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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 986 Documents
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Could Road Structures Impact the Avian Community? A Study Case from the South Coast Remained Forest in Malang Region, East Java Province, Indonesia: Impact of Road Structures on Avian Community Nurrofik, Agus; Hakim, Luchman; Septiadi, Luhur; Kurniawan, Nia
Journal of Tropical Life Science Vol. 14 No. 2 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.02.10

Abstract

The remaining tropical forest on the south coast of the Malang region is one of the secluded areas that served as an important habitat for its biodiversity, particularly for avians. Nevertheless, the presence of the road structure that crosses over the forest might impact avian communities, which needs to be investigated. The avian survey was conducted to investigate the diversity, community profiles, abundance, and feeding guild based on two different ecosystem patches (on the roads versus outside the road structures) during January–April 2022. The audiovisual encounter methods were performed during the surveys on a total of ten sampling points. Avian species were identified using field guides where the conservation status was based on the national regulation (P106 KLHK), CITES, and IUCN Redlist. The comparison through the avian community based on species richness was analyzed using Venn Diagrams and predicted using rarefaction and interpolation curves on INEXT packages. Additionally, the comparison of sizes of avian abundance was investigated using the α-diversity parameter index, and the feeding guild was determined by five diet guilds. In total, 2536 individuals from 67 species, 34 families, and 13 orders were found during the survey. The avian communities were richer outside the road structure, but their abundance qualitatively reveals that both different ecosystem patches showed relatively good condition. Overall, road structures generate both positive (unique habitat patches) and negative (physical barriers that could disrupt natural ecological processes) impacts on avian diversity. In light of these, sustainable management and conservation action plans were urgently needed to prevent the negative effects on avian communities posed by the road structure.
Different Mangrove Rehabilitation Statuses Effects to Benthic Bacterial Structure Community in the Northern Area of Java Island: Mangrove Rehabilitation to Benthic Bacterial in the Northern Area of Java Island Vidayanti, Viky; Retnaningdyah, Catur; Mustafa, Irfan; Oktaviani, Indah
Journal of Tropical Life Science Vol. 14 No. 2 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.02.15

Abstract

The study proposed identifying the changes in bacterial community and diversity and exploring the potential correlations among sediments parameters and benthic bacterial communities under different mangrove ecosystems rehabilitation statuses. There were three sites: 1. Banyuurip Mangrove Center (BMC) as a restoration site; 2. Pulau Lusi (PL) as a degraded site; and 3. Kampung Blekok (KB) as natural site. The physicochemical parameters and benthic bacteria from the mangrove sediment of the three locations were observed. The data were analyzed statistically to determine the sites' variation and the correlation between parameters. The results found that the physicochemical parameters among restoration sites varied. Soil organic matter (SOM) in natural and restoration sites was significantly higher than in degraded sites. Cation exchange capacity (CEC), calcium and potassium ions, and soil conductivity of the restoration site were considerably higher than the other sites. According to diversity indices and taxa richness, benthic bacteria in the restoration were the most diverse. Proteobacteria dominated in natural and restoration sites; meanwhile, Firmicutes dominated in degraded site. Sulfurovum aggregans was found abundant in natural and restoration sites; meanwhile, Mesobacillus subterraneus was the dominant species in the degraded site. Furthermore, the bacterial taxa richness was positively correlated with SOM and the bacterial diversity was correlated with CEC and conductivity.
In silico Characterization of Poly (ethylene) Terephthalate (PET): Degrading Enzymes from Rhizobacter sp. for Enzymatic Degradation Mechanisms: Characterization of Rhizobacter sp. PET Hydrolases Damuri, Nur Wahida; Mohd Rozdhi, Amira Azawani; Tirmizhi Abubakar, Munkaila; Wayan Gunam, Ida Bagus; Huyop, Fahrul; Oyewusi, Habeebat Adekilekun
Journal of Tropical Life Science Vol. 15 No. 1 (2025)
Publisher : Journal of Tropical Life Science

