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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 32 Documents
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Search results for , issue "Vol. 14 No. 3 (2024)" : 32 Documents clear
Possible Role of Akt in Mossy Fiber Sprouting: Akt Activity and CA3 Mossy Fiber Sprouting in a Kainate Model of Epilepsy: Akt Activity and CA3 Mossy Fiber Sprouting in Epilepsy husna, Machlusil; Handono, Kusworini; Sujuti, Hidayat; Aulanni'am, Aulanni'am
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.14.03.09

Abstract

The most prevalent pathological phenomenon observed in patients with epilepsy is hippocampal mossy fiber sprouting (MFS), which is thought to be associated with epileptic progression, such as worsening seizure control, cognitive function, and behavior. MFS is discovered in the dentate gyrus and the hippocampal Cornu Ammon 3 (CA3) area. The CA3 area is involved in memory, so disturbances in that area can affect memory impairment in patients with epilepsy. The mammalian target of rapamycin complex-1 (mTORC1) is also associated with MFS. Akt is an upstream activator of mTORC1 and a downstream target of mammalian target of rapamycin complex-2 (mTORC2) and plays a role in cytoskeleton organization. We analyzed Akt activity and MFS in the CA3 zone in an in vitro model of kainate-induced epilepsy. We divided organotypic hippocampal slice cultures (OHSCs) into a kainate (epilepsy) group and a control (untreated) group. On the 10th day in vitro (DIV), the kainate group was exposed to 8 µM kainic acid for 48 h, diluted in the medium. At 32 DIV, we measured Akt activity through western blotting and CA3 MFS through synaptoporin fluorescence intensity observed using confocal laser scanning microscopy. We found that Akt activity increased significantly (p = 0.000) in the kainate group, and the synaptoporin fluorescence intensity also increased in the stratum oriens of the CA3 area (p = 0.049) in the kainate group. Our findings implied that Akt may play a role in MFS development. Because Akt is a main downstream target of mTORC2, mTORC2 may also be involved in MFS development. Further research is required to clarify these findings.
Expression of TAD1 (Tillering & Dwarf1) Gene in Hawara Bunar and IR64 Rice Cultivars: Expression of TAD1 (Tillering & Dwarf1) Gene in Hawara Bunar and IR64 Sindiya, Vita; Fendiyanto, Miftahul Huda; Hamim, Hamim; Miftahudin , Miftahudin
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.14.03.11

Abstract

Rice cv. Hawara Bunar is a local rice cultivar tolerant to aluminum (Al) and drought stress. However, the cultivar has inferior characteristics, such as a tall habitus and a small number of tillers, making the cultivar agronomically unattractive. Many genes control plant height and tiller number; one is the TAD1 gene. Analysis of gene expression in two contrasting rice cultivars for both characters is a prerequisite for selecting certain genes for gene editing targets. This study aimed to analyze the gene expression of the TAD1 in rice cv. IR64 and Hawara Bunar, and to construct a phylogenetic tree of genes that regulate rice plant height and tiller number. Gene expression analysis was conducted using the qRT-PCR technique, while the phylogenetic tree was constructed based on the Neighbor-Joining method using PAUP4 software. The results showed TAD1 gene expression in the tillering phase of rice cv. Hawara Bunar is higher than the cv. IR64. The gene expression level in both cultivars corresponds to the plant height and tiller number characters in both rice cultivars. Phylogenetic analysis showed that the TAD1 gene clustered with genes that cause the rice to have a tall habitus with few tillers. The results of a transcriptome meta-analysis reinforced the phylogenetic tree, which shows that the TAD1 gene was found in a group of downregulated genes based on the volcano plots. Therefore, the TAD1 gene can be selected as a target gene for editing in rice cv. Hawara Bunar to obtain superior characters.
Design of Epitope-Based Vaccine Against SARS-CoV-2: An Immuno-Informatics Study: Epitope-Based Vaccine Against SARS-CoV-2 Kusuma, Kavana Hafil; Widyananda, Muhammad Hermawan; Nafisah, Wirdatun; Grahadi, Rahmat; Christina, Yuyun Ika; Dwijayanti, Dinia Rizqi; Mustikaningtyas, Dewi; Widodo, Nashi; Djati, Muhammad Sasmito
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.14.03.07

