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BIOTROPIA - The Southeast Asian Journal of Tropical Biology

biotropia
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Published by Southeast Asian Regional Centre for Tropical Biology

ISSN : 02156334 EISSN : 1907770X DOI : http://dx.doi.org/10.11598/btb

Core Subject : Health, Science, Agriculture,

Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Immunology & microbiology Veterinary

BIOTROPIA, The Southeast Asian Journal of Tropical Biology, is a scientific publication of the Southeast Asian Ministers of Education Organization (SEAMEO) – Southeast Asian Regional Center for Tropical Biology (BIOTROP). It publishes articles in the broad areas of tropical ecosystems and environmental impacts, biodiversity conservation and sustainable development and biotechnology.

Arjuna Subject : Ilmu Pertanian dan Biologi (Semua) - Ilmu Pertanian dan Biologi (Lain-Lain)

Articles 520 Documents

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Testing Reliability of Serum Samples as a DNA Source on Captive Breeding Long-tailed Macaques (Macaca fascicularis) Perwitasari-Farajallah, Dyah; Farajallah, Achmad
BIOTROPIA Vol. 21 No. 2 (2014): BIOTROPIA Vol. 21 No. 2 December 2014
Publisher : SEAMEO BIOTROP

The serum realibility was tested in captive breeding conditions on the long-tailed macaques (Macaca fascicularis). Serum and buffy coat were applied to standard protocol of DNA extration following the amplification of microsatellite DNA locus of D2S1777 by PCR and visualized PCR products by means of PAGE with silver staining.Â The amount of genomic DNA extracted from serum was sufficient for genotyping individuals at DNA microsatellite locus of D2S1777 with the allele size is approximately 160 bp.Â We show that serum can provide a reliable alternative for obtaining DNA where taking blood using anticoagulant is impracticable

Genetic Variation of Teak Mistletoe (Dendrophthoe pentandra (L.) Miq.) Based on Random Amplified Polymorphic DNA (RAPD) Markers Muttaqin, Zainal; Budi, Sri Wilarso; Wasis, Basuki; Siregar, Iskandar Zulkarnaen; Corryanti, Corryanti
BIOTROPIA Vol. 27 No. 2 (2020): BIOTROPIA Vol. 27 No. 2 August 2020
Publisher : SEAMEO BIOTROP

Mistletoes are hemiparasitic macroparasite plants that interfere with trees and other wild plants in nutrient acquisition. As the plant has low leaf water potential, it draws water from teak wood tissues during the deciduous stage of the teak host, thereby killing the twigs and eventually the teak tree. Mistletoes are also key players in plant diversity. Therefore, the mistletoe population needs to be regulated not only as a parasite but also as a keystone species affecting biodiversity. Knowledge scarcity on the status of mistletoes includes their genetic variation. Hence, the purpose of this study is to analyze the level of genetic variation of teak mistletoe (Dendrophthoe pentandra) using RAPD markers. At the Padangan teak Clonal Seed Orchard (CSO), leaf samples were randomly collected from three layers of the mistletoe crown (upper, middle, and below) taken from five host teak trees randomly selected from each of the sub-observation measure plots (OMP). Four OMP units inside the observation sample plots (OSP) (n = 3, 50 × 50 m) at different levels of infestation (light, moderate, and heavy) were established. Analysis of genetic variation and genetic distance of mistletoes across different crown layers was conducted using RAPD markers. The leaf samples from crown layers UU (upper crown, subsection upper), UM (upper crown, subsection middle), and UB (upper crown, subsection below), including U (upper crown), had significantly greater genetic variation (He = 0.181–0.255) than those from the M layer (middle crown, He = 0.227) and the B layer (below crown, He = 0.114). Furthermore, the greatest genetic distance occurred between mistletoes in the UB and B crown layers (0.310), whereas the shortest genetic distance occurred between mistletoes of the UU and UM layers in the upper crown (0.038). Practical implications of the low genetic variation include the control of D. pentandra infestation by restricting its population so that the Perhutani State-Owned Forestry Enterprise can maintain damage levels below the economic threshold.

