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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 530 Documents

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The expression of growth factor signaling genes in co-culture IVM Erif Maha Nugraha Setiawan; Hyun Ju Oh; Min Jung Kim; Geon A Kim; Seok Hee Lee; Yoo Bin Choi; Ki Hae Ra; Byeong Chun Lee
Indonesian Journal of Biotechnology Vol 22, No 2 (2017)
Publisher : Universitas Gadjah Mada

The objective of this study was to determine the expression of growth factor signaling genes in human adiposederived stem cells (ASCs), porcine oocytes, and cumulus during in vitro maturation (IVM). The human ASCs (from 2 young and 2 old donors) were used for the co-culture IVM system. The maturation rate was examined based on polar body extrusion. The expression of the growth factor signaling genes from ASCs, oocytes, and cumulus were measured using qPCR. All data were analyzed using ANOVA followed by Tukey’s test. The expression of the h-IGF1 signaling genes from human ASCs cells showed similar values in all groups and the h-FGF2 expressions were higher in the young donors than the old ones. The p-FGF2, p-FGFR2, and p-TGFβ1 expressions in the oocytes as well as p-IGFR in the cumulus that were co-cultured from the young donors showed higher values than the old and control groups. The apoptotic ratio (p-BAX/p-BCL2) from the oocytes and cumulus in both co-culture groups also showed lower levels than the control (P<0.05). Oocyte maturation rates were significantly increased in all co-cultured groups (Y1 (85.9 ± 2.2%), Y2 (91.2 ± 1.1%), O1 (86.3 ± 1.5%), and O2 (86.5 ± 2.3%)) compared with the control (76.7 ± 1.1%; P<0.05). Although the expression of growth factor signaling genes was varied, young donors’ ASCs might support in vitro maturation beħer than those from old donors.

Genotyping of Rotavirus by Using RT-PCR Methods Hera Nirwati; Tri Wibawa; Abu Tholib Aman; Yati Soenarto
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

There is a great diversity of rotavirus genotypes circulating worldwide, with dominant genotypes changing from year to year. Rotavirus genotyping was performed by using reverse transcription PCR with type-specifi c-primers. Since rotavirus is a RNA virus that has high mutation rate, there was a possibility of technical diffi culty in genotyping due to mutation in the primer binding sites. During Indonesian rotavirus surveillance study 2006-2009, it was reported that 17% of samples subjected for G type and 21% of samplessubjected for P type were untypeable. The objective of this study was to identify genotypes of the samples that were untypeable previously using RT-PCR based on the method described by Das et al. (1994) and Gentsch et al. (1992). There were 30 samples subjected to G type and 61 samples subjected to P type to be re-typed using method described by Gouvea et al. (1990) and Simmond et al. (2008) for G and P typing, respectively. By using another set of primer, the genotype of all samples was identifi ed. This study highlights the importance of a constant reconsideration of primer sequences employed for the molecular typing of rotaviruses. Key words: rotavirus, G typing, P typing

Cloning Gene Encoding Micronema 3 (Mic3) Protein of Tachyzoite Toxoplasma Gondii Local Isolate Wayan T. Artama; Ni Nyoman Ayu Dewi; Didik Tulus Subekti
Indonesian Journal of Biotechnology Vol 10, No 1 (2005)
Publisher : Universitas Gadjah Mada

Microneme 3 (MIC3) protein tachyzoites Toxoplasma gondii is one of protein which plays an important role during cell host invasion. Gene encoding MIC3 protein has been studied and it was suggested a potent vaccine candidate against Toxoplasma gondii infection. The aim of this research is to clone and sequence the gene encoding MIC3 protein of tachyzoites Toxoplasma gondii local isolate by amplification using polymerase chain reaction with specific primers. The amplified DNA fragment was cloned into pGEM-T and transformed into E. coli XL-1 Blue by heat shock method. Recombinant plasmids were isolated using alkali lysis method and analyzed by digestion using restriction endonuclease enzymes PstI, HindIII, NcoI and EcoRV. The recombinant plasmids then sequenced to find out the nucleotide sequence of insert gene by ABIPRISM 377 DNA Sequencer. The DNA sequence then were analyzed by computer software for alignment. The result showed that transformation in E. coli XL-1 Blue by pGEM-T produced one clone that was encoding MIC3 protein. Analysis of 489 bp from 5’ and 447 from 3’ of gene sequence showed 97-98% homology with gene encoding for MIC3 protein of RH isolate.

