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All Journal ILMU KELAUTAN: Indonesian Journal of Marine Sciences Narra J Makara Journal of Science
Kamarisima,
School Of Life Sciences And Technology, Institut Teknologi Bandung, Bandung, Indonesia
Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Health Professions Immunology & microbiology Medicine & Pharmacology Public Health

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Isolation of Asphaltene-Degrading Bacteria from Sludge Oil Aditiawati, Pingkan; Kamarisima,
Makara Journal of Science Vol. 19, No. 1
Publisher : UI Scholars Hub

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Abstract

Sludge oil contains 30%–50% hydrocarbon fractions that comprise saturated fractions, aromatics, resins, and asphaltene. Asphaltene fraction is the most persistent fraction. In this research, the indigenous bacteria that can degrade asphaltene fractions from a sludge oil sample from Balikpapan that was isolated using BHMS medium (Bushnell-Hass Mineral Salt) with 0.01% (w/v) yeast extract, 2% (w/v) asphaltene extract, and 2% (w/v) sludge oil. The ability of the four isolates to degrade asphaltene fractions was conducted by the biodegradation asphaltene fractions test using liquid cultures in a BHMS medium with 0.01% (w/v) yeast extract and 2% (w/v) asphaltene extract as a carbon source. The parameters measured during the process of biodegradation of asphaltene fractions include the quantification of Total Petroleum Hydrocarbon (g), log total number of bacteria (CFU/ml), and pH. There are four bacteria (isolates 1, 2, 3, and 4) that have been characterized to degrade asphaltic fraction and have been identified as Bacillus sp. Lysinibacillus fusiformes, Acinetobacter sp., and Mycobacterium sp., respectively. The results showed that the highest ability to degrade asphaltene fractions is that of Bacillus sp. (isolate 1) and Lysinibacillus fusiformes (Isolate 2), with biodegradation percentages of asphaltene fractions being 50% and 55%, respectively, and growth rate at the exponential phase is 7.17x107 CFU/mL.days and 4.21x107 CFU/mL.days, respectively.
Antibacterial compounds derived from marine Streptomyces aureofaciens A3 through in-silico molecular docking Srikandace, Yoice; Syani, Ira Rhabbiyatun; Wahhaab, Aisha; Kamarisima, Kamarisima; Putri, Sastia Prama; Aditiawati, Pingkan
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 29, No 3 (2024): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.29.3.403-413

Abstract

Streptomyces aureofaciens widely produces the antibiotic tetracycline and many other compounds during fermentation. The compounds have yet to be known for their antibacterial potential. This work aims to determine new antibiotics or other possible antibacterial compounds produced by marine S.aureofaceiens A3 through an in silico molecular docking method. The ethyl acetate (EA) extracts from fermented marine S. aureofaciens A3 in ISP4 medium enriched with seawater components showed strong antibacterial activity.  The antibacterial activity of EA extracts during 6-12 days of fermentation was carried out by the Kirby-Bauer method and the compounds of EA extracts were analyzed by GC/MS. Compounds identified by GC/MS were ligands for an in silico molecular docking study against four target proteins (DNA gyrase, topoisomerase IV, PBP 1a, and DHFR) of pathogenic bacteria. The drug-likeness of selected chemicals as antibacterial agents was assessed using Lipinski's Rule of Five. The results showed the prospective compounds as a narrow-spectrum antibacterial, including 3,5-di-tert-Butyl-4-hydroxyphenylpropionic acid against PBP 1a and Benzenepropanoic acid, and 3,5-bis (1,1-dimethyl ethyl)-4-hydroxy-, methyl esters against DHFR. Substances with broad-spectrum antibacterial activity, such as 3-Acetylphenanthrene and 3-(p-Ethoxyphenyl)-5-(O-tolyloxymethyl)-2-oxazolidone, against multitarget DNA gyrase B and DHFR, 7,9-Di-tert-butyl-1-oxaspiro (4,5) Deca-6,9-diene-2,8-dione against PBP1a and DHFR, and isobenzofuro [5,6-b] benzofuran-8-carboxylic acid, 1,3-dihydro-7,10-dimethoxy-9-methyl-1-oxo-, methyl ester against DNA gyrase B, PBP 1a, and DHFR. On the 12th day of fermentation, two compounds were identified: isobenzofuro[5,6-b] benzofuran-8-carboxylic acid, 1,3-dihydro-7,10-dimethoxy-9-methyl-1-oxo-, methyl ester, and 3-(p-Ethoxyphenyl)-5-(O-tolyl oxy methyl)-2-oxazolidone.  This is the first report that these two compounds, known as potential drugs like antibiotics through in silico molecular docking, were first produced by Streptomyces species.
Development of an inactivated viral transport medium for diagnostic testing in low-resource countries Rahmani, Silmi; Meitha, Karlia; Septiani, Popi; Priharto, Neil; Kamarisima, Kamarisima; Ningrum, Ratih A.; Angelina, Marissa; Agustiyanti, Dian F.; Wisnuwardhani, Popi H.; Nugroho, Herjuno A.; Tan, Marselina I.
Narra J Vol. 5 No. 3 (2025): December 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v5i3.2068

