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Cloning, Sequencing and Characterization of The Xylan Degrading Enzymes from Geobacillus thermoleovorans IT-08 Puspaningsih, Ni Nyoman Tri; Suwanto, Antonius; Suhartono, Maggy T
Jurnal ILMU DASAR Vol 9 No 2 (2008)
Publisher : Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Jember

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Abstract

Geobacillus thermoleovorans IT-08 is a Gram positive, thermophilic bacterium that can utilize xylan as a sole source of carbon. This strain was isolated from Gunung Pancar hot spring, Bogor, West Java, Indonesia. A plasmid genomic library in Escherichia coli DH5α was constructed and screened for xylanase activity. One positive clone, namely DH5α (pTP510) has been isolated, sequenced and showed putative exo-xylanase (exo-xyl), β-xylosidase (xyl), and α-L-arabinofuranosidase (abfa) genes (Genebank Accession No.DQ387047, DQ345777 and DQ387046 respectively). Each gene encoded 604, 511 and 502 amino acids, respectively. The BLAST search for protein database revealed that Abfa was high similar with GH51 family Abfa of Geobacillus stearothermophilus T6, but Xyl and Exo-Xyl were slight similar with GH43 family (25-34%) respectively. The deduced protein had a molecular weight of about 70 kDa (Exo-Xyl), and 60 kDa (Xyl and Abfa). These showed good accordance with the calculated molecular weight of each protein (68.64 kDa for Exo-xyl, 57.99 kDa for Xyl and 57.03 kDa for Abfa) from deduced amino acid sequence.
Purification and Charaterization of Protease from Pathogenic Bacteria Pseudomonas aeruginosa Baekhari, Ace; Suhartono, Maggy T; Palupi, Nurheni Sri; Nurhayati, Tati
Jurnal Teknologi dan Industri Pangan Vol. 19 No. 1 (2008): Jurnal Teknologi dan Industri Pangan
Publisher : Departemen Ilmu dan Teknologi Pangan, IPB Indonesia bekerjasama dengan PATPI

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Abstract

In the last decade, concern on protease as medical target for overcoming bacterial diseases and viral diseases has been rapidly increased because of the obvious involvement of this enzyme in the molecular of the diseases. The purpose of this research was to purify and characterize protease from pathogenic bacteria Pseudomonas aeruginosa. The bacteria were grown in media containing triptone 1%, NaCl 1% and Yeast extract 0.5%. protease of Pseudomonas aeruginosa was purified using column chromatography with Sephadex G-100 gel. There were three peaks of enzyme protein, which were detected on fractions 14,17 and 30. the optimum pH of the extracelluler protease from Pseudomonas aeruginosa was 8. The optimum temperature of Pseudomonas aeruginosa was 300C. Fe3+ (1dan 5 mM) was strong activator and Co 2+ was strong inhibitor. Study on the effect of metals ion and specific inhibitors indicated that protease from Pseudomonas aeruginosa was serin metaloprotease. The apparent moleculer weights, as determined by SDS-PAGE and zymogram technique, 36 kD and 42 kD. Key word : Protease, characterization, purification, pathogenic bacteria P. aeruginosa
Isolasi dan kloning fragmen cDNA dari tanaman karet dengan sifat resisten dan rentan terhadap Corynespora cassiicola menggunakan metode cDNA-AFLP Isolation and cloning of cDNA fragments from rubber plant with resistant and susceptible characters to Corynespora cassiicola using cDNA-AFLP method NURHAIMI-HARIS, .; SUWANTO, Antonius; SUHARTONO, Maggy T; ASWIDINNOOR, Hajrial
E-Journal Menara Perkebunan Vol 78, No 1: Juni 2010
Publisher : INDONESIAN RESEARCH INSTITUTE FOR BIOTECHNOLOGY AND BIOINDUSTRY

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (486.561 KB) | DOI: 10.22302/iribb.jur.mp.v78i1.78

