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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.

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Articles 518 Documents

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Application of Multiplex RT-PCR for Detection of Cucurbit-infecting Tobamovirus Budi Setiadi Daryono; Keiko T. Natsuaki
Indonesian Journal of Biotechnology Vol 16, No 1 (2011)
Publisher : Universitas Gadjah Mada

Cucumber green mottle mosaic virus (CGMMV) and Kyuri green mottle mosaic virus (KGMMV) are seed borne viruses and they are also transmitted mechanically during agricultural practice and through water. Hence, these viruses have potential diseases widely distributed throughout the world. To detect different strains of CGMMV and KGMMV, several specific primers for each virus were designed for single and multiplex RT-PCR. The results of single and multiplex RT-PCR showed that CGMMV was detected in zucchini isolated in Bali-Indonesia, while KGMMV was detected both in zucchini isolated in Bali-Indonesia and Cucumis metuliferus isolated in Thailand. Furthermore, artificial co-infection of these two viruses was prepared and carried out using two different ways of viral RNAs extraction. Based on the results, it could be reported that viral RNAs for cDNA amplification by multiplex RT-PCR could be extracted from a mixture of infected leaves or separate extraction of each viruses infected leaves. In addition, results presented in this study demonstrated the application of multiplex RT-PCR to simultaneously detect CGMMV and KGMMV from cucurbit leaves using a mixture of four primers and its feasibility as a sensitive and rapid laboratory assay. Since, no multiplex RT-PCR technique has been described for the detection of CGMMV and KGMMV, this technique can be a good option for sensitive and reliable tool for detection of two major cucurbit infecting Tobamoviruses.Keywords : Cucurbit infecting Tobamovirus, multiplex RT-PCR, seed borne viruses

Allelic diversity of butyrophilin (BTN1A1) gene in Indian bovines Manoj Kumar; Poonam Ratwan; Ramendra Das; Alka Chopra; Vikas Vohra
Indonesian Journal of Biotechnology Vol 22, No 2 (2017)
Publisher : Universitas Gadjah Mada

Indian milch bovines comprises of 58.56% of total livestock population (512.05 million) in the country and primarily includes native and crossbred cattle (37.28%) and water buffaloes (21.28%). Milk and milk products are essential food items of Indian diet especially in children, old and senile. Milk fat is an important constituent of milk and has an economic value and its percentage in milk varies betweem species and breeds within species. Butyrophilin (BTN1A1) a membrane protein regulates secretion of lipids and size of a fat globule in milk. Present study was conducted in 538 bovines of 11 breeds/populations adapted to different parts of India, with an aim to screen and determine the major allele of BTN1A1 gene using PCR-RFLP based test. Results indicate that exon 8 of BTN1A1 gene is polymorphic in Tharparkar, Sahiwal, Jhari and Belahi populations of native cattle and Holstein Friesian and Jersey crossbreds where as the same exon was monomorphic in Murrah, Chilika, Gojri, Chhattisgarhi and Bargur populations of water buffalo. We conclude that variations in BTN1A1 gene can serve as an excellent genetic marker while selecting cows for higher milk fat and can be applied while formulating their breeding plans.

A Novel Variant of HOXA10 gene, Ser19Cys, among Patients with Endometriosis and its Relationship with the Severity of the Disease Pinda Hutajulu; Djaswadi Dasuki; Ahmad Hamim Sadewa; Totok Utoro
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

Endometriosis is a gynecological disease associated with inherited genetic traits. HOXA10 gene whichis expressed in uterine plays an important role in the pathogenesis of endometriosis. The protein affects thedevelopment of pinopodes as a biomarker of endometrial receptivity in endometriosis.The aim of this study isto examine if there is a mutation or polymorphism within HOXA10 gene among patients with endometriosis.Thirty twopatients and 32 healthy women were recruited as subjects of this study. The exon 2 of HOXA10which covers most of coding region was amplifi ed using PCR. The presence of a mutation or polymorphismwas detected by direct seguencing. The distribution of genotype and allele was analyzed using Chi square test with p<0.05 is considered as signifi cantly different. A novel heterozygous variant within exon 2 of HOXA10 which substitute an adenine into thymine was detected at base position 55. This missense alteration changed amino acid serine to cystein (Ser19Cys). Interestingly, this variant was detected in 12 endometriosis cases (38%) but none in control. Patients carry HOXA10 Ser19Cys variant were associated with dismenorea and more frequent in stage I endometriosis. The role of this variant in the function of HOXA10 protein and frequency among Indonesians need to be clarifi ed. We found a novel heterozygous HOXA10 gene variant, Ser19Cys.The genotype frequency is 38% among endometriosis patients but none in control. This variant found in patient with dismenore and endometriosis stage 1. Key words: HOXA10 gene, endometriosis, Ser19Cys polymophism

