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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.
Microbiological and Physicochemical Characteristics of Inasua Traditional Fish Fermented from Maluku Islands Suwanto, Antonius; Mahulette, Ferymon; Mubarik, Nisa Rachmania; 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.
GENETIC DIVERSITY ANALYSIS OF THERMOPHILIC BACTERIA FROM CANDRADIMUKA CRATER IN CENTRAL JAVA EMPLOYING PCR-RFLP OF 16S-rRNA GENE TEMMY DESILIYARNI; ANTONIUS SuwANTOAAAo; MAGGY T. SUHARTONO; TRESNAWATI PURWADARIA
BIOTROPIA - The Southeast Asian Journal of Tropical Biology No. 14 (1999)
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (196.046 KB) | DOI: 10.11598/btb.1999.0.14.155

Abstract

The specific primers for bacteria (63f and 1387r) were used to amplify the 16S-rRNA genes from total community genomic DNA of thermophilic bacteria. The total community genomic DNA was obtained from muds and water samples of Candradimuka crater, Dieng Plateau, Central Java. PCR products were cloned into vector  pCR*2.1-TOPO (3.9 kb) and transformed into Escherichia coli TOPIC. Two  tetrameric restriction endonucleases  Rsal  and  Hhal  were employed to generate Restriction Fragment Length Polymorphisms (RFLP) paterns. These enzymes yielded 10 and 9 groups of 16S-rRNA profiles or OTU (Operational Taxonomic Units) from 27 16S-rRNA gene clones. Rsal was found to be more discriminative in differentiating the clones than Hhal. Rsal-RFLP indicated that OTU 7 and OTU 3 represented the most abundant clones, i.e. 6 and 5 clones respectively. The distribution of 16S-rRNA gene clones could  indicate relative distribution of  specific groups of  thermophilic  bacteria  in  their  natural habitat. Analysis of diversity at the DNA level could represent both culturable  and  unculturable bacteria in the  environment. Similarity analysis showed that  at level  0.600 there  were 8 different  groups from 10  RFLP  profiles generated by  Rsal  digestion. This study indicated that there were at least 8 groups of different thermophilic bacteria occupying Candradimuka crater. Key words: Thermophiles, 16S-rRNA, Candradimuka crater.
THE PROCESS OF DEVELOPING GELATINIZATION AND SACCHARIFICATION WITH VARIATIONS IN TEMPERATURE AND PERIOD OF GLUCOSE SAGO MATERIAL Megavitry, Rissa; Nurhijrah, Nurhijrah
International Journal of Environment, Engineering and Education Vol 1 No 3 (2019)
Publisher : Three E Science Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (570.762 KB) | DOI: 10.5281/zenodo.3634182

Abstract

Initial temperature variations carried out for the gelatinization stage and sampling every six hours during the saccharification process, which lasted 72 hours. The liquefaction process using the ?-amylase enzyme and then proceeds to the saccharification process with the glucoamylase enzyme. The raw material used is sago flour, which has relatively high starch content. The method in this research 1) Sample preparation; 2) Gelatinization Process; 3) Liquefaction Process; 4) Saccharification Process; 5) Reducing Sugar Analysis; 6) Sweetness Level Analysis; 7) Dextrose Equivalent Analysis; 8) Statistical Analysis. The result for analysis obtained the average value of reducing sugar at the use of 121 degrees Celsius gelatinization temperature is 108.33 g/L higher than the value of reducing sugar at the use of 87 degrees Celsius gelatinization temperature is 94.56 g/L. The analysis obtained the average value of sweetness level at the use of 121 degrees Celsius gelatinization temperature is 23.22 degrees Brix higher than the value of sweetness level at the use of 87 degrees Celsius gelatinization temperature is 20.82 degrees Brix. The analysis obtained the average value of dextrose equivalent at the use of 121 degrees Celsius gelatinization temperature is 54,17 percent higher than the value of dextrose equivalent at the use of 87 degrees Celsius gelatinization temperature is 47.28 percent. The high potential of glucose syrup made from sago expected to motivate the development of home industries that use glucose syrup in various food productions.
Molecular Dynamic Simulation for Thermal Stability Properties of Endo β-Mannanase Enzyme Yulandi, Adi; Hermosaningtyas, A A; Sutanto, Sheila; Suwanto, Antonius
UNEJ e-Proceeding Indonesian Protein Society (IPS), International Seminar and Workshop 2014
Publisher : UNEJ e-Proceeding

