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Articles by issue : Vol 4, No 2 (2010): August 2010
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Macaca nemestrina and Dengue Virus Infectivity: a Potential Model for Evaluating Dengue Vaccine Candidates

WIDJAJA, SUSANA, WINOTO, IMELDA, STURGIS, JONATHAN, MAROEF, CHAIRIN N, LISTIYANINGSIH, ERLIN, TAN, RATNA, PAMUNGKAS, JOKO, BLAIR, PATRICK J, SAJUTHI, DONDIN, PORTER, KEVIN RANDALL

Microbiology Indonesia Vol 4, No 2 (2010): August 2010
Publisher : Indonesian Society for microbiology

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Abstract

Macaca nemestrina has been shown to respond to infectious disease agents, such as HIV, and is more sensitive compared to other species of macaques such as rhesus (M. mulatta) and cynomolgus monkeys (M. fascicularis).  To evaluate M. nemestrina for the ability to support dengue (DEN) viremia and serve potentially as an improved model for testing DEN vaccines, a series of experiments were conducted using primary viral isolates from individuals with DEN virus infections.  This study shows that M. nemestrina develops consistent, measurable viremia with all four DEN serotypes and produces immune responses sufficient to protect against homologous virus.  Anti-dengue antibodies generated after infection are predominately IgG1.  This species of monkey therefore appears to be a suitable model for testing DEN virus vaccine candidates.

Fragrance Formation in Aquilaria spp. Shoot Culture Induced by Acremonium sp.

RAHAYU, GAYUH ( Bogor Agricultural University, Indonesia )

Microbiology Indonesia Vol 4, No 2 (2010): August 2010
Publisher : Indonesian Society for microbiology

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Abstract

In this research, fragrance formation in the shoot culture of three clones of Aquilaria malaccensis (Ama1, Ama7, and Ama13) and four clones of A. microcarpa (Ami5, Ami8, Ami16, and P6) as a response towards infection of four isolates of Acremonium sp. (F, G, L, and M) were studied using dual culture methods in three different concentrations of a modified Murashige-Skoog (MSmod) media (50, 75, and 100%). The result indicated that Acremonium F and M induced the formation of fragrance. The index of fragrance induced by Acremonium F was twice from that of Acremonium M, and commonly produced in shoot cultures in MSmod 50%. The index of fragrance in A. malaccensis shoot culture was 70% higher than that of A. microcarpa. Furthermore, GLC analyses of acetone extracted from fragranced shoots of A. malaccensis indicated that only one compound (RT 5.76) might determine the fragrance. Host-microbe compatibility study indicated that  the presence of Acremonium significantly affected the fitness of the shoots. In contrast, the presence of shoots did not significantly affect the growth rate of Acremonium. In general, Acremonium F, L and M significantly increased  shoot death during the 35 days of interaction.

Ecological and Taxonomical Perspective of Yeasts in Indonesia

SJAMSURIDZAL, WELLYZAR, OETARI, ARIYANTI, KANTI, ATIT, SARASWATI, RASTI, NAKASHIMA, CHIHARU, WIDYASTUTI, YANTYATI, KATSUHIKO, ANDO

Microbiology Indonesia Vol 4, No 2 (2010): August 2010
Publisher : Indonesian Society for microbiology

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Abstract

In the course of ecological and taxonomical study of yeasts in Indonesia, a total of 2147 yeast isolates from 315 samples in the year 2003, 2005, 2006, and 2008 had been obtained from eight locations e.g. Liwa (Sumatera), Cibinong (Java), Cibodas (Java), Kutai (Kalimantan), Enrekang (Sulawesi), Pucak (Sulawesi), Gili and Kuta (Lombok), and Kupang (Timor).  Leaves, flowers, litters, soils, epiphytic soils, insects and insect´s nests were collected for yeasts isolation.  Our molecular identification based on D1/D2 region of nuclear large-subunit rDNA and the internal transcribed spacer (ITS) regions sequence data on 525 representative isolates revealed that 306 isolates belong to 48 described species (18 genera) and 209 strains belong to 19 undescribed species (19 genera), and 10 isolates were discarded because of contamination.  Based on their substrates, litter had the highest yeasts genera (19) followed by soils (18), flowers (10), leaves (6), epiphytic soils (4), and insects and insect´s nests (4).  Genera found on soils were also common on litters.  Yeasts genera found on flowers and epiphytic soils were common on leaves and litters.  The genera Aureobasidium, Cryptococcus, Pseudozyma, Rhodotorula and Sporidiobolus were found in all substrates.  Based on their locations, Kutai had the highest number of genera (15) followed by Cibodas (10), Cibinong (10), Enrekang (10), Kupang (10), Pucak (9), Liwa (7), and Lombok (7).  The genus Cryptococcus was found in all locations.  Our study shed a light to detection of many new taxa of yeasts, 41% of yeasts found in this study represented novel taxa.

