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All Journal HAYATI Journal of Biosciences Microbiology Indonesia Plasma - Jurnal Kesehatan Journal of Mathematical and Fundamental Sciences Journal of Tropical Biodiversity and Biotechnology The Indonesian Biomedical Journal ANNALES BOGORIENSES 3BIO: Journal of Biological Science, Technology and Management Current Research on Biosciences and Biotechnology Narra J
Ernawati A. Giri Rachman
School Of Life Sciences And Technology, Institut Teknologi Bandung
Agriculture, Biological Sciences & Forestry Astronomy Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Earth & Planetary Sciences Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Neuroscience Physics Public Health

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The Structural Evaluations of SARS-CoV-2 Main Protease (Mpro): A Review for COVID-19 Antivirals Development Strategy Muhammad Hamzah Syaifullah Azmi; Ernawati Arifin Giri-Rachman
3BIO: Journal of Biological Science, Technology and Management Vol. 5 No. 2 (2023)
Publisher : School of Life Sciences and Technology, Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/3bio.2023.5.2.2

Abstract

It has been almost four years since the first case of COVID-19 emerged, and the antivirals that could work specifically against SARS-CoV-2with a high efficacy are still under development. Main Protease (Mpro) of this virus plays a crucial role in virion maturation during itsreplication within the host cell. This protein works together with the papain-like protease (PLpro) to cleave polyprotein 1a  and 1ab  into a total of16 functional fragments of non-structural protein. Antiviral with the ability to inhibit the activity of Mpro could potentially prevent the virion replication, and they can be developed to target the catalytic or allosteric site of this protein. Antiviral that works on the catalytic site will act as competitive inhibitors of the substrate peptide which leads to the loss of Mpro function. Targeting the allosteric site (e.g. distal site and dimerization interface) will cause allosteric modu- lation of the protomer which could alter the protein 3D conformation and disrupt the formation of homodimer structure. This will affect the geometry and surface structure of the catalytic site which in turn decreases the affinity of the substrate peptide towards the Mpro catalytic site, resulting in a completeinactivation of the protein. Mutation study of Mpro amino acids sequence also reveals that the mutation frequency for each amino acid position isextremely low and negligible. Moreover, it is found that this protein has 24 mutational cold spot residues scattered within its structure which could be targeted for the development of antivirals due to its highly conserved nature.
Anti-HBsAg IgY polyclonal antibodies potential as capture antibody for HBsAg detection kit development A'yun, Ramadhani Qurrota; Hakim, Meutia Diva; Giri-Rachman , Ernawati Arifin; Tan, Marselina; Niloperbowo, Wardono
Current Research on Biosciences and Biotechnology Vol. 5 No. 2 (2024)
Publisher : Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/crbb.2024.5.2/UBVBMKPZ

Abstract

Hepatitis B, affecting about 296 million globally, is a significant concern, with Indonesia ranking second in Southeast Asia for case numbers. The disease's latent initial phase, devoid of early symptoms upon hepatitis B virus (HBV) infection, highlights the demand for precise diagnostics. This research aimed to develop anti-HBsAg polyclonal antibodies (pAb) for application as capture agents within a sandwich enzyme-linked immunosorbent assay (ELISA). Chicken egg-derived IgY antibodies have advantages over mammalian ones due to simpler extraction and higher yield. In a study involving 21-week-old chickens, four intramuscular injections of 500 µg HBsAg antigen in Freund's adjuvant were administered at two-week intervals. Eggs as IgY source were collected daily and then IgY was isolated from eggyolk using polyethylene glycol (PEG) precipitation. The Bradford method was used to measure the total protein concentration, while the existence of IgY and pAb specific IgY against Anti-HBsAg was verified through SDS-PAGE and sandwich ELISA using HRP as a reporter, respectively. The resulting SDS-PAGE showed two distinct IgY bands: a 68 kDa heavy chain and a 23 kDa light chain. Using these anti-HBsAg IgY antibodies as capturing agents, the slightly elevation of IgY pAb against HBsAg level has been identified within the second week following the initial immunization. Subsequently, from the third to the eighth week, antibody levels escalated significantly, ranging from 2 to 13-fold higher than those observed in the second week. These findings suggest the potential use of IgY pAb as effective capture antibodies in sandwich ELISA for HBsAg antigen detection.
A Brief Review of the Global and Indonesian Diagnostic Development for Sexual Transmitted Diseases Giri-Rachman, Ernawati Arifin; Laurelia, Jessica; Marselina Irasonia, Tan; Wardono , Niloperbowo; Anindyajati
Current Research on Biosciences and Biotechnology Vol. 6 No. 1 (2024)
Publisher : Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/crbb.2024.6.1/RIQI8H4A

