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Articles by issue : Vol 1, No 1 (2007): April 2007
11
Articles
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Rapid and Simple Amplification of Genomic DNA Sequences Flanking Transposon

WAHYUDI, ARIS TRI

Microbiology Indonesia Vol 1, No 1 (2007): April 2007
Publisher : Indonesian Society for microbiology

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Abstract

A rapid and simple method to amplify genomic DNA sequences flanking mini-Tn5 transposon insertion was developed. This technique can be used to determine the location and orientation of the transposon insertion within genomic DNA of the bacteria. Based on the mini-Tn5Km1 transposon sequence, PCR primers can be designed to specifically amplify the DNA sequences flanking mini-Tn5 transposon by inverse polymerase chain reaction (inverse PCR) directly, upstream and downstream of the transposon insertion. The method involves: (i) digestion with a restriction enzyme that does not cut mini-Tn5Km1 sequence; (ii) self-ligation under conditionsfavoring the production of monomeric circles; and (iii) inverse PCR reaction using primers designed from mini-Tn5Km1 sequence to amplify the DNA sequences flanking mini-Tn5Km1 transposon insertion. Feasibility and reliability of this method were demonstrated with mini-Tn5Km1 mutants of the microaerobic magnetic bacterium Magnetospirillum magneticum AMB-1 which are defective in magnetosomes synthesis. The inverse PCR products amplified from these mutant genomes showed the correct fragments as determined through Southern hybridization and DNA sequence analysis.

Improving the Effectiveness of Crude-Oil Hydrocarbon Biodegradation Employing Azotobacter chroococcum as Co-Inoculant

PARNADI, PUJAWATI SURYATMANA, KARDENA, EDWAN, RATNANINGSIH, ENNY, WISJNUPRAPTO, .

Microbiology Indonesia Vol 1, No 1 (2007): April 2007
Publisher : Indonesian Society for microbiology

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Abstract

Azotobacter chroococcum has a great potential as biosurfactant producing bacteria and was used as co-inoculant to promote the rate of hydrocarbon biodegradation. The rate of hydrocarbon biodegradation were 0.01212, 0.01582, and 0.01766 per day for Acinetobacter sp., Bacillus cereus and the consorsium culture respectively. On the other hand, the rates of biodegradation using Azotobacter as co-inoculant were 0.1472, 0.01612, and 0.02709 g per day. Azotobacter chroococcum co-inoculant has the capability of increasing biodegradation efficiency of crude oilhydrocarbon. The biodegradation efficiency of petroleum hidrocarbon was increated by 13.4, 14.6, and 14.4% within the Petrobacter cultures.

Protein Patterns in Arbuscular Mycorrhizal Roots and Non-Mycorrhizal Roots of Oil Palm Seedling

WIDIASTUTI, HAPPY, SUKARNO, NAMPIAH, DARUSMAN, LATIFAH KOSIM

Microbiology Indonesia Vol 1, No 1 (2007): April 2007
Publisher : Indonesian Society for microbiology

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Abstract

A comparison of the protein patterns in root extracts from none mycorrhizal and mycorrhizal oil palm roots has been made. The polypeptides were analyzed every three weeks up to 11 weeks. A factorial design of fungi species (no mycorrhizal, Acaulospora tuberculata, Gigaspora margarita) and with or without fertilizer was assessed. The result showed that specific polypeptides were detected in primary and secondary roots. In unfertilized oil palm root, a 60 kDa polypeptide was detected while it was abcent in fertilized root. Inoculation of A. tuberculata with the addition of fertilizer application yielded a specific 26.7 kDa polypeptide in primary root on the 11th week after inoculation. A specific 64.2 kDa polypeptide of G. margarita was detected in unfertilized secondary root also on the 11th week.

Identification of Class 1 Integron of Escherichia coli from Street Foods in Jakarta

FRISCA, ., LAY, BIBIANA WIDYATI, WATURANGI, DIANA ELIZABETH

Microbiology Indonesia Vol 1, No 1 (2007): April 2007
Publisher : Indonesian Society for microbiology

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Abstract

A total of 43 Escherichia coli isolates were identified from school street foods located in Northern and Southern Jakarta. The isolates were examined for antibiotic resistance using five antibiotics discs (ampicillin, kanamycin, streptomycin, trimethoprim, tetracycline) and screened for the class 1 integron with specific conserved region primer using PCR amplification. The antibiotic diffusion test revealed three isolates (7%) with resistance to multiple antibiotics. PCR detection of integron regions showed one isolate possessed a class 1 integron bearing one gene cassette with ~700bp amplicon size. DNA sequencing showed that the gene cassette was resistant to trimethoprim determinant type V (dhfrV). The integron bearing E. coli strain could become a threat for the widespread distribution of an antibiotic resistance gene especially for pathogenic bacteria.