Isolation of Endophytic Bacteria from Palm Oil Fruits and Characterization of Their Lipases

DJAFAR, FANDY, PURWADARIA, TRESNAWATI, SINURAT, ARNOLD PARLINDUNGAN

Microbiology Indonesia Vol 4, No 2 (2010): August 2010
Publisher : Indonesian Society for microbiology

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Abstract

Lipases (EC 3.1.1.3)  can be produced in palm oil fruits by fruit cells or endophytic microbes. The purpose of this research is to isolate endophytic lipolytic bacteria of palm oil fruit and characterization their lipases. The bacteria were isolated and screened using medium Kouker and Jaeger containing olive oil,  minerals, yeast extract, peptone, agar, and rhodamine B as an indicator. Fifteen endophytic bacteria were isolated and identified having the microbial lipase activity. Most of them showed rod shape, positively Gram test, spore formation, and motility except one bacteria strain K which was coccus. The enzyme was produced using submerged culture in the same medium but not containing agar and rhodamine B. Based on data of enzyme activity towards p-nitrophenyl palmitate as a substrate, protein concentration, and  specific  activity, two bacteria were selected, those were BSWt2(1) and Ink 1.3 isolates. Microscopic and biochemistry analyses show that BSWt2(1) and Ink 1.3 were identified as Bacillus brevis and B. lacterosporus respectively. Crude lipase from B. brevis BSWt2(1) and B. lacterosporus Ink 1.3 showed optimum activities at pH 8.0-9.0 and 60°C, and at pH 8.5 and 60-70°C. The enzymes were stable pre-incubated at pH 7.5-9.0 and pH 7.5-8.0 respectively, and they were stable pre-incubated for 2-4 hours at 80°C and for 2-8 hours at 100°C.  Based on  stability in high temperature, lipase from both isolates were specific and might be applicable for use in waste water treatment in palm oil factories.

Physiological Characterization and Molecular Identification of Denitrifying Bacteria Possesing Nitrous Oxide High Reduction Activity Isolated from Rice Soils

SETYANINGSIH, RATNA, RUSMANA, IMAN, SETYANTO, PRIHASTO, SUWANTO, ANTONIUS

Microbiology Indonesia Vol 4, No 2 (2010): August 2010
Publisher : Indonesian Society for microbiology

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Abstract

Rice  fields are one of the main sources of high nitrous oxide N2O emission.  Soil denitrifiers possessing high N2O reduction activity are important for controlling N2O emission.  Nitrous oxide reduction is the last step of denitrification process.  The aims of this study were to characterize and to identify denitrifying bacteria isolated from rice soils possessing high activity of N2O reduction.  Soil samples were taken from 6 locations of rice fields in Bogor (West Java) and Tangerang (Banten), Indonesia.  Physiological characterization was performed using API 20 NE, while molecular identification was conducted based on the 16S rRNA gene sequence.   It was found that ten isolates of denitrifying bacteria were able to grow using N2O as an electron acceptor as indicated by decreasing N2O concentration in the headspace of the cultures.  The bacterial  growth indicated by optical density,  increased up to 0.12-0.47  after 5 days incubation.  Isolate BL2 had the highest activity of  N2O reduction followed by BL1 and BLN1 at up to 5.41, 4.09, and 3.91 μmol mL-1 bacterial cultures, respectively.  The BL1, BL2, and BLN1 isolates had some different physiological characteristics.  Based on their 16S rRNA sequence, BL1 and BLN1 were closely related to Ochrobactrum anthropi ATCC 49188 with similarity of 99%.

The Production of Blue Cheese with the Addition of Nonpathogenic Strain of Klebsiella pneumoniae and Fortification of Folic Acid and Iron

AGUSTINAH, WIDYA, WINARNO, FLORENTINUS GREGORIUS

Microbiology Indonesia Vol 4, No 2 (2010): August 2010
Publisher : Indonesian Society for microbiology

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Abstract

Blue cheese is a semi-soft ripened cheese that involves the growth of Penicillium roqueforti in the ripening process.  Cheese has a longer shelf life compared to raw milk and the production of cheese will give added value to the finished product, which, therefore, can benefit local dairy farmers in Indonesia.  The objective of this study was to produce a new variant of blue cheese which was made from a mixture of fresh cow´s milk (Frisian Holstein cow) and skimmed milk powder and which had a high vitamin B12, folic acid, and iron content. Blue cheeses for this study were made by milk fermentation with the addition of a nonpathogenic strain of Klebsiella pneumoniae in the cheese preparation and fortification of folic acid and iron. This study showed that blue cheeses had been successfully made from a mixture of fresh cow´s milk and skimmed milk at a ratio of 1:1 and acceptable by 42 untrained panelists.  Compared to the commercial blue cheese, the addition of K. pneumoniae (0.8% v/v) and fortification (0.08 g L-1 of premix) had positive effects in increasing the amount of vitamin B12, folic acid, and iron up to 2.7, 13.64, and 102.86 ppm on dry-weight basis, respectively. However, blue cheese made without K. pneumoniae was the most preferred and had the highest scores for texture, taste and aroma.

