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Characterisation of ACE2-like Enzyme from Bacillus cereus sp. as an Alternative Treatment for COVID-19 Patients Maulida, Alya Sendra; Anggraeni, Novi Arie; Fibriani, Azzania
HAYATI Journal of Biosciences Vol. 32 No. 1 (2025): January 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.1.47-54

SARS-CoV-2 infection can lead to downregulation of ACE2, raising pro-inflammatory Angiotensin II levels. Recombinant human ACE2 protein therapy can restore homeostasis but is costly. An alternative is an ACE2-like enzyme with similar effects. The previous research identified a carboxypeptidase protein from Bacillus cereus sp. (rBceCP) as a potential ACE2-like enzyme, but it has not been characterized well. This study characterizes, expresses, and tests the activity of the rBceCP). rBceCP structure and properties were predicted using Prabi and Expasy. The in vitro approach included protein expression optimization, hydrolysis tests, and inhibition tests. In silico analysis revealed the protein is a homodimer with 53.66% α-helix and a molecular weight of 58.99 kDa. The protein is stable, hydrophilic, and has an isoelectric point at pH 4.93, indicating it can be expressed using the E. coli system. Expression of rBceCP showed no significant differences across IPTG concentrations (p-value >0.05). The protein hydrolysis activity of rBceCP was similar to the control, though purified samples had lower activity than crude samples. Inhibition activity in crude and purified samples showed no significant differences (p-value >0.05) and was higher than the control. Thus, rBceCP has potential as an ACE2-like enzyme and a therapeutic candidate for COVID-19.

Development of a Fluorescence Immunoassay Based on Curcumin Carbon Dots-labeled IgY Antibodies for SARS-CoV-2 Detection Rachmadani, Nisa Amanda; Soetomo, Meilisa Keizia; Taharuddin, Audrey Angelina Putri; Santika, Arum Sinda; Abdillah, Oktaviardi Bityasmawan; Permatasari, Fitri Aulia; Iskandar, Ferry; Rachmawati, Heni; Fibriani, Azzania
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.33.1.44-57

Carbon dots (CDs) are widely utilized in biomedical applications as fluorescent labels for imaging and diagnostics due to their excellent biocompatibility and superior optical properties. These advantages often make CDs a substitute for organic fluorescent dyes, which suffer from low emission intensity and poor photostability when interacting with biomolecules. Moreover, carbon-based materials are eco-friendly and can be synthesized from natural sources, such as curcumin, a chromophore compound abundantly available in Indonesia. Therefore, this study conducted a preliminary investigation on curcumin CDs-labeled IgY antibodies (IgY-cur CDs) for fluorescence immunoassay of SARS-CoV-2 in rapid test applications. The synthesis of the fluorescent label involved a carbodiimide coupling reaction using EDC/NHS agents to conjugate IgY antibodies with curcumin CDs. The IgY-cur CDs conjugate was confirmed to detect antigens through FRET immunosensor mechanisms, showing a significant increase in fluorescence intensity with increasing antigen concentrations (p < 0.05), with a minimum sample concentration of 10 ng. Furthermore, the IgY-CDs cur conjugate was applied as a reporter in a fluorescence-based LFIA using a sandwich assay format. The test strip successfully detected synthetic multiepitope SARS-CoV-2 antigens with an estimated detection limit of 54.28 µg and nasopharyngeal samples from confirmed COVID-19 patients within 35 minutes of operation. The test strip was evaluated to be stable under cold storage at 4°C for up to 3 weeks. In conclusion, curcumin CDs-labeled IgY antibodies demonstrate promising potential for further development as fluorescent labels in rapid diagnostic applications targeting SARS-CoV-2.

SARS-CoV-2 lineages and naso-oropharyngeal bacterial communities in COVID-19 reinfection: A study in West Java, Indonesia Sativa, Alvira R.; Asyifa, Isnaini Z.; Adzdzakiy, Muhammad M.; Iryanto, Syam B.; Nugroho, Herjuno A.; Wulandari, Ari S.; Yanthi, Nova D.; Nasrulloh, Mukh F.; Rahmawati, Ema; Alamanda, Cut NC.; Ristandi, Ryan B.; Rachman, Rifky W.; Robiani, Rini; Agustiyani, Dian F.; Wisnuwardhani, Popi H.; Wardiana, Andri; Ningrum, Ratih A.; Dharmayanthi, Anik B.; Prasetyoputri, Anggia; Fibriani, Azzania; Saputra, Sugiyono
Narra J Vol. 5 No. 3 (2025): December 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v5i3.2901

