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Articles by issue : Vol 3, No 2 (2009): August 2009
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Articles
Exploration of Bacillus thuringiensis ä-Endotoxin Derived from Bacterial Isolates in Jabodetabek Region

JUSUF, EDDY

Microbiology Indonesia Vol 3, No 2 (2009): August 2009
Publisher : Indonesian Society for microbiology

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Abstract

Bacillus thuringiensis is a well-known species of bacteria producing parasporal crystalline proteins that are toxic to many insect pests, it also has strong cytocidal activity against human cancer cells. In this work we endeavoured to explore the city of Jakarta and its neighbouring regencies to obtain new strains to profile its potency. The soil samples were boiled and plated on T-3 agar; the colonies which appeared were then examined under the light microscope to check for crystalline proteins. The proteins were treated with 1% SDS-0.01% b-mercaptoethanol and visualized by SDS-PAGE to determine their molecular size. From 52 soil samples, 1248 putative colonies were obtained. After microscopic examination, 57 isolates showed the existence of crystalliferous protein, of those 30 indicated many sizes of ä-endotoxin protein from approximatively 150 kDa to the smallest 35 kDa. Most of proteins examined probably showed insecticidal activity and four of those were predicted to possess cytocidal activity against human cancer cells. The geographic condition did not appear to influence the distribution of different types of äendotoxin.

Detection and Sequence Diversity of Begomovirus Associated with Yellow Leaf Curl Disease of Pepper (Capsicum annuum) in West Sumatra, Indonesia

TRISNO, JUMSU, HIDAYAT, SRI HENDRASTUTI, HABAZAR, TRIMURTI, MANTI, ISHAK, JAMSARI, .

Microbiology Indonesia Vol 3, No 2 (2009): August 2009
Publisher : Indonesian Society for microbiology

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Abstract

Yellow leaf curl disease of pepper has become an emerging important disease in West Sumatra since early 2000. Several attempts have been made, including disease survey and detection, in order to identify the causal agent of the disease. Pepper (Capsicum annuum) plants showing yellow leaf curl from West Sumatra were analyzed for presence of Begomovirus employing Polymerase Chain Reaction (PCR) with degenerate primers pAL1v 1978 and pARc 715. A DNA fragment of 1.6 kb was successfully amplified and subjected to direct sequencing. A stem loop region was found in the nucleotide sequence obtained, which contains the conserved nucleotide signature sequence TAATATTAC present in begomoviruses. Based on the stem loop region comparisons and phylogenetic analysis, the virus isolates from West Sumatra showed the closest relationship to Pepper yellow leaf curl Indonesia virus (PYLVIV) and Tomato yellow leaf curl Indonesia virus (TYLCIV). The sequence was different from other Asia Begomoviruses reported earlier. These isolates were divided into three groups which were tentatively called Pepper yellow leaf curl Indonesia virus-West Sumatra-[group 1], -[group 2] and -[group 3] {PYLCIV-WS-[group1], -[group2], and -[group3]}.

Identification and Phylogenetic Analysis of Bacterial Isolates from Litopenaeus vannamei Shrimp Culture System and Gut Environment Based on 16SrRNA Gene Sequence Data

RAHAYU, TUBAGUS HAERU, GANDJAR, INDRAWATI, RIANI, ETTY, DJUNAIDAH, IIN SITI, SJAMSURIDZAL, WELLYZAR

Microbiology Indonesia Vol 3, No 2 (2009): August 2009
Publisher : Indonesian Society for microbiology

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Abstract

Selected bacterial isolates from a Litopenaeus vannamei shrimp culture system and gut environment were assessed using 16S rRNA gene sequencing method to identify their identity and to construct their phylogenetic relationship. In a preliminary study, a total of 19 isolates were selected as probiotics. These isolates were prepared using freeze and heat-shock method to obtain the DNA template. PCR amplification of 16S ribosomal RNA gene of isolates was carried out using bacterial universal primers 9F and 1510R and was sequenced using an automated DNA sequencer. These gene sequences were compared with other gene sequences in the GenBank database (NCBI) using a BLAST search to find closely related sequences. Alignment of these sequences with sequences available from GenBank database was carried out to construct a phylogenetic tree for these bacteria. Most of the isolates obtained, i.e. 17 out of the 19 isolates, belonged to different species of Bacillus, sharing 95 to 99% 16S ribosomal RNA identity with the respective type-strain, whereas the remaining 2 isolates belonged to Micrococcus sp. and Micrococcus luteus with 97 to 99% 16S rRNA homology, consecutively.

