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Articles by issue : Vol 8, No 3 (2014): September 2014
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Articles
Isolation and Characterization of New Antibiotics from Indonesian Coastal Marine Bacteria

VERONICA, VERONICA, LAY, BIBIANA W, MAGDALENA, STELLA

Microbiology Indonesia Vol 8, No 3 (2014): September 2014
Publisher : Indonesian Society for microbiology

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Abstract

Antibiotics are organic compounds produced by various microorganisms and have the ability to inhibit the growth or kill other microorganisms. However, the irrational application of antibiotics lead to resistance of microorganisms so that they become ineffective. The objectives of this study were to isolate and characterize new antibiotics from Indonesian coastal marine bacteria. In this study, a total of 141 isolates consisting of seven Streptomyces sp. isolates and 134 isolates of other marine bacteria, were obtained from Indonesian coastal regions. Based on antimicrobial activity assay, four Streptomyces sp. and five marine bacteria isolates showed antimicrobial activity towards Bacillus cereus and Staphylococcus aureus with the diameter of inhibition of 3-12 mm. Further, antimicrobial compounds were produced successfully extracted with six organic solvents, such as 1-butanol, dichloromethane, n-hexane, chloroform, and toluene. The best solvent to extract antimicrobial compounds from Streptomyces sp. isolates was 1-butanol, while the best solvent to extract antimicrobial compounds from other marine bacteria isolates could not be specified. Antimicrobial compounds were successfully separated by thin layer chromatography with mobile phase used were 1-butanol, acetic acid, and water at a ratio of 4:1:2 and retention values obtained at 0.50 and 0.63.

Characterization and Pathogenicity of Fusarium oxysporum as the Causal Agent of Fusarium Wilt in Chili (Capsicum annuum L.)

FERNIAH, REJEKI SITI, DARYONO, BUDI SETIADI, KASIAMDARI, RINA SRI, PRIYATMOJO, ACHMADI

Microbiology Indonesia Vol 8, No 3 (2014): September 2014
Publisher : Indonesian Society for microbiology

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Abstract

Fusarium wilt is a serious disease attacking chili plants in Central Java which cause lost of chili productivity. Fusarium wilt is caused by pathogenic fungi Fusarium oxysporum, which is host specific. The objectives of this research were to characterize the pathogenic F. oxysporum as the causal agent of fusarium wilt in chili plants and to observe the virulence of the pathogen. Fungal pathogen was isolated from Tawangmangu as an endemic area of fusarium wilt in Central Java. The fungi was characterized morphologically and identified molecularly by its internal transcribed spacer regions (ITS regions). Pathogenicity test was done to observe the virulence of the pathogen. One pathogenic strain was isolated from Tawangmangu, Karanganyar and was identified  morphologically and molecularly as F. oxysporum.  

Cloning, Expression and Bioinformatic Analysis of Human Papillomavirus Type 52 L1 Capsid Gene from Indonesian Patient

SUHANDONO, SONY, KENCANA UNGU, DEWI AYU, KRISTIANTI, TATI, SAHIRATMADJA, EDHYANA, SUSANTO, HERMAN

Microbiology Indonesia Vol 8, No 3 (2014): September 2014
Publisher : Indonesian Society for microbiology

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Abstract

Human papillomavirus (HPV) type 52 is the most prevalent type for causing cervical cancer in Indonesian population. Cervical cancer becomes the most common cancer suffered by Indonesian women. Prevention of HPV infection can be achieved using HPV virus-like particle (VLP) vaccine derived from L1 major capsid protein.  This study aimed to clone and analyze HPV-52 L1 gene. DNA obtained from biopsy of a cervical cancer patient was amplified using specific primers designed from Asian originated HPV-52 L1 gene available in the GenBank. The isolated HPV-52 L1 gene sequence was submitted to GenBank with accession number [KF225497]. Expression of HPV-52 L1 gene was performed using pRSET/EmGFPEscherichia coli expression vector. We analyzed and compared the HPV-52 L1 gene expressions from recombinant E.coli BL21 (DE3) that had been induced for 3 hours with 1 mM IPTG and without induction. The protein was expressed in insoluble form. We performed the following bioinformatic analyses: construction of phlyogenetic tree, T-cell epitopes prediction and 3D proteins structure modelling. We utilized the following softwares: MEGA5 for phylogenetic tree, IEDBann for MHC prediction, CLC DNA Workbench 6.5 for hydrophobicity analysis and PDB-Viewer Deep for 3D protein structure analysis. The phylogenetic tree which was developed based on [KF225497] sequence showed that it shared a branch with Asian countries (Philippines and Thailand). The deduced amino acid sequences of the predicted epitopes that were consistent in all of the programs were 259GTLGDPVPGDLYIQGS274 and 345KKESTYKNE353. This information may be useful to design diagnostic strategies and vaccine suitable for Indonesian population.

