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All Journal Jurnal Ilmu Pertanian Indonesia Squalen Bulletin of Marine and Fisheries Postharvest and Biotechnology Annales Bogorienses
Atikana, Akhirta
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Environmental Science Immunology & microbiology

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The Marine Actinobacterium Streptomyces sp. BTA 1-131 as a Potential Producer of Anti-Nontuberculous Mycobacterial (Anti-NTM) Paramita, Ni Luh Putu Vidya; Atikana, Akhirta; Sukmarini, Linda; Untari, Febriana; Prayoga, Muhammad Bagas; Maulidia, Faiqoh Nur; Ratnakomala, Shanti; Lisdiyanti, Puspita; Nuryastuti, Titik; Hertiani, Triana
Squalen, Buletin Pascapanen dan Bioteknologi Kelautan dan Perikanan Vol 19, No 3 (2024): December 2024
Publisher : :Agency for Marine and Fisheries Research and Human Resources, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15578/squalen.882

Abstract

Nontuberculous mycobacteria (NTM) are environmental microorganisms, also known as opportunistic pathogens, found in patients with pulmonary tuberculosis. The emergence of antibiotic resistance is increased by prolonged antibiotic treatment for NTM infections. Therefore, alternative sources of new antibiotics are essential for the treatment of NTM infections. A marine actinobacterium, Streptomyces sp. BTA 1-131, isolated from a marine sponge, Melophlus sarasinorum, has been reported as a potential source of antibacterials and anticancer agents. The present study aimed to investigate the potential of Streptomyces sp. BTA 1-131 against two NTMs: Mycobacterium smegmatis and Mycobacterium fortuitum. Streptomyces sp. BTA 1-131 was fermented in three cultivation media (SYP, ISP2, and YS), and the secondary metabolites were extracted using methanol. The bioactivity screening showed inhibition of all methanolic extracts against the growth of M. smegmatis and M. fortuitum. The methanolic extract, which could inhibit both mycobacteria, was a crude extract derived from SYP liquid medium fermentation. The isolated compounds in this study were preliminarily identified using thin-layer chromatography (TLC). The TLC results showed different potential compounds in the crude extracts of Streptomyces sp. BTA 1-131 also highlighted the impact of the fermentation medium on the production of metabolites from Streptomyces. This study also added knowledge about the importance of the Indonesian marine actinobacterium Streptomyces sp. BTA 1-131 as a promising producer of anti-NTM compounds.
Bioprospecting of Pectinase-Producing Bacteria from Marine Actinomycetes Hasanah, Neneng; Nadhifah, Hana; Rahayuningsih, Mulyorini; Atikana, Akhirta; Ratnakomala, Shanti; Lisdiyanti, Puspita; Rahmani, Nanik
Jurnal Ilmu Pertanian Indonesia Vol. 30 No. 4 (2025): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18343/jipi.30.4.689

Abstract

Pectinase is used in a variety of industries, including fruit juice production, textile processing, papermaking, biodegumming, coffee and tea manufacturing, medicines, feed, and nutraceuticals. The demand for pectinase enzymes grows year after year. Industrial applications require high-activity enzymes that can increase considerable product yields while also improving based on needs and byproduct use. Indonesia's industry continues to rely on imported pectinase enzymes. Indonesia, on the other hand, possesses megabiodiversity, particularly marine microorganisms, which have the potential to provide new enzymes with high activity for industrial applications. This work aims to undertake bioprospecting of marine actinomycetes producing pectinase enzymes that have the capacity to hydrolyze pectin polymer, both from commercial and biomass sources. A total of 20 marine actinomycetes isolates from sediment, seawater, and sponges were bioprospected, and one isolate was selected with high pectinase activity (BLH 1.20), which was then used to characterize pH, temperature, hydrolysis analysis on pectin polymers, and isolate identification using 16s rRNA analysis. The selected isolate (BLH 1.20) performed best in a sodium phosphate buffer with a pH of 6.0 and a temperature of 30°C, achieving an activity of 5.4 U/mL. The 16S rRNA analysis revealed that the isolate is from the genus Streptomyces and the species Streptomyces sampsonii. Keywords: bioprospecting, marine Actinomycetes, pectinase, Streptomyces sampsonii
Detection of Keto Synthase (KS) Gene Domain in Sponges and Bacterial Sponges Atikana, Akhirta; Naim, Mohamad Azrul; Sipkema, Detmer
Annales Bogorienses Vol. 17 No. 2 (2013): Annales Bogorienses
Publisher : BRIN

