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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.
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
EFFECT OF POVIDONE IODINE TREATMENT ON BACTERIAL COMMUNITY ASSOCIATED WITH WHITE SHRIMP (LITOPENAEUS VANNAMEI) LARVAE Pangastuti, Artini; Suwanto, Antonius; Lestari, Yulin; Suhartono, Maggy T.
Marine Research in Indonesia Vol 34, No 2 (2009)
Publisher : Research Center for Oceanography - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/mri.v34i2.471

Abstract

The efficacy of povidone iodine as a surface disinfectant was assessed in white shrimp (Litopenaeus vannamei) eggs and larvae. Eggs and nauplii were exposed to povidone iodine 20 ppm for 20 seconds. Culture-based method and Terminal Restriction Fragment Length Polymorphism (T-RFLP) were used to monitor the total number of bacteria and diversity of the bacterial community associated with shrimp eggs and larva at each developmental stage. Povidone iodine reduced the total culturable bacteria, especially Vibrio, on eggs and nauplii, as well as the total bacteria in the whole community as estimated by T-RFLP results. Povidone iodine also reduced the diversity of bacterial community and altered the evenness of phylotypes distribution suggesting that the use of povidone iodine as a surface disinfectant in shrimp aquaculture should be reconsidered.
Expression of An Immunogenic Intimin Fragment of EHEC O157:H7 in Escherichia coli Periplasm under The Control of A Rhamnose-Based Regulated Promoter Hariyatun, Hariyatun; Suwanto, Antonius; Kusharyoto, Wien
ANNALES BOGORIENSES Vol 18, No 1 (2014): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.1234/90

Abstract

Intimin is the main adhesin of Enterohemorrhagic E. coli (EHEC) O157:H7 bacteria which are the most common leading infectious cause of bloody diarrhea and acute kidney failure in children who develop hemolytic uremic syndrome (HUS). Intimin is required for persistent bacterial colonization to eukaryotic host cell and its receptor-binding activity is localized at the C-terminus 282 amino acids (Intimin282). Thus, Intimin282 is an attractive antigen candidate that could be useful in vaccine and diagnostic systems against EHEC infections. Previous studies had reported expression of Intimin in E. coli cytoplasm using commonly used prokaryotic expression systems. However, it usually encountered several problems, i.e. low expression level, leaky expression, inclusion body formation, and truncated protein. The pRHA vector, which is tightly regulated by Lrhamnose and D-glucose, represents a viable alternative E. coli expression system to overcome such problems. Moreover, E. coli periplasm has an advantage of maintaining protein functionality by providing an oxidative environment that is more efficient than cytoplasm. However, to date there is no study about Intimin expression using pRHA expression system and/or in E. coli periplasm. Accordingly, we constructed a recombinant pRHA vector harbouring the respective gene to investigate the expression of an immunogenic Intimin fragment of EHEC O157:H7 in E. coli periplasm. The gene encoding His6-tagged Intimin282 (Int282) together with pelB signal sequence was cloned into the pRHA vector, subsequently expressed in E. coli JM109 and purified. Expression and purification of Int282 were verified by SDS-PAGE and Western blot. The result showed that Int282 was successfully expressed in E. coli periplasm with a protein size of approximately 32 kDa, which corresponded with the predicted size of the protein based on its amino acid sequence.
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.
Analisis Matagenom Komunitas Bakteri Tempe dengan Teknik Terminal Restriction Fragment Length Polymorphism (T-RFLP) Barus, Tati; Griselda, Griselda; Suwanto, Antonius; Agustina, Tan Watumesa
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 15, No 2 (2010): June 2010
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (342.198 KB) | DOI: 10.24002/biota.v15i2.2726

Abstract

Bacteria have an important role in tempe fermentation in Indonesia, aside of Rhizopus oligosporus as the dominant microbe. In this study the molecular aspect of bacterial diversity in tempe were analyzed using a fingerprinting technique, Terminal-Restriction Fragment Length Polymorphism (T-RFLP). This study was aimed to examine the diversity of bacterial community during tempe making. Bacterial diversity analysis was conducted in the first hour and the thirteenth hour after the soybean soaked while the fresh tempe was analysed at one to two hours after the fermentation ended. T-RFLP can be used to describe the diversity of bacterial community during the fermentation of tempe. T-RFLP profiles revealed the presence of 24, 30 and 33 bacterial phylotypes in the first hour and the thirteenth hour after the soybean soaked as well as in fresh tempe samples. The phylotypes were dominated by unculturable bacteria group. Only several bacterial phylotypes were consistenly identified since the beginning to the end of fermentation, while most of them were only identified at certain phases along with the environmental changes (i.e: pH) that occured during the fermentation process. One of the consistently identified groups belongs to Bacillus genera.
EFFECT OF POVIDONE IODINE TREATMENT ON BACTERIAL COMMUNITY ASSOCIATED WITH WHITE SHRIMP (LITOPENAEUS VANNAMEI) LARVAE Pangastuti, Artini; Suwanto, Antonius; Lestari, Yulin; Suhartono, Maggy T.
Marine Research in Indonesia Vol 34 No 2 (2009)
Publisher : Research Center for Oceanography - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/mri.v34i2.471

Abstract

The efficacy of povidone iodine as a surface disinfectant was assessed in white shrimp (Litopenaeus vannamei) eggs and larvae. Eggs and nauplii were exposed to povidone iodine 20 ppm for 20 seconds. Culture-based method and Terminal Restriction Fragment Length Polymorphism (T-RFLP) were used to monitor the total number of bacteria and diversity of the bacterial community associated with shrimp eggs and larva at each developmental stage. Povidone iodine reduced the total culturable bacteria, especially Vibrio, on eggs and nauplii, as well as the total bacteria in the whole community as estimated by T-RFLP results. Povidone iodine also reduced the diversity of bacterial community and altered the evenness of phylotypes distribution suggesting that the use of povidone iodine as a surface disinfectant in shrimp aquaculture should be reconsidered.
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.
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 & Education Vol 1 No 3 (2019)
Publisher : Three E Science Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | 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 α-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.
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.
Co-Authors . EFRIWATI . Melani . NURHAIMI-HARIS 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 Dyah Kusuma Anggraini Edi Husen Edi Husen EDI HUSEN ERNIN HIDAYATI ESTI PUSPITASARI Esti Utarti Eunice Limantara 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 Yogiara Yogiara YULIN LESTARI YUSMINAH HALA