Abstract

Viral transport medium (VTM) is crucial for retaining clinical specimens, such as the virus or its genetic material from the mucus of respiratory tract of coronavirus disease 2019 (COVID-19) suspected patients. However, the locally produced VTM in Indonesia lacks the ability to inactivate the virus, risking the safety of diagnostic personnel. The aim of this study was to formulate inactive VTM (iVTM) incorporating chaotropic agents like guanidine salt, along with anionic detergents, chelators, buffers, and surfactants, to inactivate the virus while maintaining RNA integrity. Viral RNA stability in iVTM (pH 4 and pH 6) was evaluated for 30 days at 4°C and 25–28°C. In vitro inactivation test was performed on SARS-CoV-2 isolate (variant B1). The stability test revealed that storing the clinical specimens in iVTM at pH 6 maintained severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) detectability by qPCR for up to 30 days at cold and room temperatures. Stability assessments conducted over a 4-month period (at 25–28°C) on iVTM with a pH of 6 revealed clear appearance, consistent pH stability, no alteration in the solution color, and no indications of bacterial or fungal contamination. Results from an in vitro inactivation assay demonstrated that iVTM pH 6 eliminated SARS-CoV-2 infectivity within just five minutes of contact. These findings suggest that iVTM pH 6 offers a safer and cost-effective alternative for handling and transportation of clinical specimens.
Development of an inactivated viral transport medium for diagnostic testing in low-resource countries Silmi Rahmani; Karlia Meitha; Popi Septiani; Neil Priharto; Kamarisima Kamarisima; Ratih A. Ningrum; Marissa Angelina; Dian F. Agustiyanti; Popi H. Wisnuwardhani; Herjuno A. Nugroho; Marselina I. Tan
Narra J Vol. 5 No. 3 (2025): December 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v5i3.2068

Abstract

Viral transport medium (VTM) is crucial for retaining clinical specimens, such as the virus or its genetic material from the mucus of respiratory tract of coronavirus disease 2019 (COVID-19) suspected patients. However, the locally produced VTM in Indonesia lacks the ability to inactivate the virus, risking the safety of diagnostic personnel. The aim of this study was to formulate inactive VTM (iVTM) incorporating chaotropic agents like guanidine salt, along with anionic detergents, chelators, buffers, and surfactants, to inactivate the virus while maintaining RNA integrity. Viral RNA stability in iVTM (pH 4 and pH 6) was evaluated for 30 days at 4°C and 25–28°C. In vitro inactivation test was performed on SARS-CoV-2 isolate (variant B1). The stability test revealed that storing the clinical specimens in iVTM at pH 6 maintained severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) detectability by qPCR for up to 30 days at cold and room temperatures. Stability assessments conducted over a 4-month period (at 25–28°C) on iVTM with a pH of 6 revealed clear appearance, consistent pH stability, no alteration in the solution color, and no indications of bacterial or fungal contamination. Results from an in vitro inactivation assay demonstrated that iVTM pH 6 eliminated SARS-CoV-2 infectivity within just five minutes of contact. These findings suggest that iVTM pH 6 offers a safer and cost-effective alternative for handling and transportation of clinical specimens.
Co-Authors Agustiyanti, Dian F. Dian F. Agustiyanti Herjuno A. Nugroho Marissa Angelina Marissa Angelina Marselina I. Tan Meitha, Karlia Neil Priharto Neil Priharto Ningrum, Ratih A. Nugroho, Herjuno A. PINGKAN ADITIAWATI Popi H. Wisnuwardhani Putri, Sastia Prama RAHMANI, SILMI Ratih A. Ningrum Septiani, Popi Silmi Rahmani Srikandace, Yoice Syani, Ira Rhabbiyatun Tan, Marselina I. Wahhaab, Aisha Wisnuwardhani, Popi H.