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All Journal HAYATI Journal of Biosciences VALENSI Microbiology Indonesia Acta Biochimica Indonesiana Sarwahita : Jurnal Pengabdian Kepada Masyarakat Jurnal Riset Sains dan Kimia Terapan JSMARTech : Journal of Smart Bioprospecting and Technology Prosiding Seminar Nasional Pengabdian Kepada Masyarakat Makara Journal of Science Jurnal Bioteknologi & Biosains Indonesia (JBBI) Jurnal Kesehatan Masyarakat Jurnal Bioteknologi & Biosains Indonesia
Jefferson Lynford Declan
(1) Department Of Chemistry, Faculty Of Mathematics And Natural Science, Universitas Negeri Jakarta, Gedung KH. Hasjim Asj'ari, 6th Floor, Jl. Rawamangun Muka, Jakarta Timur, 13220, Indonesia (2) Research Center For Detection Of Pathogenic Bacteria,
Agriculture, Biological Sciences & Forestry Humanities Biochemistry, Genetics & Molecular Biology Chemistry Earth & Planetary Sciences Economics, Econometrics & Finance Education Energy Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience Public Health Social Sciences Other

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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 Vol. 29, No. 3
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.
hpmA Gene as a Detection Method of Proteus mirabilis Bacteria using real-time Polymerase Chain Reaction Nurjayadi, Muktiningsih; Putri, Gladys Indira; Fitriyanti, Anisa; Declan, Jefferson Lynford; Novitasari; Abomoelak, Bassam
Jurnal Kesehatan Masyarakat Vol. 21 No. 2 (2025)
Publisher : Universitas Negeri Semarang in collaboration with Ikatan Ahli Kesehatan Masyarakat Indonesia (IAKMI Tingkat Pusat) and Jejaring Nasional Pendidikan Kesehatan (JNPK)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/kemas.v21i2.16214

Abstract

Proteus mirabilis is pathogenic bacteria that can cause gastrointestinal infections, bacteremia, and Urinary Tract Infections (UTI). Therefore, it is necessary to have a fast, sensitive, specific, and accurate detection method to identify Proteus mirabilis. This study aims to determine the confirmation, specificity, and sensitivity test of the hpmA gene primer to detect Proteus mirabilis quick and precise using the real-time Polymerase Chain Reaction method. Gradient Polymerase Chain Reaction results showed the hpmA primer has an amplicons length of 195 bp and the optimum annealing temperature at 60°C. The primer pair produced Ct value of 10.40±0.18 and showed one peak in the melting curve with Tm value of 81.84°C±0.02 by real-time PCR. Furthermore, the hpmA primer was also able to distinguish target and non-target bacteria based on the difference in Ct and Tm value formed. Based on these results, the concentration of bacterial DNA that can be detected by primers reached 3.2 pg/μL, equivalent to the concentration of target bacteria that can be detected by primers is 10.24×102 CFU. In the next step, hmpA primer will be developed to detect Proteus mirabilis in artificial contaminated samples using real-time PCR.
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 Jurnal Kimia VALENSI, Volume 11, No. 1, May 2025
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.
DETERMINATION OF OPTIMAL ANNEALING TEMPERATURE Vibrio alginolyticus PRIMERS USING POLYMERASE CHAIN REACTION METHOD Putri, Gladys Indira; Nurjayadi, Muktiningsih; Declan, Jefferson Lynford; Krisdawati, Ismaya; Juliansyah, Dandy Akbar; Fahriza, Tiara; Azzahra, Maharanianska; Maulana, Irvan; Kartika, Irma Ratna; Kurniadewi, Fera; Sukmawati, Dalia; Saamia4, Vira; Saputro, Dwi Anna Oktaviani; Wiranatha, I Made; Abomoelak, Bassam; El-Enshasy, Hesham Ali
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol. 10 No. 2 (2023)
Publisher : BRIN - Badan Riset dan Inovasi Nasional

