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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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16s rRNA Identification of Pediococcus spp. from Broiler and Studies of Adherence Ability on Immobilized Mucus Ema Damayanti; Lies Mira Yusiati; Achmad Dinoto
Indonesian Journal of Biotechnology Vol 17, No 2 (2012)
Publisher : Universitas Gadjah Mada

The objectives of this research were to study taxonomical status of lactic acid bacteria (LAB) isolated from broiler and adherence ability on mucus in vitro. Molecular analysis was performed by analyzing 16S rRNA gene using universal primer. The adherence assay on mucus was carried out using microplate method with total plate count (TPC), absorbance (A550) and confirmed by scanning electron microscopy (SEM). The results of this studies revealed that three of LAB isolates have closed relation to Pediococcus acidilactici (99.9%) species.Three isolates of P. acidilactici have adherence ability on broiler mucus higher than that on porcine mucin with an adherence percentage of 55.5% versus 50.8% and absorbance A550 of 0.061 versus 0.051, respectively. The highest adherence ability showed by P. acidilactici R02 with adherence percentage was 59.3% and absorbance A550 = 0.068. Adherence on mucus were affected by the addition of 3 g/l of gastric juice and 0.3% (b/v) of bile salt. Adherence analysis using SEM also showed that the adherence on broiler mucus was higher than the adherence on porcine mucin. Altogether this adherence studies, suggest that three isolates of P. acidilactici LAB were capable of colonizing host intestinal mucus in vitro as important property to be promising probiotic bacteria for broiler.Key words : adherence, broiler, Pediococcus, mucus, 16S rRNA

The aqueous extract of Gerrardanthus macrorhizus caudex enhanced doxorubicin activity in MCF-7 human breast cancer cells Sari Haryanti; Yuli Widiyastuti; Slamet Wahyono
Indonesian Journal of Biotechnology Vol 23, No 1 (2018)
Publisher : Universitas Gadjah Mada

Gerrardanthus macrorhizus (GM) caudex, is traditionally used in cancer therapy by the Tetun people in Belu District, East Nusa Tenggara Province, Indonesia, where it is known as “akar batu”. This study aimed to explore the cytotoxic effects of G. macrorhizus caudex aqueous extract, as well as its combination with doxorubicin, on MCF-7 cells. Also investigated were the possible mechanisms of interaction through cell cycle progression and apoptosis induction. Single treatments of 5–320 µg/mL of the extract showed morphological alterations in MCF-7 cells, but did not show any cytotoxic effect. Combining the extract with doxorubicin resulted in a synergistic cytotoxic effect. Doxorubicin concentrations equivalent to 1/12, 1/8, and 1/5 fold of the IC50 combined with 20 µg/mL decreased viability to 48%. We then explored the combination effect of doxorubicin 0.4 µM with GM 5 and 20 µg/mL using a flow cytometer. A low concentration of the extract (5 µg/mL) combined with 0.4 µM of doxorubicin resulted in slight cell cycle modulation by G1, G2M arrested and apoptosis induction. The combination of doxorubicin and a higher concentration of the extract (20 µg/mL) did not show cell cycle modulation, and led to necrosis. Therefore, G. macrorhizus caudex at low concentrations has the potential to be developed further as a co-chemotherapeutic agent.

A Study on Production of Poly-β-Hydroxybutyrate Bioplastic from Sago Starch by Indigenous Amylolytic Bacteria Nur Arfa Yanti; Langkah Sembiring; Sebastian Margino; Nurhayani H. Muhiddin
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

Bacillus sp. PSA10 and Bacillus sp. PPK5 were two indigenous strain amylolytic bacteria from SoutheastSulawesi that have ability to produce bioplastic poly-β-hydroxybutyrate (PHB) from sago starch. The study wasattempted to determine the mechanism of PHB production by bacteria amylolytic was grown on sago starchcontainingmedia. Two amylolytic bacteria i.e. Bacillus sp. PSA10 and Bacillus sp. PPK5 was grown for 168 hin a mineral salts medium with sago starch as carbon source. Growth of amylolytic bacteria was monitoredby cell dry weight. Extraction of PHB was done by N-hexane acetone-diethyl ether method and PHB contentwas quantifi ed with UV spectrophotometer at 235 nm. Glucose level was determined by using kit of glucoseGOD 10” and was quantifi ed with spectrophotometer at 500 nm. Sago starch concentration was determinedby phenol method using specthrophotometer at 490 nm. The result of the study showed that Bacillus sp.PSA10 was produced PHB up to 66,81 % (g PHB/g cell dry weight) at 48 h and Bacillus sp. PPK5 up to 24,83% (g PHB/g cell dry weight) at 84 h. Bacillus sp. PSA10 has ability to converse sago starch to be PHB directlywithout glucose accumulation in the media, whereas Bacillus sp. PPK5 have to accumulate glucose as productof sago starch hydrolysis to produce of PHB. PHB synthesis by Bacillus sp. PHB production on sago starchof the Bacillus sp. PSA10 was found to be growth-associated whereas Bacillus sp. PPK5 was found to be nongrowth-associated. Therefore, two indigenous amylolytic bacteria were having of difference in biosynthesismechanism of PHB in sago starch medium and their characteristics of PHB synthesis should be consideredin developing cultivation methods for the effi cient production of PHB. Keywords : Production, PHB, Amylolytic bacteria, Sago starch.

