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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 DH5? was constructed and screened for xylanase activity. One positive clone, namely DH5? (pTP510) has been isolated, sequenced and showed putative exo-xylanase (exo-xyl), ?-xylosidase (xyl), and ?-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.
SOYBEAN SEEDLING ROOT GROWTH PROMOTION BY 1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE-PRODUCING PSEUDOMONADS Husen, Edi; Wahyudi, Aris Tri; Suwanto, Antonius; Saraswati, Rasti
Indonesian Journal of Agricultural Science Vol 10, No 1 (2009): April 2009
Publisher : Indonesian Agency for Agricultural Research and Development - MOA

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Abstract

Pseudomonad producing 1-aminocyclopropane-1-carboxylate(ACC) deaminase (E.C.4.1.99.4) has been known to promoteplant growth by lowering ethylene biosynthesis in higher plants,which can be induced by indole-3-acetic acid (IAA) production.The objective of this study was to examine the ability of IAAproducingPseudomonas isolated from local soil environment(rhizosphere of soybean grown in Plumbons agricultural areain Cirebon, West Java, Indonesia) to promote soybean root growthin relation to their ACC deaminase activities. The experimentswere conducted in growth room and Laboratory of Soil BiologyResearch, Indonesian Soil Research Institute, Bogor, from Januaryto August 2008. Soybean seeds were inoculated by immersing theseeds for 1 hour in bacterial cell suspension containingapproximately 108-109 cells ml-1. The seeds were then germinatedfor 2 days before planting in growth pouches containing sterilizeddistilled water. All treated and untreated seeds were grown for7 days in growth room at 24°C with 1300 lux of light intensityfor 12-hour followed by a 12-hour dark period at 22°C. ACCdeaminase activity of the isolates was assayed based on their abilityto grow in Dworkin-Foster’s salt minimal medium containingammonium sulfate or ACC as a source of nitrogen. Thirteen outof 81 isolates tested significantly increased soybean root lengthand weight, up to 50% from untreated plants. Of 13 isolates,11 demonstrated ACC deaminase activities. Two isolates thatdid not show ACC deaminase activities had lower capacity toproduce IAA. The results suggest that the effectiveness of IAAproducingPseudomonas in promoting the growth of the soybeanseedlings is associated with their ACC deaminase activities orthey produce IAA at low levels.
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 | 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.
PENGUJIAN KET AHANAN KOLEKSI GENOTIPE KEDELAI TERHADAP PENYAKIT BISUL BAKTERI Anggraini, Dyah Kusuma; Tjahjono, Budi; Suwanto, Antonius; Aswidinnoor, Hajrial
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 23 No. 3 (1995): Buletin Agronomi
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (796.084 KB) | DOI: 10.24831/jai.v23i3.1634

Abstract

The objective of the research was to evaluate the resistance of soybean genotype in the germplasm collection to pustule disease. Seventy five genotypes were evaluated using spray inoculation method. Inoculation was done on the third week after planting. The 75 genotypes evaluated consists of 29 local varieties, 8 national varieties, 23 introduction, and 15 experimental lines. Results of the experiment showed that among the 75 genotypes tested, one local variety, Si Pinang was found resistant to the pustule disease (Xanthomonas campestris pv. glycines). The resistant local variety was collected from Langkat, North Sumatra.
ISOLASI DAN IDENTIFIKASI SECARA MOLEKULER GANODERMA SPP. YANG BERASOSIASI DENGAN PENYAKIT BUSUK PANGKAL BATANG DI KELAPA SAWIT Purnamasari, Maria Indah; Prihatna, Cahya; Gunawan, Agustin Wydia; Suwanto, Antonius
Jurnal Fitopatologi Indonesia Vol 8 No 1 (2012)
Publisher : The Indonesian Phytopathological Society (Perhimpunan Fitopatologi Indonesia)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (484.212 KB) | DOI: 10.14692/jfi.8.1.9

