reaction method. The results showed that myfA and ystA primers have optimum annealing temperatures at 60°C with amplicon lengths of 181 bp and 123 bp, respectively. Primer myfA was able to amplify the target with real-time PCR at Ct 12.07±1 and Tm 81±1°C, while the ystA primer at Ct 12.38±1 and Tm 83±1°C. myfA and ystA primers were also able to distinguish target and non-target bacteria based on Ct or Tm. The designed primers successfully detected Yersinia enterocolitica bacteria with the smallest concentration of 0.000439 ng/µL equivalent to 7.024 × 102 CFU. The detection limit obtained is smaller than the contamination threshold set by the Food and Drug Administration (BPOM). Primer myfA and ystA Yersinia enterocolitica also successfully detected the target bacteria in cabbage and lettuce samples artificially. Based on these results, myfA and ystA primers successfully detected Yersinia enterocolitica in vegetable samples using real-time PCR quickly, sensitively, specifically, and accurately.
Deteksi Vibrio parahaemolyticus Menggunakan Primer Gen toxR2 dengan Gradient Polymerase Chain Reaction Nurjayadi, Muktiningsih; Krisdawati, Ismaya; Declan, Jefferson Lynford; Putri, Gladys Indira; Juliansyah, Dandy Akbar; Rahmawati, Atikah Nur; Fitriyanti, Anisa; Musie, Royna Rahma; Kurniadewi, Fera; Sukmawati, Dalia; Saamia, Vira; Wiranatha, I Made; Abomoelak, Bassam; Elenshasy, Hesham Ali
Jurnal Riset Sains dan Kimia Terapan Vol. 11 No. 1 (2025): Jurnal Riset Sains dan Kimia Terapan, Volume 11 Nomor 1, Juni 2025
Publisher : Program Studi Kimia Universitas Negeri Jakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21009/JRSKT.111.03

Abstract

Makanan adalah kebutuhan vital, dengan kriteria utama adalah keamanan, kualitas, dan nilai gizi. Untuk memastikan keamanan makanan, diperlukan metode deteksi yang cepat dan akurat, terutama untuk mendeteksi bakteri patogen penyebab keracunan makanan. Vibrio parahaemolyticus merupakan bakteri patogen yang banyak ditemukan pada makanan laut. Penelitian ini bertujuan untuk mengembangkan metode deteksi cepat V. parahaemolyticus dengan menargetkan gen toxR2 menggunakan Gradient Polymerase Chain Reaction. Gen toxR dipilih karena fungsinya sebagai pengatur penting gen virulensi. Tahapan yang dilakukan meliputi desain primer, penyiapan sampel bakteri dari biakan murni, dan uji amplifikasi menggunakan PCR Gradien. Hasil uji amplifikasi menunjukan bahwa pasangan primer toxR2 berhasil mengamplifikasi pada suhu 58-62°C dengan dihasilkan pita berukuran 137 bp. Berdasarkan hasil tersebut, dapat disimpulkan bahwa PCR Gradien dengan primer toxR2 dapat diaplikasikan untuk mengembangkan alat deteksi V. parahaemolyticus dengan dilakukan uji lanjutan seperti uji konfirmasi, uji spesifisitas, uji sensitivitas, dan uji pada pangan menggunakan Real-Time Polymerase Chain Reaction.
Detection Method for Escherichia coli Using Real-Time Polymerase Chain Reaction Targeting the yhaV Gene Nurjayadi, Muktiningsih; Fitriyanti, Anisa; Musie, Royna Rahma; Putri, Gusti Angieta; Azizah, Puan Aqila; Angelina, Helzi; Grace, Grace; Sihombing, Ananda Indah Putri; Setiawan, Agus; Declan, Jefferson Lynford; Putri, Gladys Indira; Juliansyah, Dandy Akbar; Fatimah, Siti; Berkahingrum, Ayu; Kartika, Irma Ratna; Kurniadewi, Fera; Saamia, Vira; Chen, Shyi-Tien; Aboemolak, Bassam; Enshasy, Hesham Ali El
Makara Journal of Science
Publisher : UI Scholars Hub