Abstract

Sexually transmitted diseases (STDs) are diseases with a high prevalence rate. The World Health Organization (WHO) estimates that more than 1 million STDs are transmitted every day, those diseases are chlamydia, syphillis, trichomoniasis, ghonorroea, and virus caused diseases (hepatitis B virus, immunodeficiency virus, human papillomavirus, and herpes simplex virus). Early and accurate examination and detection are important to help with the healing and control of these diseases. One of the examination methods that could be used is using the laboratory diagnostic methods which contribute to 40% to 60% of the process of diagnosing a disease. Thus, early detection not only helps control the spread of STDs but also facilitates the healing process. However, in Indonesia there are obstacles in the examination of diseases due to several factors, such as inadequate surveillance system and limited examination facilities, so that most people are undiagnosed. Therefore, this review will discuss in more depth the development of diagnostics for sexually transmitted diseases in Indonesia and globally. Global development in diagnostics is very broad and diverse, in which many diagnostic techniques has already been established. The development of diagnostic techniques has progressed rapidly from simplex assays to multiplex and also computerized assays. Diagnostic techniques in Indonesia has also developed and some of the local kits have already been in the market showing that Indonesia is already moving towards production of local diagnostics.
Microbial Count and AvBD10 Expressions in Ovaries and Oviducts of Kampung Unggul Balitbangtan (KUB)-1 Chickens Following Intravaginally CpG-ODN and S. Enteritidis Suryohastari, Raden Rara Bhintarti; Sumarsono, Sony Heru; Giri-rachman, Ernawati Arifin; Edi, Suryo Purnomo; Sukoco, Rinto; Wicaksana, Dwi Nawang
Journal of Tropical Biodiversity and Biotechnology Vol 9, No 2 (2024): June
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.88750

Abstract

Indonesia boasts diverse native chickens (Gallus gallus domesticus) known for more disease resistance in comparison to broiler chicken, and Kampung Unggul Balitbangtan (KUB)-1 is designated as Indonesia's superior breed. Salmonella Enteritidis (SE) is associated with salmonellosis, a foodborne illness that can be transmitted by transovarial, wherein colonisation in the oviduct ascends to the ovaries. However, studies mimicking transovarial salmonellosis via intravaginal treatment of chicken have been limited. Meanwhile, Cytosine-phosphate-guanine oligodeoxynucleotide (CpG-ODN) stimulation has been known to induce avian β-defensins (AvBDs). This in vivo study aimed to determine the effects of intravaginal CpG-ODN treatment and SE challenged on microbial count and AvBD10 expression regarding the potential of intravaginally CpG-ODN to enhance innate immunity as an alternative approach against transovarial Salmonellosis. A total of 39 KUB-1 chickens were divided into four groups: T1 (CpG-ODN treatment), T2 (SE treatment), T3 (CpG-ODN treatment + challenged with SE), and C (Control). Observation was carried out from day 1 to day 4 post-intravaginal (PI). We found a significant increase in ovarian microbial count (p≤0.05). Notably, ovaries and oviducts remained uncontaminated post-SE challenge. Intravaginal CpG-ODN treatment significantly upregulated AvBD10 in both ovaries (p=0.016) and oviducts (p=0.023). Therefore, KUB-1 chickens exhibit SE immunity, and intravaginal CpG-ODN administration holds promise for preventing transovarial Salmonellosis in laying hens. 
Improvement of Plasmid Volumetric Yield by Addition of Glycerol and Phosphate Buffer in Escherichia coli TOP10 Batch Culture Anindyajati; Afifah, Salma Aulia; Riani, Catur; Tan, Marselina Irasonia; Natalia, Dessy; Giri-Rachman, Ernawati Arifin; Artarini, Anita
HAYATI Journal of Biosciences Vol. 31 No. 3 (2024): May 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.3.572-580