Abstract

A number of Ganoderma spp. isolates was isolated from oil palms attacked by basal stem rot (BSR) disease in Padang and Pontianak plantations. Genetic polymorphism of these isolates was analyzed based on the internal transcribed spacer (ITS) sequence of ribosomal DNA region. In addition, a restriction fragment length polymorphism (RFLP) analysis was also performed to determine the association of the isolates with BSR disease. The isolated Ganoderma spp. showed high DNA polymorphism and there was no obvious genetic clustering of isolates that may correspond to their geographical position in Padang and Pontianak. This indicated that exchange of DNA between Ganoderma spp. infecting oil palm is not uncommon. This can be explained by the heterothallic nature of Ganoderma spp. in which DNA recombination occurs during sexual reproduction between different thalli. RFLP analysis showed that ITS fragments from all Ganoderma spp. isolates were digested with restriction enzymes MluI and SacI. This indicated that the anoderma spp. isolates were specific for oil palm and thus associated with the BSR.Key words: basal stem rot, Ganoderma spp., internal transcribed spacer, oil palm
Microbiological and Physicochemical Characteristics of Inasua Traditional Fish Fermented from Maluku Islands Mahulette, Ferymon; Mubarik, Nisa Rachmania; Suwanto, Antonius; Widanarni, Widanarni
Biosaintifika: Journal of Biology & Biology Education Vol 10, No 2 (2018): August 2018
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v10i2.13537

Abstract

Based on the raw materials, inasua consists of two types namely inasua with sap and inasua without sap. Research of inasua with sap has never been done and considered as the novelty of this research. The sensory characteristics and shelf life of two types of inasua were different. The research aims to analyze the microbiological and physicochemical characteristics of two types of inasua during fermentation. The microbiological analyzes include the total number of bacteria and lactic acid bacteria, while physicochemical analyzes include temperature, pH, water activity, proximate analysis, salt, alcohol, histamine, amino acids and fatty acids contents. The total number of bacteria and lactic acid bacteria has decreased during fermentation. At the end of the fermentation the total number of bacteria and lactic acid bacteria inasua with sap were 3.2x107 CFU/g and 3.0x107 CFU/g, while inasua without sap were 5.4x105CFU/g and 3.5x105 CFU/g, respectively. The moisture, protein, alcohol contents and water activity decreased, otherwise the salt, fat, ash, amino acids, and fatty acids contents increased during fermentation. Generally, microbiological and physicochemical characteristics of inasua with sap was better than inasua without sap. The results of this research to improve the quality of this fermentation product in the future.
Bakteri dalam Plak Gigi dan Saliva Penderita Diabetes Tipe 2, dan Hubungannya dengan Status Agregasi Trombosit Kemal, Yulianti; Chaidar, Sri Lelyati; Syafril, Yuniarti; Mangundjaja, Soeherwin; Oemardi, Maryantoro; Suwanto, Antonius
Journal of Dentistry Indonesia Vol 7, No 3 (2000): December
Publisher : Faculty of Dentistry, University of Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (461.124 KB) | DOI: 10.14693/jdi.v7i3.727

Abstract

The occurrence of coronary atherosclerosis and acute myocardianl ischemia due to the hyperaggregation of platelets, caused the death of 75-80% of type 2 diabetics. In an invitro study, the aggregation of platelets was influenced by the "Platelet Aggregation Associated Protein" on the surface of dental plaque bacteria, S. sanguis. The aim of the study was to identify bacteria in the supragingival plaque and saliva of type 2 diabetics, and their relationship to the aggregation of platelets. Dental plaque and salivary gland samples from 5 type 2 diabetics were diluted serially, and inoculated in Mitis Salivarius medium. The morphologie of the Colony Forming Units (CFU) Growth were analysed, identified physiologically and biochemically with Api 20 Strep subtrates. Aggregation of platelets of the blood were analysed with Adenosin Di Phosphate. The result of the study showed 22 colonies (CFU), in 6 morphology types. Three morphologytypes were identified as A viridans, the other 3 as Str. acidominus, Lc. lactis lactis, and E. avium. One morphology type of A. viridans, Str .acidominus, Lc. lactis lactis and E. avium were found in subjects with hypoaggregation; 2 morphology types of A. viridans were found in subjects with normal aggregation. It is presumed that type 2 diabetics with Str. acidominus, Lc. lactis actis, E. avium, and certain morphology type of A. viridans in their dental plaque and saliva, hve hyperaggregation of platelet diabetics with two morphology types of A. viridans have normal aggregation of platelets.
DIVERSITY OF PROTEASE-PRODUCING BACILLUS SPP. FROM FRESH INDONESIAN TEMPEH BASED ON 16S RRNA GENE SEQUENCE Barus, Tati; Wati, Linda; Melani, .; Suwanto, Antonius; Yogiara, .
HAYATI Journal of Biosciences Vol. 24 No. 1 (2017): January 2017
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (841.094 KB) | DOI: 10.4308/hjb.24.1.35

