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Articles by issue : Vol 5, No 1 (2011): March 2011
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Articles
Diversity of SCAR Markers of Pyricularia grisea Isolated from Digitaria ciliaris Following Cross Infection to Rice

LISTIYOWATI, SRI ( Department of Biology, Bogor Agriicultural University ) , WIDYASTUTI, UTUT ( Department of Biology, Bogor Agriicultural University ) , RAHAYU, GAYUH ( Department of Biology, Bogor Agriicultural University ) , HARTANA, ALEX ( Department of Biology, Bogor Agriicultural University ) , JUSUF, MUHAMMAD ( Department of Biology, Bogor Agriicultural University )

Microbiology Indonesia Vol 5, No 1 (2011): March 2011
Publisher : Indonesian Society for microbiology

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Abstract

Cross infection of Pyricularia grisea from grass to rice and vice versa has been reported, but genetic changes are not known yet.  This research  aimed at estimating the possibility of the genotype alteration in P. grisea dc4 isolated from Digitaria ciliaris, following cross infection to either rice cv. Kencana bali, Cisokan, and IR64 or Panicum repens, Cynodon dactylon, Digitaria sp., and Ottochloa nodosa. The genotypes were analyzed by employing three SCAR markers, Cut1; PWL2; and Erg2.  The results indicated that the dc4 was only able to infect Kencana bali, Cisokan, and P. repens.  The dc4 had only two out of three SCAR markers, Cut1 and Erg2.  Host shift was followed by genotype alteration in two loci of SCAR.  Isolates derived from lesions on Kencana bali (dc4-kb) and Cisokan (dc4-c) of the dc4 infection, both lost their Cut1 and gained PWL2. On the contrary, there was no genotype alteration from dc4 to isolate derived from P. repens of dc4 infection (dc4-pr).  Neither the isolate dc4-kb  that was cross-inoculated to Cisokan nor the dc4-c that was cross-inoculated to Kencana bali showed SCAR marker change.  In comparison,  race 173 isolate and those derived from Kencana bali and Cisokan did not show genotype alteration. All had two out of three SCAR markers, PWL2 and Erg2.  The isolate 173 was adapted to rice. This indicated that genotype diversity of the dc4 might arise following host shift from grass to rice.Pyricularia grisea merupakan cendawan blas yang telah diketahui memiliki kisaran inang luas selain pada padi. Infeksi silang cendawan blas pada rumput ke padi dan sebaliknya telah dilaporkan, tetapi perubahan genetiknya belum dilaporkan. Tujuan penelitian ini menganalisis kemampuan infeksi silang dan perubahan genotipe P. grisea dc4 asal Digitaria ciliaris dalam perpindahannya ke padi cv. Kencana bali, Cisokan, dan IR64 atau rumput Panicum repens, Cynodon dactylon, Digitaria sp. dan Ottochloa nodosa. Genotipe P. grisea dianalisis melalui tiga marka SCAR, yaitu Cut1; PWL2; dan Erg2. Isolat dc4 memiliki 2 marka SCAR, yaitu Cut1 dan Erg2; tidak memiliki PWL2. Isolat dc4 hanya mampu menginfeksi silang Kencana bali, Cisokan, dan P. repens. Turunan isolat dc4 sebagai hasil infeksi silang ke Kencana bali (dc4-kb) dan Cisokan (dc4-c) menunjukkan perubahan genotipenya, yaitu Cut1 tidak teramplifikasi pada keduanya; PWL2 teramplifikasi;, serta Erg2 tetap teramplifikasi. Sebaliknya, turunan isolat dc4 sebagai hasil infeksi silang ke P. repens (dc4-pr) tidak mengalami perubahan genotipe. Turunan isolat dc4-kb sebagai hasil infeksi silang ke Cisokan, maupun turunan isolat dc4-c dari Kencana bali, juga tidak menunjukkan perubahan genotipe, yaitu tetap menunjukkan keberadaan PWL2 dan Erg2. Sebagai pembanding digunakan isolat ras 173 yang diisolasi dari padi.  Genotipe isolat tersebut maupun turunannya, sebagai hasil infeksi silang ke Kencana bali dan Cisokan, tidak menunjukkan perubahan. Perubahan genotipe dc4 terjadi mengikuti pergantian inang dari rumput ke padi.

Glucose Biosensor Using Selected Indonesian Bacteria

ISWANTINI, DYAH ( Department of Chemistry, Faculty of Mathematics and Natural Sciences, Institut Pertanian Bogor ) , NOVIK, NOVIK ( Research Center for Biology, Lembaga Ilmu Pengetahuan Indonesia ) , TRIVADILA, . ( Department of Chemistry, Faculty of Mathematics and Natural Sciences, Institut Pertanian Bogor )

Microbiology Indonesia Vol 5, No 1 (2011): March 2011
Publisher : Indonesian Society for microbiology