Abstract

AbstractLeaf fall disease caused by Corynespora cassiicola fungi is one of the most important diseases in rubber plant. Rubber clone AVROS 2037 is considered resistant to this pathogen while clone PPN 2444 is susceptible. These two rubberclones were used to identify genes or transcripts differentially expressed during interaction between rubber plants and the fungi, using cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) method. Induced genes/transcripts expression was examined to compare differencies between plants uninfected and infected with C. cassiicola at 24, 36, 48 and 72 hours after inoculation. cDNA-AFLP analysis was performed using restriction enzyme VspI and TaqI so the adapters and primers also have the recognition site of these enzymes. By using 29 specific primers, 35 out of approximately 1450 fragments were differentially expressed between AVROS and PPN 2444 clones. All of these fragments were cloned and sequenced. The homology-based grouping of these sequences resulted in 19 contigs and nine individual sequences. Among these, 10 contigs and five sequences have significant sequence homology with known genes in gene bank data base, such as Ran binding protein, protein transporter and transcriptional regulators of some organisms; arginase, GTP-binding protein, heat shock protein (HSP) and aconitase. Ran binding protein, GTPbinding protein and protein transporter were known as membrane proteins while arginase and HSP usually expressed as a response to wounding or toxin treatment. The present of arginase is usually related to the availability of nitric oxide (NO) in plant tissue. NO is well known as a signal molecule on plant defense response. AbstrakPenyakit gugur daun yang disebabkan oleh fungi Corynespora cassiicola merupakan salah satu penyakit penting tanaman karet. Klon karet AVROS 2037menunjukkan sifat resisten terhadap patogen tersebut sedangkan klon PPN 2444 merupakan klon yang rentan. Kedua klon karet tersebut digunakan untuk mengidentifikasi gen atau transkrip yang diekspresikan secara diferensial selama terjadi interaksi antara tanaman karet dengan C. cassiicola menggunakan teknik cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP). Ekspresi gen/transkrip dipelajari untuk membandingkan perbedaan antara tanaman yang tidak diinfeksi dengan yang diinfeksi patogen pada waktu 24, 36, 48 dan 72 jam setelah inokulasi. Analisis cDNA-AFLP dilaksanakan dengan menggunakan pasangan enzim restriksi VspI dan TaqI sehingga adapter dan primer memiliki sekuen pengenalan kedua enzim restriksi tersebut. Dengan menggunakan 29 pasang primer spesifik, sebanyak 35 dari sekitar 1450 fragmen memiliki ekspresi berbeda antara klon AVROS 2037 dan PPN 2444. Semua fragmen yang berbeda tersebut kemudian diklon pada vektor kloning dan disekuen. Hasil sekuensing dikelompokkan berdasarkan homologi sekuennya dan menghasilkan 19 contigs serta sembilan macam sekuen yang tidak mengelompok. Sebanyak 10 dari 19 contigs dan lima dari sembilan sekuen tersebut memiliki homologi dengan produk gen yang telah dikenal yang terdapat di pangkalan data GenBank, seperti putative Ran binding protein, protein transporter, regulator transkripsi, arginase, GTP-binding protein, heat shock protein (HSP) dan aconitase. Beberapa di antaranya seperti putative Ran binding protein, protein transporter dan GTP-binding protein dikenal sebagai protein membran, sedangkan arginase dan HSP merupakan protein atau enzim yang ekspresinya pada tanaman antara lain dipengaruhi oleh adanya pelukaan dan perlakuan toksin. Keberadaan arginase sering berhubungan dengan ketersediaan nitric oxide (NO) pada jaringan tanaman. NO dikenal sebagai salah satu sinyal molekul dalam mekanisme pertahanan tanaman.
Molecular analysis of Hemagglutinin Gen of Highly Pathogenic Avian Influenza of H5N1 Subtype Isolated from Waterfowls Susanti, R; Soejoedono, Retno D; K Mahardika, I Gusti Ngurah; T Wibawan, I Wayan; Suhartono, Maggy T
Indonesian Journal of Animal and Veterinary Sciences Vol 13, No 3 (2008)
Publisher : Indonesian Animal Sciences Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (423.147 KB) | DOI: 10.14334/jitv.v13i3.584

Abstract

Avian influenza viruses (AIV) subtype H5N1 isolated from waterfowls in West Java pose the known characteristic of highly pathogenic strains, with polybasic amino acid sequence of cleavage site QRERRRKKR and QRESRRKKR. This research aimed to analyze the important domains of hemagglutinin (HA) gene of those isolates. Fragment of HA gene was amplified using RT-PCR method with specifically-designed primer pairs and sequenced using dideoxy termination method with ABI automatic sequencer (Applied Biosystems). Multiple alignment of nucleotide and deduced amino acid sequences were analyzed using ClustalW of MEGA-3.1 program. Some of biological domains of HA, i.e. antigenic sites, receptor binding pocket, and glycosylation sites of the isolates were polymorphic. The viruses also pose conserved glutamine (Q) and glisin (G) residues at the known receptor binding site, at the position 222 and 224 respectively. This findings clearly show that all AIV subtype H5N1 isolaed from waterfowl preservesthe α-2,3NeuAcGal avian receptor specificity. Key Words: Antigenic Sites, Glycosylation Sites, Receptor Binding Pocket, AIV H5N1, Waterfowls
Identification of Pathogenecity of Avian Influenza Virus Subtype H5N1 from Waterfowls Base on Amino Acid Sequence of Cleavage Site Hemagglutinin Protein R., Susanti; Soejoedono, Retno D.; K Mahardika, Gusti Ngurah I; Wibawan, Wayan T I; Suhartono, Maggy T
Indonesian Journal of Biotechnology Vol 13, No 2 (2008)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (635.287 KB)