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Abstract

Endo β-mannanase or mannanase hydrolyse the β-D-1,4 mannopyranoside linkages in β-mannan intomanno-oligosaccharides. Four mannanases, named MAN1, MAN2, MAN3 and MAN4, were isolated from palm kernel meal waste have potential as thermostable mannanases. Series of enzymatic assay to characterize enzyme properties may affect longer time and higher cost. Homology modeling and molecular dynamic simulation are reliable and faster alternative assay to determine enzyme properties by analyzing enzymes’ three-dimensional structure. The structureswere constructed using homology modeling approach using Modeller. Template 2QHA was chosen for having more than 98% sequence similarity with targets. The homology models and template were simulated using molecular dynamics software GROMACS 4.6 for 10 ns production time each at 300 K, 323 K and 353 K. Both targets share the same (β/α)8 TIM barrel folding type similar to template 2QHA The basic analysis of molecular dynamic simulation (root mean square deviation and root mean square fluctuation) showed that both enzymes were thermostable, albeit compared to template 2QHA amino acid residues substitution in samples contribute for different thermostable profile. However, MAN2 was appeared to be more stable at high temperature than other samples. Keywords: endo β-mananase, homology modeling, molecular dynamic simulation
Population Dynamics of Yeasts and Lactic Acid Bacteria (LAB) During Tempeh Production . EFRIWATI; ANTONIUS SUWANTO; GAYUH RAHAYU; LILIS NURAIDA
HAYATI Journal of Biosciences Vol. 20 No. 2 (2013): June 2013
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (139.422 KB) | DOI: 10.4308/hjb.20.2.57

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Yeasts and lactic acid bacteria (LAB) are commonly found in tempeh and has been studied separately. However, comprehensive study on population dynamics of yeasts and LAB during tempeh production, including the effect of the difference tempeh production methods has not been reported. This research was aimed in studying the effect of different methods of tempeh production applied in tempeh home industry on the dynamics of yeast and LAB communities. Population dynamics was expressed as both changes of colony number and its phylotype. Samples were obtained from five stages and from two different methods of tempeh production. Observations were carried out employing colony counting on selective media followed by Terminal Restriction Fragment Length Polymorphism (T-RFLP). The study indicated that the population of yeasts and LAB during tempeh production were dynamic and different between these methods. Tempeh production methods affected the presence of yeasts and LAB population as indicated by difference in colony number, the number and diversity of phylotype, as well as number of specific phylotypes grew on plates.
Xanthomonas oryzae pv. oryzae (Xoo), a causal agent of bacterial leaf blight (BLB), is one of the most important pathogens of rice. The effectiveness of ten Streptomyces spp. isolates in suppressing Xoo disease was assessed in planta and in vitro. In planta experiments were carried out in a greenhouse and arranged in a randomized completely block design (RCBD) with three replications. Twenty treatments were tested which included plants inoculated with both Streptomyces spp. and Xoo, and plants i RATIH DEWI HASTUTI; YULIN LESTARI; ANTONIUS SUWANTO; RASTI SARASWATI
HAYATI Journal of Biosciences Vol. 19 No. 4 (2012): December 2012
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.19.4.155

Abstract

Xanthomonas oryzae pv. oryzae (Xoo), a causal agent of bacterial leaf blight (BLB), is one of the most important pathogens of rice. The effectiveness of ten Streptomyces spp. isolates in suppressing Xoo disease was assessed in planta and in vitro. In planta experiments were carried out in a greenhouse and arranged in a randomized completely block design (RCBD) with three replications. Twenty treatments were tested which included plants inoculated with both Streptomyces spp. and Xoo, and plants inoculated with only Streptomyces spp. Plants inoculated with Xoo and sprayed with a chemical bactericide, and plants inoculated with only Xoo served as positive controls, whereas plants not inoculated with either Streptomyces spp. or Xoo were used as negative controls. The results showed that the effect of endophytic Streptomyces spp. on BLB disease expressed as area under disease progress curve (AUDPC) was not significantly different to that on control plants (P > 0.05). However, plants inoculated with endophytic Streptomyces spp. were significantly taller and produced higher tiller number than control plants (P < 0.05). Streptomyces spp. isolate AB131-1 gave the highest plant height. In vitro studies on biocontrol mechanisms of selected Streptomyces spp. isolates showed that isolate LBR02 gave the highest inhibition activity on Xoo growth, followed by AB131-1 and AB131-2. Two isolates (AB131-1 and LBR02) were able to produce chitinase, phosphatase, and siderophore which included biocontrol characteristics. Morphological and colonization studies under SEM and light microscopy confirmed that the three isolates were endophytic Streptomyces spp. from different species. These studies found that the paddy plant which was inoculated with endophytic Streptomyces spp. AB131-1 and infected by Xoo could increase the height of plant and number of tillers.
Cloning of Genomic DNA Flanking Transposon in the Nonpathogenic Mutant of Xanthomonas axonopodis pv. glycines M715 ALINA AKHDIYA RUSMANA; ANTONIUS SUWANTO; BUDI TJAHJONO
HAYATI Journal of Biosciences Vol. 12 No. 2 (2005): June 2005
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (107.224 KB) | DOI: 10.4308/hjb.12.2.57