Mutation and Characterization of an Albino Mutant of Monascus sp. Isolated from the Cikapundung River, Bandung

MILANDA, TIANA, WIBOWO, MARLIA SINGGIH, GUSDINAR, TUTUS, DHANUTIRTO, HARYANTO

Microbiology Indonesia Vol 1, No 1 (2007): April 2007
Publisher : Indonesian Society for microbiology

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Abstract

Monascus sp. isolated from Cikapundung River, Bandung was mutated using ethyl methanesulfonate (2.5%, 90 min). Previously, this wild type was identified as Monascus purpureus ITBCC-HD-F001 employing random amplification polymorphic DNA (RAPD). Stability of the mutant was observed using color consistency and mutant stability (sub-culturing for five generations) tests. Genetic variation of the mutant (M. purpureus ITBCC-HDF002) was confirmed by RAPD. One of the DNA bands of 1150 bp was found in the albino mutant but not in the wild type, so it was considered as a genetic variation resulting from the mutation process. The albino mutant was characterized by comparing the growth curve, biomass production curve, and the monascidin A production curve of both strains i.e. wild type and the albino mutant. Monascidin A production of the mutant was higher than that of the wild type.

Hospital Acquired Bacterial Infection in Burns Unit at Cipto Mangunkusumo Hospital, Jakarta

SUDARMONO, PRATIWI, WIWING, VERONICA

Microbiology Indonesia Vol 1, No 1 (2007): April 2007
Publisher : Indonesian Society for microbiology

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Abstract

Burn injury causes mechanical disruption to the skin, which allows environmental microbes to invade the deeper tissues. A prospective study of infections in burn patients has shown that the incidence of hospital acquired bacterial infection in burn wounds was high. In the Burns Unit, Cipto Mangunkusumo Hospital, Jakarta, 94 patients were hospitalized from January to July 2004. The objective of this study was to evaluate the hospital acquired infections in burn wounds. Using a cross sectional study, 49 patients were included. The specimens for bacterial investigation were obtained from clean eschar which has healthy tissue taken at day 1, day 5 and day 10. At the same time, bacterial investigations were conducted from the air and the water, as well as from the hand and nasal swabs of hospital personnel. The results show that Klebsiella pneumoniae is the most prominent bacterium found in the wounds, but it is also found in the air. Pseudomonas aeruginosa was the number two causative bacteria which caused a change of the bacterial infectivity on day 5 and 10. These bacteria were always found when we conducted bacterial investigations from the water resource of the burns unit. Methicillin Resistant Staphylococcus aureus is also found in the nasal swab of hospital personnel. Using the antibiogram pattern, there were similarities between bacteria found in the wounds and in bacteria found in the air and water. In conclusion, hospital acquired burn wound infection in Burns Unit, Cipto Mangunkusumo Hospital is as high as 62%. The surveillance data are very important for developing good clinical practice guidelines in burn injury treatment and management

Phenotypic, Metabolic, and Genetic Diversity of the Indonesian Isolates of Rhizopus oligosporus

PRIHATNA, CAHYA, SUWANTO, ANTONIUS

Microbiology Indonesia Vol 1, No 1 (2007): April 2007
Publisher : Indonesian Society for microbiology

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Abstract

Fifteen Rhizopus oligosporus isolates were isolated from a number of tempeh samples obtained from Mataram, Jember, and Bogor, Indonesia; and subjected for characterization based on phenotypic, metabolic, and genetic fingerprinting through internal transcribed spacer (ITS) regions and amplified fragment length polymorphism (AFLP). Based on the growth on solid medium, they can be divided into three groups. Firstly, isolates that produced thick mycelia, dumpy sporangiophore, and scarce spores in agar culture, the second group is isolates that produced thin mycelia, stretched sporangiophore, with abundant spores in agar culture. The third group that only comprises one isolate, FB-06, is morphologically intermediate of the first and the second groups. These characters correlated with their range of temperature tolerance. The first group is less tolerant to high temperature (45 oC) compared with the second group, and the third group is the most tolerant to temperature up to 45 oC. Metabolic fingerprinting showed a very high polymorphism. In general, the result may explain a correlation in which isolates obtained from the same locations shared similar patterns. There is no correlation found between metabolic fingerprints and their phenotypic fingerprints. Rhizopus oligosporus readily dominated the niche and utilized nearly all carbon sources given demonstrate the versatile nature of this fungus. ITS regions identification revealed single nucleotide polymorphisms in four representative isolates examined, whereas AFLP fingerprinting determined each of representative isolates as individually unique. Furthermore, this AFLP profile seemed to agree with their phenotypic characters..