Abstract

Identification of pathotype of Avian Influenza Virus (AIV) subtype H5N1 isolates is very important. Thisresearch aimed to identify the pathotype of AIV subtype H5N1 isolated from household waterfowls in West Javabased on molecular markers of amino acid sequences of the Hemagglutinin (HA) cleavage site. Fragments of HAgenes of 21 isolates were amplified using RT-PCR with a primer pair that flanking the cleavage site region, andsequenced with dideoxy-termination method with ABI automatic sequencer (Applied Biosystems). Multiple alignmentof nucleotide and their deduced amino acid sequence were analyzed using ClustalW from MEGA 3.1 program.The result shows that all H5N1 isolates (21 isolates) possess polybasic cleavage sites with 2 patterns ofamino acid sequence, i.e QRERRRKKR (20 isolates) and QRESRRKKR (1 isolate). This finding indicates that all ofthe viruses isolated in this research were of highly pathogenic avian influenza (HPAI) strains.Keywords: cleavage site, waterfowls, HPAI
Molecular analysis of Hemagglutinin Gen of Highly Pathogenic Avian Influenza of H5N1 Subtype Isolated from Waterfowls Susanti, R; Soejoedono, Retno D; K Mahardika, I Gusti Ngurah; T Wibawan, I Wayan; Suhartono, Maggy T
Jurnal Ilmu Ternak dan Veteriner Vol 13, No 3 (2008): SEPTEMBER 2008
Publisher : Indonesian Center for Animal Research and Development (ICARD)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (423.147 KB) | DOI: 10.14334/jitv.v13i3.584

Abstract

Avian influenza viruses (AIV) subtype H5N1 isolated from waterfowls in West Java pose the known characteristic of highly pathogenic strains, with polybasic amino acid sequence of cleavage site QRERRRKKR and QRESRRKKR. This research aimed to analyze the important domains of hemagglutinin (HA) gene of those isolates. Fragment of HA gene was amplified using RT-PCR method with specifically-designed primer pairs and sequenced using dideoxy termination method with ABI automatic sequencer (Applied Biosystems). Multiple alignment of nucleotide and deduced amino acid sequences were analyzed using ClustalW of MEGA-3.1 program. Some of biological domains of HA, i.e. antigenic sites, receptor binding pocket, and glycosylation sites of the isolates were polymorphic. The viruses also pose conserved glutamine (Q) and glisin (G) residues at the known receptor binding site, at the position 222 and 224 respectively. This findings clearly show that all AIV subtype H5N1 isolaed from waterfowl preservesthe α-2,3NeuAcGal avian receptor specificity. Key Words: Antigenic Sites, Glycosylation Sites, Receptor Binding Pocket, AIV H5N1, Waterfowls
DAUR PATOLOGIS TEGAKAN HUTAN TANAMAN Acacia mangium Willd. Nuhamara, Simon Taka; Hadi, Soetrisno; Suhendang, Endang; Suhartono, Maggy T; Syafii, Wasrin; Achmad, Achmad
BERITA BIOLOGI Vol 9, No 1 (2008)
Publisher : Research Center for Biology-Indonesian Institute of Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (858.66 KB) | DOI: 10.14203/beritabiologi.v9i1.804

Abstract

Heart rot on Acacia mangium Willd. forest stand is critical especially for mechanical or construction wood based purposes. Failure on understanding the nature and the way it get established into the tree stem may cause high economic consequences.Anticipating such a worse condition, studies on cull factor in relation to age was initiated. Eventually the study is aimed at healthy cutting cycles of the clear and purposely stand establishment. The study had been carried out at BKPH Parung Panjang, KPH Bogor. Following the cull factor measurement technique combined with the pathological rotation estimation procedures, it was found that the healthy volume was 0.0623 m and the cull factor was 31.25 %.The figures were at the age of nine years. Therefore, the pathological rotation cycle for the A. mangium stand in the area could be fitted at eight years, as being adopted so far.This is true, when the plantation is established for the production of wood, provided that the tending operation is optimal. Applying the United States Department of Agriculture (USDA) Forest Health Monitoring (FHM) indices, the general performance of the A. mangium forest stand in Parung Panjang is found to be in healthy criteria. The damage indices for all stand ages investigated varied from 2.77 (lowest) to 5.16 (highest) as compared to the 21.18 value, the possible highest FHM tree index.
Identification of Pathogenecity of Avian Influenza Virus Subtype H5N1 from Waterfowls Base on Amino Acid Sequence of Cleavage Site Hemagglutinin Protein Susanti, R.; Soejoedono, Retno D.; Mahardika, I Gusti Ngurah K; Wibawan, Wayan T I; Suhartono, Maggy T
Indonesian Journal of Biotechnology Vol 13, No 2 (2008)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (635.287 KB) | DOI: 10.22146/ijbiotech.7803