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Abstract

Microbial glucose sensors have been developed using Escherichia coli bacterial strains from Japan.  However, there is interest in developing local bacteria as glucose sensors in Indonesia.  In this research, the stability and the potential of a selected number of Indonesian bacteria as glucose biosensors was explored.  Results of this study indicate that three of them, E. coli, Bacillus subtilis, and Thermus filiformis exhibit properties of high viability and stability at high temperature (30-60 ºC). Spectrophotometrical and electrochemical measurements showed significant absorbance values and highly stable current features for E. coli as indicated by its high capacity to produce glucose dehydrogenase.  E. coli, B. subtilis, and T. filiformis produced currents of 3.25 µA, 0.2 µA, and 0.02 µA respectively, and E. coli also produced a much higher activity of glucose dehydrogenase. Electrochemical measurement using E. coli-modified carbon paste electrode allowed the determination of glucose concentration of up to 20 mM. Therefore, Indonesian E. coli has a high stability and can be used as a glucose biosensor

Screening of Actinomycetes Producing an ATPase Inhibitor of Japanese Encephalitis Virus RNA Helicase from Soil and Leaf Litter Samples

RATNAKOMALA, SHANTI, RIDWAN, RONI ( Research Center for Biotechnology LIPI ) , LISDIYANTI, PUSPITA ( Research Center for Biotechnology LIPI ) , ABINAWANTO, . ( Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia ) , ANDI, UTAMA ( Research Center for Biotechnology LIPI )

Microbiology Indonesia Vol 5, No 1 (2011): March 2011
Publisher : Indonesian Society for microbiology

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Abstract

Actinomycetes are commercially important microorganisms for the production of antibiotics, enzymes, inhibitors of enzymes, and other bioactive secondary metabolites. Some 853 isolates of actinomycetes were isolated from soil and leaf litter samples in Kupang NTT and Enrekang, South Sulawesi. Those isolates were then tested for inhibition of ATPase activity of RNA helicase from Japanese encephalitis virus (JEV), in order to identify a drug candidate for the treatment of JEV infection. Results revealed that 14 isolates have relatively high inhibition-activity on JEV ATPase activity of the JEV-RNA-helicase, which range from approximately 40.0-50.0% inhibition. The highest inhibition-activity was identified in Actinoplanes philippinensis 5-849 with 49. 9% of inhibition-activity and Streptomyces chartreusis 5-095 with 49.2% of inhibition-activity

Genome-Shuffling-Improved Acid Tolerance and Lactic Acid Production in Lactobacillus plantarum for Commercialization

TRIRATNA, LITA ( Research Center for Biotechnology, Lembaga Ilmu Pengetahuan Indonesia ) , SAKSONO, BUDI ( Research Center for Biotechnology, Lembaga Ilmu Pengetahuan Indonesia ) , SUKMARINI, LINDA ( Research Center for Biotechnology, Lembaga Ilmu Pengetahuan Indonesia ) , SUPARMAN, ASEP ( Department of Food Science and Technology, Institut Pertanian Bogor, )

Microbiology Indonesia Vol 5, No 1 (2011): March 2011
Publisher : Indonesian Society for microbiology

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Abstract

We applied genome shuffling to improve the acid tolerance of Lactobacillus plantarum, while simultaneously enhancing lactic acid production. The starting populations were mutant libraries generated by gradual low pH adaptation and ultraviolet irradiation and then which were subjected to recursive protoplast fusion. A library of shuffled mutants (fusants) with genetic exchange is achieved by repetition of this process. After three rounds of genome shuffling, we obtained the best performing fusant that grow better at low pH 4.0 and consume glucose faster than does the wild type. In addition, lactic acid production of this fusant was 64% higher than that of the wild type. These results demonstrated that the genome shuffling has been successful in engineering L. plantarum with multiple beneficial improved phenotypes. In the future, this technology is a promising candidate to accelerate poorly characterized strains for commercialization

Optimization of Human Interferon α2b Soluble Protein Overproduction and Primary Recovery of Its Inclusion Bodies

NINGRUM, RATIH ASMANA ( School of Pharmacy, Institut Teknologi Bandung ) , RETNONINGRUM, DEBBIE SOFIE ( School of Pharmacy, Institut Teknologi Bandung ) , CAHYATI, YEYET ( School of Pharmacy, Institut Teknologi Bandung ) , RACHMAWATI, HENI ( School of Pharmacy, Institut Teknologi Bandung )

Microbiology Indonesia Vol 5, No 1 (2011): March 2011
Publisher : Indonesian Society for microbiology

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Abstract

The hIFN2b open reading frame has been constructed and overexpressed in Escherichia coli BL21(DE3). The yields of protein purified using nickel column from inclusion bodies (IB) and total soluble proteins were 3.46 mg and 2.57 mg in 1 L culture, respectively. This research was aimed to obtain optimal condition for high level overproduction of soluble hIFNα2b as well as primary recovery of hIFN2b from IB. We used two different conditions for obtaining soluble protein, i.e. induction temperatures and inducer concentrations, and three different conditions for inclusion bodies, i.e. centrifugation speeds, washing and solubilizing buffers. Induction using 0.5 mM of isopropyl thiogalactopyranoside at 25 °C yielded 8.9 mg hIFN2b in 1 L culture. The best recovery of IB was achieved when 10 000 g was applied for centrifugation, 1% Triton X-100  in 50 mM Tris Cl pH 8.0 as washing buffer, and 8M guanidine HCl in 50 mM Tris Cl pH 8.0 containing 800 mM 2-mercaptoethanol as solubilizing buffer were used. At this optimal condition the yield of hIFN2b from IB was 28.85 mg in 1 L culture. The total recovery of hIFNα2b at optimal condition was 50% from IB and 14% from soluble protein. hIFN2b from IB was refolded by 9 d dialysis in refolding buffer (0.2 mM EDTA, 0.25 mM ditiothreitol, 50 mM Tris and 0.4 M urea pH 8.0).