Abstract

The investigation of mRNA development has gained substantial interest, particularly in the ex vivo and in vivo therapy. mRNA is widely used for the development of gene editing-based therapies and mRNA vaccines. The aim of this study was to optimize the medium and harvest time to increase plasmid DNA production as part of mRNA production. This study modified used a medium modification approach to achieve high density culture of Escherichia coli TOP10 pGEMT-N in batch cultivation method. Various media formulations were assessed, including LB; LB with phosphate buffer (K2HPO4 12.549 g/L and KH2PO4 2.31 g/L); LB with glycerol (50 g/L); LB with glycerol and phosphate buffer; LB with phosphate buffer, glycerol, glucose (15 g/L), and galactose (15 g/L). The effect of additional carbon sources and phosphate buffer on culture density was measured through OD600 and wet cell weight analysis. The highest OD600 and wet cell weight was observed when LB with glycerol and phosphate buffer was used, with OD600 of 4.78±0.14 and wet cell weight of 36.00±0.63 mg/ml. Plasmid DNA was subsequently isolated from these cultures following 5- and 7.5-hour incubation periods. The utilization of LB medium with glycerol and phosphate buffer resulted in a substantial increase in the volumetric concentration of plasmid DNA of 1,516.97±385.00 ng/ml after 5 hours of incubation. In conclusion, a remarkable enhancement in plasmid DNA volumetric yield within 5 hours was achieved by addition of glycerol and phosphate buffer to LB medium, leading to incubation period.
In Silico Study, Design, and Expression of an Intranasal Dual Chimeric Vaccine for Indonesian-Based Norovirus GII-2 and Hepatitis B Giri-Rachman, Ernawati Arifin; Tan, Marselina Irasonia; Novia Syari Intan; Putri Ayu Fajar; Wojciechowska, Gladys Emmanuella Putri; Hertadi, Rukman; Retnoningrum, Debbie Soefie
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.31.5.1007-1018

Abstract

Hepatitis B virus (HBV) remains an important healthcare challenge, leading to liver diseases like cirrhosis and cancer. In response, we created a prophylactic and therapeutic HBV vaccine by integrating HBcAg and HBsAg from HBV genotype B into Norovirus (NoV) GII.2 P domain (PdomGII.2-HBV) for enhanced intranasal delivery. This vaccine also aimed to simultaneously prevent NoV infection, which causes gastroenteritis. Since the selected HBV epitopes have undergone extensive research and are tailored to the Indonesian population, this study focused on identifying NoV epitopes and assessing T cell epitopes coverage of the PdomGII.2-HBV for the Indonesian population. Following that, we expressed the PdomGII.2-HBV protein using Escherichia coli BL21(DE3) and employed a gentle solubilization technique for protein purification. Our in-silico analysis identified two B cell epitopes, along with 15 CD4+T cell epitopes and 35 CD8+T cell epitopes within the GII.2 P domain. These T cell epitopes cover 100% of the Javanese-Sundanese population's HLA allele variations, which constituted the largest demographic group in Indonesia. Subsequently, we successfully purified the presumed PdomGII.2-HBV protein, revealing a molecular weight of 39.5 kDa. Following the successful expression and purification of the presumed PdomGII.2-HBV protein, it is evident that this vaccine design has significant potential, warranting further study.
The Influence of Polyethylene Glycol Precipitation Methods on Yield and Purity of White Radish Peroxidase Faizah, Nur Al; Giri-Rachman, Ernawati Arifin; Niloperbowo, Wardono
3BIO: Journal of Biological Science, Technology and Management Vol. 6 No. 2 (2024)
Publisher : School of Life Sciences and Technology, Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/3bio.2024.6.2.5

