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All Journal HAYATI Journal of Biosciences Jurnal Pengolahan Hasil Perikanan Indonesia ILMU KELAUTAN: Indonesian Journal of Marine Sciences Indonesian Journal of Cancer Chemoprevention BERITA BIOLOGI JURNAL BIOLOGI INDONESIA ANNALES BOGORIENSES Annales Bogorienses
Apon Zaenal Mustopa
Research Center for Biotechnology, Indonesian Institute of Sciences Jalan Raya Bogor km 46, Cibinong 16911, Bogor, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Earth & Planetary Sciences Immunology & microbiology Medicine & Pharmacology

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PENGARUH SUHU, PH, ENZIM DAN SURFAKTAN TERHADAP PLANTARISIN F REKOMBINAN ENKAPSULASI SEBAGAI ANTIBAKTERI STAPHYLOCOCCUS AUREUS DAN SALMONELLA TYPHI Mustopa, Apon Zaenal; Hasim, Hasim; Amelia, Suci
JURNAL BIOLOGI INDONESIA Vol 14, No 1 (2018): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v14i1.3664

Abstract

ABSTRACTStaphylococcus aureus causes diarrhea, which is one of the main cause of infant mortality, where asSalmonella typhi causes typhoid fever with the incidence rate of 180/100,000/year. Plantarisin F is anantimicrobial peptide that can inhibit the growth of S. aureus and S. typhi. The aim of this study is to determinethe effect of temperature, pH, enzymes, and surfactants of encapsulated F recombinant plantarisin. Plantarisin F(1.61%) encapsulated with maltodextrin (5.36%) and skim milk (2.68%) using the spray dry with inlettemperature 150ºC produced particles that are generally spherical with a rough texture, range in size, yield25.03%, and had good antibacterial activity against S. aureus and S. typhi. The antibakterial activity plantarisinF encapsulated is not affected by the treatment temperature (40ºC-100ºC), pH (2-12), enzyme (proteinase-K,catalase, lysozyme, pepsin, trypsin), dan surfaktan (SDS, urea, triton X-100, PMSF, EDTA) treatment.Keywords: Antibacterial, Encapsulation, Plantarisin F, Salmonella typhi, Staphylococcus aureus
AKTIVITAS ANTIBAKTERI DAN ANTIOKSIDAN PEPTIDA SUSU KAMBING HASIL HIDROLISIS DENGAN PROTEASE LACTOBACILLUS PLANTARUM S31 Herlina, Nina; Mustopa, Apon Zaenal; Surachma, Rahma Sari; Triratna, Lita; Kartina, Gina; Alfisyahrin, Wida Nurul
JURNAL BIOLOGI INDONESIA Vol 15, No 1 (2019): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v15i1.3762

Abstract

ABSTRACTResearch on the hydrolysis of milk with various protease obtained from the digestive tract, plants and animals has been widely carried out, but the hydrolysis process of goat milk with protease enzymes from Lactobacillus plantarum S31 isolated from bekasam is still widely unknown. This study aims to determine the antibacterial and antioxidant activity of peptides hydrolyzed by protease enzymes from L. plantarum S31. Isolation and purification of extracellular proteases was carried out with 80% ammonium sulfate saturation, dialysis and G50 Sephadex matrix. The results of hydrolysis showed that fraction 11 has the highest antioxidant activity. Goat milk with pH 5 has a greater inhibitory activity of about 29%, which is 5% compared to goat milk pH 7. This fraction also has a quite good antibacterial activity of Entero Phatogenic Escherichia coli (EPEC K1.1) bacteria, Staphylococcus aureus and Listeria monocytogenes.  Keywords: goat milk, hydrolysis, antibacterial, antioxidant, Lactobacillus plantarum
Cloning, Expression, and Bioinformatics Modeling of Human Papillomavirus Type 52 L1/L2 Chimeric Protein in Escherichia coli BL21 (DE3) Ikramullah, Muh. Chaeril; Mustopa, Apon Zaenal; Wibawa, Tri; Hertati, Ai; Umami, Rifqiyah Nur; Ratna, Lita Tri; Irawan, Shasmita; Firdaus, Moh Egy Rahman; Darusman, Huda Salahudin
HAYATI Journal of Biosciences Vol. 31 No. 5 (2024): September 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.5.891-902

