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All Journal Journal of Tropical Soils Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Indonesian Journal of Biotechnology Jurnal Perlindungan Tanaman Indonesia Jurnal Impresi Indonesia Acta Solum
Donny Widianto
Department of Agricultural Microbiology, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta
Religion Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Economics, Econometrics & Finance Education Environmental Science Immunology & microbiology Law, Crime, Criminology & Criminal Justice Materials Science & Nanotechnology Social Sciences

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A Single Base Substitution Adjacent to the Stop Codon in the downstream of the SMP3 gene Affects its Post-trancriptional process in Saccharomyces cerevisiae Widianto, Donny; Mukai, Yukio; Irie, Kenji; Araki, Hiroyuki; Oshima, Yasuji
Indonesian Journal of Biotechnology Vol 12, No 2 (2007)
Publisher : Universitas Gadjah Mada

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Abstract

The smp3-1 mutant allele confers increased holding stability of heterologous plasmid, pSR1, and a temperature-sensitive growth defect which is remediable by the addition of 1 M sorbitol as the osmotic stabilizer. The smp3-1 allele contains two base substitutions; one is in the open reading frame and changed the 490th CAT (encoding Histidine) to TAT (tyrosine), and the other one is an A for G substitution, at 2 bp downstream from termination codon. These base substitutions were separated each other by recombination at a BstNI site located between these two substitutions. The base substitution in the 3 untranslated region was found to be lethal and the defect was unremediable by the osmotic stabilizer, while that in the open reading frame has no appreciable effect to the cell. Thus, both the base substitutions join together confer the smp3-1 mutant phenotype. The smp3-1 mutant cells cultivated at 37 OC in nutrient medium containing 1 M sorbitol showed similar smp3 transcription as in the wild type. These facts suggest that smp3-1 mutation has a defect in its post-transcriptional process.
Ethanol Production by Fermentation of Various Sweet-Stalk Sorghum Juices Using Various Yeast Strains Widianto, Donny; Arofatullah, Akbar; Yuwono, Triwibowo; Prijambada, Irfan Dwidya
Indonesian Journal of Biotechnology Vol 15, No 2 (2010)
Publisher : Universitas Gadjah Mada

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Abstract

The ethanol production by fermentation of sweet-stalk sorghum juice is affected by the juice composition and the capability of the yeast strain to ferment it. Eight yeast strains were tested on their growth and ethanol fermentation abilities in sweet-stalk sorghum juices extracted from three cultivars of sweet sorghum. The best specific growth rate of the yeast strains grown aerobically in the yeast extract peptone dextrose (YEPD) broth and the sweet-stalk sorghum juices of KCS105, FS501, and FS902 cultivars, were achieved by OUT7903, OUT7913, OUT7903, and OUT7027 yeast strains, respectively. However, the best specific CO2 evolution rate of the yeast strain during fermentation of the juices was achieved by OUT7027 yeast strains. The highest ethanol concentration, ethanol yield, and sugar conversion efficiency (SCE) were obtained by strain OUT7921 when it was employed to ferment sweet-stem sorghum juice of FS902 cultivar. It was also observed that the juice extracted from sweet-stalk sorghum of FS902 cultivar is the most suitable medium for all yeast strains to achieve their best fermentation abilities. Thus, it is likely that the growth and ethanol production ability of a yeast strain in sweet-stalk sorghum juice depend on the physiological responses of the yeasts to nutrientcomposition of the sorghum juice and the sorghum cultivar from which the juice was extracted.Key words : Sweet-stalk sorghum juice, ethanol, fermentation, yeast
Legume Nodulating Bacterium, Achromobacter xylosoxidans Found in Tropical Shrub Agroecosystem, Sumatera, Indonesia Wedhastri, Sri; Fardhani, Dinar Mindrati; Kabirun, Siti; Widada, Jaka; Widianto, Donny; Evizal, Rusdi; Prijambada, Irfan Dwidya
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

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Abstract

Legume nodulating bacteria (LNB), known also as rhizobia, are soil bacteria, which are able to form rootnodules and fi x nitrogen in the leguminous plants. The LNB availability in the soil depends on the type ofagroecosystem, where plant grows. In this study, we isolated LNB from the shrub agroecosystem in Sumatera,Indonesia, and obtained four selected bacterial strains. Among them, the isolate UGM48a formed root nodulein Macroptilium atropurpureum and showed highest number of nitrogenase activity. UGM48a also contains nifHand nodA genes. An analysis of the PCR-amplifi ed 16S rDNA and BLASTn analysis showed that UGM48adisplayed 96% similarity with Achromobacter xylosoxidans. In addition, UGM48a were successfully nodulatedGlycine max (L.) merr var. wilis. This is the fi rst report detecting A. xylosoxidans as nodule-forming species forGlycine max possesing the positive copy of nodA gene.Keywords : Legume Nodulating Bacteria, shrub agroecosystem, Achromobacter xylosoxidans, nodA, Glycine max
The Diversity of Legume-Nodulating Bacteria from Several Agroecosystems in Sumberjaya, Lampung Wedhastri, Sri; Yuliana Prahastiwi, Yuliana; Widada, Jaka; Widianto, Donny; Kabirun, Siti
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

