Indonesian Journal of Biotechnology
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Antifungal Production of a Strain of Actinomycetes spp Isolated from the Rhizosphere of Cajuput Plant: Selection and Detection of Exhibiting Activity Against Tested Fungi
No full textActinomycetes are bacteria known to constitute a large part of the rhizosphere microbiota. Their isolation is an important step for screening of new bioactive compounds. Culturable actinomycetes populations from cajuput plant rhizosphere soils in Wanagama I Forest UGM Yogyakarta were collected to study about their antifungal activity. Among 17 of a total 43 isolates that showed activity were screened for producing antifungi substances. Screening for antifungal activity of isolates were performed with dual culture bioassay in vitro. One isolate that was designated as Streptomyces sp.GMR-22 was the strongest against all tested fungi and appeared promising for a sources of antifungal. Culture’s supernatant and mycelia were extracted with chloroform, ethyl acetate and methanol, respectively. Antifungal activity of crude extracts was tested by diffusion method against tested fungi. The result indicates that isolates of actinomycetes from cajuput plant rhizosphere could be an interesting sources of antifungal bioactive substances
Effect of Substrate Concentration to Anode Chamber Performance in Microbial Electrolysis Cell
No full textMicrobial electrolysis is a promising process for bio-hydrogen production which might be implemented in waste water treatment in a near future. Unfortunately substrate could be converted into methane by acetoclastic methanogens and will reduce the coulombic efficiency (CE). The research objective was to study the competition between electrogens and methanogens for substrate in a continuous Microbial Electrolysis Cell (MEC).The competition was studied in relation to controlling acetate influent concentration (Cin) from 35 to 1 mM with a fixed anode potential -350 mV, by assessing activity of electrogens as current density (CD), activity of acetoclastic methanogens as methanogenic consumed acetate (Cmeth), and CE and by measuring anolyte protein content to confirm a steady state condition. Controlling Cin from 35 to 1 mM resulted in tendency of both CD and Cmeth to decrease and CE to increase. At decreasing Cin from 35 to 5 mM which left excess acetate concentration in anolyte, the CEs were between 36.4% and 75.3%. At further decreasing Cin to 1 mM the acetate concentration was limited (Cef 0 mM), but the CE only reached 95.8%. Methanogenesis always occur and electrogens were not able to outcompete the acetoclastic methanogens even though the substrate concentration was limited.Keywords : microbial electrolysis cell, bio-hydrogen, metanogenesis, substrate concentratio
Early Detection and Serotyping of Dengue Viruses Clinical Isolates Using Reverse Transcription Polymerase Chain Reaction (RT-PCR) 2 Primers
No full textRecently several methods for confirming Dengue Virus have been developed involve virus isolation, detection of virus antigen, and nucleic acid using PCR. It has been reported that rapid detection method for confirming DHF by Multiplex RT-PCR had been successfully developed. It was more effective than the other methods with a high sensitivity and specivicity were 100% at the early phase (day 1-3). This study was designed to develop rapid detection and serotyping methods for Dengue Virus using RT-PCR 2 primers (Dcon and preM) with annealing temperature was 57oC. The whole blood samples were collected from suspected dengue fever patients that had been confirmed with NS1 kit from R.S. Persahabatan DKI Jakarta and R.S. Prof. Dr. Sardjito DI Yogyakarta during Februari-August 2009. The PCR products showed that in 12 samples, 100 % were postitive with different pattern among the serotypes especially for DEN1 and DEN2, but not for DEN3 and Den4. This method was also able to confirm the double infection DEN2-DEN3, but not for the other ones because of the unspecific pattern. From the results, it indicated that the 2 primers can be a promising early detection and serotyping method of Dengue Virus which infected the DHF patients. Key words: Dengue Virus, DHF, early detection, serotyping, RT-PCR 2 primers
Genetic Variation of Apolipoprotein E (ApoE) in Surabaya, Palu and Alor Populations of Indonesia
