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All Journal HAYATI Journal of Biosciences Bioma : Berkala Ilmiah Biologi Journal of Tropical Biodiversity and Biotechnology The Indonesian Biomedical Journal 3BIO: Journal of Biological Science, Technology and Management Narra J
CATUR RIANI
School of Pharmacy, Institut Teknologi bandung, Jalan Ganesha 10, Bandung 40132, West Java, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Earth & Planetary Sciences Education Environmental Science Health Professions Immunology & microbiology Medicine & Pharmacology Neuroscience Public Health

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A Mini Review on Analysis of Potential Antibacterial Activity of Symbiotic Bacteria from Indonesian Freshwater Sponge: An Unexplored and A Hidden Potency Setiawan, Edwin; Hermanto, Michael Einstein; Abdulgani, Nurlita; Prasetyo, Endry Nugroho; Riani, Catur; Wulandari, Dyah; Budiharjo, Anto
Journal of Tropical Biodiversity and Biotechnology Vol 9, No 1 (2024): March
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.82682

Abstract

Marine sponges have been investigated as potential bioresources because of their symbiotic relationship with microbes such as Actinobacteria that produce antibacterial substances. In contrast, a group of sponges, that inhabits freshwater environments called freshwater sponges (Order Spongillida Manconi & Pronzato, 2002) and consists of only one percent among all of the sponges’ species (Phylum Porifera Grant, 1836), has  not yet intensively examined.  For this reason, we screened, determined, evaluated, and reviewed by examining several databases in Scopus, Pub Med, and Google Scholar related to potential aspects of symbiotic bacteria and their antibacterial substances that can be further utilised  and developed into synthesised  antibacterial compounds, based on published metagenomic data of symbiotic bacteria in freshwater sponges. At the same time, we compared a composition of those freshwater symbionts to marine sponges’ symbionts whether those possess a similar composition or not. Moreover, a current report and a revisit study of freshwater sponges in East Java, initiate further direction on mapping of those symbiotic bacteria from Indonesia that can be nominated as potential groups possessing antibacterial properties. 
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.
Design of lipid nanoparticle (LNP) containing genetic material CRISPR/Cas9 for familial hypercholesterolemia Prasetia, I GNJA.; Kurniati, Neng F.; Riani, Catur; Mudhakir, Diky
Narra J Vol. 5 No. 1 (2025): April 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v5i1.2217

Abstract

Familial hypercholesterolemia is a genetic disorder caused by mutations in the low-density lipoprotein receptor gene (LDLR) and the current treatment still focuses on symptom management. The aim of this study was to develop a lipid nanoparticle (LNP)-based delivery system for the CRISPR/Cas9 component in correcting LDLR gene mutations. LNPs were prepared using an ultrasonic-solvent emulsification technique by varying the surfactant: oil ratio (SOR), homogenization speed and time, and sonication time. Next, the LNP surface was modified by adding DSPE-PEG2000-NH2 and polyethyleneimine. The next stage is to design the single guide RNA (sgRNA) and Donor DNA wildtype (Donor DNA wt). This genetic material was complexed with LNP and then transfected into Hepa1-6 LDLR mt cells, an in vitro representation of cells suffering from familial hypercholesterolemia. This optimization process produced LNPs with a particle size of 118.6±0.8 nm and a polydispersity index of 0.34±0.03. The LNP surface modification resulted in a zeta potential of +7.5 mV. A transmission electron microscope (TEM) analysis howed spherical morphology with size distribution following a regular pattern. LNP cell viability tests showed good biocompatibility at concentrations <15 mM with a half-maximal inhibitory concentration (IC50) value of 27.7 mM. The dominant cellular uptake mechanism of LNP was through the clathrin-mediated endocytosis (CME) pathway. The Hepa1-6 LDLR mt cell model was successfully produced with the transfecting agent Lipofectamine 3000 by homology-directed repair (HDR) mechanism. The LNP-genetic material complex with a ratio of sgRNA:Cas9:Donor DNA wt (1:1:0.04) showed an increase in LDLR gene expression of 3.3±0.2 times and LDLR protein levels reached 12.95±0.25 ng/mL on day 4 after transfection. The results of this study indicate that the developed LNP-based delivery system has the potential for gene therapy applications in familial hypercholesterolemia.
Optimization of PCR Primers for Detection of Extended-Spectrum Beta-Lactamase Targeting CTX-M and TEM Genes Kurniati, Dwi Elfira; Riani, Catur; Hardiyanti, Renny; Rachmawati, Dian
3BIO: Journal of Biological Science, Technology and Management Vol. 7 No. 1 (2025): Vol. 7 No. 1 (2025)
Publisher : School of Life Sciences and Technology, Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/3bio.2025.7.1.5

