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INDONESIA
Journal of Tropical Biodiversity and Biotechnology
Published by Universitas Gadjah Mada
ISSN : 25409573     EISSN : 25409581     DOI : -
Core Subject : Science, Agriculture, Social,
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Environmental Science Immunology & microbiology
Journal of Tropical Biodiversity and Biotechnology (JTBB) is an authoritative source of information concerned with the advancement of tropical biology studies in the Southeast Asia Region. It publishes original scientific work related to a diverse range of fields in tropical biodiversity, functional biology, and biotechnology.
Arjuna Subject : -
Articles 20 Documents
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Search results for , issue "Vol 8, No 2 (2023): August" : 20 Documents clear
Diversity and Community Structure of Dragonflies (Odonata) in Various Types of Habitat at Lakarsantri District, Surabaya, Indonesia Muhamad Azmi Dwi Susanto; Nirmala Fitria Firdhausi; Saiful Bahri
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 2 (2023): August
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.76690

Abstract

Dragonflies are insects that are very dependent on the existence of freshwater ecosystems, However, the population of dragonflies in urban freshwater ecosystems is at risk due to a number of issues. Consequently, it is essential to carry out research and efforts to preserve dragonflies in urban areas. This study aims to provide information about the diversity and structure of dragonfly communities in various habitat types in the Lakarsantri, Surabaya. Data collection in this study was carried out in the habitat types of ponds, reservoir, river, and rice field in July to September 2021. The study results show there are 22 species from 4 families with a total of 827 individuals. Analysis of the Shannon-Wiener diversity index showed that the highest value of dragonfly diversity was found in a pond, with a value of H' = 2.40, and the location with the lowest value was a river, with a value of H' = 1.77. At four research locations that have different aquatic ecosystems, the community structure of dragonfly is also different. The composition of the dragonfly community structure at the reservoir location has similarities to a pond, and at a river location, it has similarities to a paddy field. Differences in abiotic factors consisting of light intensity, humidity, and temperature at each study location have a correlation with differences in dragonfly community structure. In addition, the composition of the vegetation at each location is also one of the factors causing differences in the structure of the dragonfly community. 
In Silico and Validation Approaches for Optimum Conditions of Rattus norvegicus Target Gene qPCR Primers Gracia Alice Victoria Pollo; Nyoman Yudi Antara; Firman Alamsyah; Rarastoeti Pratiwi
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 2 (2023): August
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.71765

Abstract

The qPCR method requires an oligonucleotide pair to prime the amplification process. With the variety of qPCR reagent and primer options available, in silico and laboratory experimental validation approach was needed to validate the most suitable primer for prior use. This article aims to provide in silico analysis of actin alpha-2 smooth muscle (Acta2), fibroblast activation protein (Fap), hypoxanthine phosphoribosyltransferase-1 (Hprt1), platelet-derived growth factor subunit B (Pdgfb), phosphoinositide-3-kinase regulatory subunit-1 (Pik3r1), and vascular cell adhesion molecule-1 (Vcam1) qPCR primer with qPCR and electrophoresis validation. The procedure used in this approach was in silico analysis of primer from published articles and newly designed primer. The analysis was done with Primer-BLAST for gene specificity, Primer-Dimer, OligoCalc for hairpin formation, BLAST Nucleotide for identical sequence screening, and Clustal Omega for product length validation. Experimental validation was done using qPCR for optimal annealing temperature, priming ability, and amplificon specificity, and electrophoresis for product length validation. This assessment resulted in in silico and laboratory experimental validation of Acta2, Fap, Hprt1, Pdgfb, Pik3r1, and Vcam1 primer pairs producing suitable amplicon for qPCR using Rattus norvegicus cDNA with SYBR annealing temperature range of 60-65°C with three mM MgCl2. The primer pair can be used for further qPCR analysis under similar conditions and the procedure stated can be used as starting point for qPCR Primer preparation.
Essential Oils of Etlingera acanthodes A.D. Poulsen, An Endemic Ginger from Sulawesi Island Hurria Hurria; Anggra Alfian; Muhammad Fajri Ramadhan Muslim Saleh; Heder Djamaludin; Murni Mursyid; Witno Witno; Asri Subkhan Mahulette
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 2 (2023): August
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.72117

