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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 986 Documents
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Genome-wide investigation and characterization of heat shock transcription factors in papaya (Carica papaya): Mining of the HSF transcription factor in papaya Le, Thi Man; Azar, Sahar; Thi Thanh Tran, Huyen; Chu, Ha Duc; Vu, Quyen Thi Xuan; Tran, Lan Thi Mai; La, Hong Viet; Le, Chi Toan; Cao, Phi Bang
Journal of Tropical Life Science Vol. 14 No. 3 (2024): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.02

Abstract

Heat shock transcription factors (Hsf-s) have been considered one of the major regulatory proteins that play important roles in various biological processes during the growth and development of plants. Unfortunately, no comprehensive studies of the Hsf family in papaya (Carica papaya), a popular tropical fruit crop, have been performed, even the papaya genome assembly has been released recently. In this study, a total of 18 members of the Hsf family, namely CpHsf-s have been identified in papaya. Based on various computational tools, a systematic characterization of the CpHsf family, such as gene structure, physic-chemical features, categorization, and protein-protein interaction, has been conducted. We found that the physic-chemical properties of the CpHsf proteins were highly variable, while all proteins were hydrophilic and localized in the nucleus. Our classification indicated that the CpHsf proteins could be categorized into three groups, including HsfA, HsfB, and HsfC, and members in the same clade share similar gene structure. According to the previous RNA-Seq datasets, our re-analysis revealed that the CpHsf genes exhibited different expressions in various major organs or tissues during fruit ripening and under the ultra-low temperature stress. Taken together, our study could provide a list of candidate genes for further functional characterization towards the improvement of stress tolerance in papaya.
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
Molecular Recognition of Polyaromatic Hydrocarbons (PAHs) by Naphthalene Dioxygenase through the Action of Rhamnolipid: PAHs Recognition by NDO with Rhamnolipid Azhary, Nabihah; Abdul Hamid, Azzmer Azzar; Mohd Ashaari, Mardiana
Journal of Tropical Life Science Vol. 14 No. 3 (2024): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.01

Abstract

Rhamnolipids are a type of glycolipid biosurfactant that has garnered significant attention in various industries, including healthcare and petroleum. Their remarkable properties, such as highly biodegradable and good emulsification, have propelled extensive research on their potential role in the biodegradation of polycyclic aromatic hydrocarbons (PAHs). While numerous empirical studies have focused on PAH biodegradation, the molecular interactions between biosurfactants and PAHs remain elusive. This study aims to provide insights into the molecular recognition of PAHs by naphthalene dioxygenase (NDO) in the presence of rhamnolipid by molecular docking and molecular dynamics (MD) simulations. The results indicated that selected PAH compounds, phenanthrene (PHE), fluoranthene (FLU), and benzo[a]pyrene (BAP), interact with NDO’s active site mostly through hydrophobic interactions. The presence of rhamnolipid changes NDO’s structural conformation, which leads to a more stable binding between PAHs and NDO, as demonstrated during simulation runs. In addition, the MD simulation analysis by using root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), solvent accessible surface area (SASA), and minimum distance parameters for the systems with rhamnolipid provided better results compared to the system without rhamnolipid, especially for NDO-BAP complex. Moreover, the number of consensuses interacting residues (Phe224, His195, Leu307) for the NDO-BAP complex with rhamnolipid presence was higher compared to without rhamnolipid (Val209, Leu253). Phe224 was identified as a consensus interacting residue for the NDO-BAP complex with rhamnolipid; assuming its important role for substrate binding when rhamnolipid is present. Hence, this study offers molecular insights into the role of biosurfactants during hydrocarbon degradation, especially for high molecular weight PAHs.
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.
Identification of Gene Candidates in Diterpenoid Biosynthesis of Curcuma longa: An mRNA Sequencing Approach: Identification of Gene Candidates in Diterpenoid Fadhullah, Hafizh; Purwoko, Devit; Zulaeha, Siti; Hanifah, Nurul Fitri; Hartuti, Endah Dwi; Rahmadara, Gemilang; Safarrida, Anna; Reninta, Rikania; Evawati, Evawati; Roza, Irwan; Tajuddin, Teuku
Journal of Tropical Life Science Vol. 14 No. 3 (2024): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.08