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Escherichia coli is a foodborne pathogenic bacterium that can cause diarrhea, while yhaV is a virulence-associated gene linked to the toxin–antitoxin system in E. coli. This study was aimed at evaluating the confirmation, specificity, and sensitivity of a yhaV gene primer using real-time polymerase chain reaction. The yhaV-targeting PCR successfully amplified a DNA fragment with an amplicon length of 207 bp (base pairs) under an annealing temperature optimized to a range of 54 °C to 62 °C via gradient PCR. The PCR using the primer pair produced a consistent Ct (cycle threshold) of 14.14 ± 0.05 and showed a single peak in the melting curve at a Tm (melting temperature) of 83.67 °C ± 0.02. The specificity test indicated that the yhaV primer effectively distinguished E. coli from nontarget bacteria on the basis of differences in Ct and Tm values. The sensitivity analysis showed that the PCR directed toward the primer pair successfully detected E. coli at a minimum concentration of 2.24 pg/µL, with a Ct value of 29.93 and a detection limit of 31.5 × 102 CFU. These results suggest that yhaV-based real-time PCR quickly and accurately identifies E. coli. Primer designs that target yhaV have the potential to be developed as components of a rapid, specific, and sensitive kit for detecting E. coli in food samples.
Real-time PCR-based Detection of Foodborne Pathogen Cronobacter sakazakii DNA in Infant Formula Milk with Specific Targeting on the hfq Gene Nurjayadi, Muktiningsih; Juliansyah, Dandy Akbar; Declan, Jefferson Lynford; Putri, Gladys Indira; Krisdawati, Ismaya; Rahmawati, Atikah Nur; Azzahra, Maharanianska; Maulana, Irvan; Putri, Gusti Angieta; Kurniadewi, Fera; Kartika, Irma Ratna; Saamia, Vira; Wiranatha, I Made; Abomoelak, Bassam; El-Enshasy, Hesham Ali
HAYATI Journal of Biosciences Vol. 32 No. 6 (2025): November 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.6.1597-1607

Abstract

Cronobacter sakazakii has been linked to cause meningitis, necrotizing enterocolitis, and sepsis in infants and newborns, with case fatality rates ranging from 40 to 80%. The most common source of infection has been identified as Cronobacter sakazakii-contaminated infant formula. With a relatively specific target hfq gene, this study aims to develop a real-time PCR method to identify Cronobacter sakazakii in infant formula milk. Real-time PCR is used as a detection method because rt- PCR has higher specificity and sensitivity compared to conventional PCR methods. The real-time PCR method also has a higher level of effectiveness and time efficiency compared to conventional PCR. Cronobacter sakazakii ATCC 29544 genomic DNA was isolated and used in a real-time PCR assay. Cronobacter sakazakii DNA was amplified using a primer targeting the hfq gene, yielding a 145 bp amplicon. The results of the real-time PCR test showed that Cronobacter sakazakii DNA with a concentration of 53 ng/µL could be amplified by the primer pairs of hfq gene with Ct values of 11 respectively then had Tm values of 81.7°C±0.5. The specificity test showed that the hfq primer pairs could differentiate between the target and some non-target bacteria. The sensitivity test showed the ability of the primer to detect the smallest concentration of 3.392 pg/µL with a Ct of 26.16. Based on the results obtained, it can be concluded that the hfq primer has the potential to be used as a fast detection method for Cronobacter sakazakii bacteria in infant formula using real-time PCR.
Assessing Methods for Enhanced Recovery of Touch DNA from Fingerprints: A Pilot Study Saamia, Vira; Yudianto, Ahmad; Nurjayadi, Muktiningsih; Novitasari
HAYATI Journal of Biosciences Vol. 33 No. 1 (2026): January 2026
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.33.1.79-86