Abstract

Etlingera acanthodes A.D. Poulsen is a ginger endemic to Sulawesi, and there is no research on its essential oils. The Essential oil information of E. acanthodes is the first reported and has a high novelty. The objective of the study is to analyze the component of E. acanthodes essential oils, which are endemic to Sulawesi. The essential oils obtained by hydrodistillation of the leaves, stems, flowers, and rhizomes of E. acanthodes A.D. Poulsen. The samples were analyzed by GC-MS method using the Agilent Technologies 7890 Gas Chromatograph with Auto Sampler. Data analysis of essential oils of GC-MS results were determined based on comparing mass spectra from the NIST 2005 v.2.0 library and Wiley 7 library 2003. The oils of E. acanthodes contain terpenoids, phenolic, steroids, and other compounds. Phenolic compounds (39.56%) predominate in leaves, other compounds (41.25%) on stems, diterpenes hydrocarbons (77.3%) in flowers, and other compounds (43.5%) and steroids (40.4%) on rhizomes. The five main compounds of E. acanthodes are Neophytadiene; (+)-De-O-Methylcentrolobine; Cholest-5-En-3-Ol,23-Ethyl-,(3. Beta.23S)-; 9,12-Octadecadienoic Acid, Phenol, 2-ethyl-. The analysis found several compounds that can be used for industry and medicine in the future.  
DNA Authentication of Indonesian Leaffish Pristolepis grooti from Kelekar River and Ogan River in South Sumatra Based on Cytochrome C Oxidase Subunit I (COI) Gene Mochamad Syaifudin
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 2 (2023): August
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.74133

Abstract

Indonesian leaffish Pristolepis grooti, an endemic species, are distributed in the region of Sumatra, Riau, Bangka Belitung and Kalimantan. However, there has been a decline in the population recently. This research purposed to investigate the mitochondrial DNA cytochrome c oxidase subunit I (COI) gene, the genetic distance, the genetic tree of the leaffish and characterize the chemical physics of water of its habitat in the Kelekar River Muara Enim Regency and the Ogan River, Ogan Ilir Regency. The method used in species authentication was DNA isolation, amplification using PCR (Polymerase Chain Reaction) and sequencing of COI gene. The size of the COI mtDNA gene fragment was 704 bp (PM 1, PM 4, PP 2 and PP 4) and 723 bp (PM 2, PM 3, PP 1 and PP 3). A cryptic diversity of the species P. grooti is found based on the genetic distance value of 4.5-6%, both in the Kelakar and Ogan Rivers. The phylogenetic tree of the leaffish of this study formed 2 separate sub-clusters with a bootstrap value of 50%. The properties of water qualities in the two rivers included temperatures 28.3-31.8°C, pH 5.6-8.3, dissolved oxygen 4.82-10.89 mg L-1, alkalinity 10-28 mg L-1 CaCO3, water transparency 16-45 cm, ammonia 0.47-0.70 mg L-1, water current 0.17-0.30 m s-1 and TDS 7-44 mg L-1. 
Butterfly Diversity from Isolated Lowland Area: An Assessment in Langsa Urban Forest, Langsa, Aceh, Indonesia Herlina Putri Endah Sari; Andri Yusman Persada; Wendy Achmmad Mustaqim; Kartika Aprilia Putri; Imti Yazil Wafa
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 2 (2023): August
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.74610