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

Abstract

Dienelactone hydrolase (DHL) from Rhizobacter sp. is an enzyme from the β‐ketoadipate pathway that belongs to the α/β hydrolase family. It involves the conversion of chloroaromatics, such as nitrophenols and hydrocarbons, into harmless metabolites. The sequence-based analysis of Dienelactone hydrolase from Rhizobacter sp. shows significant homology to the extensively studied polyethylene terephthalate hydrolase of Ideonella sakaiensis (IsPETase). IsPETase can degrade the polymer, polyethylene terephthalate (PET), at room temperature. It was chosen as a template for dienelactone hydrolase from Rhizobacter sp. that was studied as a putative PET hydrolase. This study employs bioinformatics tools such as Expasy Protparam, Clustal Omega, SWISS-MODEL, GROMACS and Autodock vina to analyse the amino acid sequence of this enzyme, predict its three-dimensional structure and study its binding interaction. The structure of the putative PET hydrolase has been determined with 0.9 GMQE value and an overall quality factor of 96%. The residues responsible in substrate binding interactions are Leu88, Ser160 and Trp185. Thus, this in silico analysis depicts the ability of the putative PET hydrolase to bind to the polymer polyethylene terephthalate.
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 (2025): In Press
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.
Synthesis of Nanoflowers using Garcinia gummi-gutta Leaf Extract via Green Route for Enhanced Antifungal and Anti-cancerous Activities: Silver Nanoflowers with Biological Applications Theresa Kurian, Jissa; Kadanthottu Sebastian, Joseph
Journal of Tropical Life Science Vol. 14 No. 2 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.02.05

Abstract

Due to its envisaged relevance in nanomedicine and materials research, the bio-engineering of nanoparticles (NPs) is becoming progressively more promising. Compared to physical and chemical processes, green synthesis produces NPs that are less hazardous to the environment. The usage of phytochemicals in Garcinia gummi-gutta (L.) leaf extract (GGL) in the bio-reduction of GGL-Ag NPs with potential antifungal and anti-cancerous activities was the main focus of the current study. UV-vis spectrophotometry at 442 nm verified the synthesized GGL-Ag NPs. The average diameters of the synthesized GGL-Ag NPs were determined by scanning electron microscopy (SEM and zeta-sizer studies to be 166.69 nm and 148.2 nm, respectively. Energy dispersive X-ray spectroscopy (EDS) and X-ray diffraction (XRD) examinations of the GGL-Ag NPs confirmed the crystalline nature and the elemental constitution of the NPs. Additionally, the synthesized GGL-Ag NPs' FTIR spectra demonstrated the presence of Phyto components acting as capping agents. Zeta potential measurements (-26.2± 4.13 mV) authenticated the stability of the synthesized GGL-Ag NPs. Antimicrobial activity testing of the GGL-Ag NPs demonstrated considerable suppression against Candida tropicalis and Candida albicans at a dose of 100 µg/ml and 60 µg/ml. Additionally, the synthesized GGL-Ag NPs have demonstrated considerable cytotoxic effects on the Hep-G2 cell line. The current study results show that GGL- Ag NPs may be produced at a low cost and with minimal environmental impact for nanobiotechnology and biomedicine usage.
Antioxidant Activity of Baby Java Citrus Peel Extract Promotes Lung Tissue Repair in Mice Challenged by Lipopolysaccharides: Antioxidant Activity of BJE Promotes Lung Tissue Repair Rachmawati, Farida; Sari, Fikriya Novita; Sakti, Sefihara Paramitha; Sakti, Muhammad Wisam Wira; Rahayu, Sri; Soewondo, Aris; Rifa'i, Muhaimin
Journal of Tropical Life Science Vol. 14 No. 2 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.02.03