Abstract

The rapid advancement of science and technology, particularly in forensic science, has significantly enhanced crime investigation methodologies. One such advancement is the utilization of Scientific Crime Investigation methods, specifically the analysis of touch DNA from fingerprints. This research investigates the efficiency of fingerprint powders and swabbing agents in improving the quality and quantity of touch DNA for forensic applications. Touch DNA, derived from cellular materials like sweat and skin cells, presents a valuable source of genetic material for identification purposes. The study involved experimental analyses using Regular Silk Black Fingerprint Powder and Magnetic Dual-Purpose Powder, coupled with non-ionic detergent surfactants as swabbing agents. DNA samples were collected from volunteers with varying DNA shedding levels, processed, and analyzed using quantitative PCR and capillary electrophoresis. Results indicated that fingerprint powders significantly reduce the quantity and quality of recovered DNA due to DNA damage caused by the powders' chemical composition. Conversely, using non-ionic surfactants like Triton™ X-100 in swabbing improved DNA recovery and stability, leading to more complete DNA profiles. This study underscores the importance of optimizing fingerprint powder formulations and DNA sampling techniques to enhance forensic DNA analysis. The findings advocate for the development of less damaging fingerprint powders and improved DNA extraction protocols to preserve the integrity of touch DNA evidence in forensic investigations.
Efficacy Test of Prototype Kit for Detection Bacillus cereus and Listeria monocytogenes in Processed Meat using Real-time PCR Method Nurjayadi, Muktiningsih; Fahriza, Tiara; Putri, Adinda Myra Amalia; Rahmawati, Atikah Nur; Berkahingrum, Ayu; Anggraeni, Rosita Gio; Putri, Gladys Indira; Declan, Jefferson Lynford; Akbar, Dandy; Maulana, Irvan; Azzahra, Maharanianska; Shangkara, Muhammad Arkent; Kartika, Irma Ratna; Kurniadewi, Fera; Sukmawati, Dalia; Rahayu, Sri; Saamia, Vira; Wiranatha, I Made; Abumoelak, Bassam; El Enshasy, Hesham
Jurnal Kimia Valensi Vol. 11 No. 1 (2025): Jurnal Kimia VALENSI
Publisher : Department of Chemistry, Faculty of Science and Technology Syarif Hidayatullah Jakarta State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/jkv.v11i1.44280

Abstract

According to the World Health Organization (WHO), harmful agents such as Bacillus cereus and Listeria monocytogenes are responsible for 600 million cases of disease and 420,000 deaths annually. This research aims to test the effectiveness of the real-time PCR method for developing a prototype kit to detect pathogenic bacteria in processed meat. As a comparison, the and conventional PCR methods were used to obtain the accuracy, specificity, sensitivity, and effectiveness of the real-time PCR method. All the samples were cultured in solid media agar, performed amplification using specific primers cyt-K 2 and hly using PCR and real-time PCR. Meatballs, nuggets, and sausages, five samples each, were found to be positive positively contaminated with all targeted bacteria. However, they did not provide specific results using solid media culture and the PCR method. In addition, the real-time PCR method using prototype kit formulas accomplished that all contaminated samples had a Ct value smaller than the negative control, NTC (No Template Control), and had a similar melting curve to the positive control. This establishes that the real-time PCR method clarifies that all samples were contaminated with target bacteria. A formula was developed in the prototype kit with real-time PCR methods that can be used and applied on a commercial scale efficiently and precisely.
Co-Authors Aboemolak, Bassam Abomoelak, Bassam Abumoelak, Bassam Agus Setiawan Ahmad Yudianto Akbar, Dandy Angelina, Helzi Anggraeni, Rosita Gio Azizah, Puan Aqila Azzahra, Maharanianska Berkahingrum, Ayu Chen, Shyi-Tien Dalia Sukmawati El Enshasy, Hesham El-Enshasy, Hesham Ali Elenshasy, Hesham Ali Enshasy, Hesham Ali El Fahriza, Tiara Fitriyanti, Anisa Furqoni, Abdul Hadi Grace, Grace Jefferson Lynford Declan Juliansyah, Dandy Akbar Kartika, Irma Ratna Krisdawati, Ismaya Kurniadewi, Fera Maulana, Irvan Muktiningsih Nurjayadi Musie, Royna Rahma NOVITASARI Novitasari Novitasari Putri, Adinda Myra Amalia Putri, Gladys Indira Putri, Gusti Angieta Rahmawati, Atikah Nur Shangkara, Muhammad Arkent Sihombing, Ananda Indah Putri Siti Fatimah SRI RAHAYU Wiranatha, I Made