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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 995 Documents
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Utilization of Chitosan Elicitation on Biomass, Total Flavonoids, and Antioxidant Activity of Black Betel Callus (Piper betle L. var Nigra): Utilization of Chitosan Elicitation on Black Betel Callus (Piper betle L. var Nigra) Nurindah Wanti, Yulia Tri; Wida Utami, Edy Setiti; Junairiah
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: 10.11594/3d65dk31

Abstract

Callus culture is a suitable method for the production of secondary metabolites. Elicitors can increase the content of secondary metabolites through the elicitation process. This study aims to determine the effect of chitosan elicitation on biomass, total flavonoids, and antioxidant activity of black betel callus. The research method is callus production by growing leaf explants on Murashige and Skoog (MS) medium with the addition of growth regulators Benzyl Amino Purin (BAP) 0.5 mg/L and 2,4-Dichlorophenoxy Acetic Acid (2,4-D) 2.0 mg/L. Furthermore, the callus was sub-cultured on MS medium with chitosan elicitor for four days. The data obtained was callus biomass. Extraction of callus to measure flavonoid content and antioxidant activity. The results showed that chitosan elicitation at 1.5 mg/L showed the most optimal biomass results, 1.22  ± 0.39 g fresh weight and 0.81 ± 0.17 g dry weight. Chitosan elicitation with 1.5 mg/L treatment showed the highest total flavonoid content of 9.52 ± 0.37 µg QE/g. The methanol extract of black betel callus resulting from chitosan elicitation has antioxidant activity. Callus treated with 2 mg/L chitosan showed the most substantial IC50 value of 53.60 ± 14.45 mg/L. Chitosan elicitation can effectively increase biomass, total flavonoids, and antioxidant activity of black betel leaf callus. Chitosan 1.5 mg/L is the optimum concentration for increasing biomass and total flavonoids, and chitosan 2 mg/L is the concentration that has the most effect on the antioxidant activity of black betel leaf callus.
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
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.
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.
A Novel System for the Production of the Bioactive N-alkylamide ‘Spilanthol’ Through Somatic Embryogenesis in Acmella ciliata Kunth (Cass.): Production of the Bioactive N-alkylamide ‘Spilanthol’ in Acmella ciliata Neethu Mohan, S; Hemanthakumar, AS; Preetha, TS
Journal of Tropical Life Science Vol. 13 No. 3 (2023)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.13.03.05

Abstract

Acmella ciliata Kunth (Cass.), a medicinally important plant in the family Asteraceae, has high commercial value because of its traditional phytomedicinal uses. The plant contains many phytochemicals like alkyl amides, alkaloids, tannins, saponins and flavonoids accountable for most of its pharmacological applications. The study presented here reports the callus culture and somatic embryogenesis of this plant thereby raising a novel system for the subsequent production of the N-alkyl amide ‘spilanthol’, the valuable secondary metabolite presents in it. Murashige and Skoog (MS) medium supplemented with auxins either alone or in combination with cytokinins were used for the induction and maturation of somatic embryos. MS medium supplemented with 2,4-D (0.5, 1.0 and 2.0 mg.L-1) produced black friable callus whereas, 1.0 mg.L-1 NAA in combination with 0.5 mg.L-1 BA induced white, slightly purple coloured friable callus which on further subculture to fresh medium induced somatic embryos that germinated into plantlets upon transfer to MS basal medium. The mode of regeneration via somatic embryogenesis was confirmed by histological analysis through free-hand sectioning and stereomicroscopic observation. The plantlets raised through somatic embryogenesis after a short hardening period, were found to acclimatise in the field at 83.33% efficiency and exhibited genetic uniformity with 96.6% similarity in the ISSR analysis. HPLC analysis of in vitro raised embryogenic callus showed 239.512 µg.g-1 spilanthol content which was comparatively higher than the mother plants (92.19 µg.g-1). The bioproduction of the N-alkylamide ‘spilanthol’ through embryogenic callus can be extended for the scale-up production of this bioactive compound using bioreactor technology for the formulation of phytodrugs.
Morpho-Anatomical, Ex-situ Conservation and Haemolytic Activity of Pentaphragma grandiflorum Kurz.: Morpho-anatomy, Ex-situ Conservation and Haemolytic Activity of Pentaphragma grandiflorum Kurz Amoroso, Victor; M. Maghanoy, Lalaine Grace; Aser, Cristine Mea
Journal of Tropical Life Science Vol. 13 No. 3 (2023)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.13.03.04