Continuous emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants may influence viral transmission dynamics and alter interactions with the respiratory microbiota, potentially increasing the risks of reinfection. This study investigated cases of coronavirus disease 2019 (COVID-19) reinfection in West Java, Indonesia, with the aim of identifying the SARS-CoV-2 variants involved, characterizing their genomic mutations, and profiling the nasal and oropharyngeal microbiota associated with reinfection. Naso-oropharyngeal swab samples were collected from 42 COVID-19 reinfection cases and nine new infection cases. Whole genome sequencing was performed using Oxford Nanopore Technologies (ONT) MinION Mk1C and variant analysis was conducted using ARTIC workflow. Nexstrain and PANGOLIN were used to determine the lineages. Phylogenetic trees were constructed using IQ-tree and FigTree. Key mutations were identified by Cov-GLUE. Additionally, 16s rRNA amplicon sequencing was conducted on nine samples from each group to analyze bacterial communities using EPI2ME and MicrobiomeAnalyst. All identified SARS-CoV-2 strains in this study were Delta variant (B.1.617.2), predominantly lineage AY.23 (n=46, 90%), followed by AY.24 (n=3) and AY.109 (n=2). No differences in SARS-CoV-2 lineages were observed between reinfection and new infection cases. Unique hotspot mutations found only in COVID-19 reinfections included NSP3, V220A, S_T676I, ORF7a_V82A, and ORF7a_TI20I. Bacterial community analysis revealed no significant diversity differences (alpha and beta) between the two groups. While the most dominant phylum remained Terrabacteria in both groups, Streptococcus was dominant in COVID-19 reinfections, whereas Prevotella was dominant in new infection cases. Notably, Haemophilus parainfluenzae, Fusobacterium periodonticum, Fusobacterium nucleatum, and Leptotrichia buccalis had significant increases in reinfection cases. Despite the similarity in SARS-CoV-2 lineages causing both COVID-19 reinfection and new infection cases, the presence of distinct key mutations and bacterial species suggest their potential as biomarkers within this group.

Evaluation of Curcumin-derived Carbon-dots' Inhibitory Activity as SARS-CoV-2 Antiviral Candidate Using Chemical Crosslinking Taharuddin, Audrey Angelina Putri; Yamahoki, Nicholas; Stephanie, Rebecca; Agustiyanti, Dian Fitria; Wisnuwardhani, Popi Hadi; Angelina, Marissa; Rubiyana, Yana; Ningrum, Ratih Asmana; Wardiana, Andri; Desriani, Desriani; Hariyatun, Hariyatun; Iskandar, Ferry; Permatasari, Fitri Aulia; Giri-Rachman, Ernawati Arifin; Fibriani, Azzania
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.33.1.232-239

In our previous work, we demonstrated that curcumin-derived carbon dots (Cur-CDs) have potential as antivirals for COVID-19. However, the precise mechanism of action remains unclear. This study investigated the potential of Cur-CDs against SARS-CoV-2 by targeting the dimerization of the C-terminal domain of nucleocapsid protein (N-CTD) using chemical crosslinking. Recombinant SARS-CoV-2 N-CTD was expressed, purified, and subjected to chemical crosslinking. The dimerization inhibition ability of Cur-CDs was assessed with ligand concentrations ranging from 0 to 2,000 μg/mL. Successful inhibition —defined as a noticeable reduction in SARS-CoV-2 N-CTD dimer band intensity on SDS-PAGE—was observed when Cur-CDs were present at 8 to 16 times the protein concentration. We hypothesize that Cur-CDs bind to the dimerization residues, preventing non-covalent interactions between monomers and limiting dimer formation. Our findings suggest that Cur-CDs could be a promising antiviral strategy for SARS-CoV-2, especially targeting the dimerization of the nucleocapsid protein. Additionally, this study also highlights the use of chemical crosslinking as a valuable tool for interaction-based drug screening.

