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Indonesian Journal of Biotechnology

ijbiotech
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Published by Universitas Gadjah Mada

ISSN : 08538654 EISSN : 20892241 DOI : -

Core Subject : Science,

Biochemistry, Genetics & Molecular Biology Immunology & microbiology Materials Science & Nanotechnology

The Indonesian Journal of Biotechnology (IJBiotech) is an open access, peer-reviewed, multidisciplinary journal dedicated to the publication of novel research in all aspects of biotechnology, with particular attention paid to the exploration and development of natural products derived from tropical—and especially Indonesian—biodiversity. IJBiotech is published biannually and accepts original research articles featuring well-designed studies with clearly analyzed and logically interpreted results. A strong preference is given to research that has the potential to make significant contributions to both the field of biotechnology and society in general.

Arjuna Subject : -

Articles 518 Documents

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Selection of Phalaenopsis amabilis L. Blume Orchid Resistance to Hygromycin Ixora Sartika Mercuriani; Aziz Purwantoro; Sukarti Moeljopawiro; Seonghoe Jang; Endang Semiarti
Indonesian Journal of Biotechnology Vol 17, No 2 (2012)
Publisher : Universitas Gadjah Mada

Examination of Phalaenopsis amabilis orchid resistance to hygromycin antibiotic is an important step to doprior to Agrobacterium-mediated genetic transformation in this orchids using Hygromycin phosphotransferase(HPT) gene as a selection marker in the T-DNA that harboring a desired gene to be transfered. We exposedthe plant on hygromycin containing medium. The experiment was conducted using 6 weeks old P. amabilisprotocorms. These protocorms were subcultured onto NP medium supplemented with various concentrationof Hygromycin (0, 5, 10, 20, 1nd 40 mg/l). The number of survival protocorms were examined every week for4 weeks after subcultured (WAS). The resistancy of hygromycin was calculated as ratio of death protocormsper total protocorms). The result showed that 10 mg/l hygromycin with 1 weeks of application caused deathclose to LD 50. This data indicate that P. amabilis resistance to hygromycin treatment on the appropriateconcentration 10 mg/l, and this concentration can be used for other purposes in orchid system.

The Aquaeous Extract of Root Nodules Vigna radiata (rnVr) which Inoculated by Rhizobium as an Orally Available Anemia Therapeutic Candidate Dewi Hidayati; Tutik Nurhidayati; Shinta Hartanto; N. Nurjannah
Indonesian Journal of Biotechnology Vol 13, No 2 (2008)
Publisher : Universitas Gadjah Mada

The extract of root nodules Vigna radiata (rnVr) which inoculated by Rhizobium is considered beneficial as an orally available anemia therapeutic candidate, because it contain the leghemoglobin. The positive control mice (group I) were fed with the high nutrient pellet.The twelve mice (Mus musculus) was treated with the “taking rice pellet” that representing the low nutrient food for 21 days until they suffered anemia. Then, the anemia mice were treated orally with rnVr in different concentration groups:II. 0% III.33%; IV.67% and V.100%, respectively and fed with the “aking rice pellet”. After 14 days, the blood mice were collected from orbital sinus. The hemoglobin (Hb) concentration were analyzed by spectrophotometry and blood plasma profile protein were analyzed with electrophoresis (SDS-PAGE). All anemia mice that treated with rnVr showed the increasing of Hb and group that treated with 100% extract of rnVr could reach a normal Hb value, raising from 9.85 to 12.68 g/dL. There were observed the proteins which have molecule weight 36.5 and 35.7 kDa that indicated the existing erythropoietin. The increasing haemoglobin concentration and erythropoietin suggested if extract of rnVr could increasing red blood production and potential as an orally available anemia therapeutic candidate.

The genetic variations and relationship of Madura tobacco (Nicotiana tabacum L.) based on molecular characteristics Fitri Nadifah; Budi Setiadi Daryono
Indonesian Journal of Biotechnology Vol 21, No 2 (2016)
Publisher : Universitas Gadjah Mada

Madura has at least 22 genotypes of local tobaccos (Nicotiana tabacum L.). This diversity could potentially produce new genotype of tobaccos with superior characters. However, information of the genetic diversity of Madura tobaccos is still limited. The aim of this study was to determine the genetic variation and relationship of 24 genotypes of Madura tobaccos with Random Amplified Polymorphic DNA (RAPD) analysis. In this research we were used 6 single primers for amplification: (OPA-18, OPB-12, OPB-14, OPC-1, OPC-8 and OPC-19) and 2 mixture primers ((OPB-12+OPC-8) and (OPC-1+OPC-19)). Genetic similarity and clustering was analyzed with Unweighted Pair Group Method Arithmetic (UPGMA) method with Numerical Taxonomy and Multivariate Analysis System (NTSYS) version 2.10 software. From this research we found that OPA18425, OPB12450, OPC8500, (OPC19+OPC1)550 and OPC8800 can be used as specific markers. Polymorphic bands percentage with mixture primers was relatively equal with single primers (<60%). The dendogram showed that Madura tobacco genotypes consist of 2 main clusters: cluster A (22 genotypes) and cluster B (2 genotypes: Bukabu Sa’ang and Prancak-95). Madura tobaccos had high genetic similarity between genotypes ranging from 0.80-1.00.

