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INDONESIA
Indonesian Journal of Biotechnology
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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-429 T/C and -374 T/A Polymorphisms in Receptor Advanced Glycation Endproducts (RAGE) gene in Type 2 Diabetic Patients with Diabetic Retinopathy at the Dr. Sardjito General Hospital Yogyakarta Djuma, Agustina Welhelmina; ., Sunarti; Hastuti, Pramudji
Indonesian Journal of Biotechnology Vol 17, No 1 (2012)
Publisher : Universitas Gadjah Mada

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Abstract

Receptor of advanced glycation endproduct (RAGE) plays an important role in the pathogenesis of diabetic vascular complications, such as diabetic retinopathy. The interaction between the RAGE and advanced glycation end product (AGE) leads to oxidative stress and could result in cellular activation and infl ammation. The production of AGE occurs normally during aging but it increases in hyperglycemia condition. The objective of this research was to investigate the association between -429 T/C and -374 T/A polymorphisms in RAGE gene with the risk of diabetic retinopathy (DR) of type 2 diabetic patients in Javanese population. This was a case control study which consisted of 40 type 2 diabetic patients with DR as case subjects and 40 type 2 diabetic patients without DR (NDR) as control subjects. Genotyping of polymorphism was performed by PCR-RFLP. Chi-square test and odds ratio models were used to evaluate the association of both polymorphisms and DR risk and to examine 2-SNP haplotype of -429 T/C and -374 T/A polymorphisms in RAGE gene on DR. The genotype frequencies of -429 T/C polymorphism in RAGE gene in DR subjects were TT = 72.5% and TC/CC = 27.5%; while in NDR subjects were TT = 80% and TC/ CC = 20%, with p = 0.431. The allele frequencies of -429 T/C polymorphism in DR subjects were T = 83.7% and C= 16.3%, while in NDR subjects were T = 87.5% and C = 12.5%, with p = 0.499. The genotype frequencies of -374T/A polymorphism in RAGE gene in DR subjects were TT = 67.5%, TA = 32.5% while in NDR subjects were TT =82.5%, TA = 17.5%, with p = 0.121. In DR subjects, the frequencies of T and A were 83.7% and16.3%, while in NDR subjects the frequencies of T and A were 91.2 % and 8.8%, with p = 0.151. Odds ratios of -429 T/C polymorphism were 1.52 (95% CI = 0.54 – 4.29) for TC/CC genotype and 1.358 (95% CI = 0.56 – 3.31) for C allele. Odds ratios of -374 T/A polymorphism were 2.27 (95% CI = 0.79 – 6.49) for TA genotype and 2.02 (95% CI = 0.76 – 5.37) for A allele. χ2-value for 2-SNP haplotype was p = 0.127. The -374 T/A polymorphism in RAGE gene was a stronger risk factor of DR than -429 T/C polymorphism in RAGE gene. There were not signifi cantly different of frequencies of genotypes, allele, and two-SNP haplotype of -429 T/C and -374 T/A polymorphisms in RAGE gene between DR subjects and NDR subjects.
Legume Nodulating Bacterium, Achromobacter xylosoxidans Found in Tropical Shrub Agroecosystem, Sumatera, Indonesia Wedhastri, Sri; Fardhani, Dinar Mindrati; Kabirun, Siti; Widada, Jaka; Widianto, Donny; Evizal, Rusdi; Prijambada, Irfan Dwidya
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

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Abstract

Legume nodulating bacteria (LNB), known also as rhizobia, are soil bacteria, which are able to form rootnodules and fi x nitrogen in the leguminous plants. The LNB availability in the soil depends on the type ofagroecosystem, where plant grows. In this study, we isolated LNB from the shrub agroecosystem in Sumatera,Indonesia, and obtained four selected bacterial strains. Among them, the isolate UGM48a formed root nodulein Macroptilium atropurpureum and showed highest number of nitrogenase activity. UGM48a also contains nifHand nodA genes. An analysis of the PCR-amplifi ed 16S rDNA and BLASTn analysis showed that UGM48adisplayed 96% similarity with Achromobacter xylosoxidans. In addition, UGM48a were successfully nodulatedGlycine max (L.) merr var. wilis. This is the fi rst report detecting A. xylosoxidans as nodule-forming species forGlycine max possesing the positive copy of nodA gene.Keywords : Legume Nodulating Bacteria, shrub agroecosystem, Achromobacter xylosoxidans, nodA, Glycine max
Alternative Oxidase (AtAox) c78s Mutant Expression at Escherichia coli (SASX41DB) Djajanegara, Ira
Indonesian Journal of Biotechnology Vol 12, No 1 (2007)
Publisher : Universitas Gadjah Mada