Activity of Proteolytic and Amylolytic Enzymes from Bacillus spp. Isolated from Shrimp Ponds

JAMILAH, IT, MERYANDINI, ANJA, RUSMANA, IMAN, SUWANTO, ANTONIUS, MUBARIK, NISA RACHMANIA

Microbiology Indonesia Vol 3, No 2 (2009): August 2009
Publisher : Indonesian Society for microbiology

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Abstract

Accumulation of feed excess in commercial shrimp ponds due to overfeeding could decrease water quality. Protein and starch are the primary components of shrimp feed. This study was conducted to characterize extracellular proteases and amylases of Bacillus spp. isolated from shrimp ponds. 72 proteolytic and amylolytic Bacillus spp. isolates were screened from shrimp ponds in Karawang, West Java. Ten isolates were selected for further characterization for their growth and ability to reduce total suspended solid generated from commercial shrimp feed. Bacillus sp. DA 5.2.3 and L5 showed excellent activity in reducing total suspended solid, by 37 and 30% respectively. Protease and a-amylase activities of Bacillus sp. DA 5.2.3 isolate were consistently higher than that of L5. Maximum total and specific protease activity of DA 5.2.3 isolate was 2.0 U mL-1 and 40.9 U mg-1 respectively, while the activities of the L5 isolate were 2.1 U mL-1 and 23.0 U mg-1 respectively. Based on its 16S rRNA gene sequences, Bacillus sp. DA 5.2.3 showed 99% similarity to Bacillus cereus XHJ-2-6. Bacillus sp. DA 5.2.3 could potentially be applied to maintain water quality by reducing total suspended solid in water columns of shrimp ponds.

Development of Rapid Agglutination Test to Detect Chicken Marek Antibody

WIBAWAN, I WAYAN TEGUH, HALIMAH, LIA SITI, DJANNATUN, TITIEK, ZARKASIE, KAMALUDDIN

Microbiology Indonesia Vol 3, No 2 (2009): August 2009
Publisher : Indonesian Society for microbiology

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Abstract

To our knowlege, there is no rapid agglutination test to detect antibodies to viruses which might be due to the small dimension of viral particles. Through complex formation of Staphylococcus aureus bearing protein A-rabbit IgG-anti IgY-IgY anti Marek virus, agglutination of antibodies to viruses can be achieved and visualized. To design the prototype of the test, the bacterial cells of Staphylococcus aureus were coupled to a complex compound consisting of IgG-IgY-Marek antigen. This protocol was able to detect clearly the presence of Marek antibody in chicken sera, showing the rapid, clear and distinct agglutination reaction on the glass objects. No agglutination reaction was observed in the reaction of specified pathogen free chicken sera with this prototype showing the specificity of the test. This finding demonstrates a novel rapid agglutination which can be used for the detection of antibodies to various agents.

Molecular Analysis of H5N1 Avian Influenza Virus from Avian Species: Compared with Genbank Data of the Indonesian H5N1 Human Cases

DHARMAYANTI, NI LUH PUTU INDI

Microbiology Indonesia Vol 3, No 2 (2009): August 2009
Publisher : Indonesian Society for microbiology

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Abstract

In Indonesia, the H5N1 avian influenza (AI) disease has been circulating for more than five years and has infected various types of avian species and human beings. Generally, avian influenza cases in human beings are suspected to be spread by chicken, birds or waterfowl previously infected by avian influenza. The data supporting this assumption were very limited, therefore the molecular characterization on four avian influenza genome segments such as hemagglutinin, neuraminidase, matrix and non structural that was isolated from the avian species surrounding the avian influenza cases in human was conducted. The analysis was conducted on these genes which were responsible for binding receptors, the pathogenicities, and the resistance to antiviral drugs, thus the virus changes can be detected by comparing the sequence data of GenBank from human cases related to the avian species. The four avian influenza viruses used in this study isolated from avian influenza cases surrounding the avian influenza cases in human in 2007. The results of genetic analysis showed that these four viruses and the available sequence data from the GenBank for of avian influenza virus in human and avian have the receptor a-2,3 of sialic acid which is the avian receptor. The A/Ck/West Java/Bks2/2007 virus is collected from the chicken surrounding the avian influenza cases in human that resembles the data of avian influenza virus from human, A/Indonesia/CDC1031/2007 from GenBank. The viruses conferred similarities amino acid sequence of hemagglutinin, neuraminidase, matrix and non structural protein. All viruses used have deletion at the position 80-84 of the NS1 protein and possessed the ESEV motif which may contribute to an increased virulence. The avian influenzaviruses examined in this study also show resistance to amantadine