Abstract

Curcuma longa is a medicinal plant renowned for its therapeutic properties and potential treatment of cancer. This study focused on the biosynthesis of diterpenoids in the rhizome and leaves of C. longa. The genes responsible for producing these medicinal compounds were analyzed using BLASTx, Gene Ontology (GO) annotation, differential expression, and homology. The substantial dataset was obtained from the National Center for Biotechnology Information (NCBI), comprising 151,730,334 clean reads and 167,264 transcripts for the analysis. The results of the BLASTx analysis were as follows: NR yielded 65.93%, Swiss-Prot yielded 44.52%, and COG yielded 17.35%. Subsequently, GO annotation was performed using Blast2GO, resulting in an annotation rate of 56.79%. Differential expression analysis revealed a total of 636 genes that were significantly differentiated between the rhizome and leaves. The homology analysis resulted in 11 proteins associated with diterpenoid biosynthesis and nine proteins related to CYP450. Approximately three class I proteins were highly expressed in the rhizome. Additionally, seven CYP450 enzymes from the CYP71D and CYP726 subfamilies were identified; three were highly expressed in the rhizome. The expression patterns of these enzymes were similar to the aforementioned three class I diTPSs, indicating their potential involvement in macroditerpenoid biosynthesis in C. longa. These findings provide valuable genomic resources for future functional genomics research on C. longa, facilitating targeted efforts to enhance the production of bioactive compounds.
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.
Toxicity of Clove Oil Nanoparticle Againts (Aphis gossypii) on Chili (Capsicum annum) and Its Predator (Cheilomenes sexmaculata): Toxicity of CO-NPs againts A. gossypii and C. sexmaculata Ikawati, Silvi; Boangmanalu, Maslina; Choliq, Fery Abdul; Aji Pamungkas, Bayu
Journal of Tropical Life Science Vol. 14 No. 3 (2024): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.04

Abstract

One of the pests that cause economic losses in Chili (Capsicum annum L.) is aphid (Aphis gossypii Glover) (Hemiptera: Aphididae). Therefore, it is necessary to carry out alternative controls that are not damaging and detrimental to the surrounding environment including against beneficial organisms such as the natural enemy Cheilomenes sexmaculata Fabricius (Coleoptera: Coccinellidae). Clove oil and the formulation of essential oils in the form of nanoparticles have been used as a botanical pesticide. The purpose of this work is to determine the toxicity of a clove oil nanoformulation against aphids (A. gossypii) and the six-spotted zigzag ladybird predator C. sexmaculata. This work has six treatments and four replications using a fully randomized design. The results showed that clove oil nanoparticles (CO-NPs) significantly affected mortality and decreased the number of offspring of A. gossypii. The average size of the tested nanoparticles was 166.38 nm and the average zeta potential value of the tested nanoparticles was -19 mV. The CO-NPs can affect the increase in mortality and decrease in the offspring number of A. gossypii. The LC50 value of A. gossypii was 0.32% at the time of observation 48 hours after application while the LT50 value was 3 hours at a concentration of 1.2%. The percentage of decrease in the number of offspring reached 95.01% at a concentration of 1.2%. Results of calculating the selectivity ratio value (SR) showed that CO-NPs are selective against predators C. sexmaculata, with the SR value <1.
Monitoring the Success of Hydroseeding Application Using Microbial Diversity in Some Post-Coal Mining Revegetation Areas, South Kalimantan: Monitoring the Success of Hydroseeding Application Using Microbial Diversity Fadhil Anshari, Muhammad; Achmad Rinaldo Fernandes , Adji; Setyo Leksono, Amin; Arisoesilaningsih, Endang
Journal of Tropical Life Science Vol. 14 No. 3 (2024): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.06