Biodegradation of Used Engine Oil by Acinetobacter junii TBC 1.2 Witono Basuki; Khairul Syahputra; Ayu Tri Suryani; Ilham Pradipta
Indonesian Journal of Biotechnology Vol 16, No 2 (2011)
Publisher : Universitas Gadjah Mada

The isolates have capability to degrade used engine oil was obtained from soil in the beach contaminatedwith used engine oil. One of the selected isolates TBC 1.2 was identified by its 16s rDNA as Acinetobacterjunii. The microorganism can use hydrocarbons in used engine oil as the sole carbon source and energy, alsoit significantly degraded almost all hydrocarbon compounds in used engine oil. With its ability Acinetobacterjunii TBC 1.2 has a potency to be utilized for bioremediation of soil polluted with used engine oil.

Molecular cloning of gene fragment encoding 4-coumarate: Coenzyme A ligase of Sengon (Paraserianthes falcataria) Sri N. Hartati; Enny Sudarmonowati; S. Suharsono; Kurnia Sofyan
Indonesian Journal of Biotechnology Vol 15, No 1 (2010)
Publisher : Universitas Gadjah Mada

4-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, sengon

Anthocyanin, nutrient contents, and antioxidant activity of black rice bran of Oryza sativa L. ‘Cempo Ireng’ from Sleman, Yogyakarta, Indonesia Pratiwi Apridamayanti; Rarastoeti Pratiwi; Yekti Asih Purwestri; Woro Anindito Sri Tunjung; Rumiyati Rumiyati
Indonesian Journal of Biotechnology Vol 22, No 1 (2017)
Publisher : Universitas Gadjah Mada

The chemical contents and health benefits of black rice bran of some rice cultivars have been investigated. However, there has been little research on the ‘Cempo Ireng’ cultivar from Sleman, Yogyakarta. The aim of this present study was to determine the anthocyanin, antioxidant activity, and macro- and micronutrients contents of black rice bran from this local cultivar. The anthocyanin in the black rice bran was extracted using the maceration method with methanol as a solvent. The extract obtained was separated through a preparative thin layer chromatography (TLC) of silica GF254 and a mobile phase composed of n-butanol, acetic acid, and water. Two fractions were collected and analyzed for the anthocyanin content. The preparative TLC spots were separated for further detection and measurement of cyanidin 3-O-glucoside using HPLC followed by LC-MS. The antioxidant activity of the fractions were measured using the DPPH free radical scavenging method. The results showed that the anthocyanin in fraction 1 was identified as cyanidin 3-O-glucoside (66.1 ± 10.6 µg/g). The IC50 of fractions 1 and 2 were 200.96 and 218.36 µg/mL, respectively. Analysis of the macro- and micronutrients revealed that the black rice bran of ‘Cempo Ireng’ had nutrient contents comparable with other rice cultivars. Therefore, this local black rice bran can be used as a source of antioxidants and macro-- and micronutrients.

Expression analysis of antioxidant genes in response to drought stress in the fl ag leaf of two Indonesian rice cultivars R. Refli; Sukarti Muljopawiro; Kumala Dewi; Diah Rachmawati
Indonesian Journal of Biotechnology Vol 19, No 1 (2014)
Publisher : Universitas Gadjah Mada

The objective of this study was to analysis the expression of antioxidant genes in response to droughtstress in Indonesian rice. The malondialdehyde (MDA) content and the expression of Cu-ZnSod1, cCu-ZnSod2,MnSod1, cApxa, cApxb, chl-sApx, Cat1, Cat2, Cat3, Gr1, Gr2, and Gr3 genes were assayed in the rice fl ag leaf ofCiherang and Situ Bagendit cultivars subjected to control, mild and severe drought during the grain fi llingphase. Increase in MDA content of Ciherang treated to mild and severe drought was almost two-fold andthree-fold respectively, while MDA content in Situ Bagendit subjected to mild and severe drought increasedapproximately one-fold and two-fold as compared to the control. The semi quantitative reverse transcriptionpolymerase chain reaction (sqRT-PCR) analysis showed that the expression of cCu-ZnSod1, MnSod1, Cat2, Gr3genes of Ciherang, and cCu-ZnSod2, MnSod1, cApxa, cApxb, chl-sAPX, Cat2 and Gr1 genes of Situ Bagendit increasedin fl ag leaf of plant treated to drought. Expressions of cApxb, chl-sApx, Cat3 of Ciherang and Cu-ZnSod1 and Gr2genes of Situ Bagendit were not changed signifi cantly by drought stress. Decreased expression was shownby cCu-ZnSod2, cApxa, Cat1, Gr1 and Gr2 genes of Ciherang, and Cat1, Cat3 and Gr3 genes of Situ Bagendit. Theresults indicated that the activity of oxidative defense was regulated by four genes; cCu-ZnSod1, MnSod1, Cat2,Gr3 in Ciherang, and eight genes; cCu-ZnSod1, cCu-ZnSod2, MnSod1, cApxa, cApxb, chl-sApx, Cat2 and Gr1 in SituBagendit. Therefore, differences in the number of antioxidant genes controlling oxidative defense systemmight determine the difference of the oxidative defense capacity between both cultivars in response to droughtstress during grain fi lling.