Abstract

Acute lung injury tends to be induced by infection or sepsis that disrupt alveolar and vascular permeability, neutrophil influx, and edema. Those impairments are worsened by the increase of oxidative stress along with hyperinflammation response. Oxidative stress in lung tissue could be indicated by malondialdehyde (MDA) and nuclear factor erythroid 2-related factor 2 (Nrf2) expression. This research aimed to evaluate the efficacy of Baby Java citrus peel extract (BJE) in suppressing oxidative stress and preventing lung injury in lipopolysaccharides (LPS)-induced mice. Twenty-five male BALB/c mice were divided into five groups consisting of untreated (N), LPS (A), and LPS-induced followed by treatment using BJE at various doses: 75 mg/kg BW (BJE-1), 105 mg/kg BW (BJE-2), and 150 mg/kg BW (BJE-3). Lungs were isolated for histopathological analysis also detection of MDA and Nrf2 using flow cytometry. BJE at the dose of 105 mg/kg BW could inhibit the alteration of lung histology following LPS challenge including alveolar and interstitial neutrophil infiltration, proteinaceous debris, and septal thickening. The same dose also showed good potency in suppressing MDA and Nrf2 levels as oxidative stress indicators. Our findings demonstrated protective effects of Baby Java citrus peel in acute lung injury and oxidative stress prevention after LPS exposure.
Cytotoxic of Usnic Acid Isolated from Ramalina sp.: Cytotoxic of Usnic Acid Isolated from Ramalina sp. Darmawan, Akhmad; Maulidiyah; Megawati; Ariani, Novita; Aisya, Sitti; Sukirno; Randy, Ahmad; Primahana, Gian; Hendra, Medi; Nurdin, Muhammad
Journal of Tropical Life Science Vol. 14 No. 2 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.02.14

Abstract

Ramalina sp. (Ramalinaceae) is a type of lichen known to contain many active secondary metabolite compounds that have the potential to be used as medicine or medicinal raw materials. One of the biological activities possessed by Ramalina sp. lichen is its anticancer activity. This research aims to isolate and identify active secondary metabolite compounds from the methanol extract of the Ramalina sp. lichen and to find out the cytotoxic activity of the isolated compound against MCF7 breast cancer cells. Compound 1 (usnic acid) was successfully isolated from fraction A. The isolation and purification process was carried out starting with a maceration process using acetone solvent, followed by silica gel column chromatography using a gradient solvent system consisting of n-hexane, n-hexane:EtOAc, EtOAc, EtOAc:MeOH, and MeOH with 5% increment of polarity to obtain 17 fractions (F-1 to F-17). From the 17 fractions obtained, fraction 3 (F-3) and fraction 4 (F-4) (eluted with n-hexane:EtOAc 30%), which had the same TLC profile, were combined and named as fraction A. Compound 1 (50 mg) is a yellow needle crystal that was formed in a bottle of fraction A, which was obtained after the process of combining fractions F-3 and F-4 and solvent evaporation process. The crystals were then separated and purified with CHCl3 and MeOH. Compound 1 was then characterized based on spectroscopic data. Various spectroscopic analysis data, including FTIR, 1D- and 2D-NMR, and LC-ESI-MS, show that Compound 1 is a dibenzofuran derivative compound with 18 carbons (3 from carbonyl groups (C=O) and 3 from methyl groups) and 2 hydroxyl (-OH). Cytotoxicity assay showed that at a low concentration of 18.75 ug/mL, Compound 1 caused a 67.06% decrease in MCF7 viability
Unlocking the Mysteries of Reproduction: Exploring Fecundity and Gonadosomatic Index in the Enigmatic Bornean Pygmy Halfbeak, Dermogenys colletei (Meisner, 2001) (Beloniformes: Zenarchopteridae): Breeding Biology of Bornean Pygmy Halfbeak Latif, Kamil; Abit, Lirong Yu; Al-Asif, Abdulla-; Pengarah, Leonard Umban
Journal of Tropical Life Science Vol. 14 No. 2 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.02.06