Cloning of cDNA Encoding GRA1 Protein of Tachyzoite Toxoplasma Gondii Local Isolate Erma Sulistyaningsih; Sukarti Moeljopawiro; Jarot Subandono; Wayan T. Artama
Indonesian Journal of Biotechnology Vol 10, No 1 (2005)
Publisher : Universitas Gadjah Mada

Gene encoding GRA1 protein is potent DNA-vaccine candidate against toxoplasmosis. The aim of the research was to clone the gene encoding GRA1 protein of tachyzoite Toxoplasma gondii local isolate by DNA recombinant technology. Tachyzoite was grown in Balb/c mice in vivo. Messenger RNA was isolated from total RNA and it was used to synthesis cDNA. Complementary DNA encoding GRA1 protein of tachyzoite Toxoplasma gondii local isolate was amplified and cloned in a prokaryote cloning vector. The recombinant GRA1-encoding gene was then digesting using EcoRI restriction endonuclease and sequencing. The result showed that the recombinant GRA1- encoding gene consisted of DNA sequences encoding all signal peptide and mature peptide of GRA1 protein. Alignment of recombinant GRA1 sequence to gene encoding GRA1 protein of Toxoplasma gondii RH isolate showed 100% homologous.

Biofilm formation analysis and molecular identification of copper-resistant bacteria isolated from PT Freeport Indonesia’s tailings Maria Massora; Erni Martani; Eko Sugiharto; Roberth Sarwom; Tumpal Sinaga
Indonesian Journal of Biotechnology Vol 22, No 1 (2017)
Publisher : Universitas Gadjah Mada

Copper is an essential macronutrient for living organisms. Nevertheless, at high concentrations, it is toxic to most forms of life, including microorganisms. In this research, we examined the biofilm formation ability and identified the molecular characteristics of copper-resistant bacteria isolated from PT Freeport Indonesia’s tailings. Four bacteria isolates from PT Freeport Indonesia’s tailings were used in this study. Qualitative analysis of biofilm formation by copper-resistant bacteria was performed using the Scanning Electron Microscopy (SEM) method and Microtiter Plate Biofilm Assay. The results showed that the C53 isolate could be categorized as a strong biofilm former, and three other isolates (C38, C40, and C43) as medium biofilm formers. The identity of the selected isolates was based on 16S rRNA gene sequence analysis: C38 isolate had a 99% similarity to Bacillus cereus strain HM85, C43 isolate had a 99% similarity to Bacillus subtilis strain EN16, C40 isolate had a 99% similarity to Lycinibacillus fusiformis strain MB52, and C53 isolate had a 98% similarity to Pseudomonas aeuruginosa strain GGRJ21. The capability of the C53 isolate to form strong biofilm can be exploited in bioremediation processes aiming to remove copper from tailings.

An Actinomycetes Producing Anticandida Isolated from Cajuput Rhizosphere: Partial Identification of Isolates and Amplification of pks-I genes A. Alimuddin; Widya Asmara; Jaka Widada; M. Mustofa; Reni Nurjasmi
Indonesian Journal of Biotechnology Vol 15, No 1 (2010)
Publisher : Universitas Gadjah Mada

Actinomycetes have been the most prolific producer of various kinds of antifungal metabolites, and many of them are described as being produced by polyketide synthetases (pks). We present strain of Actinomycetes producing anticandida isolated from rhizosphere plant for amplification of Pks-I genes. The isolate was obtained from Wanagama I Forest UGM Yogyakarta. Gene of seven isolates, from total of 173 isolates, were amplified using degenerate primer to detect the presence of pks genes. One strain that is named Streptomyces sp. GMR-22 was partialy identified as anticandida producing actinomycete. The strain shown the strongest activity against Candida albicans. Based on bioautography assay, one spot active with Rf 0.57 was appeared as bright yellow by cerrium sulphate but it was and not visible on UV254 and 366 lights. Key words : pks genes, anticandida, Streptomyces sp GMR-22, rep-PCR, cajuput rhizosphere

Assessment of genetic diversity among surian Toona sinensis Roem in progenies test using random amplified polymorphic DNA markers Jayusman Jayusman; Muhammad Na’iem; Sapto Indrioko; Eko Bhakti Hardiyanto; ILG Nurcahyaningsih
Indonesian Journal of Biotechnology Vol 22, No 1 (2017)
Publisher : Universitas Gadjah Mada

Surian Toona sinensis Roem is one of the most widely planted species in Indonesia. This study aimed to estimate the genetic diversity between a number of surian populations in a progeny test using RAPD markers, with the goal of proposing management strategies for a surian breeding program. Ninety-six individual trees from 8 populations of surian were chosen as samples for analysis. Eleven polymorphic primers (OP-B3, OP-B4, OP-B10, OP-H3, OP-Y6, OP-Y7, OP-Y8, OP-Y10, OP-Y11, OP-Y14, and OP-06) producing reproducible bands were analyzed for the 96 trees, with six trees per family sampled. Data were analyzed using GenAlEx 6.3, NTSYS 2.02. The observed percentage of polymorphic loci ranged from 18.2% to 50%. The mean level of genetic diversity among the surian populations was considered to be moderate (He 0.304). Cluster analysis grouped the genotypes into two main clusters, at similarity levels of 0.68 and 0.46. The first two axes of the PCoA explained 46.16% and 25.54% of the total variation, respectively. The grouping of samples into clusters and subclusters did not correspond with family and their distances, but the grouping was in line with the genetic distances of the samples.

