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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.
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Articles 15 Documents
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Search results for , issue "Vol. 15 No. 2" : 15 Documents clear
Structural Comparison of α-agarase (α-AgaD) from Thalassomonas sp. LD5: An in-silico study: Structural Comparison of α-agarase (α-AgaD) from Thalassomonas sp. LD5 Oyewusi, Habeebat Adekilekun; Oladipo, Oluwatosin; Abdul Wahab, Roswanira; Adekilekun , Habeebulahi Ajibola; Wayan Gunam, Ida Bagus; 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/

Abstract

The significance of agarase enzymes spans various high-value industries, including food, cosmetics, and medicine. These enzymes play a crucial role in the hydrolysis of agar to produce bioactive oligosaccharides, enabling wide-ranging applications across multiple fields. Among them, α-AgaD is a novel α-agarase enzyme produced by the Thalassomonas sp. LD5 strain. However, the structural and functional characteristics of α-AgaD within biological systems remain largely unexplored. This study therefore aims to provide a comprehensive in silico analysis of α-AgaD, focusing on its physicochemical properties, phylogenetic relationships, secondary structure composition, and 3D homology modelling. A range of computational tools was employed to validate the findings and enhance the structural understanding of this newly identified α-AgaD enzyme. The α-AgaD protein consists of 1,466 amino acids with a molecular weight of 158,787.82 Da. It has a theoretical isoelectric point (pI) of 4.14, indicating an overall acidic nature. Structural analysis revealed that alpha helices and random coils are the predominant secondary structures. Hydrophobic amino acids were more abundant than hydrophilic ones, with glycine accounting for approximately 10.4% of the total residues. The protein's aliphatic index was 72.05, and the instability index was 28.28, suggesting that α-AgaD is stable and likely to maintain its structure across a wide temperature range. Three-dimensional models of α-AgaD were constructed using I-TASSER, NCBI-PDB, SWISS-MODEL, and AlphaFold2, and subsequently validated using ERRAT, Verify3D, and PROCHECK. Among the models generated, AlphaFold2 produced the most accurate prediction, with nearly all amino acid residues located in the preferred regions of the Ramachandran plot. This further confirmed the reliability and quality of the refined models. The in silico structural analysis of α-AgaD offers valuable insights into the enzyme’s primary sequence, functional domains, and overall structural architecture, enhancing our understanding of α-agarase from Thalassomonas sp. LD5.
First Report of Microalgae Associated with Velamen Aerial Roots of Epiphytic Orchids in the Philippines: Microalgae in Velamen Roots of Orchids in the Philippines Arguelles, Eldrin
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.15.02.01

Abstract

Velamen roots of epiphytic orchids are unique environment for growth and proliferation of rare and novel microalgal species.  This taxonomic study presents the first floristic survey of microalgal communities inhabiting the velamen roots of epiphytic orchids (Vanda ampullacea, Vanda denisoniana, Vanda bensonii) in the Philippines, documenting these taxa for the first time in this unique aerial habitat as new distributional records for the country. Overall, 16 species of microalgae were described taxonomically, of which four species each were identified belonging to Cyanophyceae, Bacillariophyceae, and Chlorophyceae, while two species each for Trebouxiophyceae and Zygnematophyceae. The survey reports an additional of fifteen species (Chlorella vulgaris, Mucidosphaerium pulchellum, Chlorococcum infusionum, Desmodesmus abundans, Ankistrodesmus falcatus, Pediastrum angulosum, Cosmarium formosulum, Closterium moniliferum, Cocconeis euglypta, Diatoma vulgaris, Nitzschia palea, Fragilaria vaucheriae, Chroococcus minutus, Pseudanabaena minima, and Nostoc verrucosum) as new records of microalgae associated with velamen roots of orchids found in Asia. In addition, the study documented the existence of three rare microalgae, Mucidosphaerium pulchellum (H.C. Wood) C.Bock, Proschold & Krienitz, Pediastrum angulosum Ehrenberg ex Meneghini, and Cosmarium formosulum Hoff which are taxonomically described as new records in the Philippines. The floristic survey enriches the diversity of algae from velamen roots of epiphytic orchids and provides important taxonomic and distributional records of microalgae found in terrestrial plants in the Philippines.
Genomic Characterization and Transcriptomic Profiling of Phospholipase A Superfamily in Cocoa (Theobroma cacao): Genome-wide analysis of the phospholipase A genes in cocoa Nguyen, Quy Phuong; Vu, Xuan Duong; Chu, Ngoc Thi Bich; Tran, Lan Thi Mai; Chu, Ha Duc; La, Hong Viet; Dong, Huy Gioi; Tran, Huyen Thi Thanh; Cao, Phi Bang
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/res8c250