Abstract

The objective of this work is to clone flanking DNA derived from Tn-5 mutagenesis of wild type strain Xanthomonas axonopodis pv. glycines as first step to clone and to identify the gene involved in pathogenicity mechanism. We have localized the flanking DNA fragment from a nonpathogenic mutant of Xag M715. Southern hybridization analysis using 2.8 kb EcoRI from pYR103 as a probe showed that the fragment is located within 2.0 kb PstI fragment. A 0.7 kb flanking DNA was amplified using inverse PCR technique, and inserted into pGEM-T Easy vector generating a 3.7 kb recombinant plasmid (pAA01). Southern hybridization analysis of the wild type (YR32) with pAA01 as a probe indicated a hybridization signal located at approximately 3.0 kb PstI fragment. DNA sequence analysis revealed that the DNA fragment has a 64% identity to a vir gene of Bacillus anthracis.
SOYBEAN SEEDLING ROOT GROWTH PROMOTION BY 1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE-PRODUCING PSEUDOMONADS Edi Husen; Aris Tri Wahyudi; Antonius Suwanto; Rasti Saraswati
Indonesian Journal of Agricultural Science Vol 10, No 1 (2009): April 2009
Publisher : Indonesian Agency for Agricultural Research and Development

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/ijas.v10n1.2009.p19-25

Abstract

Pseudomonad producing 1-aminocyclopropane-1-carboxylate (ACC) deaminase (E.C.4.1.99.4) has been known to promote plant 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 IAAproducing Pseudomonas isolated from local soil environment (rhizosphere of soybean grown in Plumbon's agricultural areain Cirebon, West Java, Indonesia) to promote soybean root growth in relation to their ACC deaminase activities. The experiments were conducted in growth room and Laboratory of Soil Biology Research, Indonesian Soil Research Institute, Bogor, from January to August 2008. Soybean seeds were inoculated by immersing the seeds for 1 hour in bacterial cell suspension containing approximately 108-109 cells ml-1. The seeds were then germinatedfor 2 days before planting in growth pouches containing sterilized distilled water. All treated and untreated seeds were grown for 7 days in growth room at 24°C with 1300 lux of light intensity for 12-hour followed by a 12-hour dark period at 22°C. ACC deaminase activity of the isolates was assayed based on their ability to grow in Dworkin-Foster’s salt minimal medium containing ammonium sulfate or ACC as a source of nitrogen. Thirteen out of 81 isolates tested significantly increased soybean root length and weight, up to 50% from untreated plants. Of 13 isolates, 11 demonstrated ACC deaminase activities. Two isolates that did not show ACC deaminase activities had lower capacity to produce IAA. The results suggest that the effectiveness of IAA producing Pseudomonas in promoting the growth of the soybean seedlings is associated with their ACC deaminase activities or they produce IAA at low levels.
Genetic Diversity of Klebsiella spp. Isolated from Tempe based on Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction (ERIC-PCR) TATI BARUS; IVAN HANJAYA; JOANITA SADELI; BIBIANA W LAY; ANTONIUS SUWANTO; ADI YULANDI
HAYATI Journal of Biosciences Vol. 20 No. 4 (2013): December 2013
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (625.021 KB) | DOI: 10.4308/hjb.20.4.171-176