Abstract

Human papillomavirus (HPV) L1 major capsid protein generates a highly immunogenic virus like particles (VLPs), which have been used as the main component of its prophylactic vaccine. However, the neutralizing antibodies against L1 VLPs are mostly type specific and may not be effective to prevent infection from different strains of HPV. On the other hand, HPV L2 minor capsid protein has low antigenic variation, thus can induce cross-neutralization. This study aims to obtain HPV 52 L1/L2 chimeric protein, which is designed based on HPV type 52 as one of the most circulated high-risk types in Indonesia, to develop a broad-spectrum HPV vaccine. Substitution of HPV 52 H4 helix L1 region with an HPV 52 L2 epitope was carried out using overlap extension PCR. HPV 52 L1/L2 chimeric gene was constructed into pET-SUMO expression vector and expressed in Escherichia coli BL21 (DE3). Bioinformatics modeling suggested that L2 epitope was located inside of the loop region in monomer form, and on the contrary, it was located outside of the pentamer surface. Furthermore, B cell and T cell epitopes predictions were conducted using Immune Epitope Database (IEDB) analysis. The B cell epitopes prediction revealed eleven potential epitopes, whereas the T cell epitopes prediction showed seven potential epitopes for each MHC class I and MHC class II. This study showed that HPV 52 L1/L2 chimeric protein has the potential to induce cross-neutralizing antibodies and can be developed as a promising candidate for a new HPV vaccine.
Potential Probiotic Yeasts of the Pichia Genus Isolated from ‘Dadih’, a Traditional Fermented Food of West Sumatra, Indonesia Chihombori, Tatenda Calvin; Mustopa, Apon Zaenal; Astuti, Rika Indri; Mutiara, Ilma; Refli, Redoyan; Umami, Rifqiyah Nur; Fatimah; Irawan, Herman; Ekawati, Nurlaili; Trinugroho, Joko P; Akmaliyah, Rizna; Chairunnisa, Sheila; Amani, Febriyanti Nur; Manguntungi, Baso; Hertati, Ai; Mamangkey, Jendri
HAYATI Journal of Biosciences Vol. 32 No. 2 (2025): March 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.2.320-340

Abstract

Fermented buffalo milk, known as dadih, serves as a reservoir of potential probiotic yeasts. Over the past two decades, probiotic yeasts have gained increasing attention in both basic and clinical sciences due to their health benefits. This study aimed to isolate and characterize probiotic yeasts from dadih. Yeasts were isolated using yeast Extract, peptone, and dextrose (YPD) medium, and molecularly identified through 18S-rRNA sequencing. Probiotic potential was assessed by evaluating resistance to acidic pH, bile salts, proteolytic, lipolytic, and hemolytic activities. Secondary metabolites produced during fermentation were tested for antimicrobial properties. GBT30 and GBT37 isolates were selected based on their superior performance in probiotic property assays for further analysis. Molecular identification revealed these isolates as Pichia occidentalis (GBT30) and Pichia kudriavzevii (GBT37). Both strains demonstrated in vitro survivability under simulated gastrointestinal conditions and exhibited antimicrobial activity. Whole-genome sequencing of P. kudriavzevii GBT37 identified a genome size of 10,906,850 base pairs, distributed across four chromosomes with a GC content of 38.26%. Notably, secondary metabolite biosynthesis genes were located on contig 7. In addition, 26 probiotic-related genes, including GSY1, HSC82, HSP104, TPS1, ARN1, FLO1, ALA1, SIR2, and others, were identified in P. kudriavzevii GBT37, indicating its potential as a probiotic yeast. The traditional fermentation process of dadih offers probiotic yeasts with promising health benefits, supporting its potential as a functional food.
The Gene Analysis and Probiotic Potential Characterization of Pseudomonas alcaligenes SG03 Manguntungi, Baso; Rusmana, Iman; Mustopa, Apon Zaenal; Meryandini, Anja
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.32.4.1039-1052