Ultrastucture of Wolbachia are Found in Somatic and Reproductive Tissue of Drosophila simulans and D. melanogaster

KUSMINTARSIH, ENDANG SRIMURNI ( Faculty of Biology, Jenderal Soedirman University )

Microbiology Indonesia Vol 5, No 1 (2011): March 2011
Publisher : Indonesian Society for microbiology

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Abstract

Ultrastructural observations shows Wolbachia in the testis of Drosophila melanogaster, where Wolbachia and cytoplasm are excluded from the mature sperm, and also found either in somatics and reproductive organ of D. simulans. Details of the ultrastructure of Wolbachia pipientis from the reproductive and somatic organs of D. melanogaster harbour Wolbachia-induce popcorn-effect and D. simulans harbour Wolbachia-induce cytoplasmic incompatibility are described as follows: the ultrastructure of Wolbachia in both of them were similar, distribution of Wolbachia in D. simulans was not restricted to the reproductive organs, they were also found in somatic tissues (muscle). Wolbachia can be present without causing detrimental effects. They are pleomorphic (rod shaped, elongate, oval or slightly bent).   The size varies between 0.04 µm and 0.47 µm in diameter and between 0.26 µm and 1.2 µm in length.  In a few cases Wolbachia seem to have been undergoing fission, but are still joint together by a vacuolar membrane. The microorganisms appear to have two membranes, a host membrane and a bacterial membrane.  However, in some cases the microorganism seems to be surrounded by only one membrane, the possibility why only one membrane was visible might be due to loss during the embedding process

Process Design of Microbiological Chitin Extraction

WAHYUNTARI, BUDIASIH ( Center for Bioindustrial Technology, Laboratoria Pengembangnan Teknologi Agro-Biomedika, Badan Pengkajian dan Penerapan Teknologi, Pusat Penelitian Ilmu Pengetahuan dan Teknologi, ) , JUNIANTO, . ( Faculty of Fishery and Marine Sciences, Universitas Padjajaran ) , SETYAHADI, SISWA ( Center for Bioindustrial Technology, Laboratoria Pengembangnan Teknologi Agro-Biomedika, Badan Pengkajian dan Penerapan Teknologi, Pusat Penelitian Ilmu Pengetahuan dan Teknologi, )

Microbiology Indonesia Vol 5, No 1 (2011): March 2011
Publisher : Indonesian Society for microbiology

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Abstract

Chitin extraction from shrimp shells involves two processing steps, these are the deproteination and demineralization process. The aim of this experiment was to compare the order of the chitin extraction process. The first experiment was deproteination of fresh shrimp shells followed by demineralization process and the second one was demineralization of fresh shrimp shells followed by deproteination. Bacillus licheniformis F11.1, a proteolytic producing bacterium, was used for the deproteination process. Lactobacillus acidophilus FNCC116, a lactic acid bacterium, was used for the demineralization process. The deproteination was done in a 1 liter fermenter jar at 55 ºC, 250 rpm and 2.5 vvm aeration for 60 h. The demineralization was done in the same size fermenter at 30 ºC and 50 rpm agitation for 48 h. The experimental results showed that demineralization followed by the deproteination process resulted in a better chitin yield than when the process was conducted in the opposite order. The first process reduced 47.37% protein and 50.23% ash, whereas the second process reduced 79.61% protein and 88.65% ash

Screening of Quorum Quenching Activity of Bacteria Isolated from Ant Lion

Christianto, Billy, Yogiara, . ( Faculty of Biotechnology, Universitas Katolik Indonesia Atma Jaya )

Microbiology Indonesia Vol 5, No 1 (2011): March 2011
Publisher : Indonesian Society for microbiology

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Abstract

Bacterial intercellular communication or quorum sensing controls the pathogenesis of many medically important organisms. Therefore, it is important to isolate bacteria that can disintegrate the communication, in a process called quorum quenching. Bacteria from ant lion (Myrmeleon sp.) were grown on Luria agar, and approximately 1.85 x 109 CFU mL-1 was obtained. Eleven morphologically different colonies were screened for quorum quenching activity using wild type Chromobacterium violaceum as an indicator. Two isolates (Myr7 and MyrB) were found to possess quorum quenching activity. Isolates with quorum quenching activity were later identified employing 16S rRNA.  Both isolates were similar to bacteria in the genus Aeromonas