Abstract

Pentaphragma grandiflorum Kurz. is one of the five (5) species of Pentaphragma that is found in the Philippines. It is an edible flowering plant consumed as a vegetables and utilized for its medicinal value by the locals. It is categorized as one of the Other Threatened Species with a high economic value. Despite the many uses of P. grandiflorum, there is still inadequate information on its morpho-anatomical characteristics conservation and lack of scientific evidence to support the claim of its safe utilization by the locals. The collected wildlings of the P. grandiflorum were nurtured and monitored in the canopy greenhouse of Central Mindanao University, Philippines. The safe utilization of the leaf extract of P. grandiflorum was assessed through a haemolytic assay. The following are the morpho-anatomical features described in this study: fleshy erect shrub with primary and aerial roots; stem puberulous at a young stage and glabrous upon maturity with dictyostele type of stele; petiole fleshy, puberulous, dissected vascular bundle with dictyostele arrangement; leaf finely puberulous adaxial and glabrous abaxial, dictyostele arrangement, midrib amphibrical arrangement, with tri- to tetracytic stomates; inflorescence arises singly in axil, bisexual, elongated, with yellow and/or purple corolla. Fifty-three out of 130 wildlings survived and abundantly produced bisexual flowers in the succeeding months. The 1 mg/mL concentration of ethanolic and methanolic leaf extracts of P. grandiflorum were found to have an average haemolysis percentage of 0.32 ± 6.78 and 0.45 ± 0.65, respectively. The result of the haemolysis assay revealed that the ethanolic and methanolic leaf extract of P. grandiflorum is safe to utilize and do not pose any toxic effects to humans.
In-Silico Molecular Phylogeny of Philippine Myxomycetes using 18S rRNA and small subunit rRNA (SSU) Gene Sequences: Molecular Phylogeny of Myxomycetes using 18S rRNA and SSU Sequences in the Philippines Ong, Christian Joseph; Clemente, Richard; Alaijos, Oliver; Pascual, Lady Janine; Aguilar, Russell Neil; Desacula, Raizza
Journal of Tropical Life Science Vol. 13 No. 3 (2023)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.13.03.01

Abstract

Myxomycetes, commonly called plasmodial slime molds, are eukaryotic organisms usually thriving on terrestrial ecosystems, manifesting attributes of fungi and protists. The current taxonomy of myxomycetes poses serious problems and does not clearly reflect the evolutionary relationships of this group. The literature on myxomycetes in the Philippines has primarily focused on species identification, ecological and diversity studies. However, no attempts have been made yet to elucidate the evolutionary relationships of this class using molecular evidence. The use of 18S rRNA and small subunit rRNA (SSU) sequences in this study to construct phylogenies has revealed that certain taxa, traditionally considered monophyletic, exhibit inconsistencies that warrant further investigation. However, the molecular evidence that supports the division of myxomycetes into two distinct groupings (Lucisporidia and Columellidia) according to spore color remains consistent with the constructed phylogeny using 18S rRNA gene sequences. Therefore, the present study aims to assess Philippine myxomycetes' diversity and evolutionary relationships. In addition, the study aims to compare the conventional taxonomy and molecular phylogeny of myxomycetes species in the Philippines using two molecular barcode markers - the 18S rRNA and SSU sequences. The study demonstrated that it is not always possible for morphology to agree with molecular data. On the other hand, molecular data can be more beneficial in reconstructing phylogenies but only to a certain extent and should be further evaluated.
Nutritional Properties Evaluation of Blowfly Larvae from Fish and Chicken Wastes for Asian Sea Bass Feed Formulation Application: Nutritional Properties Evaluation of Blowfly Larvae Anuar, Nurazira; Omar, Nur Faizah Moidu; Zakaria, Zainoha; Abdul Keyon, Aemi Syazwani; Muda, Nor Wajihan; Abd. Manaf, Mohammed Suhaimee; Mahat, Naji Arafat
Journal of Tropical Life Science Vol. 13 No. 3 (2023)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.13.03.02

Abstract

This present research characterized the proximate nutrient, fatty acids and amino acids compositions of the wild third instar blowfly larvae collected from fish and chicken wastes as well as its mixture, in view of aquaculture feeding for Asian sea bass (Lates calcarifer). Analyses of crude protein, crude lipids, crude fiber, ash, carbohydrates, amino as well as fatty acids were performed. Results revealed that the larvae that fed on the mixed substrates (chicken and fish, 50:50 ratio) had significantly the highest nutritional values (51.47 ± 0.32% of crude protein, 29.4 ± 1.47% of crude fat, 4.81 ± 0.83% of crude fiber, 4.85 ± 0.01% of ash and 12.71 ± 1.67% of carbohydrate) for formulating feeds for Asian sea bass when compared with that of chicken and fish wastes alone (P < 0.05). Similarly, significantly higher percentages of fatty acids (DHA and EPA) and amino acids (Arg, Lys, Met, Trp, His, Val, Ile, Leu and Phe) were observed in the larvae from mixed-substrates when compared with that of the remaining two substrates (P < 0.05). The findings supported the utilization of blowfly larvae harvested on mixed substrate as a possible candidate of nutrients for Asian sea bass feed formulations

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