Abstract

Successful revegetation improves the whole ecosystem's integrity, including microbe habitat. The goal of this study is to monitor the success of hydroseeding applications in some post-coal mining revegetation areas using microbial diversity. This study was conducted by sampling soils at a reference site (HS) and three revegetation areas (Kuni, AR07, AH). Kuni represents a 12-year-old monoculture replantation area while AR07 and AH are representations of hydroseeded areas with different ages, 5.5 years and 3 months old. Soil samples were then analyzed to determine N, P, K, and CEC, and extracted using the CTAB/SDS method, resulting in the total genome DNA. The genes of 16S rRNA were amplified using a specific primer, followed by product quantification and purification. Sequencing libraries were generated using the NEBNext® UltraTM DNA Library Pre Kit for Illumina. The library was sequenced on Illumina platform, and 250 bp paired-end reads were generated. The data were then analyzed using Anova, biplot, and cluster analysis. Results showed that AR07 was the most similar site to HS based on soil chemical properties and had the highest value of all alpha diversity indices. The dominant presence of Burkholderiales in AH indicated improvement in soil chemical properties. The soil microbial diversity PCA analysis revealed that the similarity between HS and AH was high. It was indicating a better success of hydroseeding at AH with shorter revegetation time as compared to the monoculture replantation site in Kuni. Hydroseeding using local pioneer species is highly recommended for postcoal mining revegetation.
The Ecological Character of Water-Bioindicator Macroinvertebrates on Various Agricultural Management: Ecology of Water-Bioindicators in Agriculture kurnianto, Agung sih; Septiadi, Luhur; Hamidah, Wanda; Magvira, Nur Laila; Sholikah, Ummi
Journal of Tropical Life Science Vol. 14 No. 3 (2024): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.12

Abstract

In Indonesia, horticulture is a crucial part of agriculture, heavily reliant on agrochemicals. This study in East Java's Jember and Bondowoso regencies compared conventional and organic farming methods, focusing on their effects on aquatic macroinvertebrates as bioindicators. Research included sites practicing conventional horticulture (cabbage, chili) and organic rice farming. Measurements of water current, pH, conductivity, dissolved oxygen, and temperature were taken, along with macroinvertebrate sampling. Significant differences were found in pH, conductivity, and water current, but not in dissolved oxygen and temperature. Organic farming showed higher macroinvertebrate diversity and lower dominance, especially the Baetidae family. While BMWP-ASPT and EPT scores were similar across methods, organic farming rated unpolluted in biotilik scores. Hierarchical cluster analysis, PCA, and CCA revealed factors influencing the ecological impacts of farming practices. The study underscores how different agricultural methods affect macroinvertebrate diversity, highlighting their role as environmental indicators. This reflects the diverse ecological impacts of agricultural management practices.
Allometry and condition factor of Faunus ater (Cerithioidea: Pachychilidae) from An Estuarine Habitat of Kerala, Southern India: Allometry and condition factor of Faunus ater Nair Rajendran, Akhil; Jisha, Sasidharan; Hari , Bharathan
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.14.02.17

Abstract

Faunus ater is a pachychilid gastropod known to inhabit brackish water habitats of Western Indo-Pacific countries. This study aimed to analyse the morphometric relationships and condition factor of F. ater collected from the Edava-Nadayara brackish water lake of Kerala, India.  Hydrographic parameters of sampling stations were recorded. A total of 1,522 specimens were collected every month from March 2019 to February 2020. The mean values recorded for total length, shell width, body whorl length, opercular length, opercular width, and total weight were 45.38±13.44 mm, 14.47±3.88 mm, 20.81±5.83 mm, 7.71±3.08 mm, 4.62±1.62 mm, and 6.97±3.72 g, respectively. The length-weight relation was obtained as Log W= -1.005+2.871 Log L.  The b value (<3) indicated a negative allometric growth of the organism. Regression analysis of other morphometric measurements also showed a positive correlation (P<0.001).  The analysis of Fulton’s condition factor indicated a state of well-being of F. ater in this habitat, with condition factors ranging from 5.87 to 6.99 spatially and 5.48 to 7.00 temporally.  This study provides the first detailed investigation of morphometric relationships and condition factors in F. ater.

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