Optimization of β-Cyclodextrin Production from Sago Starch using Recombinant Cyclodextrin Glycocyltransferase from Bacillus sp. A2-5a

NOVARYATIIN, SUSI, RIANI, CATUR, RETNONINGRUM, DEBBIE SOFIE

Microbiology Indonesia Vol 8, No 3 (2014): September 2014
Publisher : Indonesian Society for microbiology

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Abstract

Cyclodextrin (CD) is a cyclic oligosaccharide molecule which is classified into three types: α-CD, β-CD, and γ-CD, each consists of 6, 7, and 8 glucose units. CDs are produced enzymatically using starch as the substrate catalyzed by CD glycosyltransferase (CGTase). This research was aimed to determine optimum condition of β-CD production from sago starch using recombinant CGTase (rCGTase) from Bacillus sp. A2-5a, and using the optimum condition, β-CD production was done at 100 mL scale using complexing agents. In this study, rCGTase was overproduced in Escherichia coli BL21(DE3) and purified applying Ni-NTA affinity chromatography with gradual elution of imidazole and concentrated using Nanosep column. The purified rCGTase was 76.39 kDa in size and displayed β-cyclization and hydrolysis activities using zymography. The results showed that optimum conditions for β-CD production was achieved when preheated sago starch of 0.5% (w/v), enzyme of 2.6x10-2 U, and N,N-dimethylformamide (DMF) as complexing agent of 1% (v/v) were used and the reaction time was 8 h. When DMF of 1% (v/v) was added repeatedly at 100 mL scale production, the highest concentration of β-CD was obtained at the reaction time of 8 h. This research reported for the first time the optimum condition of b-CD production at 100 mL scale using rCGTase from Bacillus sp. A2-5a with DMF as complexing agent.

Identification and characterization of virulence factor of several Indonesian Xanthomonas oryzae pv. oryzae

FATIMAH, FATIMAH, MUSTOPA, APON ZAENAL, KUSNANDARSYAH, IQBAL

Microbiology Indonesia Vol 8, No 3 (2014): September 2014
Publisher : Indonesian Society for microbiology

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Abstract

Xanthomonas oryzae pv. oryzae (Xoo) is the bacterial causative agent of leaf blight in rice (Oryza sativa L.), the most serious bacterial disease of rice in many rice growing areas worldwide. This study aimed to identify and characterize several virulence factors of seven Xoo isolates from Yogyakarta, West Java, and West Sumatera. The identification of Xoo using 16S rRNA confirmed high homology to Xanthomonas oryzae pv. oryzae PXO99A and revealed three groups. The first group was Xoo93229, the second group containing Xoo1110, Xoo1122, Xoo1130, Xoo7624 and Xoo8024 as the same cluster with PXO99A and the third group was KACC10331 and MAFF311018. The amounts of exopolysaccharide (EPS) and cellulase produced were varying depending on the Xoo isolates. The EPS were produced more by isolate Xoo1130, Xoo1122 and Xoo8024. All tested isolates revealed similar cellulase activity except for isolate Xoo8024. The pathogenicity assay among the Xoo isolate showed that all tested isolates were virulent except Xoo7624. The in planta assay revealed that the tested isolates have multiplied and continued increasing the population size except for Xoo1110 and Xoo7624. High yield of EPS, cellulase activity, more virulence, and increasing population size revealed from isolate Xoo1130 and Xoo1122.

Modeling and Optimising the Growth of Lasiodiplodia theobromae During Gathotan Fermentation

PURWANDARI, UMI ( Universitas Trunojoyo Madura ) , NAVA, NOVIA ( Department of Agroindustrial Technology, Universitas Trunojoyo Madura ) , HIDAYATI, DARIMIYYA ( Universitas Trunojoyo Madura )

Microbiology Indonesia Vol 8, No 3 (2014): September 2014
Publisher : Indonesian Society for microbiology

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Abstract

Gathotan is fungal fermented cassava, and a raw material for a Javanese snack called ‘gathot’. This type of food is now hardly to find, and the process of making gathotan is relatively lack of process control, leads to failure in process. To make gathotan, peeled cassava tubers are left on the ground or roof for several weeks or months until they become black inside an important characteristic of gathotan. This work aims to improve gathotan fermentation by optimizing fermentation process. The effect of incubation temperature and time, inoculum level, soaking time, and drying, on the growth of Lasiodiplodia theobromae, the main gathotan fungus, in cassava tubers was studied. Experimental design was set up according to response surface methodology. Five parameters measured were pH, titratable acidity, and fungal growth. Results showed that incubation temperature affected pH in linear (P<0.01) and quadratic functions (P<0.05). Titratable acidity was not affected by any treatment. Fungal growth was significantly affected by incubation time (P<0.01) or inoculum level (P<0.05), and interaction of several factors: incubation time and incubation temperature (P<0.05) or drying time (P<0.01). Optimization model indicated that incubation temperature at 34.5°C for 2.4 days, soaking for 26.4 hours, drying time of 3.7 hours at 40°C, and inoculum level of 2% resulted in maximum growth of L. theobromae in gathotan.

Modified Slide Culture Method for Faster and Easier Identification of Dermatophytes

ROSANA, YEVA, MATSUZAWA, TETSUHIRO, GONOI, TOHRU, KARUNIAWATI, ANIS

Microbiology Indonesia Vol 8, No 3 (2014): September 2014
Publisher : Indonesian Society for microbiology

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Abstract

Basic slide culture as a morphological identification was known as the most common method for the identification of pathogenic mold fungi. This method preserved the morphological features relatively undisturbed compared with adhesive tape preparations. However, it was necessary to modify method of basic slide culture to improve its usability and shorten the time it needed to identify mold fungi. There were four kinds of method carried out in this study; two kinds of modified slide culture, one kind of direct culture on slant agar plate, and a basic slide culture for identifying mold fungi, which result would be compared with each other. These four methods were tested to 4 species of dermatophytes which were known as mold fungi that could infect skin, hair, and nails in human; those were Trichophyton mentagrophytes, Microsporum canis, Microsporum gypseum, and Epidermophyton floccosum. Result of this study showed that both modified slide culture and direct culture on slant agar plate could visualize the structure of dermatophytes faster than basic slide culture method. These methods were also easier to prepare compared to basic culture method. Conclusion of this study showed that basic slide culture method needed to be modified for better identification of mold fungi.