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Journal Articles

Permanent URI for this collectionhttps://repository.unesco.gov.ph/handle/123456789/50

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    Genome mining of a novel marine sponge symbiont Nocardia sp. BML-15-R-026U reveals high biosynthetic potential for secondary metabolites, including a non-ribosomal peptide and a polyketide of high novelty
    Gloria, Paul Christian; Romines, Elaine; Punzalan, Marc Jeremie; Florece, Christine Marie; Cadorna, Kreighton; Salvador-Reyes, Lilibeth; Lluisma, Arturo (Philippine-American Academy of Science and Engineering, 2023-11-28)
    Antibiotic and drug resistance poses serious global public health threats, leading to substantial infections and fatalities annually. Addressing these issues requires the discovery of novel bioactive compounds and a faster and more cost-effective discovery process. However, traditional approaches, which require isolation and multi-step purification of compounds from organisms and running of initial assays, suffer from serious limitations such as the need for substantial amounts of biological material and high rates of compound rediscoveries. Because the biosynthetic capabilities of organisms are encoded in their genomes, genome mining provides a promising solution that would complement traditional approaches. This study conducted long-read whole genome sequencing on a marine sponge symbiont, Nocardia sp. BML-15-R-026U, to explore its genomic repertoire of secondary metabolite-encoding Biosynthetic Gene Clusters (BGCs). A four-contig genome assembly was generated for this isolate with a high degree of completeness and an estimated genome size of 4.84 Mbp. Its genome displays remarkable biosynthetic potential by containing at least 34 distinct secondary metabolite BGCs, predominantly Non-Ribosomal Peptide Synthetase (NRPS) and Polyketide Synthase (PKS) systems capable of producing novel chemical structures. Further analysis was focused on two genomic regions. In region 3.10, the study predicted a BGC for a novel, serine-rich non-ribosomal peptide with a predicted molecular weight of 2754 g/mol. Region 3.12 contained an iterative type-I PKS BGC, suggesting the potential synthesis of a polyketide compound with oxidoreductase-inhibiting properties. This study highlights genome mining as a productive early-phase approach for identifying promising drug leads and has identified the most promising candidates among this isolate’s BGCs for experimental validation.
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    Optimized agar extraction from Gracilaria eucheumoides Harvey
    Villanueva, R. D.; Pagba, C. V.; Montaño, N. E. (Walter de Gruyter, 1997)
    A 33 factorial experimental design was utilized to determine the optimum alkali pretreatment conditions in the extraction of agar from Gracilaria eucheumoides. Three levels from each of three factors were considered: Temperature, 70, 80, 90 °C; NaOH concentration, 4, 7, 10% and; treatment duration, 0.5, 1, 2 h. The optimum conditions were found to be 90 °C, 10% and 2 h. The gel strength of the agar yielded under these conditions was 432 ± 43 g/cm2. The effects of the different alkali pretreatment conditions to the agar yield and 3, 6-anhydrogalactose and sulphate contents were also determined. Agar yield was higher at lower temperature, stronger alkali solution and shorter treatment duration. Higher 3, 6-ahydrogalactose content and lower sulphate level were obtained at higher temperature, higher alkali concentration and longer duration of treatment.
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    Total synthesis and bioactivity evaluation of hydrophobic microcionamide‐inspired peptides
    Inocentes, Carl Rogel V.; Salvador‐Reyes, Lilibeth A.; Villaraza, Aaron Joseph L. (Wiley, 2023-01)
    In this report, we describe the facile synthesis of four microcionamide-inspired peptides where the atypical 2-phenylethylenamine (2-PEA) functional group in the marine natural product, microcionamide A, was replaced with a similarly-aromatic but more easily incorporated tryptophan (Trp) residue. Compounds 1–4 were synthesized using a standard Fmoc-based solid-phase synthesis strategy followed by iodine-mediated on-resin cyclization for disulfide-bridged compounds 1–3. Compound 1 showed antimicrobial activity against Staphylococcus aureus and Pseudomonas aeruginosa, with minimum inhibitory concentrations (MICs) of 9.1 μM and 15 μM, respectively. The inactivity of alanine analogs 2–4 against these pathogens suggests that the N-terminal Val, the cyclic scaffold, the contiguous Ile residues, and consequently, the hydrophobicity of compound 1 are essential for antibacterial activity. Compound 1 also favorably exhibited minimal cytotoxicity against normal mammalian cell lines. In summary, we have synthesized an analog of microcionamide A where replacement of the 2-PEA moiety with a Trp residue retained the antibacterial activity and with favorably low cytotoxicity.
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    Development of autonomous multi-sensor ocean monitoring instrument designed for complex archipelagic waters
    Purba, Noir P.; Faizal, Ibnu; Valino, Darryl Anthony; Kang, Hooi Siang; Sugianto, Erik; martasuganda, marine kenzi; Abimanyu, A.; Bratasena, T.; Zenyda, K. S.; Prayogo, N.; Ramdhani, F.; Khan, A. M. A. (Springer, 2023-01-22)
    This paper presents the development of low-cost multi-sensor ocean monitoring instrument to measure oceanographic parameters. The aim of this instrument is to fulfil the monitoring specifically for archipelagic countries with complex waters, and it allows for both vertical and horizontal measurements. The platform contains removable sensors, rechargeable batteries, satellite system, and micro-controller. Inside the instrument, the probes are primarily to measure acidity level (pH), water temperature (°C), salinity (ppt), conductivity (ms/cm), turbidity (NTU), and depth (m). Furthermore, data are stored in an internal SD card and simultaneously transmitted to a website portal data via satellite after it goes to the surface water. For validation, several tests had been conducted in controlled laboratory conditions and field setting, in which the test results had shown satisfactory results. In the future, the system will be upgraded by adding extra units of antenna, chlorophyll sensors, and a power changer made from thrusters. Currently, this instrument is operational and available for use in archipelagic countries with dynamics depth.