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INDONESIA
Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences
Published by Universitas Brawijaya
ISSN : 20875517     EISSN : 25274376     DOI : -
Core Subject : Agriculture, Social,
Agriculture, Biological Sciences & Forestry Environmental Science
The Journal of Tropical Life Science (JTLS) provides publication of full-length papers, short communication and review articles describing of new finding or theory in living system, cells and molecular level in tropical life science and related areas. The journal publishes articles that report novel findings of wide Tropical Life system phenomenon in the areas of biodiversity, agriculture, fisheries, health, husbandry, forestry and environmental technology. JTLS has 1 volume with 3 issues per year.
Arjuna Subject : -
Articles 15 Documents
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Search results for , issue "Vol. 15 No. 2" : 15 Documents clear
Rational Design of Peptide Inhibitor Targeting BRCA1-Associated Protein 1 Through Homology Modeling and Molecular Dynamics Simulation: Rational Design of BRCA1-Associated Protein 1 Peptide Inhibitor Husain, Syarifuddin; Mohamed, Ruzianisra; Abd Halim, Khairul Bariyyah; Mohd Mutalip, Siti Syairah; Hairuddin, Omar Nafiis
Journal of Tropical Life Science Vol. 15 No. 2
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/qf88a179

Abstract

Cancer remains a complex and heterogeneous disease, with the BRCA1-Associated Protein 1 (BAP1) recognized as a tumour suppressor gene playing a vital role in various cellular processes. Interestingly, BAP1 is overexpressed in certain cancers, and inhibition of its ubiquitin C-terminal hydrolase (UCH) domain may offer a promising therapeutic strategy. This study aims to identify the key residues involved in the interaction between ubiquitin and BAP1 and to design peptide inhibitors capable of selectively targeting BAP1’s deubiquitinating activity. A 3D protein model of the BAP1–ubiquitin complex was generated using AlphaFold, followed by molecular dynamics (MD) simulations to identify critical interacting residues. Peptide inhibitors were designed based on the β-turn region of ubiquitin, and molecular docking was performed using the HADDOCK 2.4 server. Based on the result, it was observed that mutating Lys6 and Thr9 to arginine improved binding affinity between the cyclic peptide inhibitors and the BAP1, probably due to the complementary attraction between the positively charged arginine residue and the negatively charged surface electrostatic potential of the BAP1 distal site. MD simulations were conducted to assess the stability and interactions of the BAP1-peptide complexes, showing that the CP3K6R/T9R mutant exhibited the highest average number of hydrogen bonds and the strongest binding affinity. The study suggests that electrostatic interactions and residue-specific mutations can be used to optimise peptide inhibitors for BAP1. The findings support the possibility of developing therapeutic strategies to inhibit BAP1 and suppress tumour progression.
Medicines in medicines: Challenges and Prospects in Drug Discovery from Fungal Endophytes of Medicinal Plants in Southeast Asia: Challenges and Prospects in Drug Discovery from Fungal Endophytes of Medicinal Plants Guerrero, Jonathan Jaime G.; General, Mheljor; Balendres, Mark Angelo; Tan, Mario; Buiza, Marielle; Huyop, Fahrul
Journal of Tropical Life Science Vol. 15 No. 2
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/xvfdnn97

Abstract

Fungal endophytes engage in a balanced symbiotic continuum with their host plants, from mutualism to commensalism and parasitism. These host-endophyte interactions play a pivotal role in shaping the biosynthetic and chemical space of the host plants and their associated mycobiomes, resulting in a wealth of biologically active natural products that are attractive for drug discovery. Endophytic fungi in medicinal plants continue to attract attention, highlighting a holistic view of plant-based therapeutics that considers the plant and its endophytic partners as sources of medicinal compounds. In this review, we assembled recent Southeast Asian studies related to fungal endophytes from plants with traditional medicinal uses and their potential biomedical applications. Here, we present a comprehensive analysis of the interactions within the region, identifying prolific fungal classes that produce compounds of biomedical significance. This analysis is based on a consolidated dataset of over 1,300 interactions. We noted an association between plant-endophyte-synthesized compounds and their related chemistry. However, the majority are preliminary and lack comprehensive follow-through research. While fungal endophytes in the region produce important compounds, their applicability in drug discovery necessitates extensive long-term studies.
Genetic Variation of Siam Orange (Citrus nobilis Lour.) in Several Sumatran Production Centers using RAPD Marker: Genetic Variation of Citrus nobilis Lour in Several Sumatran Production Centers Arifa Setriani; Mansyurdin; Nurainas
Journal of Tropical Life Science Vol. 15 No. 2
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/7mr9as38