Genetic Variation Analysis of Mold (Magnaporthe oryzae B.Couch) Using Random Amplified Polymorphic DNA Ajeng Kusumaningtyas Pramono; Budi Setiadi Daryono
Indonesian Journal of Biotechnology Vol 17, No 2 (2012)
Publisher : Universitas Gadjah Mada

Magnaporthe oryzae B.Couch is a host-specific fungi, certain strain only infect certain host plant species. Genetic variety among M. oryzae isolates was explained by dendogram which was constructed using similarity data of Random Amplified Polymorphic DNA (RAPD). Dendogram construction was achieved by computer software, Numerical Taxonomy System (NTSYS). The aim of the research were to study the genetic variation among M. Oryzae using RAPD and to construct a dendogram of genetic similarities among the ten isolates from green foxtail (Setaria viridis L.), finger millet (Eleusine coracana L.) and rice (Oryza sativa L.).RAPD was performed in 30 cycles using 5 primers (OPA-02, OPA-03, OPA-04, OPA-05, OPA-07). Polymorphism data was used to constructed dendogram using Dice index and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) in NTSYS software. There were 68 polymorphism fragments from 74 amplified fragments.Three clusters were formed in the dendrogram, based on host pathotype: foxtail millet type, finger millet type and rice type. There were two subclusters in foxtail millet type based on mating type, MAT1-1 dan MAT1-2. Thus, RAPD could be used as a method for genetic variation analysis of Magnaporthe oryzae to show host-specific specificity.Key words: Magnaporthe oryzae, RAPD, mating type

Use of microsatellite markers to detect heterozygosity in an F2 generation of a black rice and white rice cross Kristamtini Kristamtini; Taryono Taryono; Panjisakti Basunanda; Rudi Hari Murti
Indonesian Journal of Biotechnology Vol 23, No 1 (2018)
Publisher : Universitas Gadjah Mada

The aim of this research was to know the heterozygosity of F2 generation from black rice and white rice crossing using microsatellite marker. The research material consisted of F2 Sx G plant population from black rice (S) and white rice Situbagendit (G) crosses, female parent of black rice (S), male parent of white rice (G), chemical and organic fertilizer, chemicals and tools for molecular activity and 3 microsatellite markers related to color properties (RM 220, RM 224 and RM 252). All of plant populations (generation F2, parent female, parent male) were planted in fields up to harvest. Young leaves (30 days after planting) all of plant populations were molecularly analyzed using 3 microsatellite markers (RM 220, RM 224 and RM 252). Stages of this activity include DNA isolation, PCR reaction, and visualization of PCR results using Metaphore Agarose Gel Electrophoresis. The results showed that the percentage of the number of individual plants showing heterozygous pattern in F2 S × G plant generation was 50% (RM 220); 40% (RM 224) and 60% (RM 252), so the RM 252 microsatellite marker was effectively used as a DNA-assisted selection tool on the crossbreed of black rice with white rice.

The Development of Pathogenicity of Avian Influenza Virus Isolated from Indonesia Michael Haryadi Wibowo; Agus Eko Srihanto; Khrisdiana Putri; Widya Asmara; Charles Rangga Tabbu
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

Highly pathogenic avian infl uenza outbreak in Indonesia has been reported in various poultry due toH5N1 subtype. The presence of multiple basic amino acids within the cleavage site of HA glycoprotein hasbeen identifi ed to be associated with the pathogenicity of avian infl uenza virus. The study was retrospectivestudy which was designed to characterize the cleavage site and fusion site region of haemagglutinin gene ofAIV isolated from various poultry in 2003 to 2013. Isolation, Identifi cation and propagation were carried outto collect viral stock. For virus detection, reverse transcriptase PCR (RT-PCR) method on H5 and N1 genefragment was performed. All of RT-PCR HA gene positive products were sequenced for further nucleotideanalysis and to determine the nucleotide composition at the targeted fragment. The results are all AIV isolateswere identifi ed as H5N1 subtype. The sequence analyses revealed some motives of basic amino acid motivethat were classifi ed as highly pathogenic avian infl uenza virus. Further analyses on fusion domain of all AIVisolated during the period 2003 to 2013 showed conserved amino acid. Keywords: avian infl uenza, haemagglutinin, cleavage site, basic amino acid, fusion site