Eco-bioremediation potential of mealworm gut microbiome for polystyrene degradation in nutrient-based media Afandi, Afandi; Septiani, Popi; Fibriani, Azzania
Asia Pacific Journal of Sustainable Agriculture, Food and Energy Vol. 13 No. 2 (2025): December 2025
Publisher : Asia Pacific Network for Sustainable Agriculture, Food and Energy Network (SAFE Network)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.36782/apjsafe.v13i2.535

Polystyrene is a petroleum-based polymer widely used in single-use packaging and thermal insulation. Its high molecular weight and structural stability make it highly resistant to degradation, leading to persistent environmental accumulation. Recent studies have highlighted the potential of insect gut microbiota, particularly from mealworms, to biodegrade plastic waste. In this study, gut extracts were inoculated into Nutrient Broth (NB) and Potato Dextrose Broth (PDB), each supplemented with polystyrene as emulsion, powder, or film. NB showed the highest reduction in polystyrene weight (0.93%) by day 28, compared to PDB (0.73%). Total plate count and yeast-mold count analyses revealed microbial proliferation in both media, with NB exhibiting a higher final bacterial count (7.562 log cfu/mL) than PDB (6.510 log cfu/mL), while fungal counts were comparable. Scanning Electron Microscopy confirmed structural damage to polystyrene films, including surface roughening and micro-pitting, especially in NB. These findings indicate that media composition significantly influences microbial growth and degradation efficiency. NB appears to favor bacterial communities with enhanced plastic-degrading capabilities, demonstrating superior biodegradation potential in liquid culture.

SARS-CoV-2 lineages and naso-oropharyngeal bacterial communities in COVID-19 reinfection: A study in West Java, Indonesia Sativa, Alvira R.; Asyifa, Isnaini Z.; Adzdzakiy, Muhammad M.; Iryanto, Syam B.; Nugroho, Herjuno A.; Wulandari, Ari S.; Yanthi, Nova D.; Nasrulloh, Mukh F.; Rahmawati, Ema; Alamanda, Cut NC.; Ristandi, Ryan B.; Rachman, Rifky W.; Robiani, Rini; Agustiyani, Dian F.; Wisnuwardhani, Popi H.; Wardiana, Andri; Ningrum, Ratih A.; Dharmayanthi, Anik B.; Prasetyoputri, Anggia; Fibriani, Azzania; Saputra, Sugiyono
Narra J Vol. 5 No. 3 (2025): December 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v5i3.2901

Continuous emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants may influence viral transmission dynamics and alter interactions with the respiratory microbiota, potentially increasing the risks of reinfection. This study investigated cases of coronavirus disease 2019 (COVID-19) reinfection in West Java, Indonesia, with the aim of identifying the SARS-CoV-2 variants involved, characterizing their genomic mutations, and profiling the nasal and oropharyngeal microbiota associated with reinfection. Naso-oropharyngeal swab samples were collected from 42 COVID-19 reinfection cases and nine new infection cases. Whole genome sequencing was performed using Oxford Nanopore Technologies (ONT) MinION Mk1C and variant analysis was conducted using ARTIC workflow. Nexstrain and PANGOLIN were used to determine the lineages. Phylogenetic trees were constructed using IQ-tree and FigTree. Key mutations were identified by Cov-GLUE. Additionally, 16s rRNA amplicon sequencing was conducted on nine samples from each group to analyze bacterial communities using EPI2ME and MicrobiomeAnalyst. All identified SARS-CoV-2 strains in this study were Delta variant (B.1.617.2), predominantly lineage AY.23 (n=46, 90%), followed by AY.24 (n=3) and AY.109 (n=2). No differences in SARS-CoV-2 lineages were observed between reinfection and new infection cases. Unique hotspot mutations found only in COVID-19 reinfections included NSP3, V220A, S_T676I, ORF7a_V82A, and ORF7a_TI20I. Bacterial community analysis revealed no significant diversity differences (alpha and beta) between the two groups. While the most dominant phylum remained Terrabacteria in both groups, Streptococcus was dominant in COVID-19 reinfections, whereas Prevotella was dominant in new infection cases. Notably, Haemophilus parainfluenzae, Fusobacterium periodonticum, Fusobacterium nucleatum, and Leptotrichia buccalis had significant increases in reinfection cases. Despite the similarity in SARS-CoV-2 lineages causing both COVID-19 reinfection and new infection cases, the presence of distinct key mutations and bacterial species suggest their potential as biomarkers within this group.

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