Abstract

Proteins are widely used in various industries as highly valued biotechnology products. One example is horseradish peroxidase isolated from horseradish (Armoracia rusticana) that used as enzyme label in immunochemistry. However, the cultivation of horseradish is limited to subtropical countries, making the dependency on horseradish peroxidase unsustainable for tropical countries. Numerous studies have explored alternative peroxidases, and white radish peroxidase isolated from Raphanus sativus L. has emerged as a promising candidate. In this study, white radish peroxidase is isolated using the polyethylene glycol (PEG) precipitation method which is widely used as a simple and cost-effective method. This study aims to evaluate the effectiveness of the one-step and two-step PEG precipitation method. The one-step PEG precipitation method used in this study was done by mixing the white radish juice with PEG 6000 30% (w/v), while the two-step method was done by mixing it with PEG 400 20% (w/v) and PEG 6000 30% (w/v) consecutively. This study compares the yield and recovery levels of total protein and white radish peroxidase, as well as the enzymatic specific activity of white radish peroxidase isolated both by the one-step PEG precipitation and the two-step PEG precipitation. The results indicate that both extraction methods yield the same level of white radish peroxidase. However, they differ in terms of purity. The two-step extraction method results in white radish peroxidase with higher purity, as evidenced by its specific activity towards the chromogen ABTS in the presence of H2O2.
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

Abstract

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.
Development of a novel multi-epitope peptide vaccine candidate against Mycobacterium tuberculosis using reverse vaccinology: A promising strategy for enhanced immunoprotection Nur AHM. Hasan; Ernawati A. Giri-Rachman; Husna Nugrahapraja
Narra J Vol. 6 No. 1 (2026): April 2026
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v6i1.2897

Abstract

Tuberculosis (TB) is a leading cause of death worldwide, caused by Mycobacterium tuberculosis (Mtb). The existing Bacillus Calmette-Guerin (BCG) vaccine has limitations, especially its reduced effectiveness in adults. This research focuses on developing a multi-epitope Mtb vaccine candidate through reverse vaccinology, aiming for a more effective and widely applicable solution. The study used the Vaxign2 pipeline to identify Mtb antigenic proteins, including PPE35, mpt83, mrsA, and rplK. Cytotoxic T cells (CTL), helper T cells (HTL), and B-cells, were predicted and selected based on their antigenicity, non-allergenicity, and non-toxicity. The chosen epitopes from these proteins, 4 CTL, 1 HTL, and 1 B cell epitope, were assembled into a multi-epitope vaccine construct, incorporating the adjuvant PADRE and linkers (EAAAK, AAY, and GPGPG). The vaccine candidate has a molecular weight of 10.68 kDa, with stability, hydrophilicity, and solubility confirmed. Its 3D structure was validated for quality and accuracy. Docking and molecular dynamics simulations with immune receptors TLR2 and TLR4 showed strong, stable interactions. The global population coverage of the vaccine candidate was reaching 98.19%. In silico cloning into the pET30a(+) vector in Escherichia coli BL21(DE3) was successful, with codon optimization (CAI: 0.98) and a GC content of 54.6%. Immunity simulations indicated enhanced activation of antigen-presenting cells, CTL, HTL, B cells, and antibody production. Overall, this study suggests vaccine candidate is a promising multi-epitope vaccine candidate, warranting further in vivo testing, including protein expression in E. coli.
Molecular Characterization of HLA-B27 in Anterior Uveitis: Integrated Serological and Genetic Analysis Reveals Elevated Antigen Levels and Variants Concentrated in Exons 2 and 3 Shinta Stri Ayuda Nur Setyaningsih; Arief Akhdestira Mustaram; Angga Fajriansyah; Patriotika Muslima; Elfa Ali Idrus; Muhammad Hamzah Syaifullah Azmi; Elsa Gustianty; Ernawati Arifin Giri-Rachman; Marselina Irasonia Tan
The Indonesian Biomedical Journal Vol 18, No 3 (2026)
Publisher : The Prodia Education and Research Institute (PERI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18585/inabj.v18i3.4239