No full textApolipoprotein E (ApoE) has been considered to play an important role in cardiovascular disorders.Several studies reported that genetic variation in ApoE locus influence plasma lipoprotein level. The objectivesof this study was to compare the frequency of ApoE genotypes and alleles in some populations of Indonesia.One hundred and ninety five voluntarily unrelated apparently healthy individuals were recruited fromSurabaya, Palu and Alor representing the western, middle and eastern populations of Indonesia, respectively.Blood samples were collected from each subject for DNA extraction. The common allelic variants of ApoE werescreened using polymerase chain reaction (PCR) and restriction fragment length polymorphism. Three allelesi.e. ε2, ε3 and ε4 were identified and five genotypes i.e. ApoE ε2/ε2, ApoE ε2/ε3, ApoE ε3/ε3, ApoE ε2/ε4, ApoE ε3/ε4 were found in three populations studied, while ApoE ε4/ε4 was absent in Surabaya, representing the westernpopulations of Indonesia. The frequency of ε2, ε3 and ε4 alleles in the western population were 0.208, 0.701and 0.092 respectively; in the middle population were 0.242, 0.618 and 0.140 respectively and in the easternpopulation of Indonesia were 0.267, 0.466 and 0.267 respectively. The highest frequency of ε2 and ε4 allelewas found in the eastern population of Indonesia. The distribution of ε2 allele were not significantly differentamong all Indonesian populations, but significantly different were found in ε3 and ε4 allele in the easternpopulation compared to those in the western and middle populations of Indonesian. It can be concluded thatthe frequency of three ApoE alleles in the western and middle populations of Indonesia was not significantlydifferent however, significantly different was observed in the frequency of ApoE ε3 and ε4 alleles from theeastern compared to those in the western and middle populations of Indonesia
The Detection of Mutational Changes in Sorghum using RAPD
No full textSorghum is a multifunction plant due to its high economic value as a source of food, feed and industrial raw material of biofuel. Sorghum improvement can be done through mutation breeding and this research was conducted to evaluate the power of mutation breeding by observing the difference between mutant and its original counterpart. Varieties of sorghum Durra, Zhengzu and their mutants B-100 and Zh-30 were arranged in completely randomized design. DNA extraction was done using a modified CTAB method. After purification, quantification, and dilution, PCR was carried out for RAPD analysis. The result showed that Durra and Zhengzu varieties were significantly different in plant height, number of leaves and seed colour, however the mutant and its original counterpart cannot be differentiated morphologically. RAPD can be used to differentiate mutant and its original counterpart by observing the specific band pattern from each primer
Molecular cloning of gene fragment encoding 4-coumarate: Coenzyme A ligase of Sengon (Paraserianthes falcataria)
No full text4-coumarate:Coenzyme A ligase (4CL) plays an important role in lignin biosynthetic pathway thatcatalyzed the activation of coumaric acid, caffeic acid or ferulic acid to be a syringil monomer. Ligninbiosynthesis control through 4CL down regulating would support lower lignin wood production. Theobjective of this study was to clone conserved region cDNA of gene encoding 4CL. Gene fragment isolation wasconducted by means of reverse transcriptase polymerase chain reaction (RT-PCR) using degenerateheterologous primer. The RT-PCR products were purified, sequenced and analyzed to select the highlyhomologous fragment to 4CL. BLASTanalysis result showed that deduction of amino acid sequences from oneof two RT-PCR product nucleotide was highly homologous with the 4CL conserved region from Rubbus ideaus,Oryza sativa, Populus tomentosa, Populus balsamifera, Betulla platyphilla, Nicotiana tabacum, and Arabidopsisthaliana with identity ranging from 78-90%.Key words: 4-coumarate: Coenzyme A ligase, lignin, sengo
Characterization of envelope-transmembrane Gene of Jembrana Disease Virus Tabanan 1995 Isolate