Abstract

Langsa Urban Forest (LUF) is a 10-ha of the isolated urban forest in Langsa, Aceh, which is maintained to preserve urban biodiversity such as the butterfly. No recent study has been done in this area on butterfly biodiversity including the diversity and plant's potential for host and food plant sources. A one-month survey in July 2021 using the standard walk method on four transects was conducted. There are 36 species recorded during this study including 5 families, with Nymphalidae as the most abundant family and Leptosia nina as the most abundant species. Shannon-Wiener diversity index was used for this recent research with the value of H’ 1.78–2.78 and the Evenness index with scale 0.66–0.94. Most of the species have broad geographical ranges, with 3 of them restricted to the Indomalayan realm. There are 117 plants were recorded which 33 species supposed as host and food plants divided into 26 as host plants, 11 as food plants, and 4 for both. No specific plants threatened the collected butterflies, but it's important since providing diversity data. 
Isolation and Characterization of Rhizospheric Bacteria Associated with Canna Plant for Production of Maltooligosaccharide Amylase Rina Dwi Agustiani; Oedjijono Oedjijono; Nanik Rahmani; Nuraeni Ekowati
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 2 (2023): August
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.78346

Abstract

The objectives of the study were to isolate amylolytic bacteria from the rhizosphere and plant tissue of Canna edulis Ker., as well as litter; to know oligosaccharide compounds produced from starch hydrolyzed by the bacterial enzymes, and to identify the amylolytic bacteria based on phenetic and 16S rRNA gene sequences. From the rhizosphere, Canna plant tissue, and litters obtained thirty-two amylolytic bacterial isolates. Eight isolates (TH6, TH7, T5, T10, D2, D3, A3, S1) produced high clear zone diameters ranging from 18-30 mm; especially an isolate T10, which was consistent in producing a total clear zone diameter of 20 mm. The hydrolysate of starch hydrolysed by the T10 amylase resulted in three oligosaccharide compounds maltotriose, maltotetraose, and maltopentose. The amylase activity of isolate T10 was optimal at a temperature of 40°C and pH at 0.801 U/mL. The isolate T10 was identified as a species member of Bacillus toyonensis based on phenotyphic characterization and 16S rDNA gene sequencing analysis with a similarity value of 99.93%
Molecular Identification of Several Morphologically Distinct Flowerhorn Fish (Family) Using Mitochondrial COI Gene Marker Dini Wahyu Kartika Sari; Himawan Achmad; Hafit Rahman; Harya Bimasuci
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 2 (2023): August
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.78459

Abstract

Flowerhorn fish has been known as a breed of fish produced by artificial hybridization between several cichlid fish. Other ornamental cichlid fish generally known to be crossed to make flowerhorn variant includes Amphilophus citrinelus, Amphilophus labiatus, Vieja melanurus, and Amphilophus trimaculatus. Our study identified a variety of flowerhorn samples with distinct morphotypes, dubbed as Cencu (LH1CC), Kamfa (LH2KF), Thai Silk (LH3TS), Kirin (LH4KR), Parrot (LH5PR), and Vieja (LH6VJ) using mtDNA COI-based DNA barcoding. Molecular analysis and phylogenetics showed that all sample had 0% genetic divergence and conspecific with A. trimaculatus sequence. Hence, we concluded that despite having varied morphotypes, all flowerhorn samples were identified as A. trimaculatus and were a variation of flowerhorn from A. trimaculatus lineage. The findings should be used as a precaution as the fish is identified as an invasive species. 
Diversity and Distribution of Ficus (Moraceae) in The Karst Ecosystem of Bantimurung Bulusaraung National Park Yelastri Yelastri; Sulistijorini Sulistijorini; Nina Ratna Djuita
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 2 (2023): August
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.78811