Abstract

This study aimed to develop an epitope-based vaccine of SARS-CoV-2 S protein through an immuno-informatics study. The whole genome of SARS-CoV-2 sequences was obtained from the GISAID database and then trimmed to obtain the S protein sequences. The alignment was done by Clustal-W of MEGA software. Epitope prediction and modeling were performed by Discotope BepiPred and the PepFold3 web server. The allergic responses and physicochemical characteristics of predicted epitopes were analyzed using the AlgPred and ProtParam from ExPASy. Molecular docking and dynamic stimulation were performed using AutoDock Vina and YASARA. Biovia Discovery Studio 2019 was used to visualize the molecular docking results. The study predicted 3 potential epitopes, including ‘GDEVRQIAPGQTGKIADYNYKLP’ (epitope 1), ‘YTMSLGAENSVAYSNN’ (epitope 2), and ‘VNNSYECDIPI’ (epitope 3) located in the spike head specifically RBD region. The epitopes did not show an allergen reaction based on IgE epitope mapping. The suitable overexpression for the host of epitopes was mammalian cells. Only epitopes 1 and 2 were stable (instability index above 40). Epitopes 1, 2, and 3 interacted with BCR with binding affinity values -6.6, -7.8, and -7.5 kcal/mol. Epitope 2 wasere stable when interacting with the BCR. Therefore, three epitopes were predicted to have high potency as the SARS-CoV-2 epitope-based vaccine.
The Attenuated Effects of Topical Empagliflozin on Imiquimod-induced Model of Psoriasis in Mice: The attenuated effects of Topical Empagliflozin on Imiquimod-induced Model of Psoriasis in Mice Abbas , Alaa H.; Abbas, Zahraa H; Salman, Hayder Ridha; Jabar, Hayder E; H. Abd, Abdulkareem
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.14.03.03

Abstract

Empagliflozin is a sodium-glucose cotransporter inhibitor (SGLT2) that drops blood glucose levels by inhibiting glucose reabsorption and encouraging glucose excretion. Other benefits of empagliflozin include cardiovascular protection, lowering uric acid levels, and reducing liver damage brought on by non-alcoholic fatty liver disease (NAFLD). to investigate the possible influence of two different concentrations of empagliflozin gel on psoriasis induced via imiquimod in mice. dividing 40 mice into five groups (8 mice for each group). All groups gated imiquimod to induce psoriasis (except group I) for seven days. The induction group (Group II) received imiquimod cream for seven days. The rest of the groups gated Clobetasol propionate cream 0.05%, empagliflozin 1% gel, and empagliflozin 3% gel, respectively, once daily for seven days after seven days of induction by imiquimod. The outcomes exhibited that topical empagliflozin had important anti-psoriatic activity by diminishing the Psoriasis Area Severity Index (PASI) score and improving histological alterations during imiquimod application; moreover, it elevated anti-inflammatory biomarker IL-37 and lowered inflammatory biomarkers TNF-α and IL-17. Empagliflozin has substantial anti-psoriatic action against imiquimod-induced psoriasis through its anti-proliferative and anti-inflammatory effects. Also, empagliflozin has a restorative effect on the histopathological alterations of mice's skin induced by imiquimod
Green Synthesis of Silver Nanoparticles using the Algae: Green Synthesis of Silver Nanoparticles using the Algae Ali, Doaa Oday; Ali, Liqaa Oday; Ali, Samara Oday
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.14.03.10

Abstract

Green methods of nanoparticle production have gained prominence due to their environmental and safety advantages. As reducing agents, these techniques employ biological substances, including bacteria, fungi, algae, and plants. In this study, the algae Chara vulgaris was used for the biosynthesis of silver nanoparticles as an environmentally friendly method. The synthesized nanoparticles were characterized using UV, FTIR, SEM, atomic absorption spectrometry, and zeta analysis. These nanoparticles have potential environmental applications in water treatment, especially in the removal of heavy metals such as cadmium, lead, and nickel at different concentrations (1, 3, 5, 7, and 9 ppm) over 12 and 24 hours. The results showed that lead had the highest removal rate of 99.5% for a concentration of 3 ppm at 24 hours. Cadmium showed the highest removal rate of 100% at 3 and 5 ppm concentrations at 24 h, and nickel recorded a removal rate of 83.2% for 1 ppm concentration at 24 h. This study highlights a low-cost, effective, and safer biological method with promising results in removing heavy metals from water.
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.
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.
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.
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.

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