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Abstract

Alternative oxidase (AOX) is the terminal oxidase operating in the mitochondrial electron transport chain. Theenzyme is activated by organic acid such as pyruvate and by reduction process. Based on sequences alignment ofalternative oxidase gene (Aox) found in several organisms, there are 2 conserved cysteine residues. In order toinvestigate the importance of those cysteine residues on the activity of AOX, mutation at cysteine residue number 78of Aox gene isolated from Arabidopsis thaliana (AtAox) was conducted. Cysteine at position number 78 was changedinto serine and the c78s mutant was expressed in Escherichia coli strain SASX41DB. This particular E. coli strain isunable to grow aerobically unless transformed with Arabidopsis Aox gene (AtAox). Expression studies on c78smutant showed that this mutant cannot be oxididized and can not be activated by pyruvic acid. This mutant isacivated by succinate instead of pyruvate. Mutation at cysteine closer to the N residue is affecting both organic acidand redox activation. Therefore, it is concluded that cysteine residue closer to the N residue is the site for bothactivation by pyruvate as well as activation by reduction process.Keywords : Alternative oxidase, site-directed mutation, SASx41DB, cysteine residues
Analysis of Toxoplasma gondii Repeat Region 529 bp (NCBI Acc. No. AF146527) as a Probe Candidate for Molecular Diagnosis of Toxoplasmosis Pratama, Dyah Ayu Oktavianie A; ., Sumartono; Artama, Wayan T.
Indonesian Journal of Biotechnology Vol 14, No 1 (2009)
Publisher : Universitas Gadjah Mada

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Abstract

            Toxoplasmosis is a disease caused by protozoan parasite Toxoplasma gondii. The infection is commonly asymptomatic. The availability of confirmative and accurate detection system is really needed. This research was aimed to develop a molecular diagnosis based on the conserved and high copy number repeat region of Toxoplasma gondii with hibridization method. Nucleic acid was isolated from tachyzoites. The repeat region of T. gondii was amplified using PuRe Taq Ready To Go-PCR Beads (Amersham Bioscience),  forward primer 5’- GAC TCG GGC CCA GCT GCG  -3’ and reverse primer 5’- CCT CTC CTA CCC CTC CTC -3’. The amplicon was sequenced using ABI Prism 3100-Avant Genetic Analyzer (PT. Charoen Pokphand, Jakarta). Probe was labeled using digoxigenin-11-dUTP. Application of probe to detect it’s complementary nucloeic acid was done by hibridization method. The research concluded that probe toxo-103 bp was highly homolog with several strain of T. gondii and it has no homology either with host’s genome or other parasites which have close genetic relationship with T. gondii.   Hybridization analysis showed that probe could detect the complementary nucleic acid up to 10 ng/ul concentration.      
Determination of Haemaglutinin and Gene Encoding Fibronectin Binding Proteins Staphylococcus aureus Isolated from Dairy Milk Cows Pratomo, Feny Prabawati; Salasia, Siti Isrina Oktavia; Tato, Syarifudin
Indonesian Journal of Biotechnology Vol 16, No 2 (2011)
Publisher : Universitas Gadjah Mada

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Abstract

AbstractStaphylococcus aureus is a major pathogen causing clinical and subclinical mastitis in dairy milk cows. The mastitis has immense economical impacts, where it reduces of the quantity and quality of milk production. The aims of the research were to analyse haemaglutinin and gene encoding fibronectin binding proteins. Nineteen Staphylococcus aureus isolates used in the present study were isolated from dairy milk cows from Yogyakarta, Solo, Boyolali and Sumedang. The haemagluitinin of S. aureus were determined based on haemaglutination reaction to erythrocytes of rabbit. Detection of gene encoding fibronectin binding proteins could be performed with specific primers using polymerase chain reaction (PCR). The results of studies showed that most of S. aureus (78,95%) expressed haemaglutinin based on their ability to aglutinate rabbit erythrocytes. Analysis of gene encoding fibronectin binding proteins of S. aureus revealed gene fnbA with size of approximately 1300 bp for 57,89% isolates, gene fnbB with size of approximately 900 bp for 31,58% isolates and both of gene fnbA and fnbB could be detected for 31,58% isolates. The characters of S. aureus based on haemaglutinin, gene fnbA and fnbB of the present study could be used as an information to control of S. aureus infection in dairy herds.Keywords : Staphylococcus aureus, haemaglutinin, gene encoding fibronectin binding protein, milk cow
The Diversity of Legume-Nodulating Bacteria from Several Agroecosystems in Sumberjaya, Lampung Wedhastri, Sri; Yuliana Prahastiwi, Yuliana; Widada, Jaka; Widianto, Donny; Kabirun, Siti
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