Abstract

Extended-Spectrum Beta Lactamase (ESBL) is an enzyme that inhibit the activity of third-generation cephalosporin antibiotics. CTX-M and TEM are the genes encoding the ESBLs. The horizontal spread of these gene from one bacteria to another leads to increased bacterial resistance. Molecular-based bacterial identification methods such as Polymer Chain Reaction are methods that are currently used because they provide faster and more specific results. Therefore, in this study, a method for identifying bacteria that produce ESBL was created by targeting CTX-M and TEM genes. In this study, two pairs of primers were designed using in silico method, then the characteristics of the primers were analyzed. The primer annealing temperature was optimized using 55 and 60oC temperatures. The results of the in silico analysis showed that both pairs of primers met the ideal characteristics of a primer, as the Tm, %GC content, and secondary product values fulfilled the required criteria. Meanwhile, the results of the primer annealing temperature optimization indicated that the optimal temperature for the PCR method using both primers was 60°C.
Antibacterial Activity of Freshwater Sponge Oncosclera asiatica Against Escherichia coli and Staphylococcus aureus Wulandari, Dyah; Dewantoro, Giwang; Lunggani, Arina Tri; Suprihadi, Agung; Riani, Catur; Setiawan, Edwin; Farikha, Siti Lutfiatul; Budiharjo, Anto
Bioma : Berkala Ilmiah Biologi Vol. 24, No 2, Tahun 2022
Publisher : Departemen Biologi, Fakultas Sains dan Matematika, Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/bioma.24.2.120-129

Abstract

Freshwater sponges are animals from the Porifera phylum that live in freshwater. The sponge used is Oncosclera asiatica was taken from Kali Porong, East Java. Seventeen isolates of bacteria have been obtained from isolation. Antibacterial potential testing was performed by paper disc inhibition assay using Escherichia coli and Staphylococcus aureus as pathogenic bacteria and amoxicillin as a positive control. The antibacterial activity test showed that four isolates have the potential activity. The isolates with the highest inhibition zones were identified using a 16S rRNA.The results of BLAST showed isolate number 2 was Pseudomonas moraviensis with 99.51% similarity. The phylogenetic tree analysis was build using the MEGA X program. The results of the phylogenetic tree analysis showed that P.moraviensis had a bootstrap value of 100% with a  genetic distance value of 0.001. P. moraviensis isolates screened for the presence of Non-Ribosomal Peptide Synthetase (NRPS) gene by A2gamF and A3gamR primers. The amplification result from NRPS gene showed positive meaning that P.moraviensis genome contained NRPS gene.
T118N Substitution of Hepatitis B X Protein Reduces Colony Formation of HepG2 Cells Artarini, Anita; Nurmalasari, Dewi Riskha; Permanasari, Silmi Citra; Riani, Catur; Tjandrawinata, Raymond Rubianto; Retnoningrum, Debbie Soefie
The Indonesian Biomedical Journal Vol 15, No 1 (2023)
Publisher : The Prodia Education and Research Institute (PERI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18585/inabj.v15i1.2095

Abstract

BACKGROUND: The acute Hepatitis B virus (HBV) infection usually ceases before six months, but chronic infection that lasts for more than six months might develop into liver cirrhosis and hepatocellular carcinoma (HCC). Viral particle load, HBV genotypes and association to the HBV x (HBx) gene mutations are the probable factors related to HCC occurrence. The mutation which leads to HBx T118N was found as the second most common HBx mutation in Indonesia, as compared to the known cancer-related HBx K130M/V131I mutant. However, the effect of T118N mutation and its combination with K130M/V131I on human hepatoma cells has not been elucidated well. Hence, this study was conducted to dissect the role of HBx T118N and its mutant combination in colony formation, as compared to the wild type HBx and cancer-related HBx K130M/V131I.METHODS: In this study, the genes encoding wild type HBx, HBx T118N, and HBx K130M/V131I mutations were obtained as synthetic gene. Meanwhile, the gene encoding HBx T118N/K130M/V131I mutations was successfully generated using site-directed mutagenesis. The optimum condition for colony formation assays was determined through Zeocin sensitivity test of HepG2 cells.RESULTS: Selection of HepG2 cells using Zeocin was determined at 200 µg/mL. Colony formation assays performed upon expression of HBx T118N and HBx T118N/K130M/V131I mutant proteins showed reduced colony numbers as compared to the expression of wild type HBx, similar to the effect from HBx K130M/V131I mutant expression.CONCLUSION: The HBx T118N and HBx T118N/K130M/V131I mutation caused less colony formation of HepG2 cells, similar to the K130/M131I mutation. This indicates a possible role of the T118N mutation in liver cancer development.KEYWORDS: colony formation assay, hepatitis B virus, HBx, T118N, K130M/V131I
Co-Authors Afifah, Salma Aulia Anindyajati Anto Budiharjo Arina Tri Lunggani ARTARINI, ANITA DEBBIE SOEFIE RETNONINGRUM DESSY NATALIA Dewantoro, Giwang Dewi Riskha Nurmalasari Dian Rachmawati Diky Mudhakir Dyah Wulandari Edwin Setiawan ERNAWATI ARIFIN GIRI-RACHMAN Farikha, Siti Lutfiatul Hardiyanti, Renny Hermanto, Michael Einstein I Gusti Ngurah Jemmy Anton Prasetia Kurniati, Dwi Elfira Kurniati, Neng F. Nurlita Abdulgani Permanasari, Silmi Citra Raden Mohamad Herdian Bhakti Raymond R. Tjandrawinata Setyo Nugroho Tan, Marselina Irasonia