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All Journal HAYATI Journal of Biosciences Microbiology Indonesia Journal of Tropical Biodiversity and Biotechnology 3BIO: Journal of Biological Science, Technology and Management Current Research on Biosciences and Biotechnology
ERNAWATI ARIFIN GIRI-RACHMAN
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Earth & Planetary Sciences Environmental Science Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience

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Molecular Analysis of Immune-Escape Mutants of Hepatitis B Virus from Local Clinical Samples CHANDRA JINATA; ERNAWATI ARIFIN GIRI-RACHMAN; DEBBIE SOEFIE RETNONINGRUM
Microbiology Indonesia Vol. 6 No. 1 (2012): March 2012
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (379.113 KB) | DOI: 10.5454/mi.6.1.2

Abstract

Small hepatitis B surface antigen (sHBsAg) is used as a component of hepatitis B vaccine. Even though this vaccine is known to be effective in preventing hepatitis B disease, natural mutation may induce Hepatitis B Virus (HBV) to form immune-escape mutant. This mutant is not only capable of infecting hepatitis B-vaccinated people, but also causing commercial diagnostic assay failure. Immune-escape mutant is generally detected from amino acid change at Major Hydrophilic Region (MHR) of sHBsAg while the change occurred outside the region may also lead to immune-escape mutant formation. This research was aimed to investigate the presence of HBV immune-escape mutants in local clinical samples in Indonesia. sHBsAg gene of seventeen HBV samples from local patients were amplified by polymerase chain reactions then subjected to two-directional sequencing. The DNA sequences later were analyzed by bioinformatics programs. Fifteen out of seventeen samples were genotype B and subtype adw2, while the other two were genotype C and subtype adrq+. Among fifteen genotype B samples, twelve of them were not immune-escape mutants, two were immune-escape mutants that have been previously reported (Gln129Arg and Met133Leu), and one was a mutant outside MHR that has not been previously reported as an immune-escape mutant (Tyr161Ser). Both samples of genotype C group were not immune-escape mutants. As conclusion, by investigating seventeen local clinical HBV samples, it was known that two of seventeen samples were confirmed as immune-escape mutants and one of seventeen samples was a mutant outside MHR.
Cloning, Overexpression, and Purification of PhoR CytoplasmicDomain Protein from Mycobacterium tuberculosis strain H37Rv OKTIRA ROKA AJI; DYSHELLY NURKARTIKA PASCAPURNAMA; FENRYCO PRATAMA; IHSANAWATI IHSANAWATI; MAELITA RAMDHANI MOEIS; ERNAWATI ARIFIN GIRI-RACHMAN
Microbiology Indonesia Vol. 8 No. 4 (2014): December 2014
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (758.166 KB) | DOI: 10.5454/mi.8.4.1

Abstract

Tuberculosis still becomesa major health problem in the world. This infectious disease is caused by Mycobacterium tuberculosis (Mtb). Novel anti-tubercular drug is urgently needed to counter multidrug resistant cases and Mtb's spread. The cytoplasmic domain of PhoR histidine kinase, a part of the two-component system PhoR-PhoP in Mtb, is one of the potential candidates for anti-tubercular drug target.Three dimensional protein of drug target is needed to screen potential drug candidate using rational drug design approaches. Previous studies have successfully characterized and isolated putative cytoplasmic domain of PhoR (CytoPhoR) from Mtb strain H37Rv. This study aimed to clone, overexpress and purify of CytoPhoR protein. CytoPhoR was fused with thioredoxin protein in expression vector pET32b and overexpressed in Escherichia coli (E.coli)BL21 (DE3) as soluble fraction by induction  1 mM IPTG. Purification of his-tagged CytoPhoR was carried out using IMAC Ni-NTA Agarose his-tag affinity column. SDS-PAGE analysis showed that another protein was co-purified (~35 kDa) along with the CytoPhoR protein. Subsequent protein purification using DEAE-ion exchange column generate a strong single band of 37 kDa on SDS–PAGE which is indicated as CytoPhoR protein. The purified CytoPhoR protein was successfully obtained and can be used for further analysis on determining three dimensional structure of CytoPhoR protein.
Expression and Purification of PhoR Sensor-Domain Histidine Kinase of Mycobacterium tuberculosis in Escherichia coli ERNAWATI ARIFIN GIRI-RACHMAN; FENRYCO PRATAMA; OKTIRA ROKA AJI; ARUM PATRIATI; IHSANAWATI IHSANAWATI; MAELITA RAMDANI MOEIS; EDY GIRI-RACHMAN PUTRA
Microbiology Indonesia Vol. 9 No. 2 (2015): June 2015
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1382.183 KB) | DOI: 10.5454/mi.9.2.1

Abstract

Globally, tuberculosis (TB) remains a leading cause of death. The emergence of multidrug-resistant strains (MDR-TB) and extensively drug-resistant strains (XDR-TB) has fuelled the discovery for novel drugs and drug targets for its successful and better treatment. One of the potential candidates for drug target is PhoR sensory protein histidine kinase, a part of the Two Component System (TCS) PhoP/PhoR in Mycobacterium tuberculosis (Mtb). This protein system was known for its role on regulating hundred of Mtb virulence factors, from genes for cell wall and lypid synthesis to genes for adaptation in human leukocyte and hypoxia response. Previous studies have successfully characterized, isolated, and cloned the putative sensory domain of PhoR protein gene into pRSET vector expression system. In this study, Escherichia coli was transformed with pRSET-SensPhoR and cultivated at 37oC under IPTG induction to express PhoR sensor-domain protein. Most of the proteins were overexpressed in the form of inclusion bodies.  Subsequent protein purification in Ni-NTA system under refolding condition on urea gradient was performed to isolate PhoR sensor-domain protein in soluble form. Arginine was supplemented in purified protein solution to prevent aggregation during long term storage.  While highly purified protein was acquired, small angle X-ray scattering (SAXS) analysis was conducted to obtain 3-dimensional (3D) protein structures in solution.    doi:10.5454/mi.9.2.1 
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.
Co-Authors Afifah, Salma Aulia Agustiyanti, Dian Fitria Andri Wardiana, Andri Anindyajati ARTARINI, ANITA ARUM PATRIATI CATUR RIANI CHANDRA JINATA DEBBIE SOEFIE RETNONINGRUM Desriani Desriani DESSY NATALIA DYSHELLY NURKARTIKA PASCAPURNAMA Edi, Suryo Purnomo EDY GIRI-RACHMAN PUTRA Faizah, Nur Al FENRYCO PRATAMA Ferry Iskandar Fibriani, Azzania Hariyatun, Hariyatun IHSANAWATI IHSANAWATI Laurelia, Jessica MAELITA RAMDANI MOEIS MAELITA RAMDHANI MOEIS Marissa Angelina Marselina Irasonia, Tan Niloperbowo, Wardono Novia Syari Intan Oktira Roka Aji Permatasari, Fitri Aulia Popi Hadi Wisnuwardhani, Popi Hadi Putri Ayu Fajar RATIH ASMANA NINGRUM Rinto Sukoco RUKMAN HERTADI SONY HERU SUMARSONO Stephanie, Rebecca Suryohastari, Raden Rara Bhintarti Taharuddin, Audrey Angelina Putri Tan, Marselina Irasonia Wardono , Niloperbowo Wicaksana, Dwi Nawang Wojciechowska, Gladys Emmanuella Putri Yamahoki, Nicholas Yana Rubiyana, Yana