Abstract

AHPND causes up to 80% of shrimp mortality, severely impacting Indonesia's aquaculture. Rising antibiotic resistance necessitates sustainable alternatives. This study investigates the probiotic potential of Pseudomonas alcaligenes SG03, a bacterium with unique genomic traits, to address antibiotic resistance and promote animal health. Genome analysis revealed a 6.17 Mb genome with 4,446 protein clusters, including genes for carbohydrate metabolism (26.63%), amino acid metabolism (19.93%), and energy metabolism (10.88%). Key probiotic-related genes, such as acid resistance (rpoS, actP), salinity tolerance (gshA, cysK), antibiotic resistance (vanB, gyrA), and metal resistance (copZ, zwf), were identified. In vitro, assays evaluated probiotic properties under conditions mimicking the shrimp gastrointestinal tract. Osmo-tolerance tests showed optimal growth at 10% glucose, with a significant drop in viability at higher concentrations. Autoaggregation increased progressively, reaching 0.78 at 18 hours and 0.13 at 48 hours. Optimal growth occurred at 30°C, with a 2.5-fold increase in optical density compared to 25°C. NaCl tolerance peaked at 2% (20.33×1012 CFU at 48 hours), while bile salt tolerance was highest at 0.1% (27.00×1012 CFU at 48 hours). pH tolerance was optimal at pH 5 (20.00×1012 CFU at 48 hours). Antioxidant (53.00%) and anti-inflammatory (60.33%) activities peaked after 48 hours. Phenotypic antibiotic resistance was observed against Tetracycline, Amoxicillin, Cefixime, Streptomycin, and Chloramphenicol, with proteolytic activity but no lipolytic or hemolytic properties. These findings highlight P. alcaligenes SG03’s potential as a probiotic in aquaculture to support shrimp health and reduce antibiotic dependency. Future studies should focus on in vivo validation and formulation development.
Truncation on N-Terminal Hydrophobic Domain of L1 Major Capsid Protein of Human Papillomavirus Type 52 Enhances Its Expression in Hansenula polymorpha Arifah, Rosyida Khusniatul; Firdaus, Moh Egy Rahman; Chairunnisa, Sheila; Irawan, Shasmita; Ekawati, Nurlaili; Irawan, Herman; Nurfatwa, Maritsa; Hertati, Ai; Swasthikawati, Sri; Novianti, Ela; Mustafawi, Wike Zahra; Nur Umami, Rifqiyah; Mustopa, Apon Zaenal
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.32.4.1062-1072

Abstract

Human papillomavirus (HPV) infection is the main cause of cervical cancer. The administration of the HPV prophylactic vaccine, which is commonly produced based on HPV L1 major capsid protein, significantly reduces the incidence of cervical cancer. However, the coverage of the HPV vaccination program is often hindered due to its relatively high cost. This study aimed to evaluate the impact of N-terminal hydrophobic domain truncation on the expression of L1 major capsid protein of HPV type 52 in Hansenula polymorpha. The truncation enhanced the yield of L1 protein expression compared with the full length, which was confirmed by Western blot and ELISA. Furthermore, the truncated L1 protein formed virus-like particles (VLPs), which were confirmed by transmission electron microscopy (TEM). Bioinformatics analysis showed that the truncated L1 protein was more soluble compared with the full length, possibly increasing the protein expression. These findings could pave the way for the development of a more cost-effective HPV type 52 L1 protein production in H. polymorpha to be used as a VLP-based prophylactic vaccine.
Medium Optimization for Recombinant Human Papillomavirus Type 52 L1 Protein Production in Pichia pastoris GS115 Platform on Bioreactor Scale Mustopa, Apon Zaenal; Nur Amani, Febriyanti; Irawan, Herman; Novianti, Ela; Swasthikawati, Sri; Ekawati, Nurlaili; Nurfatwa, Maritsa; Joko Wahyono, Daniel; Juanssilfero, Ario Betha; Mamangkey, Jendri; Purnomo, Yudi; Hertati, Ai; Wijaya, Hans; Dewi, Kartika Sari; Ningrum, Ratih Asmana
HAYATI Journal of Biosciences Vol. 32 No. 5 (2025): September 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.5.1283-1294

Abstract

Human papillomavirus (HPV) stands as the primary etiological agent in the development of invasive cervical cancer worldwide. The L1 protein is a pivotal constituent of prophylactic HPV vaccines. Notably, HPV type 52 is one of the most prevalent genotypes found in squamous cell carcinoma cases in Indonesia. This research endeavor aims to enhance the productivity of recombinant HPV-52 L1 protein by optimizing the culture conditions of P. pastoris GS115 cells. In this study, we conducted trials employing 17 different media variants to optimize the expression of recombinant HPV-52 L1 protein. The results from small-scale experiments revealed three media, namely SYN6.10, BMMY, and SYN6.1, which exhibited promising yields of recombinant HPV-52 L1 protein as assessed through ELISA or immunoassay analysis. We succeeded in refining the SYN6.10 derivative, denoted as SYN6.10b, specifically designed for use in 1-L and 5-L bioreactors. This achievement was realized by adjusting Trace Element Solution (TES) and Vitamin Solution (VS) concentrations and implementing a methanol fed-batch phase with the addition of 0.3% methanol after 24 and 48 hours of fermentation in the P. pastoris medium. Further visualizations through SDS-PAGE and western blot analysis confirmed the protein after 72 hours of fermentation in a 1-L bioreactor using the SYN6.10b medium. In conclusion, the SYN6.10b medium required a 72 hours fermentation period to successfully express recombinant HPV-52 L1 protein in the P. pastoris platform.
Metagenomic Analysis of Bacterial Communities in the Musi River Estuary, South Sumatra, Indonesia Melki; Mustopa, Apon Zaenal; Meiyerani, Jeni; Ramadhian, M. Zalfa; Purwiyanto, Anna Ida Sunaryo; Putri, Wike Ayu Eka; Hartoni
HAYATI Journal of Biosciences Vol. 32 No. 5 (2025): September 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.5.1157-1173