Abstract

Tempe is an Indonesian fermented food prepared by fermenting dehulled cooked soybeans with Rhizopus oligosporus. Many types of bacteria are also involved during tempe fermentation, and one of these is Klebsiella spp.  Some isolates of K.  pneumoniae produces vitamin B12 in tempe but it has also been classified as an opportunistic pathogen. For this reason Klebsiella spp. in tempe is important to be studied. The aim of this study was to investigate the genetic diversity of Klebsiella spp. from tempe employing ERIC-PCR method. Sixty-one isolates of Klebsiella have been isolated from sixteen tempe producers  in Bogor, Jakarta, Malang, Tengerang, Bandung and Cianjur. 63F and 1387R primers were used to amplify 16S rDNA sequences, and 1R and 1F primers were used for ERIC analysis. The results of this research showed that sixty-one strains of Klebsiella were clustered into 17 groups. Based on ERIC-PCR analysis, isolates of Klebsiella could be grouped into different profiles which some of these groups consisted of isolates with identical ERIC-PCR profiles. Several identical ERIC-PCR profiles were found in tempe from the same producer. There was no correlation observed between genetic similarity  among isolates with the origin of tempe.
Co-Authors . EFRIWATI . Melani . NURHAIMI-HARIS . Yogiara A A Hermosaningtyas A A Hermosaningtyas, A A ADI YULANDI Agus PURWANTARA Agus Purwito Agustin Wydia Gunawan ALINA AKHDIYA RUSMANA AMARILA MALIK AMARILA MALIK Andi Khaeruni Andi Khaeruni ANJA MERYANDINI Anja Meryandini Anja Meryandini ARI SUSILOWATI ARIS TJAHJOLEKSONO Aris Tri Wahyudi ARTINI PANGASTUTI Asmini Budiani Basil J NIKOLAU BIBIANA W LAY Budi Tjahjono BUDI TJAHJONO Budi Tjahjono BUDI TJAHJONO C Hanny Wijaya CAHYA PRIHATNA Cahya Prihatna CECILIA ANNA SEUMAHU DEBORA HADISUSANTO Desniar . DIAH ISKANDRIATI DIANA ELIZABETH WATURANGI Djoko Santoso Dondin Sajuthi DWI SURYANTO DWI SURYANTO DWI SURYANTO Dyah Kusuma Anggraini Edi Husen Edi Husen EDI HUSEN ERNIN HIDAYATI ESTI PUSPITASARI Esti Utarti Eunice Limantara EVELINE AYU Felicia Kartawidjajaputra Ferymon Mahulette Ferymon Mahulette, Ferymon G. A. Wattimena Gayuh Rahayu Griselda Griselda Griselda, Griselda Hajrial ASWIDINNOO HAJRIAL ASWIDINNOOR Hariyatun, Hariyatun Iman Rusmana Inez H.S. Loeddin Suharsono It Jamilah IVAN HANJAYA JOANITA SADELI KATHARINA JESSICA Kusharyoto, Wien Lilis Nuraida Linda Wati Maggy T Suhartono Maggy T Suhartono MAGGY T. SUHARTONO MAGGY T. SUHARTONO Maggy T. Suhartono MAGGY THENAWIJAYA SUHARTONO Maria Indah Purnamasari Meity S. Sinaga MEITY SURADJI SINAGA MUHAMMAD ZAIRIN Jr. Ni Nyoman Tri Puspaningsih NISA RACHMANIA MUBARIK NURITA TORUAN-MATHIUS NURUL AINI Prihasto Setyanto PRIHASTO SETYANTO QURROTA A’YUN R. Sapto Hendri Boedi Soesatyo RAHAYU WIDYASTUTI Rasti Saraswati RASTI SARASWATI Rasti Saraswati RASTI SARASWATI RATIH DEWI HASTUTI RATNA SETYANINGSIH RATNA SETYANINGSIH RIDWAN AFFANDI ROB HARLING ROHANI CINTA BADIA GINTING Sheila Sutanto Sheila Sutanto, Sheila Suryo Wiyono SUSAN SOKA SUSILOWATI1 SUSILOWATI1 Tan Watumesa Agustina TARUNI SRI PRAWAST MIEN KAOMINI ANY ARYANI DEDY DURYADI SOLIHIN Tati Barus TEMMY DESILIYARNI TRESNAWATI PURWADARIA VICKY MEICY WALTER ERDELEN Widanarni Widanarni YULIN LESTARI YUSMINAH HALA