Abstract

Bantimurung Bulusaraung National Park is an area that has the largest karst ecosystem in Indonesia. Karst is prone to damage and difficult to reuse, so it requires conservation efforts. One of the plant species that can maintain this sustainability is Ficus which acts as key species in karst ecosystems. However, at this time the species is experiencing disturbances, one of which is due to the experience of invasive plants that can threaten the existence of Ficus because the weeds can colonize habitats and are dominant which can change species diversity. This study aimed to analyze the diversity and distribution of Ficus, compare species composition, and analyze environmental factors that affect Ficus spp. in Pattunuang Resort and Bantimurung Resort. Vegetation analysis method with nesting plots placed by purposive sampling and supported with environmental and soil data measurements to determine the factors that indicate the habitat preference of Ficus. We found 18 plant species of Ficus spp. in total. At Resort Pattunuang we found 14 Ficus species with the highest abundance being Ficus sundaica (27.55%), while we recorded 15 Ficus species at Resort Bantimurung with the highest abundance being Ficus ampelas (29.23%). Ficus species were uniformly distributed with a relatively high ratio of species composition in both resorts. Principal Component Analysis (PCA) showed that the presence of Ficus in Pattunuang Resort is influenced by wind speed, soil temperature, air temperature, soil moisture, soil pH, and air humidity. In Bantimurung Resort, the existence of Ficus is influenced by wind speed, soil temperature, soil moisture, and air humidity. 
Detection of AtRKD4 Gene and Induction of Somatic Embryo in Transformant of Phalaenopsis amabilis Carrying 35S::GR::AtRKD4 Dika Sundari; Naufal Ghozi Aditya Perdana; Windi Mose; Jose Gutierrez -Marcos; Endang Semiarti
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 2 (2023): August
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.71211

Abstract

Phalaenopsis amabilis (L.) Blume is a native Indonesian orchid that plays an important role in the breeding of orchid’s hybrid worldwide. The high consumer demand causes a decline in the population of orchids for commercial trade. Plant propagation through induction of somatic embryogenesis will be very beneficial, because plants can be obtained in large numbers and uniform. AtRKD4 gene is an important gene in the model plant Arabidopsis thaliana which functions very early in development stage to initiate embryo formation. The AtRKD4 gene has been inserted into the P. amabilis orchid and several transformants have been obtained. This study aims to determine the stability integration of the AtRKD4 gene in the transformant P. amabilis genome and induce somatic embryo formation on transformant orchids. Plantation of leaf explants from P. amabilis transformants on hormone-free New Phalaenopsis basic medium induced somatic embryo formation by 20%.  Anatomical analysis showed that there is no difference stage between anatomy of somatic embryo development pattern in P. amabilis transformant and somatic embryo development pattern of monocot plants in general, PCR analysis using AtRKD4 specific primers showed that the embryos still contained 198 bp fragments of the AtRKD4 gene. In conclusion, the AtRKD4 gene is stably integrated in the P. amabilis orchid genome and can continuously induce the formation of somatic embryo from somatic cells of orchid transformants.
In silico Determination of Host-Viral Interaction of Apoptotic Mimicry Pathway Proteins During Hepatitis B Viral Pathogenesis Prachie Sharma; Kamal Rawal; kapila Kumar
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 2 (2023): August
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.72578

Abstract

Viruses are the opportunistic pathogens that have developed several elegant strategies to deploy their host systems for a pathogenic invasion. Viral apoptotic mimicry is characterized by the exposure of host cell phospholipid, the phosphatidylserine which marks the host cell for apoptotic activation. The Hepatitis b virus, an enveloped virus has recently been found to interact with Phosphatidylserine (Ptdser) on the host through its large surface protein experimentally. Nonetheless, the employment of apoptotic mimicry during the pathogenesis of HBV has not been determined.  Therefore, in the present study, we attempt the in-silico exploration of the interaction of the apoptosis initiating receptors activated by Phosphatidylserine Receptors such as TIM3, AXL, MERTK and GAS6 by Hepatitis B Virus L protein. Molecular Docking of Phosphatidylserine Receptor were studied to observe protein – protein interaction against Surface L Protein of Hepatitis B Virus by using online protein  interaction software. It was found from the in-silico studies that Phosphatidylserine Receptors i.e. TIM3 (PDB: 5F71), AXL (PDB: 5U6B), MERTK (PDB: 2POC) and Gas6 (Growth Arrest Specific protein 6) (PDB: 2C5D) have shown effective binding efficacy against Surface L Protein of Hepatitis B Virus, whereas TIM3 (PDB: F71) and Gas6 (PDB: 2C5D) has shown maximum binding energy with respect to both the software used to analyse the protein-protein docking. This interaction study can form the basis of the experimental attempt in understanding the viral-host protein interaction pattern during hepatitis b viral infection.

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