Abstract

Understanding the diversity, function, and ecological dynamics of bacterial communities depends on unique transitional environments, estuaries. Knowledge on bacterial taxa in the Musi River estuary, South Sumatra still eludes, however. This effort aims to identify bacterial species in estuary waters using metagenomic analysis based on 16S rRNA gene. Surface water samples from three study locations were analysed by DNA isolation, nanodrop spectrophotometer qualitative assessment, 16S rRNA gene amplification, electrophoresis, and Illumina NovaSeq sequencing. Results showed that Proteobacteria predominated at all sites, followed by Campilobacterota, Cyanobacteria, and Bacteroidota. At the class level, Gammaproteobacteria was most common, followed by Alphaproteobacteria and Campylobacteria. Dominant bacterial orders were Campylobacterales, Rhodobacterales, and Pseudomonadales while the most common families were Arcobacteraceae, Rhodobacteraceae, and Pseudomonadaceae. The most plentiful genera were Rheinheimera, Pseudomonas, and Pseudarcobacter. Variations in bacterial spread among stations suggest environmental factors including salinity, nutrient availability, and human activities influencing microbial community composition. Ternary plots, heat maps, and krona diagrams were employed to disclose distinct patterns of bacterial community dispersion in the estuary. This paper underscores the importance of metagenomic research in illuminating microbial diversity in estuarine environments and its impact on ecological dynamics and water quality.
Antibacterial and Antifungal of β-sitosterol Isolated from Hydroid Aglaophenia cupressina Lamoureoux Against Xanthomonas campestris and Fusarium oxysporum Johannes, Eva; Manguntungi, Baso; Tuwo, Mustika; Litaay, Magdalena; Mustopa, Apon Zaenal; Vanggy, Leggina Rezzy
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 30, No 2 (2025): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.30.2.192-202

Abstract

This study aimed to isolate and characterize β-sitosterol from the marine hydroid Aglaophenia cupressina Lamoureoux and evaluate its antibacterial and antifungal activities against Xanthomonas campestris and Fusarium oxysporum. β-Sitosterol was extracted, purified, and identified using spectroscopic techniques, including infrared and nuclear magnetic resonance spectroscopy. Antimicrobial activity was assessed through agar diffusion method to determine its inhibitory effects on bacterial and fungal growth at varying concentrations. β-sitosterol is a crystalline compound, with a melting point of 138-139°C, consistent with the reported range for pure β-sitosterol, indicating high purity. Infrared (IR) spectroscopy revealed key functional groups, including a hydroxyl group at 3433 cm⁻¹, C-O stretching at 1050 cm⁻¹, and aliphatic hydrocarbon chain vibrations at 2956, 2938, and 2869 cm⁻¹. The C=C stretching at 1634 cm⁻¹ and C-H bending at 1465 cm⁻¹ confirmed its unsaturated sterol structure. ¹H NMR spectroscopy further confirmed the structure with characteristic methyl and olefinic proton signals. The antibacterial activity of β-sitosterol against Xanthomonas campestris showed a concentration- and time-dependent effect, with the highest efficacy observed at 60 ppm, demonstrating potential as a natural antibacterial agent. Additionally, its antifungal activity against Fusarium oxysporum revealed both fungistatic and fungicidal effects, with lower concentrations exhibiting fungistatic behavior and higher concentrations displaying fungicidal activity, thereby offering versatility for both fungal inhibition and eradication. This dual action, combined with its well-characterized molecular structure, positions β-sitosterol as a promising candidate for further development as an antimicrobial compound. The findings underscore the accuracy of the identification process and highlight β-sitosterol's potential in pharmaceutical and agricultural applications, particularly in combating bacterial and fungal infections.
Partial purification and identification of antibacterial peptides from the endophytic fungus KT31 isolated from Kappaphycus alvarezii: Purifikasi parsial dan identifikasi peptida antibakteri dari kapang endofit KT31 yang diisolasi dari makroalga Kappaphycus alvarezi Sofyana, Neng Tanty; Mustopa, Apon Zaenal; Iriani Setyaningsih; Tarman, Kustiariyah; Maulidiani, Maulidiani
Jurnal Pengolahan Hasil Perikanan Indonesia Vol. 28 No. 9 (2025): Jurnal Pengolahan Hasil Perikanan Indonesia 28(9)
Publisher : Department of Aquatic Product Technology IPB University in collaboration with Masyarakat Pengolahan Hasil Perikanan Indonesia (MPHPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.17844/vyxqk974