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Abstract

Bacteria that capable of forming root nodules on legumes are known as Rhizobia. They have also known as Legume- Nodulating Bacteria (LNB). They can fi x nitrogen from the atmosphere. Diversity of Legume-Nodulating Bacteria is affected by biotic factors (such as their genetic factors, plants, and competition with the other soil microbes) and abiotic factors (such as land use, soil’s temperature, pH, chemistry and soil’s properties). The aim of this experiment is to know the diversity of eleven Legume- Nodulating Bacteria based on their phenotypic and genotypic characters. The eleven LNB used in this experiments were isolated from several agroecosystems in Sumberjaya, Lampung. The analysis of these LNB diversity were carried out by characterizing both phenotypic and genotypic properties. The diversity analysis showed that the eleven LNB isolates had high diversity, based on nodule formation, and classifi ed into two groups of cross inoculation group.Key words: Rhizobia, phenotypic diversity, genotypic diversity
Detection of eae, bfpA, espA Genes on Diarrhoeagenic Strains of Escherichia coli Isolates Harti, Agnes Sri; Iravati, Susi; Asmara, Widya
Indonesian Journal of Biotechnology Vol 11, No 1 (2006)
Publisher : Universitas Gadjah Mada

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Abstract

The Enteropathogenic Escherichia coli (EPEC) is one of pathogenic strain of diarrheagenic E. coli group in children andinfant that occurs in developing countries. The significant virulence factors in pathogenic EPEC are eaeA (E. coli attachingeffacing), bfpA (bundle-forming pilus A) and espA (encoding secreted protein A) genes. The use of DNA probes to detect thevirulence genes in E. coli in Indonesia is not common yet. In this experiment the gene fragments of eae, bfpA, and espA were usedas probes to detect the EPEC among E. coli isolates from stool specimensin of diarrheic children attending Public Health Centersin Yogyakarta. The DNA samples were isolated from 49 diarrheagenic E. coli isolates. The DNA probes of eae, bfpA and espAwere obtained by amplification of DNA fragment of EPEC O126 using PCR technique. Furthermore, those probes were used toidentify the presence of those genes among E. coli isolates using hybridization technique. The results showed that 42 (85.7%)isolates were espA+, 25 isolates (51%) were eaeA+ (EPEC strains). Therefore among 25 isolates of EPEC, 20 isolates (80 %)among EPEC were bfpA+ (typical EPEC strains).Keywords : DNA probe, eae, bfpA, espA, EPEC.
Actin Distribution in Lamina Neuralis During Cranial Neurulation of Wistar Rats Embryo (Rattus rattus) Prahastuti, Indriayuni; R, Issoegianti S.M.
Indonesian Journal of Biotechnology Vol 13, No 1 (2008)
Publisher : Universitas Gadjah Mada

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Abstract

such as craniorachisis and exencephaly. One of the processes is changing in lamina neuralis cells shape, which iscaused by actin microfilament rearrangement within lamina neuralis cells. To examine the distribution of actinmicrofilament during cranial neurulation Wistar rats embryo were used. Embryos were obtain at following days ofdevelopment; 8 days 18 hours, 9 days, 9 days 6 hours, 9 days 12 hours, 9 days 18 hours, and 9 days 20 hoursrespectively. Immunohistochemistry Avidin Biotin-peroxidase Complex (ABC) method was used to examine andidentify the distribution of actin in lamina neuralis cells. Light microscopic observation shows positive reaction foractin immunoreactivity in the apical surface of bending lamina neuralis cells. In contrast, actin is not observed in nonbendinglamina neuralis. Actin is not detected at 8 days 18 hours embryos. At 9 days embryos, positive reaction isobserved over the entire apical surface of lamina neuralis.Key words: Cranial neurulation, Actin, lamina neuralis, Rats embryo.
Antifungal Production of a Strain of Actinomycetes spp Isolated from the Rhizosphere of Cajuput Plant: Selection and Detection of Exhibiting Activity Against Tested Fungi A, Alimuddin; Widada, Jaka; Asmara, Widya; M, Mustofa
Indonesian Journal of Biotechnology Vol 16, No 1 (2011)
Publisher : Universitas Gadjah Mada

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Abstract

Actinomycetes 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.
Partial Purifi cation, Stability Analysis, and Preservation of Xylanase from Xylanolytic Alkalophylic Bacteria Hanim, Chusnul; Cahyanto, Muhamad Nur; Yusiati, Lies Mira; Wibowo, Ali
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

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Abstract

A xylanase, which produces xylose from oat spelt xylans, was isolated from the culture medium of  xylanolytic alkalophylic bacteria mutant. The enzyme was purifi ed by ammonium sulphate with level 30, 40, 50, 60, 70, 80, and 90%. The purify of the fi nal preparation was demonstrated by sodium dodecyl sulphatepolyacrylamide gel electrophoresis. The molecular masses of the purifi ed xylanase were 137.61 and 165.34 kDa. Result of ammonium sulphate saturation with the highest activity was used as standart for saturation for enzyme production and preservation, using corn, tapioca, soy bean meal and gaplek fl our as carriers. Addition of 60% ammonium sulphate showed the highest xylanase activity (62.03 U/g), and produced 89.40% enzyme recovery. Tapioca, as a carrier, produced the highest xylanase activity.Key words: preservation, purifi cation, stability analysis, xylanase.

Page 8 of 52 | Total Record : 518

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