Abstract

Siam orange (Citrus nobilis Lour.) is a key horticultural commodity in Indonesia, valued for its adaptability, potential to improve farmer welfare, and contribution to the national economy. In Sumatra, four main production centres are located in Berastagi (North Sumatra), Gunung Omeh and Pasaman (West Sumatra), and Bangkinang (Riau). However, the origin of seedlings from these centres remains unclear. Despite high productivity, inconsistencies in fruit quality and genetic diversity among production centres highlight the need for molecular-level analysis to ensure superior varieties and maintain market competitiveness. This study aimed to determine the intra- and interpopulation genetic variations of Siam orange in these four production centres using RAPD markers. DNA isolation followed the Doyle and Doyle (1987) method, and amplification used 12 primers, of which OPA03, OPA10, and OPA01 produced the highest polymorphism (95.25%). Intrapopulation genetic variation was relatively low (H = 0.1061–0.1919), with Berastagi showing the lowest (H = 0.1061) and Gunung Omeh the highest (H = 0.1919). Interpopulation genetic diversity was classified as high (DST = 0.0619), with GST = 0.2946, and gene flow was Nm = 1.1975. UPGMA cluster analysis revealed that Gunung Omeh and Berastagi had the most significant genetic distance (0.1622), while Gunung Omeh and Bangkinang were the closest (0.0614). Principal Coordinates Analysis (PCoA) indicated that Berastagi individuals were more clustered, whereas Gunung Omeh, Pasaman, and Bangkinang were more dispersed. These findings indicate that while genetic variation within populations is limited, genetic differentiation among populations is substantial, offering opportunities to select and combine diverse genetic sources. This diversity can be strategically exploited in breeding programs to develop superior cultivars, improve fruit quality uniformity, and strengthen the commercial competitiveness of Siam orange cultivation in Sumatra.
Duplex SYBR RT-qPCR for SARS-CoV-2 Detection in Malaysia: Duplex SYBR RT-qPCR for SARS-CoV-2 Detection in Malaysia Mahali, Helyatul Rasmah; Amin, Zarina; Yusof, Nur Athirah
Journal of Tropical Life Science Vol. 15 No. 2
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/mh764874

Abstract

TaqMan probe-based commercial real-time PCR kits are the gold standard for COVID-19 diagnosis but are expensive. The large scale of SARS-CoV-2 infections necessitates affordable testing for humans, animals, and environmental samples. COVID-19 symptoms overlap with other respiratory infections like influenza, common cold, MERS, and SARS, requiring precise diagnostic tests such as real-time PCR. This study introduces a cost-effective method using melting curve analysis of a SYBR green multiplex assay with gel electrophoresis. We developed a duplex SYBR Green real-time PCR assay to detect the spike (S), envelope (E), RNA-dependent RNA polymerase (RdRp), and nucleocapsid (N) gene of SARS-CoV-2 using two sets of tubes. Specific primers were designed from conserved regions of the SARS-CoV-2 genome sequences isolated from Malaysia, retrieved from the GISAID database. Initial singleplex SYBR Green RT-PCR reactions for the N, E, S, and RdRp genes were optimized. After several rounds of optimization, we targeted the S and N genes in one tube and the E and RdRp genes in another. The assay uses real-time PCR to detect four genes with two primer sets distinguished by melting temperatures: 81.5°C and 88°C for the S and N genes, and 79.5°C and 85.5°C for the E and RdRp genes. It demonstrated high specificity and sensitivity, with a detection limit of 0.1 pg/μL of DNA. We compared this method to the LyteStar 2019-nCoV RT-PCR Kit (China), approved by Malaysia's Ministry of Health. Both kits accurately detected all positive SARS-CoV-2 samples without false positives. In conclusion, the newly developed duplex SYBR Green I-based real-time PCR assay demonstrates high sensitivity, specificity, and reliability, making it a valuable and effective alternative for the detection of SARS-CoV-2.
Production of Bacterial Cellulose from Coffee Waste Extract Enriched with Carbon Source of Molasses and Pineapple Peel Waste: Production of Bacterial Cellulose from Coffee Waste Extract Mora, Giral Baines; Permatasari, Dewi; Wahyudi, Aleyda; Ardyati , Tri
Journal of Tropical Life Science Vol. 15 No. 2
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.15.02.15

Abstract

Coffee waste is an agricultural by-product that has been commonly used as compost and animal feed. It contains complex carbohydrate sources that can be further utilized for the production of bacterial cellulose. However, the sugar content in coffee waste is limited, so additional sugar sources such as molasses and pineapple peel extract are needed. Molasses and pineapple peel extract serve as substitutes for glucose and are expected to optimize the production of bacterial cellulose. This study aimed to determine the effect of different concentrations of molasses (0.5%, 2.5%, and 5% v/v) and pineapple peel extract (20% and 40% v/v) in coffee waste extract medium on bacterial cellulose production and to characterize the resulting membranes. The research stages included: (1) enrichment of starter culture and standardization of bacterial cell density; (2) extraction of coffee waste and pineapple peel; (3) production of bacterial cellulose using coffee waste extract medium supplemented with molasses or pineapple peel extract at varying concentrations; (4) physicochemical characterization of bacterial cellulose including weight, thickness, surface area, pH change, and tensile strength; and (5) analysis of membrane surface structure using SEM. The best physicochemical characteristics were obtained from the medium supplemented with 5% molasses and 20% pineapple peel extract. These treatments also yielded the best results in terms of SEM analysis and tensile strength.

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