Abstract

Tempeh is a type of traditional fermented food in Indonesia. The fermentation can be performed by Rhizopus microsporus as a main microorganism. However, Bacillus spp. is found in abundance in tempeh production. Nevertheless, information regarding the diversity of Bacillus spp. in tempeh production has not been reported yet. Therefore, the aim of this investigation was to study the genetic diversity of Bacillus spp. in tempeh production based on the 16S ribosomal RNA sequence. In this study, about 22 of 24 fresh tempeh from Jakarta, Bogor, and Tangerang were used. A total of 52 protease-producing Bacillus spp. isolates were obtained. Based on 16S ribosomal RNA results, all 52 isolates were identified to be similar to B. pumilus, B. subtilis, B. megaterium, B. licheniformis, B. cereus, B. thuringiensis, B. amyloliquefaciens, Brevibacillus brevis, and Bacillus sp. All the identified isolates were divided into two large clusters: 1) a cluster of B. cereus, B. thuringiensis, Bacillus sp., and B. brevis and 2) a cluster of B. pumilus, B. subtilis, B. megaterium, B. licheniformis, and B. amyloliquefaciens. Information about the Bacillus spp. role in determining the quality of tempeh has not been reported and this is a preliminary study of Bacillus spp. from tempeh.
Keragaman Genetika Xanthomonas axonopodis pv. glycines Asal Kedelai Varietas Edamame di Indonesia Khaeruni, Andi; Suwanto, Antonius; Tjahjono, Budi; Sinaga, Meity S.
Jurnal Perlindungan Tanaman Indonesia Vol 13, No 1 (2007)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jpti.11814

Abstract

Xanthomonas axonopodis pv. glycines cause bacterial pustule disease caused a serious disease in Edamame cultivation in Indonesia. We collected a total of 29 X. axonopodis pv. glycines isolates from Edamame fields at Jember, Ciawi, Cipanas and Bogor. The genetic diversity analysis of all isolates employing ARDRA and ISR technique showed six and seven different DNA profile, respectively. Therefore there are at least seven strains of X. axonopodis pv. glycines infected Edamame in Indonesia. Both CPI from Cipanas and JA4 from Sukorejo Jember isolates possess unique DNA profle and genetically are not closely related to other isolates.
ANALYSIS OF INTESTINAL MUCOSAL IMMUNOGLOBULIN A IN SPRAGUE DAWLEY RATS SUPPLEMENTED WITH TEMPEH SOKA, SUSAN; SUWANTO, ANTONIUS; RUSMANA, IMAN; SAJUTHI, DONDIN; ISKANDRIATI, DIAH; JESSICA, KATHARINA
HAYATI Journal of Biosciences Vol. 22 No. 1 (2015): January 2015
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1507.883 KB) | DOI: 10.4308/hjb.22.1.48

Abstract

Tempeh is a well-known Indonesian fermented food made from soybean. During the fermentation process, microorganisms play an important role in the flavor, texture, and nutritional quality of tempeh. Tempeh has been show to have immuno-modulatory and immune-stimulating properties that may also be caused by the microorganisms in tempeh as they interact between the microbial population in the intestinal tract. The objective of this study was to quantify IgA gene expression at both the transcription and translation levels in Sprague Dawley (SD) rats supplemented with tempeh. A total of 6 female SD rats were divided into 3 groups of 2 rats. The first group was the control and was fed a standard diet without tempeh. The second- and third group were fed with a standard diet supplemented with raw and cooked tempeh, respectively. Ileum tissue samples were collected after tempeh supplementation for 28 days. RNA was extracted from ileum samples, and measurement of IgA gene expression was further analyzed using semi quantitative real-time PCR. The concentration of IgA protein was quantified from ileum lysate using the half sandwich ELISA method. IgA gene expressions in rats supplemented with raw, and with cooked tempeh, were 1.18 and 1.17 fold higher, respectively, compared to the control group. Moreover, IgA protein secretion levels also increased 2.46 and 2.08 fold, respectively, compared to the control group. The result of this study indicates that both raw and cooked tempeh may stimulate IgA secretion, and also that both viable and non-viable microorganisms might stimulate IgA gene expression.