Abstract

This study investigates the phospholipase A (PLA) superfamily in cocoa (Theobroma cacao), providing a comprehensive analysis of its genomic organization, structural diversity, and functional roles. A total of 19 PLA1 and 20 PLA2 genes were identified, with detailed assessments of their chromosomal locations, protein properties, and exon-intron structures. Phylogenetic analysis established evolutionary relationships with PLA proteins from other species, such as Arabidopsis thaliana and rice (Oryza sativa). Of our interest, transcriptomic profiling under biotic stress caused by Phytophthora megakarya infection and during embryo development revealed distinct expression patterns, demonstrating the involvement of PLA genes in stress responses and key developmental processes. Taken together, these findings provide valuable insights into the roles of PLA genes in cacao biology and offer a foundation for future applications to improve cacao’s resilience and productivity through genetic and biotechnological strategies.
Comprehensive Analysis of the Aldehyde Dehydrogenase Gene Superfamily in Cassava (Manihot esculenta): Genome-Wide Identification and Transcriptional Insights: Genome-wide analysis of the ALDH genes in cassava Tran, Vinh Thanh; Le, Man Thi; Nguyen, Anh Thi Ngoc; Dong, Huy Gioi; Le, Quynh Thi Ngoc; Cao, Phi Bang; Chu, Ha Duc
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/qc82wn93

Abstract

Aldehyde dehydrogenases (ALDHs) are a vital enzyme superfamily involved in cellular detoxification, metabolism, and stress responses in plants. Despite their known roles in various species, a comprehensive genome-wide analysis of the ALDH gene superfamily in cassava (Manihot esculenta), a key drought-tolerant crop, remains limited. This study systematically identified and characterized 29 ALDHs in the cassava genome, classifying them into distinct families based on sequence similarity and phylogenetic relationships. Structural and physicochemical analysis revealed notable variations in gene length, exon-intron organization, and protein properties, indicating functional diversity within the family. Of our interest, expression profiling across 11 different organs/tissues showed that several ALDHs exhibit tissue-specific expression patterns, suggesting their potential roles in diverse physiological processes. Moreover, transcriptomic analysis under drought stress conditions revealed significant changes in ALDH gene expression, with specific members being strongly up-regulated and down-regulated, implying their involvement in drought tolerance mechanisms. The findings provide new insights into the potential roles of ALDHs in cassava's ability to mitigate oxidative stress and enhance drought resilience. This study serves as a foundation for further functional characterization of ALDHs and offers valuable genetic resources for breeding programs aimed at improving cassava’s adaptation to environmental stresses. Understanding these genetic mechanisms will contribute to developing stress-resistant cultivars, ensuring sustainable cassava production in drought-prone regions.
Population Density and Habitat Preferences of the Rinjani Scops Owl (Otus jolandae) in the Mandalika Special Economic Zone, Lombok, Indonesia: Population density and habitat preference of Otus jolandae Permatasari, Baiq Dewi; Suana, I Wayan; Hadiprayitno, Gito; Tresnani, Galuh
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/e0jyvz11

Abstract

The Rinjani Scops Owl (Otus jolandae) is an endemic species of Lombok, closely associated with Mount Rinjani National Park. In 2023, its range was newly recorded in the Mandalika Special Economic Zone (SEZ), extending its known distribution. Understanding the population density and habitat preferences of this bird is crucial for effective management and conservation. From April to June 2024, a study was conducted in Mandalika SEZ, covering an area of 1,175 hectares. The point count method was used to record individuals based on sightings and calls. Vegetation analysis was performed at observation sites to identify preferred tree species and calculate habitat preferences using the selection index. Twenty-three individuals of O. jolandae were observed across seven sites, with a population density of 0.02 individuals per hectare—lower than densities recorded in Mount Rinjani National Park—which reflects the significant ecological pressures from development activities. The habitat includes 21 tree species, but the owl actively uses only 14 for activities such as perching, roosting, and nesting. Samanea saman had the highest preference index (3.424), making it the most favored tree, followed by Gmelina arborea and Nauclea orientalis. The species relies heavily on large-diameter trees and the middle canopy layer, reflecting its need for stable and protective habitats. This study provides essential data for future conservation programs and highlights the Mandalika SEZ’s potential as a birdwatching ecotourism destination featuring this unique endemic species
Design, Construction and Expression of Spike Highly Conserved Region (HCR) SARS-CoV-2 and Cholera Toxin Subunit B Fusion Protein in Lactococcus lactis NZ3900: Construction of recombinant plasmid in Lactococcus lactis Kesuma, Suryanata; Adianingsih, Oktavia Rahayu; Winarsih, Sri; Widodo, Nashi; Yurina, Valentina
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: 10.11594/2xf1qp96