Abstract

Endophytic fungi produce a wide array of secondary metabolites with diverse biological activities, including antibacterial, antifungal, insecticidal, and immunosuppressive effects. The increasing prevalence of infections caused by pathogenic bacteria, such as Escherichia coli, Bacillus subtilis, Salmonella typhi, Pseudomonas aeruginosa, Listeria monocytogenes, Bacillus pumilus, and Staphylococcus aureus, highlights the urgent need for novel antibacterial agents. This study aimed to determine the optimal concentration of ammonium sulfate for the isolation of endophytic fungus KT31 from Kappaphycus alvarezii based on its antibacterial activity. Fungal proteins were extracted using ammonium sulfate precipitation at varying saturation levels and subsequently tested for antibacterial activity against a panel of seven pathogenic bacterial strains. Crude protein extracts demonstrating promising activity were further purified using gel filtration chromatography with Sephadex G-50, followed by molecular weight determination usingDS-PAGE and protein quantification using a Bicinchoninic Acid (BCA) assay. The highest antibacterial activity was observed in the protein fraction precipitated at 80% ammonium sulfate saturation, exhibiting inhibition zones of up to 14 mm against E. coli and B. pumilus. A notable inhibition zone of 12 mm was observed for the most active chromatographic fraction. SDS-PAGE analysis revealed that the active protein had an estimated molecular weight of 11.27 kDa. These findings suggest that endophytic fungi, particularly the isolate KT31, represent a promising source of novel antibacterial peptides, warranting further investigation for therapeutic applications.
Co-Authors Ai Hertati, Ai Akhmad Solikhin Akmaliyah, Rizna Alfisyahrin, Wida Nurul Amani, Febriyanti Nur Amelia, Suci Amelia, Suci Andi Asmawati Azis Anika Prastyowati, Anika Anja Meryandini Anna Ida Sunaryo Purwiyanto Arifah, Rosyida Khusniatul Ario Betha Juanssilfero Chairunnisa, Sheila Chihombori, Tatenda Calvin DWI SUSILANINGSIH Ekawati, Nurlaili Eva Johannes Farida, Hilda Farida, Hilda Fatimah fatimah Fatimah Fidien, Khadijah Alliya Fidien Firdaus, Moh Egy Rahman GINA KARTINA Harsi D. Kusumaningrum Hartati Chairunnisa Hartoni Hasim - Hasim Hasim Huda Shalahudin Darusman Hudaida Syahrumsyah, Hudaida Ikramullah, Muh. Chaeril Iman Rusmana Irawan, Herman Irawan, Shasmita Isworo, Rhestu Isworo, Rhestu Jendri Mamangkey Joko Wahyono, Daniel Kartika Sari Dewi Kusdianawati Kusmajadi Suradi Kustiariyah Tarman Kusumawati, Arizah LINDA SUKMARINI Lita Triratna Magdalena Litaay Maggy Thenawidjaja Suhartono Mala Nurilmala Manguntungi, Baso Maulidiani, Maulidiani Meilina, Lita Meiyerani, Jeni Melki Mustafawi, Wike Zahra Mustika Tuwo, Mustika Mutiara, Ilma Nina Herlina Novianti, Ela Nur Amani, Febriyanti Nur Umami, Rifqiyah Nurfatwa, Maritsa Pandayu, Iga Firmansyah Popi Hadi Wisnuwardhani, Popi Hadi Puspo Edi Giriwono Putri, Andini Setyanti Putri, Prabawati Hyunita Putri, Prabawati Hyunita Ramadhian, M. Zalfa RATIH ASMANA NINGRUM Ratna, Lita Tri Refli, Redoyan Rifqiyah Nur Umami, Rifqiyah Nur Rika Indri Astuti Saputri, Dinar Suksmayu Saputri Sofyana, Neng Tanty Sri Swasthikawati, Sri Suharli, Lili Suharsono Suharsono Surachma, Rahma Sari Tri Wibawa Trinugroho, Joko P Urnemi Urnemi, Urnemi Vanggi, Leggina Rezzy Vanggy, Leggina Rezzy Wahyuni, Ike Wahyuni, Ike Wardhani, Widdya Kusuma Wardhani, Widdya Kusuma Wendry Setiyadi Putranto Wibowo, Krisna Dwi Aria Wijaya, Hans Wike Ayu Eka Putri Yudi Purnomo