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All Journal HAYATI Journal of Biosciences AL-HAYAT: Journal of Biology and Applied Biology
Ikramullah, Muh. Chaeril
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences

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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.
Starter Culture Modulates Microbial Diversity During Wine-Coffee Fermentation: A DGGE-Based Molecular Study Nasir, Fitri Handayani; Astuti, Dea Indriani; Taufik, Intan; Fitriagustiani; Ikramullah, Muh. Chaeril; Putri, Nurul Febriani; Pasmawati
Al-Hayat: Journal of Biology and Applied Biology Vol. 8 No. 2 (2025)
Publisher : Fakultas Sains dan Teknologi, UIN Walisongo Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21580/ah.v8i2.28269

Abstract

Wine-flavored coffee is a unique post-harvest product characterized by fruity, acidic, and winey notes, highly favored by Indonesian consumers and possessing strong potential in the global market. However, maintaining consistency in flavor and quality remains a challenge due to the variability of natural fermentation. This study aimed to evaluate the impact of yeast and bacterial starter culture inoculation on microbial community dynamics during wine-coffee fermentation, using a molecular approach based on PCR-DGGE. DGGE analysis revealed that natural fermentation without inoculation involved diverse populations of bacteria, yeasts, and filamentous fungi, with eukaryotic microbes dominating from the early stages. Sequencing identified prevalent yeast genera including Pichia, Torulaspora, Hanseniaspora, Saccharomyces, and Candida, as well as Aspergillus among filamentous fungi. Bacterial communities were dominated by lactic acid bacteria and members of Lactobacillus, Klebsiella, Enterobacter, Pantoea, and Bacillus. In contrast, controlled fermentation with inoculated starter cultures (Pichia kudriavsevii and Klebsiella sp.) showed a more stable microbial profile throughout the process. Shannon-Wiener diversity indices demonstrated a significant difference (p = 0.05) between natural and inoculated fermentations, with species dominance observed in the latter. Cluster analysis confirmed that starter culture inoculation significantly influenced microbial succession and community structure. These findings highlight the importance of controlled fermentation using selected microbial starters to ensure consistent microbial ecology, which in turn contributes to reproducible quality in wine-flavored coffee. The molecular profiling approach provides valuable insights for improving fermentation practices and developing reliable starter culture formulations tailored to enhance flavor consistency and product quality.
Co-Authors Ai Hertati, Ai Apon Zaenal Mustopa Dea Indriani Astuti Firdaus, Moh Egy Rahman Fitriagustiani Huda Shalahudin Darusman Irawan, Shasmita Nasir, Fitri Handayani Pasmawati Putri, Nurul Febriani Ratna, Lita Tri Rifqiyah Nur Umami, Rifqiyah Nur Taufik, Intan Tri Wibawa