Structural and Functional Analysis of FLAG Tagged-Subunit 8 of Yeast Saccharomyces cerevisiae Mitochondrial ATP Synthase

ARTIKA, I MADE

Microbiology Indonesia Vol 1, No 1 (2007): April 2007
Publisher : Indonesian Society for microbiology

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Abstract

Yeast mitochondrial ATP synthase is a multisubunit complex composed of at least 17 different subunits. Subunit 8 of yeast mitochondrial ATP synthase is a hydrophobic protein of 48 amino acids encoded by the mitochondrial ATP8 gene. Although ATP synthase from eukaryotes and prokaryotes shows a similar basic structure, no homologue of subunit 8 is found in prokaryotes such as Escherichia coli. Subunit 8 has three distinct domains; an N-terminal domain, a central hydrophobic domain and a C-terminal domain. In order to elucidate its structure and function, a set of nuclear genes encoding subunit 8 variants was designed to incorporate a FLAG tag at the C-terminus and a mitochondrial signal peptide at the N-terminus. Each gene was cloned into a yeast expression vector and then allotopically expressed in a yeast strain lacking endogenous subunit 8. Structural and functional analysis showed that the hydrophobic character of the central hydrophobic domain of subunit 8 is critical for the ATP synthase function. Subunit 8 is sensitive to charge manipulation at the C-terminus. The positively charged residues at the C-terminal domain are important for subunit 8 assembly and hence its function.

16S Ribosomal RNA-Based Analysis of Thermophilic Bacteria in Gedongsongo Hot Spring

AMININ1, AGUSTINA LULUSTYANINGATI NURUL, MADAYANTI, FIDA, ADITIAWATI, PINGKAN, AKHMALOKA, .

Microbiology Indonesia Vol 1, No 1 (2007): April 2007
Publisher : Indonesian Society for microbiology

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Abstract

Denaturing gradient gel electrophoresis was used to identify the bacterial community at the Gedongsongo (WGS-2) hot spring. The bacterial samples were obtained from both culture dependent and independent strategies. Partial 16S rRNA genes were amplified by a set of primers to produce at around 400 bp fragments, including the highly variable V9 region of the 16S rRNA genes. The DGGE profiles showed that there were a few distinct bands, namely G1-G3, and G8-G12, which represent the predominant bacteria in natural habitat and the medium.Further analysis of these bands showed that most of them, except for G7, have a high homology to the 16S rRNA gene sequences of Thermus sp. As for G7, the highest homology was shown to unculturable bacteria. In addition to the distinct bands in DGGE, there were other three thin bands, namely G4, G5, and G6, which possibly represent non dominant microorganisms in the natural habitat, but could grow on GS-A medium. Further analysis of these bands showed that G6 has 80% similarity to the 16S rRNA of Burkholderia sp., while G4 and G5 have a high homology to each other but only contained 10-15% homology to the sequences of 16S rRNA from unculturable microorganisms. The phylogenetic analyses of the last organisms showed that there was branching from Burkholderia. From all the data obtained it was suggested that the WGS-2 hot spring was predominantly occupied by the genus Thermus. In addition, there were a few novel microorganisms found in the hot spring.

Effects of Temperature on Denitrifying Growth and Nitrate Reduction End Products of Comamonas testosteroni Isolated from Estuarine Sediment

RUSMANA, IMAN ( Bogor Agricultural University )

Microbiology Indonesia Vol 1, No 1 (2007): April 2007
Publisher : Indonesian Society for microbiology

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Abstract

Predictions of seasonal changes in N2O emission that occur in natural estuaries are important to anticipate the future implications of global warming. This study showed the effect of temperature on denitrifying growth and nitrate reduction end product of Comamonas testoteroni isolated from estuarine sediment using both batch and continuous cultures. The μmax values of Comamonas testosteroni grown in anaerobic batch culture were increased with increasing temperature, and the highest μmax was found at 26 oC. Concentrations of nitrate reduced (mg-1 dried weight cells) were higher at low temperature. Concentrations of N2 produced were higher at low temperature and the production of N2 was higher than both NO2- and N2O productions