Abstract

Identification of pathotype of Avian Influenza Virus (AIV) subtype H5N1 isolates is very important. Thisresearch aimed to identify the pathotype of AIV subtype H5N1 isolated from household waterfowls in West Javabased on molecular markers of amino acid sequences of the Hemagglutinin (HA) cleavage site. Fragments of HAgenes of 21 isolates were amplified using RT-PCR with a primer pair that flanking the cleavage site region, andsequenced with dideoxy-termination method with ABI automatic sequencer (Applied Biosystems). Multiple alignmentof nucleotide and their deduced amino acid sequence were analyzed using ClustalW from MEGA 3.1 program.The result shows that all H5N1 isolates (21 isolates) possess polybasic cleavage sites with 2 patterns ofamino acid sequence, i.e QRERRRKKR (20 isolates) and QRESRRKKR (1 isolate). This finding indicates that all ofthe viruses isolated in this research were of highly pathogenic avian influenza (HPAI) strains.Keywords: cleavage site, waterfowls, HPAI
Optimization of Culture Conditions for Production of β-Mannanase by Strain Nonomuraea sp. ID06-379 using Submerged Substrate Fermentation Ratnakomala, Shanti; Yopi, Yopi; Suhartono, Maggy T; Meryandini, Anja; Prasetya, Bambang
ANNALES BOGORIENSES Vol 18, No 2 (2014): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (685.031 KB) | DOI: 10.1234/96

Abstract

The objective of this study was to investigate the effect of media compositions on the production of β-mannanase by Nonomuraea sp.ID06-379. The study was focused on the influence of carbon, nitrogen,phosphorus and detergents on β-mannanase synthesis through manipulating media compositions on production medium. The results indicated that for carbon sources, locus bean gum (0.745 ± 0.036 U/ml) showed maximum mannanase activity. Malt extract was the best nitrogen source for producing β-mannanase (1.075 ± 0.006 U/ml),(NH4)2HPO4 as phosphate source (1.733 ± 0.026 U/ml) and Tween 80 (1.145 ± 0.003 U/ml) as surfactants effect on increasing permeability of bacterial cell membrane, enhancing membrane transport and excretion of extracellular enzymes into the production media. The results showed that 1% malt extract, 0.5% locus bean gum and 0.05% (NH4)2HPO4 were good substances for nitrogen source, carbon source and phosphate respectively. The highest production of β-mannanase by Nonomuraea sp. ID06-379 (5.33 U/mg) was reached in the medium optimization (Vogel’s minimal medium) contained the following ingredients: 0.5% locus bean gum, 1% malt extract and 0.05% (NH4)2HPO4, under submerged fermentation with shaking at 120 rpm and 28 C for 2 days incubation.
Characterization of Phenol Degrading Bacteria from Buntal Lake of Central Kalimantan ., Nursaadah; Santosa, Dwi Andreas; Suhartono, Maggy T
Jurnal Ilmu Tanah dan Lingkungan Vol 3 No 2 (2000): Jurnal Ilmu Tanah dan Lingkungan
Publisher : Departemen Ilmu Tanah dan Sumberdaya Lahan, Fakultas Pertanian, IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1135.116 KB) | DOI: 10.29244/jitl.3.2.24-31

Abstract

Three bacterial isolates (ICBB 1168, ICBB 1169, ICBB 1170), being capable to utilizing phenol as sole carbon and energy source, were isolated from Buntal Lake of Central Kalimantan. Growth of all isolates were optimum at 37OC. Optimum pH for growth and phenol degradation of ICBB 1168, lCBB 1169, and ICBB 1170 were 7-8, 6, and 6-7, respectively. Among the isolates, ICBB 1170 showed best phenol degrading activity. ICBB 1170 able to degrade 16 mM phenol to 0.71 mM in 4days. Phenol degradation ability of ICBB 1170 could be increased by adding 0.01-0.1% yeast extract. Addition of 0.05-0.1% glucose in medium inhibited phenol degradation by ICBB 1170. Cell-free extracts of ICBB 1170 had specific activity 2.92 Ulmg. Degradation of benzoate by ICBB 1170 wasstudied. However, the ability to degrade phenol were higher than that of benzoate.