Abstract

Prevention of SARS-CoV-2 transmission has primarily been achieved through vaccination, which is generally administered via injection and may cause discomfort. No commercially available SARS-CoV-2 vaccines can be administered via the mucosal route. However, recent advancements have demonstrated that vaccination with Lactococcus lactis enables vaccine delivery through the mucosa. A promising target for SARS-CoV-2 vaccine materials is the highly conserved region (HCR) of the SARS-CoV-2 spike (SARS-CoV-2 HCR Spike). Vaccine efficacy is enhanced by adding Cholera Toxin Subunit B (CTB) as an adjuvant. HCR and CTB proteins were recombinantly fused using a synthetic gene with optimized codons. This study aimed to construct a fusion protein of the SARS-CoV-2 spike protein and CTB in L. lactis strain NZ3900. The construction and expression of fusion proteins were analyzed using sequencing and protein electrophoresis. Codon optimization resulted in a Codon Adaptation Index value of 0.93 and a GC content of 27.06%. The cloning results revealed the formation of L. lactis colonies expressing the Fusion protein of the SARS-CoV-2 HCR Spike and CTB, which formed yellow colonies on the selection Elicker medium. PCR and sequencing confirmed the presence of the hcr-ctb gene, with a length of 981 bp and 100% sequence similarity. The Fusion protein of the SARS-CoV-2 HCR Spike and CTB was successfully expressed with a molecular weight of >35 kDa. In conclusion, we successfully constructed a Fusion protein of the SARS-CoV-2 HCR Spike and CTB in L. lactis NZ3900 as a potential vaccine candidate for oral administration to prevent SARS-CoV-2 infection.
The Ecophysiology of Guppy Fish (Poecilia reticulata) in the Pucung River, A Former Fossil Excavation Site: The ecophysiology of guppy fish in the Pucung river Beanal, Yohanis; Nugroho, Rully Adi
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/bvykkg34

Abstract

Exposing land surfaces through fossil excavation activities can increase sediment loads and toxic chemicals that are discharged into water bodies. This can have negative effects on receiving environments and their habitats. The aim of this study was to evaluate the dry body weight and physiology (whole body lipid and protein contents) of guppy fish (Poecilia reticulata) in Pucung River, a former archaeological excavation site in Sangiran, Indonesia. Little is known about their physiology in this river. Guppy fish and water were sampled from eight sites along the Pucung River, two sites (Site 1 and Site 2) were situated upstream of the archeological excavation site, one site (Site 3) was at the archeological excavation site, and five sites (Site 4 - Site 8) were situated downstream of the archeological excavation site. The distance between the two sites was 500 m. The length and total weight of captured male fish were measured. Lipid and protein contents of male fish were determined gravimetrically, and the results were conveyed as Joules. A total of 240 male individuals were captured with a length between 1.24 and 3.95 cm. The weight of male guppies varied between 13.0 and 38.2 mg. Male guppies' average lipid and protein contents ranged from 0.0509 J to 0.2635 J and 0.0842 J to 0.1648 J, respectively. The smallest weights and lipid contents among individuals were found in the excavation site (Site 3) and a site downstream (Site 4). These individuals also had the smallest protein contents, along with those from Site 5 to Site 7. Fish dry weight and lipid content were positively correlated with water pH and dissolved oxygen, and negatively correlated with biological oxygen demand. These findings showed that guppy dry weight and lipid content may be utilized to assess the impact of human activities on river health.
Evaluation of Jackfruit Peel Extract as a Low-Cost Medium for Spirulina platensis Culture: Evaluation of Jackfruit Peel Extract for Spirulina Platensis Culture Hossain, Md. Amzad; Fahmida Jahan Riya; Das, Mousumi; Fouzia Sultana Bristy; Taslima Akter; Md. Shah Alam Sarker
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/xq937835

Abstract

Spirulina platensis is a nutrient-rich blue-green alga, ideal for use as a human food and an animal feed supplement. The Kosaric medium (KM) provides optimal biomass production for Spirulina sp.; however, it is expensive and inaccessible. This study evaluated the potential of jackfruit peel powder extract (JPE) as a low-cost source of nutrients for S. platensis cultivation. The production performance of S. platensis was evaluated for 24 days in four concentrations of JPE medium (2.5, 5, 7.5, and 10%), each supplemented with 3.0 g/l NaHCO₃ and 1.25 g/l NaNO₃. Cultivation of S. platensis with KM served as the control. Maximum cell biomass (48.27 ± 0.36 mg/l), optical density (1.51 ± 0.02), specific growth rate (0.60 ± 0.02 μg/day), chlorophyll a (5.14 ± 0.03 μg/ml), chlorophyll b (3.95 ± 0.04 μg/ml), and β-Carotene (2.58 ± 0.05 μg/ml) of S. platensis were observed in KM (control) at the 20th days of culture. Similar results were obtained at 2.5% JPE medium (cell biomass: 47.47 ± 0.49 mg/l; optical density 1.49 ± 0.02, specific growth rate: 0.58 ± 0.02 μg/day; chlorophyll a 5.09 ± 0.04 μg/ml; chlorophyll b 3.93 ± 0.04 μg/ml, β-carotene 2.55 ± 0.05 μg/ml). All the growth parameters tend to decrease gradually with the further increase in concentration of the JPE medium. JPE medium of 2.5% supplemented with NaHCO3 and NaNO3 produced comparable growth and pigment content of S. platensis to KM, suggesting its potential as a cost-effective alternative culture medium for S. platensis.
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.

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