Isolation and Characterization of Antimicrobial Substance from Marine Streptomyces sp.

SUNARYANTO, ROFIQ, MARWOTO, BAMBANG, IRAWADI, TUN TEDJA, HARTOTO, LIESBETINI

Microbiology Indonesia Vol 4, No 2 (2010): August 2010
Publisher : Indonesian Society for microbiology

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Abstract

Isolation and purification of antimicrobial active substance produced by marine Actinomycetes has been carried out.  Marine sediment samples were obtained from six different places at Banten West Coast.  Isolation was conducted using two pretreatment methods,  acid and heat shock pre-treatment.  A total of 29 Actinomycetes isolates were obtained from the various sediment samples collected, then tested for antimicrobial activity against Escherichia coli ATCC 25922, Staphylococcus aureus ATCC25923, Pseudomonas aeruginosa ATCC27853, Bacillus subtilis ATCC 66923, Candida albicans BIOMCC00122, and Aspergillus niger BIOMCC00134.  Among the isolates, isolate A11 was the most activity to Gram-positive and Gram-negative bacteria, and morphological observation and identification using 16S rRNA showed that the isolate was similar to Streptomyces sp.  Production of active compound from A11 isolate used yeast peptone medium.  Purification of active compounds was carried out using silica-gel-column chromatography and preparative HPLC.  A single peak of active compounds was detected by HPLC, which showed a retention time of 8.35 min and maximum absorbance in UV visible at 210 nm and 274.5 nm respectively.

Sequence Analysis of Putative potB, potC, and potD Genes from Serratia rubidae

SUHANDONO, SONY, FITRIA, RASI, RACHMAN, ERNAWATI ARIFIN GIRI

Microbiology Indonesia Vol 4, No 2 (2010): August 2010
Publisher : Indonesian Society for microbiology

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Abstract

Amplification of putative potBCD genes from Serratia rubidae was conducted by PCR using a pair of primers FERC and RERC.  A fragment with ~1800 bp size was ligated to pGEM-T Easy vector then cloned to competent Escherichia coli DH5α.  The recombinant plasmid was sequenced using SP6, T7 and two internal primers, FPC and RPC.  A sequence similarity search and analysis was performed with the BLASTN program.  The sequence was found to have 83% similarity to potABCD genes from E. coli.  Those genes encoded a spermidine-preferential uptake system that consists of four kinds of protein: PotA is a membrane-associated ATPase, PotB and PotC are transmembrane proteins that form channels, and PotD is a periplasmic substrate-binding protein. Alignment analysis showed that the isolated clone consisted of potB (partial), potC (full length) and potD (partial).  The sequences for potBCD genes from S. rubidae are not available in the NCBI database.  Furthermore, we have submitted this sequence, potBCD from S. rubidae, on GeneBank with Acc. number FJ447342.

Isolation and Identification of Mycorrhizosphere Bacteria and Their Antagonistic Effects Towards Ganoderma boninense in vitro

BAKHTIAR, YENNI, YAHYA, SUDIRMAN, SUMARYONO, WAHONO, SINAGA, MEITY SURADJI, BUDI, SRI WILARSO, TAJUDDIN, TEUKU

Microbiology Indonesia Vol 4, No 2 (2010): August 2010
Publisher : Indonesian Society for microbiology

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Abstract

Basal stem rot caused by Ganoderma boninense is the most serious disease of oil palm (Elaeis guineensis) in Indonesia and it has caused major loss in palm oil production.  Mycorrhizosphere bacteria offer possible advantages as biocontrol agents as they live and proliferate together with arbuscular mycorrhizal fungi, which have an ability to increase plant resistance against pathogens.  A study was conducted to isolate mycorrhizosphere bacteria from spores of arbuscular mycorrhizal fungi and test their antagonistic effects against G. boninense in vitro.  All bacterial isolates were identified based on 16S rDNA analysis and it revealed that eleven out of twenty mycorrhizosphere bacteria isolated were related to Bacillus with similarity ranging from 97 to 100%, whereas other isolates were identified as Pseudomonas, Streptomyces, Kocuria, Enterobacter, Brevundimonas, and Alcaligenes with similarities ranging from 96 to 100%.  Fourteen out of twenty mycorrhizosphere bacteria showed a varying degree of inhibition towards the growth of G. boninense in vitro.  Of these, isolate B10 (closely related to Bacillus subtilis ZJ06) showed the highest inhibitory effect followed by B17 (closely related to Bacillus subtilis N43).  Therefore, these bacteria have a potential to be used as biocontrol agents to control basal stem rot disease caused by G. boninense in oil palm.