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55981/jbbi.2023.2976

Abstract

Food poisoning is a global issue of grave concern. If food is not properly cooked, it can be a medium for the spread of pathogenic bacteria. Vibrio alginolyticus is one of the pathogenic bacteria that can cause food poisoning. real-time Polymerase Chain Reaction (rt-PCR) can detect pathogenic bacteria in food, so it is necessary to determine the optimal annealing temperature. This research aims to obtain the optimal annealing temperature of the Va_Chr1_FR primer using Gradient PCR. The DNA concentration used was 174.5 with an A260/A280 purity of 1.94. The temperature range tested, 53°C-62°C, corresponds to the melting temperature of the Va_Chr1_FR primers. The primers designed were F5'-TTCTTCTGTTGTAGGTTCCG-F3' and R5'-CCAGCCCTCACATCTAATAC-R3'. Based on these results, a temperature of 60°C is deemed as the most optimal annealing temperature because it produces one of the brightest bands on electrophoresis with an amplicon length of 146 bp. The findings of this study will be beneficial to the development of Va_Chr1_FR Vibrio alginolyticus primers testing on food samples using the real-time PCR method. 
DETERMINATION OF OPTIMAL ANNEALING TEMPERATURE Vibrio alginolyticus PRIMERS USING POLYMERASE CHAIN REACTION METHOD Putri, Gladys Indira; Nurjayadi, Muktiningsih; Declan, Jefferson Lynford; Krisdawati, Ismaya; Juliansyah, Dandy Akbar; Fahriza, Tiara; Azzahra, Maharanianska; Maulana, Irvan; Kartika, Irma Ratna; Kurniadewi, Fera; Sukmawati, Dalia; Saamia4, Vira; Saputro, Dwi Anna Oktaviani; Wiranatha, I Made; Abomoelak, Bassam; El-Enshasy, Hesham Ali
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol. 10 No. 2 (2023)
Publisher : BRIN - Badan Riset dan Inovasi Nasional

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55981/jbbi.2023.2976

Abstract

Food poisoning is a global issue of grave concern. If food is not properly cooked, it can be a medium for the spread of pathogenic bacteria. Vibrio alginolyticus is one of the pathogenic bacteria that can cause food poisoning. real-time Polymerase Chain Reaction (rt-PCR) can detect pathogenic bacteria in food, so it is necessary to determine the optimal annealing temperature. This research aims to obtain the optimal annealing temperature of the Va_Chr1_FR primer using Gradient PCR. The DNA concentration used was 174.5 with an A260/A280 purity of 1.94. The temperature range tested, 53°C-62°C, corresponds to the melting temperature of the Va_Chr1_FR primers. The primers designed were F5'-TTCTTCTGTTGTAGGTTCCG-F3' and R5'-CCAGCCCTCACATCTAATAC-R3'. Based on these results, a temperature of 60°C is deemed as the most optimal annealing temperature because it produces one of the brightest bands on electrophoresis with an amplicon length of 146 bp. The findings of this study will be beneficial to the development of Va_Chr1_FR Vibrio alginolyticus primers testing on food samples using the real-time PCR method. 
Co-Authors Aboemolak, Bassam Abomoelak, Bassam Abumoelak, Bassam Adinda Myra Amalia Putri Adinda Myra Amalia Putri Agus Setiawan AGUS SETIAWAN Akbar, Dandy Ananda Indah Putri Sihombing Angelina, Helzi Anggraeni, Rosita Gio Anisa Fitriyanti Annisa Maharani Athiyah Layla Atikah Nur Rahmawati Ayu Berkahingrum Azizah, Puan Aqila Azzahra, Maharanianska Bassam Abomoelak Bassam Abomoelak Berkahingrum, Ayu Chen, Shyi-Tien Dalia Sukmawati Dandy Akbar Juliansyah Dandy Akbar Juliansyah Dandy Akbar Juliansyah Dwi Ana Oktaviani El Enshasy, Hesham El-Enshasy, Hesham Ali Elenshasy, Hesham Ali Enshasy, Hesham Ali El Fahriza, Tiara Fera Kurniadewi Fera Kurniadewi Fitriyanti, Anisa Gladys Indira Putri Gladys Indira Putri Gladys Indira Putri Grace Grace, Grace Gusti Angieta Putri Hairishah, Nazrisya Helzi Angelina Hesham A. El Enshasy Hesham Ali Al-Enshashy Hesham Ali El-Enshasy I Made Wiranatha I Made Wiranatha Irma Ratna Kartika Irvan Maulana Irvan Maulana Irwan Saputra Ismaya Krisdawati Ismaya Krisdawati Ismaya Krisdawati Juliansyah, Dandy Akbar Kartika, Irma Ratna Krisdawati, Ismaya Kurniadewi, Fera Maharani Azka Azzahra Maharanianska Azzahra Maulana, Irvan Mellyna Fitriani Muktiningsih Nurjayadi Musie, Royna Rahma Nabilla Anisa Putrie Nasywa Fhelia Salta Nida Nur Afifah NOVITASARI Pardiana Puan Aqila Azizah Putri, Adinda Myra Amalia Putri, Gladys Indira Putri, Gusti Angieta Rahmawati, Atikah Nur Ririn Gustini Rizkahana Syehfia Rosita Gio Anggraeni Royna Rahma Musie Saamia, Vira Saamia4, Vira Saputro, Dwi Anna Oktaviani Sarah Adilisa Kartini Shangkara, Muhammad Arkent Shyi-Tien Chen Sihombing, Ananda Indah Putri Sintia Mardita Siti Fatimah SITI FATIMAH Sri Rahayu SRI RAHAYU Tiara Fahriza Uswatul Nisa Vira Saamia Vira Saamia Vira Saamia Wiranatha, I Made