Abstract

BACKGROUND: Anterior uveitis is the most common form of intraocular inflammation and an important cause of visual morbidity worldwide. Human leukocyte antigen B27 (HLA-B27) is a well-established immunogenetic risk factor; however, its molecular diversity remains insufficiently characterized in Indonesian populations. This study was conducted to characterize HLA-B27 at both the serological and genetic levels by quantifying serum antigen levels and identifying sequence variations in the HLA-B27 gene associated with anterior uveitis in Indonesian patients.METHODS: Thirteen anterior uveitis patients who were clinically evaluated through the Standardization of Uveitis Nomenclature (SUN) criteria were involved in this study. Blood sample was collected from subjects, and serum HLA-B27 concentrations were measured by enzyme-linked immunosorbent assay (ELISA). Genomic DNA was analyzed using combined Sanger and Oxford Nanopore sequencing. Variant calling and annotation were performed using a custom bioinformatics pipeline.RESULTS: Serum HLA-B27 antigen levels were significantly higher in anterior uveitis patients than in healthy reference controls. Sequence analysis identified 43 patient-exclusive variants after exclusion of shared polymorphic changes, from which 13 recurrent or potentially functionally relevant variants were prioritized for downstream analysis. These variants were predominantly distributed within exons 2 and 3 and comprised single-nucleotide substitutions, coding-region insertion–deletion events, and one promoter-region insertion. Several coding variants resulted in amino acid substitutions, while adjacent compensatory indel pairs were also identified among exon 2 frameshift-associated variants.CONCLUSION: Anterior uveitis is associated with both elevated circulating HLA-B27 antigen levels and sequence variation within functionally important regions of the HLA-B27 gene, particularly exons 2 and 3. The identified missense substitutions, coding-region indels, and promoter insertion suggest potential effects on peptide binding, molecular stability, immune interaction, intracellular protein handling, or transcriptional regulation.KEYWORDS: anterior uveitis, HLA-B27, genomic variants, peptide-binding groove, protein misfolding
Co-Authors . Anindyajati A'yun, Ramadhani Qurrota Afifah, Salma Aulia Afina Firdaus Syuaib Afina Firdaus Syuaib Agustiyanti, Dian Fitria Aluicia Anita Artarini Amy Estiati Anastasia Armimi Andri Wardiana, Andri Angga Fajriansyah Anita Artarini Apsari Supraba Arief Akhdestira Mustaram ARTARINI, ANITA ARUM PATRIATI Azzania Fibriani CATUR RIANI CHANDRA JINATA Chikako Ono David Virya Chen Debbie Retnoningrum, Debbie DEBBIE SOEFIE RETNONINGRUM Desriani Desriani Dessy Natalia DESSY NATALIA Dessy Natalia DYSHELLY NURKARTIKA PASCAPURNAMA Edi, Suryo Purnomo EDY GIRI-RACHMAN PUTRA Elfa Ali Idrus Elsa Gustianty Elvi Restiawaty Faizah, Nur Al FENRYCO PRATAMA Ferry Iskandar Hakim, Meutia Diva Hariyatun, Hariyatun Hotma Hutapea, Hotma Husna Nugrahapraja Ihsanawati Ihsanawati Ima M. Zainuddin Katherine Vanya Laurelia, Jessica Lia Dewi Juliawaty MAELITA RAMDANI MOEIS MAELITA RAMDHANI MOEIS Marissa Angelina Marselina Irasonia Tan Marselina Irasonia Tan Marselina Irasonia, Tan Marselina Tan Meutia Diva Hakim Muhammad Hamzah Syaifullah Azmi Muhammad Hamzah Syaifullah Azmi Neni Nurainy Noriko Yamano- Adachi Novia Syari Intan Nur AHM. Hasan Oktira Roka Aji Patricia Gita Naully Patriotika Muslima Permatasari, Fitri Aulia Popi Hadi Wisnuwardhani, Popi Hadi Putri Ayu Fajar Putri Dwi Utari RASI FITRIA RATIH ASMANA NINGRUM Rinto Sukoco RUKMAN HERTADI Shinta Stri Ayuda Nur Setyaningsih SONY HERU SUMARSONO Sony Suhandono SONY SUHANDONO Stephanie, Rebecca Suryohastari, Raden Rara Bhintarti Taharuddin, Audrey Angelina Putri Takeshi Omasa Tan, Marselina Irasonia Tina Rostinawati Wardono Niloperbowo Wicaksana, Dwi Nawang Wojciechowska, Gladys Emmanuella Putri Yamahoki, Nicholas Yana Rubiyana, Yana Yoshiharu Matsuura