Reviewers For Vol 14 No. 2 -, Editor
BIOTROPIA Vol. 14 No. 2 (2007): BIOTROPIA Vol. 14 No. 2 December 2007
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11598/btb.2007.14.2.19

Prof. Dr. Haryono Semangun, Faculty of Agriculture, Gadjah Mada University (UGM),Yogyakarta 55281, Indonesia Dr. N.C. Rachaputi, Farming Systems Institute Queensland, Department of Primary Industries and Fisheries, Kingaroy, QLD 4610, Australia Dr. Noviar Handayani, Postgraduate Program for Biology, University of Indonesia (UI), Depok, Jakarta, Indonesia Dr. (Eng.) Sukma Nuswantara, MPHIL. Sandia Biotech Diagnostic Centre, Santosa Bandung International Hospital, Jl. Kebonjati 38, Bandung, Indonesia Dr. Tresnawati Purwadaria, Indonesian Research Institute for Animal Production, P.O. Box 221, Bogor 16002, Indonesia Dr. Soetijoso Soemitro, Biochemistry Laboratory, Department of Chemistry, Faculty of Science and Mathematics (FMIPA), Padjadjaran University, Bandung 40133, Indonesia Dr. Tri Panji, Laboratory of Microbes and Bioprocess, Biotechnology Research Institute for Estate Crops, Bogor, Indonesia Dr. Puspita Lisdiyanti, R & D Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Cibinong 16911, Jakarta, Indonesia Dr. Sigit A.P. Dwiono, Mataram Marine Bio Industry Tech. Implementation Unit, Research Center for Oceanography, Indonesian Institute of Sciences (LIPI), Teluk Kodek, Malaka, Pemenang, Lombok Barat 83352, Indonesia Dr. Estu Nugroho, Research Institute for Freshwater Aquaculture, Jl. Sempur, Bogor 16154, Indonesia Dr. Sudarto, Indonesian Research Institute for Aquaculture (RIFA), Depok, Jakarta, IndonesiaÂ Â Â Â Â Â Â Â

HETEROLOGOUS EXPRESSION OF A CHITINASE GENE FROM AEROMONAS CAVIAEIN PSEUDOMONAS FLUORESCENS ANTONIUS SUWANTO; AMARILA MALIK; BUDI TJAHJONO; ROB HARLING
BIOTROPIA - The Southeast Asian Journal of Tropical Biology No. 20 (2003)
Publisher : SEAMEO BIOTROP

A transcriptional fusion for an Aeromonas caviae chitinase gene was constructed under the control of a constitutive promoter of the kanaraycin resistance gene (PKmR). The construct was inserted into a medium copy number broad host range plasmid vector to yield recombinant plasmid pAM340, which harbored transcriptional fusion PKmR- chi. Another transcriptional fusion, Ptac-chi, in a recombinant plasmid pAM630, was conducted as comparison. Triparental mating of E. coliÂ carrying the recombinant plasmids with Pseudomotws fluorescensÂ 5100, a phyllosphere bacterium, was performed. Pseudomonas fluorescensÂ 5100 exconjugants were examined for constitutive expression of chitinase employing a spectrophotometric assay; they showed stronger chitin degradation activity than Escherichia coli transformants. Using a fungal antagonism plate assay, this chitinolytic P. fluorescens, however, could not inhibit selected phytopathogenic fungi. Keywords:Â Â Â AeromonasÂ Â caviae/Â chitinaseÂ Â gene/transcriptionalÂ Â fusion/PKm'VÂ Â Vtac-chilPseudomonas fluorescens

Effects of Blue Light and Paclobutrazol on Seed Germination, Vegetative Growth and Yield of Black Rice (Oryza sativa L. ‘Cempo Ireng’) Dewi, Kumala; Agustina, Rizkika Zakka; Nurmalika, Farida
BIOTROPIA Vol. 23 No. 2 (2016): BIOTROPIA Vol. 23 No. 2 December 2016
Publisher : SEAMEO BIOTROP