Genetic Relatedness among Duku, Kokosan, and Pisitan in Indonesia Based on Random Amplified Polymorphic DNA Markers Laila Hanum; Rina Sri Kasiamdari; S. Santosa; R. Rugayah
Indonesian Journal of Biotechnology Vol 17, No 2 (2012)
Publisher : Universitas Gadjah Mada

Genetic relatedness among duku, kokosan, and pisitan from Indonesia were investigated using random amplified polymorphic DNA (RAPD) markers. Eleven primers (OPA-01, OPA-02, OPA-10, OPB-07, OPB-11, OPB-12, OPB-15, OPT-16, OPU-14, OPU-19, and OPU-20) were used for amplification and yielded a total of 174 DNA bands, of which 167 were polymorphic. Primer OPA-10, OPB-11, OPB-12, OPB-15, and OPU-19 produced all of the polymorphic DNA bands. The size of the amplified DNA fragments ranged from 41-1546 bp. The dendrogram separated into two clusters at a genetic similarity coefficient of 0.76. The cluster 1 consisted of subclusters duku and several pisitan (pisitan OKI, pisitan Sleman, pisitan Hatu, pisitan Punggur, and pisitan Tanjung), and cluster 2 consisted of subclusters kokosan and pisitan. In the kokosan subclusters, including duku Drendan. Dendrogram supported the determination of taxonomic status of duku, kokosan, and pisitan as one species, namely Lansium domesticum Corr. and its divided into two groups, namely L. domesticum ’duku group’ and L. domesticum ’pisitan-kokosan group’. Thus, RAPD analysis was useful tool for determining the genetic variation and the genetics relatedness among duku, kokosan, and pisitan in Indonesia.Key words: duku, kokosan, pisitan/langsat, genetic relatedness, RAPD

Effects of Light Quality on Vegetative Growth and Flower Initiation in Phalaenopsis Kumala Dewi; Yekti Asih Purwestri; Yohana Theresia Maria Astuti; Lila Natasaputra; P. Parmi
Indonesian Journal of Biotechnology Vol 19, No 1 (2014)
Publisher : Universitas Gadjah Mada

The effects of LEDs (Light-Emitting Diodes) emitting different colours namely red, blue, red andblue, and white lights on vegetative growth and fl ower initiation of Phalaenopsis have been evaluated.Phalaenopsis“otohine/taisuco fi re bird” seedlings in vitro were subjected to different light qualities for either2 or 4 weeks, and then each seedling was planted in a plastic pot containing sphagnum and grown in thegrowth chamber under similar light quality for 3 months. For fl ower induction, mature Phalaenopsis plantshaving 4 – 6 leaves were grown for 3 months in the growth chamber under different light qualities. The leafspan, chlorophyll, gibberellin and cytokinin content were determined. In addition, the expressions of FT-likegene in the leaf, axillary bud, fl ower bud and stalk were examined.Vegetative growth was enhanced under blue, red-blue or white LEDs compared to that of the control.Gibberellin and cytokinin content increased in the seedlings subjected to white LEDs. Based on the averageof leaf span increment it was suggested that the growth of Phalaenopsis seedlings can be promoted by givingeither blue, red-blue or white LEDs. From the second experiment, it was found that fl ower induction inPhalaenopsis can be obtained in plants that had just fi nished fl owering without the application of LEDs. Theexpression of FT-like gene in the leaf as well as fl ower bud and stalk suggests that this gene is involved infl ower regulation of Phalaenopsis.

Development of Intergeneric Canine Embryo Using Bovine and Porcine Oocyte as Cytoplasm Recipient Yuda Heru Fibrianto
Indonesian Journal of Biotechnology Vol 10, No 1 (2005)
Publisher : Universitas Gadjah Mada

This study was conducted to increase the efficiency of canine embryo production by intergeneric somatic cell nuclear transfer (SCNT) technology. The effect of oocyte recipient for development of intergeneric canine somatic cell cloning embryos were examined. Bovine and porcine cumulus oocyte complexes (COCs) were collected from slaughterhouse ovaries and matured in TCM-199 medium depend on species. Adult dog fibroblasts collected from 3.5 years old Afghanhound dog, and cell between passage 1 and passage 10 used for intergeneric somatic cell cloning using bovine and porcine oocytes as oocyte cytoplasm donor. The result showed that oocytes from bovine and porcine can de-differentiated canine nucleus and no different between bovine and porcine oocyte in fusion and embryo development in vitro. Canine intergeneric cloned embryos developed to morula stages in vitro.

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