Marker Assisted Selection for Bacterial Leaf Blight Rice Mutant Lines Resistant A. Aryanti; A. Almaida; Rika Heryani; Nana Supriatna
Indonesian Journal of Biotechnology Vol 20, No 1 (2015)
Publisher : Universitas Gadjah Mada

Induction of mutation using gamma rays for improving of Mira-1 rice variety has been conducted.Rice mutant lines M2 generation have been obtained from mutation by the doses of 25, 50, 75, 100, 150 and200 Gy of gamma rays. Selection of mutant lines tolerant to the disease was only observed in the field neithergenetically. Marker assisted selection is a tool to obtain a new rice variety tolerant to the disease of bacterialleaf blight (BLB) genetically. Xanthomonas oryzae pv.oryzae (Xa) was the pathogen of BLB, and the identificationof rice mutant lines which were containing of Xa5, Xa13 and Xa21 genes have been done using PolymeraseChain Reaction ( PCR ) method. The result showed that one mutant line, and four mutant lines from mutationby the doses of 25 Gy and 150 Gy were containing Xa5, Xa13 and Xa21 genes the same as that of Code ricevariety as positive control, and none in Kencana Bali rice variety as negative control. Mira-1 rice variety as theparent plant was only contains Xa5 and Xa21 genes. The doses of 50 Gy and 100 Gy were very affective onremoving of all bands for identification of those genes. The purpose of this research was to obtain the mutantlines which were contain of those Xa genes as indicator for resistant to BLB disease genetically.

Biochemival Characterization of an Antibactrial Glycoprotein from Achatina fulica ferussac Snail Mucus Local Isolate and Their Implication on Bacterial Dental Infection Titiek Berniyanti; Edy Bagus Waskito; S. Suwarno
Indonesian Journal of Biotechnology Vol 12, No 1 (2007)
Publisher : Universitas Gadjah Mada

Snails crawl over a variety of potentially contaminated surfaces and their foot is the primary site of entry forpathogens, parasites and a range of opportunistic organisms, so it is a little wonder that they must have a defensivesystem to protect them. The mucus secreted on the body surfaces of mollusks is known to play crucial role inlocomotion, feeding, osmoregulation, reproduction and protection of epithelial surfaces. The snail mucus alsocontains Glycoaminoglycans (GAGs) which are complex polysaccharides that participate in the regulation ofphysiological processes through the interactions with a wide variety of proteins. GAGs, such as heparin, serve as keyto biological response modifiers, in example for acting asa a target for pathogen and parasitic factors for attachment,invasion, and immune system.For years, it has been known that the mucus secretions from snails Achatina fulica ferussac local isolate can be usedas a medication, and even empirically it is used to treat infected teeth tahat is suffered by people in rural area. Theantibacterial factor was surveyed in the aqueous extract and the mucin fraction of snail Achatina fulica ferussac, andthey exhibited positive antibacterial for Gram-positive, Escherichia coli and Gram negative, Streptococcus mutans. Inthe following study, it has been proved that an antibacterial content in the mucus was a Glycoprotein. It wascomposed of two subunits of Molecular Weight (MW) 71-73 kDa. The GelCode Glycoprotein Staining Kit detectedglycoprotein sugar moieties in polyacrylamide gel and on nitrocellulose membrane, while the glycoproteincarbohydrate estimation kit detected glycoprotein and estimated carbohydrate content. The glycoprotein contentwas 4.537 ± 0.876 for carbohydrate and 6.420 ± 1.242 for protein.Keywords : characterization, glycoprotein, Achatina fullica Ferussac snail mucus, galur Jawa, antibacterialfactor

The effects of population size on genetic parameters and mating system of sandalwood in Gunung Sewu, Indonesia Yeni Widyana Nurchahyani; Sapto Indrioko; Eny Faridah; Atus Syahbudin
Indonesian Journal of Biotechnology Vol 20, No 2 (2015)
Publisher : Universitas Gadjah Mada

We combined feld observations with isoenzyme analysis to compare population demographic and its effects on genetic diversity and mating systems, among six populations of sandalwood in Gunung Sewu, Indonesia, during March to August 2015. This endangered economic-important species was originated from the southeastern parts of Indonesia, but is recently occured as new landraces in Gunung Sewu, Java island. The observed heterozygosity varied from Ho 0.184 to 0.385 in parents, and from Ho 0.083 to 0.348 in offspring levels, based on the degree of clonality and genetic base. Most of genetic variation is distributed within populations, and only 2.7% were presented among populations, that was indicated by the low DST and FST value (HT 0.30; HS 0.276; DST 2.4%; FST 7.98%). A dendrogram indicated a grouping of populations into three clusters. However, there were seemed to be no association between geographical and genetic distance. Genetic depletion occured due to (i) clonality events as result of heavy-exploitation and/or natural disturbance which induced root suckering, (ii) genetic drifts and bottleneck effects, (iii) the founder effects due to parental low diversity, and (iv) the alteration on mating systems to be more inbreeders. Some of the results confrmed a “reproductive assurance prediction” while some others were contradicting this. It seemed that genetic diversity and mating systems are not much affected by population size, but more by the parental heterozygosity and the degree of clonality. Our results emphasized the importance of populations’ genetic base or parental genetic diversity to naturally maintain the genetic and evolutionary processes under equilibrium conditions.