Application of Molecular Biology for Identification of Virus Resistance Gene in Melon Budi Setiadi Daryono
Indonesian Journal of Biotechnology Vol 20, No 1 (2015)
Publisher : Universitas Gadjah Mada

Source of resistance to an Indonesia isolate of Cucumber mosaic virus (CMV-B2) in melon cultivarYamatouri has been reported. Moreover, Creb-2, a locus that confers resistance to CMV-B2 in Yamatouri hasbeen determined as a single dominant gene. To elucidate the resistance mechanism conferred by Creb-2 inmore detail, it is necessary to clone the Creb-2 gene and determine its molecular structure. One approach isby amplification and cloning of melon resistance gene analogs (MRGAs) based on degenerated PCR primersdesigned from conserved amino acids in the NBS-LRR motifs (P-loop, Kinase-2, and the GLPL) and Toll/Interleukin-1 receptor-like region (TIR). This study was aimed to identify and characterize the resistance geneanalogs from Cucumis melo L. cv. Yamatouri by employing polymerase chain reactions (PCR) as a molecularbiology tools with degenerate primers based on conserved motifs of cloned R genes. The application of molecularbiology such as DNA isolation, degenerate primers and PCR condition, cloning, sequencing, linkage analysisand mapping of resistance gene analogs to Creb-2 gene in melon will be widely discussed in this paper

Rapid Detection and Molecular Typing of Dengue Virus by Using Multiplex-Nested-RT-PCR Nastiti Wijayanti; Hera Nirwati; Tri Wibawa; Aris Haryanto; S. Sutaryo
Indonesian Journal of Biotechnology Vol 11, No 2 (2006)
Publisher : Universitas Gadjah Mada

world. We have evaluated the combination of one-step RT-PCR and multiplex nested PCR assays for detectingdengue viruses from clinical samples. Twelve patients were screened for the dengue virus, using a pair of primersthat conserve for several Flavivirus. The results showed that in 12 suspect patients, 100% were positive for Flavivirusand there are some genotypic variation among them, that indicated by several RT-PCR products higher than 511 bp,the expected product for RT-PCR. Further assay was performed to clarify the presence and serotypes of dengue virususing multiplex nested PCR. Serotyping results indicated that 83,3% of samples can be confirmed for dengue virus.Among the dengue virus positive 16,7 % are dengue-2, 16.7 % are dengue-3, and the most common 50% are dengue-4,whereas dengue-1 were not found among the patients. The combination of RT-PCR and multiplex nested PCR assaycan be used for rapid analysis dengue samples in early phase which is potentially useful for clinical, epidemiologyand also evolutionary studies.Key words: Flavivirus, dengue virus, serotype, RT-PCR, multiplex nested PCR

Identifcation of antibiotic producing endophytic microbe isolates from a national park in Java island Sri Yuwantiningsih; Sebastian Margino; Subagus Wahyuono
Indonesian Journal of Biotechnology Vol 20, No 2 (2015)
Publisher : Universitas Gadjah Mada

Endophytic microbes are potential sources of antibiotics. Some numbers of endophytic bacteria were isolated from plants in Ujung Kulon, Kaliurang, Meru Betiri and Baluran National Park, Bogor Botanical Garden, and Nusakambangan forest, Indonesia. Previous studies have been conducted to examine and obtain endophytic bacteria isolates from the selected plants, which resulted in three selected isolates, namely OOH-1, STG-1, and CMB-2. This research was conducted to determine the molecular identity of OOH-1 and STG-1 isolates, as well as to identify antibiotic compounds produced by STG-1 isolate. Molecular identifcation of selected isolates was based on 16S rRNA gene analysis and amplifed using primers 27F and 1492R. A phylogeny tree was then constructed by comparing the resulting sequences with data from Gene Bank using the BLAST-N program. The identifcation showed that STG-1 isolate had a 99% similarity with Pseudomonas brenneri strain SFML 97-391, and OOH-1 isolate had a 99% similarity with Enterobacter xiangfangensis. Identifcation of antibiotic compounds was done by purifcation and separation of the compounds. Antibiotic activity was also examined based on Lethal Concentration (LC50) on Fusarium oxysporum with a LC50 of 0.01–0.02% against Fusarium oxysporum.

Early Detection and Serotyping of Dengue Viruses Clinical Isolates Using Reverse Transcription Polymerase Chain Reaction (RT-PCR) 2 Primers Abdul Rahman Siregar; Tri Wibawa; Nastiti Wijayanti
Indonesian Journal of Biotechnology Vol 16, No 2 (2011)
Publisher : Universitas Gadjah Mada

Recently 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.

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