No full textThe availability of specific and rapid detection methods is essential for monitoring the health status of farmed species, particularly in viral disease as in this case early diagnosis is a critical factor in containing disease outbreaks. Jembrana Disease Virus (JDV) is a lentivirus that causes an acute, severe disease syndrome in infected Bali cattle in Indonesia, resulting in heavy economic losses because of the high mortalities. The virus-host interaction and the modes of transmission are still unknown. The goal of the research was to designa probe candidate of Jembrana Disease Virus based on envelope-transmembrane (env-tm) gene to optimize Jembrana disease detection method. The DNA fragment derived from env-tm of JDV was used, cloned in pGEX-TM and expressed in E.coli DH 5α. Sequence analysis was conducted with BLAST programs from NCBI. Sequence analyses of the fragments of env-tm clone, indicated that it has a very closed genetic relation with 97,68% homology identity. Probe was designed based on the conserved region of env-tm using Geneious resulted in JT2 252 bp long. BLAST analyses showed that probes had high specifity to other strains of JDV in Indonesia.Key words : probe, env-tm, JDV, specifity, sensitivity
Purification and Characterization of Streptomyces sp. IK Chitinase
No full textStreptomyces sp. IK isolated from compost inoculants, could produce extra cellular chitinase in a medium containing 0.2% (w/v) colloidal chitin, fermented for 96 hours at 30oC. The enzyme was purified by a combination of ammonium sulphate precipitation and DEAE-Cellulose anion-exchange chromatography. On SDS-polyacrylamide gel electrophoresis analysis, the purified enzyme showed a mass of 71 kDa. Chitinase was optimally active at pH of 6.7 and at 37oC. Km value and Vmax of the protein for colloidal chitin were 2.92 mg/ml and 4.26 ìg/h, respectively.Key words : chitinase, Streptomyces, purification, characterizatio
Identification of Metabolic Intermediates in Microbial Degradation of Chrysene by Armillaria sp. F022
No full textTo degrade chrysene, a polycyclic aromatic hydrocarbon (PAH), Armillaria sp. F022, a fungus collected from a soil, was used. Maximal degradation (77%) was obtained when Armillaria sp. F022 was incubated in cultures agitated at 120 rpm for 30 days, as compared to just 41% degradation in stationary culture. Furthermore, the degradation of chrysene was affected by the addition of surfactants. The mechanism of degradation was determined through identification of the intermediates. Several enzymes (manganese peroxidase, lignin peroxidase, laccase, 1,2-dioxygenase and 2,3-dioxygenase) produced by Armillaria sp. F022 were detected in the culture. The highest level of activity was shown by 1,2-dioxygenase after 20 days (143.6 U l-1). Theseligninolytic and dioxygenase enzymes played an important role in the oxidation of chrysene. Chrysene was indeed degraded by Armillaria sp. F022 through several intermediates, chrysenequinone, 2-((1E,3E)-4-carboxy-3-hydroxybuta-1,3-dien-1-yl)-1-naphthoic acid , 1-hydroxy-2-naphthoic acid, and gentisic acid.Keywords : Biodegradation, Chrysene, Metabolites, Armillaria sp. F02
Comparative Analysis of Rice Transformation Using Agrobacterium tumefaciens and Rhyzobium leguminosarum
No full textThis study was aimed to study the effectiveness of Rhizobium transformation system compared to the most widely used Agrobacterium mediated transformation system on three rice cultivars, Ciherang (Indica), Nipponbare (Japonica), and Rojolele (Javanica). Six day old calli induced from immature embryos were inoculated with Rhizobium leguminosarum bv trifolii ANU845 and Agrobacterium tumefaciens LBA288 that harbored with vector pCAMBIA 5106. This plasmid contained a minimum set of transfer machinery genes and had a gusplus and an hptII gene driven by 35S CaMV promoter in the T-DNA. The results showed that the transformation frequencies (number of PCR positive plants per number of calli inoculated) ranging from 0 to 12.05 % depend on the genotype and transfer agent used. The highest transformation frequency (12.05%) was obtained in Ciherang transformed with R. leguminosarum. Most of the transgenic rice obtainedby Rhizobium transformation were normal in morphology and fertile similar to those obtained by Agrobacterium transformation. Integration, expression and inheritance of transgenes were demonstrated by molecular and genetic analysis in T0 and T1 generations.Key words : Rhizobium leguminosarum, immature embryos, Agrobacterium tumefacien