Selection of Yeast Strains for Ethanol Fermentation of Glucose-FructoseSucrose Mixture J. Jasman; Irfan Dwidya Prijambada; Chusnul Hidayat; Donny Widianto
Indonesian Journal of Biotechnology Vol 17, No 2 (2012)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.16001

This study was aimed to compare the ability of some yeast strains to consume sugars (sucrose, glucoseand fructose) and to convert them into ethanol during fermentation. The results of this comparison will be thebasis of considerations in choosing the right strain to be used as a mixed culture to increase the productionof ethanol from substrate containing a mixture of sucrose, glucose and fructose, such as juice of cane andsweet sorghum. The study was conducted using fermentation in substrate consisting of glucose, fructose,and sucrose separately, glucose-fructose mixture, and glucose-fructose-sucrose mixture using some yeaststrains: FNCC3012, OUT7009, OUT7027, OUT7055, OUT7080, OUT7096, OUT7903, OUT7913, and OUT7921.Following the fermentation, analysis of the produced ethanol and the remaining sugar was conducted. Theresults of study indicated that the strains with the highest substrate consumption were OUT7921, OUT7096,OUT7055, OUT7027, and OUT7913 for glucose, fructose, glucose-fructose mixture, sucrose, and glucosefructose-sucrose mixture, respectively. Strains that produced highest concentration ethanol were OUT7096 inglucose and sucrose substrates, OUT7921 in substrate of glucose-fructose mixture and sucrose, OUT7913 insubstrate of glucose-fructose-sucrose mixture. Upon consideration of each strain capacity, both in consumingsugar and producing ethanol, the recommended strains for use in mixed culture in bioethanol fermentationusing mixed substrate of glucose, fructose and sucrose are OUT7096, OUT7913, and OUT7921.

Identification of Pathogenecity of Avian Influenza Virus Subtype H5N1 from Waterfowls Base on Amino Acid Sequence of Cleavage Site Hemagglutinin Protein R. Susanti; Retno D. Soejoedono; I Gusti Ngurah K Mahardika; Wayan T I Wibawan; Maggy T Suhartono
Indonesian Journal of Biotechnology Vol 13, No 2 (2008)
Publisher : Universitas Gadjah Mada

Identification of pathotype of Avian Influenza Virus (AIV) subtype H5N1 isolates is very important. Thisresearch aimed to identify the pathotype of AIV subtype H5N1 isolated from household waterfowls in West Javabased on molecular markers of amino acid sequences of the Hemagglutinin (HA) cleavage site. Fragments of HAgenes of 21 isolates were amplified using RT-PCR with a primer pair that flanking the cleavage site region, andsequenced with dideoxy-termination method with ABI automatic sequencer (Applied Biosystems). Multiple alignmentof nucleotide and their deduced amino acid sequence were analyzed using ClustalW from MEGA 3.1 program.The result shows that all H5N1 isolates (21 isolates) possess polybasic cleavage sites with 2 patterns ofamino acid sequence, i.e QRERRRKKR (20 isolates) and QRESRRKKR (1 isolate). This finding indicates that all ofthe viruses isolated in this research were of highly pathogenic avian influenza (HPAI) strains.Keywords: cleavage site, waterfowls, HPAI

Study of creatinine transport through chitosan/pectin/poly(vinyl alcohol) blend membranes Ni Putu Sri Ayuni; Ni Wayan Yuningrat
Indonesian Journal of Biotechnology Vol 21, No 2 (2016)
Publisher : Universitas Gadjah Mada

Creatinine was final product of creatine metabolism inskeletal muscle. Increasing of creatinine showed decreasing of kidney function. Kidney fuction decreased could be treated by hemodialysis (HD). One of the natural polymer was cellulose which often used as hemodialysis membrane. Chitosan as natural membrane was used as membrane in this research because the structure was almost similar to cellulose. Chitosan was complexed by pectin and poly(vinil alcohol) (PVA) to fixed mechanical characteristic of membrane. The objective of this research were to synthesize, characterize, and know efficiency of creatinine transport using chitosan/pectin/PVA blend membranes. The functional groups of synthesized membrane were characterized by FTIR spectrophotometer. Efficiency of optimum creatinine transport was known by using membrane with chitosan and pectin ratio70:30 while PVA used 0.5%; 1.0% and 1.5%. The source and acceptor phase resulted were complexed by picric acid and analyzed by Ultraviolet-Visible (UV-Vis) Spectrophotometer. The result of membrane synthesized which was analyzed by FTIR Spectrophotometer shows that there is a band broadening on wave number 3448.72 cm-1. It is indicated that there are an overlapped stretching of hydrogen bond -OH on PVA and NH2 on chitosan. The optimum creatinine 70 ppm transported using membrane with 1.5% PVA addition is 59%.

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