Abstract

The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
Three-Dimensional Structure of Human Epididymis Protein 4 (HE4): A Protein Modelling of an Ovarian Cancer Biomarker Through In Silico Approach: HE4 Protein Structure Modelling and Validation Abdul Rashid, Nur Nadiah; Mohd Nasir, Mohd Hamzah; Hamzah, Nurasyikin; Ismail, Che Muhammad Khairul Hisyam; Nor Hishamuddin, Siti Aishah Sufira; Mohamed Suffian, Izzat Fahimuddin; Abdul Hamid, Azzmer Azzar
Journal of Tropical Life Science Vol. 14 No. 2 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.02.13

Abstract

The Human Epididymis Protein 4 (HE4) biomarker has been extensively investigated for its potential in diagnosing ovarian cancer (OC). For the application of diagnostic techniques and drug delivery, it is crucial to understand the protein tertiary structure. However, the Protein Data Bank (PDB) does not currently contain the three-dimensional (3D) structure of HE4. Therefore, an in silico analysis was conducted to model the HE4 protein using AlphaFold, I-TASSER, and Robetta servers, with the sequence retrieved from UniProt (ID: Q14508). These three servers employed deep learning algorithms, threading templates, and de novo methods, respectively. Subsequently, Molecular Dynamics (MD) simulation using the GROMACS software package improved each 3D structure model, resulting in optimised and refined structures: RF1, RF2, and RF3. PROCHECK and ERRAT programmes were employed to assess the structure quality. The Ramachandran plots from PROCHECK indicated that 100% of residues were within the allowed regions for all servers except for I-TASSER. For the refined structures, RF1 and RF3, all residues were concentrated within the allowed regions. According to the ERRAT programme, the RF1 model exhibited the highest overall quality factor of 97.701, followed by RF3 and AlphaFold models with scores of 94.643 and 93.750, respectively. After these validations, RF1 emerged as the most accurately predicted 3D structure of HE4 and has one tunnel identified by CAVER 3.0 tool that facilitates the transportation of small particles to the active site, supported by FTsite and PrankWeb binding site predictions. This model holds potential for various computational studies, including the development of OC diagnostic kits. It will enhance our comprehension of the interactions between the protein and other biomolecules.
Improvement of Home Garden Diversity and Structure by SRFG Program to Support Food Security in Pacitan Regency, Indonesia: SRFG Program to Support Food Security in Pacitan Regency, Indonesia Wijayanti, Titik; Endang Arisoesilaningsih; Yayuk Yuliati; Amin Setyo Leksono
Journal of Tropical Life Science Vol. 15 No. 1 (2025)
Publisher : Journal of Tropical Life Science

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

Abstract

The research aimed to analyze the contribution of diversity and vegetation structure of the Sustainable Reserve Food Garden (SRFG) Program in Pacitan Regency to support food security. The sampling was carried out using a purposive random sampling on 315 respondents, who were active members of the SRFG Program. Information on the condition of the SRFG home garden was obtained through interviews and questionnaires administered directly to each respondent. The SRFG home gardens were clustered into eight based on vegetation density using multivariate clustering K-Means. Spatial variations in diversity were analyzed using descriptive statistics, density of each vegetation, Shannon-Wiener index diversity, and polynomial model regression analysis using Software PAST 4.13. The research results show that clusters 1-3 had the highest density of trees (302 individuals/ha), of shrubs (11 individuals/ m2), and of herbs (46 individuals/100 m2), with a medium level of diversity (H’ trees 2.09; H’ shrubs 1.91; H’ herbs 1.88). Meanwhile, cluster 2 excelled in herbs density, with the same level of diversity. A low level of diversity (H’ 0.8) was only found in cluster 8 in that of trees. Additionally, the questionnaire results show that the impacts of food availability, food access, food utilization and nutritional health on cluster 1-3 were better than those on cluster 4-8. This is shown on a Likert’s Scale (1-4), where the means of cluster 1-3 were 3.12 in food availability, 3.74 in food access, 3.35 in food utilization and 3.65 in nutritional health. Meanwhile, cluster 4-8 indicated food availability (3.03), food access (3.69), food utilization (3.22) and nutritional health (3.52). The results implies that improving home garden diversity and structure by the SRFG program in Pacitan Regency supports food security.

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