Black rice (Oryza sativa L. “Cempo Ireng”) is one of the local rice varieties in Sleman Regency, Yogyakarta. Its black color is caused by a high anthocyanin content, which is an important source of antioxidants. The cultivation of black rice is still limited due to its tall phenotype, long vegetative stage, and lower productivity compared to white rice. Paclobutrazol is a growth retardant that causes dwarfing in several crop plants and reduces lodging. Blue light can improve plant quality. This research aimed to evaluate the effects of blue light and paclobutrazol on seed germination, vegetative growth, and yield of black rice. The results showed that the average seed germination and the α-amylase activity of seeds exposed to blue light were lower compared to those exposed to sunlight; however, paclobutrazol concentrations did not affect the seed germination percentage. The height of rice plants treated with paclobutrazol decreased in accordance with increasing paclobutrazol concentration. Chlorophyll content and tiller numbers increased with 12.5 ppm paclobutrazol treatment. Nitrate reductase activity was higher in rice seedlings subjected to blue light compared to sunlight. Iron (Fe) content in rice plants treated with 25 or 50 ppm paclobutrazol increased compared to the control. In conclusion, paclobutrazol application at 12.5 ppm effectively reduced plant height, and higher concentrations caused greater height reduction. Blue light treatment during black rice seed germination slightly reduced germination percentage and α-amylase activity. However, when combined with paclobutrazol application, blue light treatment increased chlorophyll content, tiller numbers, and Fe content in black rice grains.

Transposition and expression of GEP gene in the genome of Vibrio harveyi to monitor its adherence in shrimp larvae Suwanto, Antonius
BIOTROPIA Vol. 13 No. 1 (2006): BIOTROPIA Vol. 13 No. 1 June 2006
Publisher : SEAMEO BIOTROP

Expression of green fluorescent protein encoded by GFP gene in Vibrio harveyi was investigated to understand the ability of the gene as a molecular marker for adherence of this pathogenic Vibrio in shrimp larvae. The GFP gene was inserted into pUC18Not and pUTmini-Tn5 to generate a recombinant plasmid pWGO2 and pWGO3, respectively, which was transferred into the three isolates of V. harveyi employing diparental mating. Recombinant E. coli carrying pWGO2 and pWGO3 resulted in green-fluorescent colonies and cells due to the production of GFP. However, al1 of mini-Tn5, including mini-Tn5-gfp were not successful1y transferred to V. harveyi. Therefore, we used mini-Tn10 (pLOFKm-gfp) for inserting of gfp gene into V. harveyi genome. Although we could obtain relatively high (l0 pangkat -8) transconjugans employing Tn10, only one of Tnl0 derived isolate of V. harveyi G3 (G3-Tn1Ogfp) showed gfp expression and was further employed for adherence assay. Fluorescent 03-TnlOgfp cells could be observed inside the digestive tract of shrimp larvae and could be distinguished from vibrio that naturally exist in shrimp larvae.

CURRENT MICROBIOLOGICAL ASPECTS IN HIGH MOUNTAIN LAKE RESEARCH YUHANA, MUNTI; HANSELMANN, KURT
BIOTROPIA Vol. 13 No. 1 (2006): BIOTROPIA Vol. 13 No. 1 June 2006
Publisher : SEAMEO BIOTROP

Remote and normally unpolluted high mountain lakes provide habitats with no or very limited anthropogenic influences and, therefore, their hydrodynamics are mostly regulated by the natural conditions. Researches in high mountain lakes deal with measuring and modeling the response of the habitats to environmental changes especially correlated to acid deposition, pollutants influx and climatic variability. The microbial world has also become a focus in many studies of these extreme ecosystems. Despite the pressure of harsh and extreme conditions, microbial communities living in these habitats developed flexible strategies and show quick adaptation to climate oscillation. New aspects in microbiological studies in recent high mountain lake research are presented in this paper.Key words : High mountain lake, extreme environment, microbial communities, microbial diversity, psychrotolerant microbe, molecular microbe

Isolating Microsatellite From Amorphophallus variabilis and Its Application for Population Study in Dramaga Conservation Forest, Indonesia Santosa, Edi; Lian, Chun Lan; Mine, Yoko; Takahata, Ken; Sugiyama, Nobuo
BIOTROPIA Vol. 25 No. 1 (2018): BIOTROPIA Vol. 25 No. 1 April 2018
Publisher : SEAMEO BIOTROP

Amorphophallus variabilis Blume, a member of Araceae, is a fleshy perennial tuber crop endemic in Java Island, Indonesia. The plant produces white edible corm; and it was used as food during famine time before 1960s. Rapid ecological changes and land fragmentations in Java in recent times threaten populations of A. variabilis. Here, compound microsatellite markers were developed in order to develop conservation strategies in the populations. Twelve primers pairs produced high polymorphism ranging from 5 to 22 alleles per locus. The observed and expected heterozygosities ranged from 0.191 to 0.851 and 0.380 to 0.943, respectively. This high allelic diversity indicates that these markers are suitable for the study on population genetic structure. Cross-amplification on related and non-related species was performed. Application of the markers on populations from Dramaga Conservation Forest revealed high allelic richness, high diversity within and among populations. Genetic distance among populations increased with an increase of geographic distance. Present study suggested that, it is important to study population of A. variabilis in Java in order to understand the population genetic structure and develop effective in situ conservation programs.