Development of Random Amplified Polymorphism DNA Markers Linked to Powdery Mildew Resistance Gene in Melon Budi Setiadi Daryono; Ganies Riza Aristya; Rina Sri Kasiamdari
Indonesian Journal of Biotechnology Vol 16, No 2 (2011)
Publisher : Universitas Gadjah Mada

A random amplified polymorphic DNA (RAPD) marker linked to powdery mildew resistance gene (Pm-I) in melon PI 371795 was reported. However, the RAPD marker has problem in scoring. To detect powdery mildew resistance gene (Pm-I) in melon accurately, the RAPD marker was cloned and sequenced to design sequence characterized amplified region (SCAR) markers. SCAPMAR5 marker derived from pUBC411 primer yielded a single DNA band at 1061 bp. Segregation of SCAPMAR5 marker in bulk of F2 plants demonstrated that the marker was co-segregated with RAPD marker from which the SCAR marker was originated. Moreover, results of SCAR analysis in diverse melons showed SCAPMAR5 primers obtained a single 1061 bp linked to Pm-I in resistant melon PI 371795 and PMAR5. On the other hand, SCAPMAR5 failed to detect Pm-I in susceptible melons. Results of this study revealed that SCAR analysis not only confirmed melons that had been clearly scored for resistance to Pm-I evaluated by RAPD markers, but also clarified the ambiguous resistance results obtained by the RAPD markers. Key words: Cucumis melo L., Pm-I, RAPD, SCAPMAR5

Nuclear Maturation of Porcine Oocytes in vitro: Effect of the Cumulus-Oocyte Complexes Quality Ni Wayan Kurniani Karja
Indonesian Journal of Biotechnology Vol 13, No 2 (2008)
Publisher : Universitas Gadjah Mada

The objective of this study was to examine the effect of the cumulus-oocyte complexes (COCs) quality on the ability of porcine oocytes to mature in vitro. Porcine COCs were collected from 2-6 mm follicles of slaughterhouse ovaries. The oocytes used for IVM were classified into three categories based on the compactness and transparency of the cumulus investment and homogeneity and transparency of the ooplasm. The oocytes were then matured in vitro for 44 h. At 22 of maturation culture, most of the oocytes in all</div><div>groups were identified still at germinal vesicle (GV) stage and metaphase I (M-I) stage. After 44 h of culture, a greater proportion of Category I and II oocytes completed in vitro maturation through the second meiotic as compared with that of Category III oocytes (P<0.05). The proportion of oocytes remaining at M-I stage and the degenerative oocytes in Category III oocytes were significantly higher than those of oocytes in other groups (P<0.05). These data indicate that porcine oocytes with high quality cytoplasm and a cumulus cell complement have a much greater chance of maturing in vitro than that lower quality oocytes. The morphological grading of immature oocytes is an appropriate selection criterion for their developmental ability.

The Use of Genetic Variability Analysis of Fusarium oxysporum f. sp. cubense for Breeding Resistance of Banana against Fusarium Wilting Disease Faria Ruhana
Indonesian Journal of Biotechnology Vol 12, No 2 (2007)
Publisher : Universitas Gadjah Mada

Fusarium wilting on banana crop caused by Fusarium oxysporum f. sp. cubense is one of the important disease in banana plant in Indonesia. This disease can cause plant to wilt and die, therefore bringing loss to the banana farmer and entrepreneur. F. oxysporum f. sp. cubense genetic variability analysis techniques can be done by in vitro or in vivo. One of F.oxysporum f. sp. cubense genetic variability analysis techniques by in vitro is RAPD-PCR. In this research, analysis is continued with pathogen test. Genetic variability analysis by in vivo is needed to determine the level of pathogen and the race. The result of genetic variability techniques by RAPD-PCR done by this writer indicates that there is a big relation/link difference between isolats from different island. Isolat from Mojokerto (East Java) is 100% genetically different compared to the one from West Sumatera. Later, result of pathogen test shows that Pisang Ambon Kuning is the most resilient compared to Pisang Raja and William Cavendish. Based on the level of pathogen, there are two race grouping, which are race 1 that attacks Pisang Ambon Kuning and race 4 that attacks Pisang Raja and William Cavendish. Scott-Knott analysis on 26 isolats results in no real difference between isolats tested.

Identification of Metabolic Intermediates in Microbial Degradation of Chrysene by Armillaria sp. F022 Tony Hadibarata; Risky Ayu Kristanti
Indonesian Journal of Biotechnology Vol 15, No 2 (2010)
Publisher : Universitas Gadjah Mada

To 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. F022

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