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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Mutiara Medika: Jurnal Kedokteran dan Kesehatan ANNALES BOGORIENSES
BUDI SAKSONO
Research Center for Biotechnology, Lembaga Ilmu Pengetahuan Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Environmental Science Health Professions Immunology & microbiology Medicine & Pharmacology

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Site-Directed Mutagenesis of Glu-269 L-Arabinose Isomerase from Geobacillus stearothermophilus Isolated from Tanjung Api Poso, Indonesia Fitriani, Dewi Fitriani; Wulandari, Puspita Suci; Saksono, Budi
ANNALES BOGORIENSES Vol 14, No 2 (2010): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (600.974 KB) | DOI: 10.1234/55

Abstract

Industrializing of tagatose requires enzymes that meet to industrial need such as thermophile, slightly acidic and metal independent.  Previously,  we  cloned,  sequenced  and  expressed  L-arabinose  isomerase  from  Geobacillus stearothermophilus  isolated  from Tanjung  Api, Poso, Indonesia. Based on DNA alignment analysis, the gene had  high  homology  with  those  of  G.  stearothermophilus  T6  (Gene  Bank  Acc  No:  AAD45718)  which  has optimum  activity  at  high  temperature  and  alkaline  condition.  In  this  p aper,  we  described  site-directed mutagenesis approach to mutate Glu-269 (Q269) to Lys-269 (K269) to decrease the optimum pH of the strain. Sequencing  result  showed  that  mutagenesis  had  been  successful  to  mutate  amino  acid  at  position  269  from glutamine (Q) into lysine (K). Expression of mutant Q269 showed protein with molecular mass ~56 kDa. Keywords: site-directed mutagenesis, Q269K, L-arabinose isomerase, Geobacillus stearothermophilus
Non Invasive Detection of Dengue Viruses from Saliva: In vitro Study Saksono, Budi
ANNALES BOGORIENSES Vol 22, No 2 (2018): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (214.71 KB) | DOI: 10.14203/ann.bogor.2018.v22.n2.75-80

Abstract

      In the previous paper, we had succeeded in developing an early detection system of dengue viruses using Sugar liganded Gold Nano Particle (SGNP) only from 6 μL serum. It has been reported that dengue virus is also detected in the saliva and urine of the patient. The evidences lead to the possibility of developing non-invasive methods of dengue virus detection. In this in vitro study, we evaluated the utility of SGNP to capture and concentrate dengue virion in 10% saliva solution. The results showed that dengue virion was successfully detected in 10% of saliva solution. Analysis of virion stability during storage showed that virions in salivary samples were stable up to 3 days at temperature wherease the RNA has significantly degraded. Although still a preliminary study, the data obtained show the prospect of SGNP as a non-invasive dengue virus detection method, as well as the development of POC (Point of Care) method. Clinical trials using saliva from dengue viruses infected patients need to be done to prove the effectiveness of the SGNP method.
The Cytotoxicity of Agaro-Oligosaccharides and Neoagaro-Oligosaccharides on Macrophage Cells Pratitis, Visi Endah; Puspitasari, Pinki Anggrahini; Hanbal, Mayland Muhammad; Tsabitah, Khansa; Juliadmi, Dian; Saksono, Budi; Wijayanti, Nastiti
Mutiara Medika: Jurnal Kedokteran dan Kesehatan Vol 24, No 2 (2024): July
Publisher : Universitas Muhammadiyah Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18196/mmjkk.v24i2.21059

Abstract

Agarose is a polysaccharide from red algae. Enzymatic hydrolysis of agarose can produce Agaro-Oligosaccharidess (AOS) and Neoagaro-Oligosaccharidess (NAOS). Different times of enzymatic hydrolysis can produce different types of AOS and NAOS based on their degree of polymerization (DPs). This study aims to examine the cytotoxicity of AOS and NAOS with different hydrolysis times on the macrophage cell line RAW 264.7. The parameters used were the percentage of cell viability and IC50 value. The cytotoxicity test using MTT assay and One-way ANOVA were used as statistical tests. The results showed that AOS-0 at a concentration below 125 µg/mL was not toxic and showed moderate toxicity up to a high concentration of 1000 µg/mL, while AOS hydrolyzed for 24 h (AOS-24) was not toxic to RAW 264.7 cells at all concentrations tested. The different results were shown in all NAOS samples, which were highly toxic to RAW 264.7 cells in the 125 to 1000 µg/mL, indicating that it was concentration dependent. The results showed that different hydrolysis times caused differences in the structure of AOS and NAOS compounds and influenced the toxicity level. Research development for further studies on antioxidants and anti-inflammatory needs more attention to the sample type and hydrolysis time.
In-Silico Optimization of α-agarase for Sustainable Bioprospecting of Agaro-oligosaccharides: In-Silico Optimization of α-agarase for Sustainable Bioprospecting of Agaro-oligosaccharides Hanbal, Mayland Muhammad; Wijayanti, Nastiti; Tsabitah, Khansa; Zulfa, Amania; Tasania, Nadia Nisa; Saksono, Budi
Journal of Tropical Life Science Vol. 15 No. 2 (2025): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/gg6mkk56

Abstract

Enzymatic synthesis is a sustainable alternative to chemical methods, offering high substrate specificity, reduced byproducts, and environmentally friendly processes. Despite its advantages, agaro-oligosaccharides (AOS) production largely depends on chemical synthesis due to the limited exploration of α-agarase. Therefore, this study aims to identify, analyze, and redesign a suitable α-agarase candidate for AOS production using in-silico approaches. Biological databases from CAZy, UniProtKB, and PDB, along with journal references, were used to curate α-agarase candidates. Non-catalytic regions were removed to retain only the GH96 catalytic domain, with a His-tag added for easier purification. Subsequently, structural modeling using SWISS-MODEL was performed to facilitate blind docking with CB-Dock2. Modeling also facilitated physicochemical properties predictions incorporating OphPred, Protein-Sol, and SCooP for pH, solubility, and thermal stability. The results showed that AgaA33, obtained from Thalassomonas agarivorans JAMB-A33, was selected due to its high annotation score and optimal temperature. Structural modeling and blind docking confirmed that the functional domains were preserved after redesign. In-silico physicochemical assessments revealed that the redesigned enzyme exhibited improved pH tolerance and thermal stability, despite a slight reduction in solubility. This study showed the use of computational tools for enzyme redesign and showed the potential of α-agarase as a green and sustainable biocatalyst for AOS production. By combining database-driven candidate selection with in-silico structural and functional analyses, these results set the foundation for further optimization of α-agarase to meet industrial needs. Future efforts must focus on improving solubility and refining activity predictions to fully realize the enzyme’s potential for eco-friendly bioprocesses.
Co-Authors A.A. Ketut Agung Cahyawan W Hanbal, Mayland Muhammad Juliadmi, Dian Nastiti Wijayanti Pratitis, Visi Endah Puspitasari, Pinki Anggrahini Tasania, Nadia Nisa Tsabitah, Khansa Wulandari, Puspita Suci Zulfa, Amania