MOLECULAR IDENTIFICATION AND PHYLOGENETIC RELATIONSHIP AMONG LOCAL, SANGKURIANG, AND AFRICAN CATFISH BASED ON RAPD MARKER Nuryanto, Agus
BIOTROPIA Vol. 19 No. 1 (2012): BIOTROPIA Vol. 19 No. 1 June 2012
Publisher : SEAMEO BIOTROP

Catfish species are commercially cultivated freshwater fish by fish farmer. Formerly, only one species of catfish had been cultivated, namely local catfish (walking catfish) Clarias batrachus.Â However, since 1985, local catfish was replaced by a new commodity from Africa called African catfish (C. gariepinus).Â In 2004, BBPBAT Sukabumi had introduced a new strain of catfish, namely Sangkuriang catfish.Â Taxonomic analysis needed, especially for Sangkuriang catfish using molecular marker, in order to get a clearer picture about its genetics departure from their parental, so their taxonomic status and relationships with local and African catfish is clearer. Â One of the molecular markers is randomly amplified polymorphic DNA (RAPD) markers. Species status defined based on the presence and absence of specific band on each catfish.Â Phylogenetics relationships was inferred from phylogenetic tree which was built using UPGMA tool as implemented in NTSYS software based on the similarity of RAPD band pattern. The result showed that Sangkuriang and local catfish had specific RAPD markers, while African catfish was not. This means that all RAPD markers of African catfish were shared with those of two others catfish. Local catfish phylogenetically distantly related to African and Sakuriang catfish. Only one individual of African catfish (D4) genetically close related to Sangkuriang catfish while the rest individuals of African catfish genetically closed related to green catfish. This means that African catfish showed very divergence genetic constituent.Â Â Key words: catfish, molecular identification, phylogenetic relationships, RAPD

Inhibitory Activities of Myristica fragrans Essential Oil on Aflatoxigenic Strains Sukcharoen, Oratai; Sirirote, Pramote; Thanaboripat, Dusanee
BIOTROPIA Vol. 26 No. 1 (2019): BIOTROPIA Vol. 26 No. 1 April 2019
Publisher : SEAMEO BIOTROP

Aflatoxin B1 is a highly toxic and carcinogenic metabolite produced by aflatoxigenic strains that commonly contaminate food and agricultural commodities. This study evaluates the inhibitory effects of Myristica fragrans Houtt (nutmeg) essential oil extracted by hydrodistillation on the mycelial growth, sporulation, and aflatoxin B1 production of Aspergillus flavus IMI 242684 and Aspergillus parasiticus IMI 283883 by fumigation and contact application. An analysis of M. fragrans essential oil using the chromatography-mass spectrometry showed that its major components are safrole (42.50%), 4-terpineol (23.81%) and methyl eugenol (11.14%). At a concentration of 1000 ppm of essential oil, the mycelial growths of both Aspergillus strains were completely inhibited by vapor treatment but only reduced by about 70% by contact treatment. However, the sporulation and aflatoxin B1 production were completely inhibited by both contact and vapor treatments. Vapor treatment induced a higher level of inhibition than contact treatment. In conclusion, nutmeg essential oil is a potential biochemical agent that can help prevent contamination of stored foods and feeds.

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Editorial Address SEAMEO BIOTROP Jl. Raya Tajur Km. 6 Bogor 16134 INDONESIA

Location Kota bogor, Jawa barat INDONESIA

Abstract

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Contact Name
Knowledge Management Department

Contact Email
kmd@biotrop.org

Phone
+62251-8323848

Journal Mail Official
biotropia@biotrop.org

Editorial Address
SEAMEO BIOTROP Jl. Raya Tajur Km. 6 Bogor 16134 INDONESIA

Location
Kota bogor,

Jawa barat

INDONESIA