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Abstract

Sponges are sources of various useful natural products. The natural compounds derived from sponges are mostly complex polyketide. The polyketide synthase genes (PKS) is responsible for the biosynthesis of complex polyketides. During this research, we detected ketosynthase (KS) gene domain from 10 species of marine sponges, collected from Mediterranean Sea (Aplysina aerophoba, Petrocia ficiformis, Axinella damicornis, Axinella veronicas, Crambe crambe) and North Sea (Halichondria panicea, Haliclona xena, Haliclona oculata, Suberites massa, Ephydatia fluviatilis). We also detected KS gene domain from 12 bacterial sponge isolated from H. panicea. We used a PCR-based approach to detect the ketosynthase (KS) gene domain of Polyketosynthase (PKS) genes. Our result showed that the sponges and the bacterial sponges are mostly KS positive (700 bp). The presence of the PKS gene indicates the ability of the sponges to produce bioactive compound and potential natural product. The presence of the KS domain in both of the sponges and the bacterial sponges might also indicate that the bacterial sponges involved in the biosyntesis of secondary metabolite of the sponges.
A Preliminary Report on The Syntheses of Oligonucleotide Primers in The National Research and Innovation Agency (NRIA) Atikana, Akhirta; Prasetyoputri, Anggia; Rubiyana, Yana; Herawati, Neng; Desriani, Desriani; Pratiwi, Riyona Desvy; Wulandari, Dwi; Sukmarini, Linda; Kusharyoto, Wien; Santoso, Adi; Putra, Masteria Yunovilsa; Lisdiyanti, Puspita
Annales Bogorienses Vol. 26 No. 1 (2022): Annales Bogorienses
Publisher : BRIN

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/ann.bogor.2022.v26.n1.21-27

Abstract

A PolyGen DNA Synthesizer is equipment that is used for synthesizing oligonucleotide primers for any amplification targets. Oligonucleotide primers are indispensable components for any Polymerase Chain Reaction (PCR)-based detections. In the present study a number of oligonucleotide primer sets were synthesized to target (1) the Human Insuline Glargin (HIG) and (2) the Human Erythropoietin (EPO), as well as (3) the RNA-dependent RNA Polymerase (RdRp) and (4) the Nucleocapsid (N) genes of the severe acute respiratory syndrome virus 2 (SARS-CoV-2). A solid-phase oligonucleotide synthesis method was used according to the default protocol of the Polygen’s instrument to synthesize primers at a 40 nmol scale. The synthesized primers in this study were compared to commercially produced primers in their ability to amplify the gene target(s) in PCR and quantitative real-time PCR (qPCR) reactions. The first two sets of primers showed similar results in PCR compared to commercial primers; however, these primers were not tested for qPCR due to sample limitation. In contrast, the primer sets 3 and 4 were not able to produce amplicons in PCR reactions and only the primer set 4 successfully amplified the gene target in qPCR. These results indicate that the crude primers synthesized in this study are promising candidates for molecular detection and diagnostics, but these primers would benefit from further optimization for routine applications.
Co-Authors Adi Santoso Desriani Desriani Dwi Wulandari Kusharyoto, Wien LINDA SUKMARINI Maulidia, Faiqoh Nur Mulyorini Rahayuningsih Nadhifah, Hana Naim, Mohamad Azrul NANIK RAHMANI Neneng Hasanah Neng Herawati, Neng Ni Luh Putu Vidya Paramita Prasetyoputri, Anggia Prayoga, Muhammad Bagas PUSPITA LISDIYANTI Putra, Masteria Yunovilsa Riyona Desvy Pratiwi, Riyona Desvy SHANTI RATNAKOMALA Sipkema, Detmer Titik Nuryastuti Triana Hertiani Untari, Febriana Yana Rubiyana, Yana