The Relatedness between Hepatitis B Virus from Non-Papuan Blood Donors in Jayapura and the Papuan Clusters

NUGRAHAPUTRA, VICTOR EKA, AMIN, MOCHAMAD, MERTANIASIH, NI MADE, LUSIDA, MARIA INGE

Microbiology Indonesia Vol 3, No 2 (2009): August 2009
Publisher : Indonesian Society for microbiology

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Abstract

The genotypes (A-H) and subtypes (adw2, adw4, adrq-, adrq+, ayw1-4, ayr) of HBV show distinct geographical distributions, which have been associated with anthropological history. The novel finding of the HBV subgenotypes C6 and D6 from Papuans formed a specific cluster distinct from the previous HBV subgenotypes C1-C5 and D1-D5. In this study we determined the most recent genotype-subtype patterns of the HBV from non-Papuan blood donors who live in Jayapura and their phylogenetic relatedness, especially with the Papuan clusters. Fifteen HBsAg-positive serums were obtained from non-Papuan blood donors including from people in Java (46.7%), Maluku (26.7%), Sulawesi (20%) and East Nusa Tenggara (6.7%). S gene of all HBV serum isolates were partially sequenced and analyzed. Most HBV isolates (53.3%) were classified as genotype B, followed by genotype C(26.7%) and D (20.0%). The subtype adw2 (33.3%) was predominant, followed by adrq+ (26.7%) and ayw1/ayw2 (20.0%). All HBV isolates with subtype adw2 and ayw1 belonged to genotype B, while adrq+ belonged to genotype C and ayw2 belonged to genotype D. The most predominant HBV genotype-subtype (B/adw2) was consistent with the ethnic background (mostly from Java people). Nevertheless, based on the phylogenetic relatedness, many non Papuan isolates (40%) were classified into HBV/C6 and HBV/D6 of the Papuan clusters. Other isolates were classified into HBV/C1, HBV/B3 and HBV/B7. In conclusion, many HBV isolates from non-Papuans in Jayapura belonged to the Papuan clusters, but others had different genotype-subtype patterns with frequencies dependent on ethnicity.

Expression of Simian Retrovirus Type D Serotype 2 Envelope in Insect Cell Using Baculovirus Expression Vector System

ISKANDRIATI, DIAH, SADIKIN, MOHAMAD, PAMUNGKAS, JOKO

Microbiology Indonesia Vol 3, No 2 (2009): August 2009
Publisher : Indonesian Society for microbiology

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Abstract

Simian retrovirus type-D (SRV) is a causative agent of simian acquired immunodeficiency syndrome in Asian macaques, and can serve as a viral model in understanding of retrovirus infection because of some similarities to human AIDS pathogenesis. Study of infection and pathogenesis of SRV in macaques could be a strategy of vaccine and antiviral development for preventive and therapeutic purposes. We expressed the SRV-2 envelope gene using baculovirus expression vector system and transfected it to Spodoptera frugiferda insect cell line for SRV-2 recombinant protein production. Analysis using PCR and sequencing technique of recombinant in the passage-3 viral stock indicated the occurrence of recombination between SRV-2 envelope and baculovirus genome. Purification using immobilized metal ion affinity chromatography Ni2+-NTA to recombinant protein could minimize the presence non-specific proteins. The SDS-PAGE analysis showed a specific protein for SRV-2 gp70 envelope. Western blot analysis of this purified protein indicated a specific reaction with anti-SRV-2 antibody positive of Macaca fascicularis serum shown as SRV-2 gp70 envelope band.

Survival Mechanism of Puccinia abrupta var. partheniicola Urediniospores During Summer Season

FAUZI, MOHAMAD TAUFIK

Microbiology Indonesia Vol 3, No 2 (2009): August 2009
Publisher : Indonesian Society for microbiology

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Abstract

The success of applying plant pathogens as biological control agents of weeds relies on the ability of the biological control agent to persist at all parts of the year and to successfully go through all of its life cycle stages in the course of a single year. One important aspect of any plant disease life cycle is the ability to survive during unfavorable parts of the season. The research aimed at understanding the mechanism involved in the survival of Puccinia abrupta var. partheniicola, a potential biological control agent of parthenium weed (Parthenium hysterophorus), during simulated summer conditions had been undertaken in the field plot at the Alan Fletcher Research Station, Brisbane. The urediniospores that were placed either on plant debris or on intact plants were exposed to summer conditions and were regularly tested their viability after being exposed. The results showed that the urediniospores could only survive for less than six weeks, which is less than half of the Queensland summer where the weed is abundant. This indicates that the rust spores do not survive on infected parthenium weed debris during summer season.