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Abstract

Bacteria that capable of forming root nodules on legumes are known as Rhizobia. They have also known as Legume- Nodulating Bacteria (LNB). They can fi x nitrogen from the atmosphere. Diversity of Legume-Nodulating Bacteria is affected by biotic factors (such as their genetic factors, plants, and competition with the other soil microbes) and abiotic factors (such as land use, soil’s temperature, pH, chemistry and soil’s properties). The aim of this experiment is to know the diversity of eleven Legume- Nodulating Bacteria based on their phenotypic and genotypic characters. The eleven LNB used in this experiments were isolated from several agroecosystems in Sumberjaya, Lampung. The analysis of these LNB diversity were carried out by characterizing both phenotypic and genotypic properties. The diversity analysis showed that the eleven LNB isolates had high diversity, based on nodule formation, and classifi ed into two groups of cross inoculation group.Key words: Rhizobia, phenotypic diversity, genotypic diversity
Ethanol Fermentation on Mixed Sugars Using Mixed Culture of Two Yeast Strains ., Jasman; Prijambada, Irfan Dwidya; Hidayat, Chusnul; Widianto, Donny
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

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Abstract

The objective of this study was to evaluate the use of mixed cultures of the recommended yeast strainsfrom a previous study on ethanol fermentation using a substrate mixture consisting of sucrose, glucose, andfructose. There were three mixed (combination) cultures namely OUT7096/OUT7913, OUT7096/OUT7921,and OUT7913/OUT7921. The fermentation medium contained sugar mixture consisting of glucose, fructose,and sucrose with a composition generally close to the composition of sugars in sweet sorghum juice. Overall,fermentation is carried out in two stages. First fermentation was performed using the three mixed culturesto determine the best combination based on the concentration of ethanol produced and the concentration ofresidual sugar. Second fermentation was conducted using the best mixed culture obtained from the fi rst stage.This second stage was intended to describe the pattern of the changes in the concentration of ethanol, sugarsand biomass during the fermentation progresses and to determine some kinetic parameters namely ethanolyield (Yp/s), growth yield (Yx/s) and specifi c growth rate (μ). The results of the fi rst fermentation showed thatthe best mixed culture was OUT7913/OUT7921 and the subsequent fermentation using this culture providethe highest ethanol yield (Yp/s) = 0.47 g.g-1 that was reached at 53rd hour, growth yield (Yx/s) = 0.425 g.g-1, andμ = 0.12 hour-1.Keywords : fermentation, ethanol, mixed culture, mixed sugar
PENGARUH BAHAN ORGANIK DAN SUHU PENGERINGAN TERHADAP KETAHANAN HIDUP ASPERGILLUS NIGER DALAM PUPUK PELET BIO-FOSFAT Sastro, Yudi; Widianto, Donny; Prijambada, Irfan D.
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 12, No 2 (2007): June 2007
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (183.053 KB) | DOI: 10.24002/biota.v12i2.2667

Abstract

This research was aimed to investigate the effect of organic matter and drying temperature on Aspergillus niger survivability in the rock phosphate pellet fertilizer namely bio-phosphate. The research was arranged by a completely randomized design 3x3x6. Addition of the mixing of tapioca waste, rice bran, and starch (BOC) and the humic substance (BH) in the bio-phosphate, and its drying temperature (SP) were the treatments. Aspergillus niger inoculums survivability in the bio-phosphate was determined using plating methods. The result showed that the addition of BOC decreased amount of A. niger in the bio-phosphate up to 28.0%, while the BH increased the amount of A. niger up to 24.4%. The ideal drying temperature of bio-phosphate pellet fertilizer was 600C.
Sekresi Asam-asam Organik oleh Aspergillus niger YD 17 yang Ditumbuhkan dengan Batuan Fosfat Sastro, Yudi; Widianto, Donny; Shiddieq, Dja'far
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 11, No 3 (2006): October 2006
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (446.464 KB) | DOI: 10.24002/biota.v11i3.2544

Abstract

Information on ability of Aspergillus niger to secrete organic acid is important in using A. niger as phosphate rock-solubilizing microorganism. This research was aimed to examine the ability of A. niger YD 17 secreting organic acid when it was grown with phosphate rock. An A. niger YD 17 was obtained from Laboratory of Microbiology, Faculty of Agriculture, GMU. The phosphate rock used was Christmas Island phosphate rock. Organic materials consisted of tapioca waste industry, rice bran, and starch. The study was conducted in Pikovskaya liquid medium and soils that were taken from Jasinga, Banten, West Java (ultisol) and Karang Jati, Ungaran, Central Java (inceptisol). The type and level of organic acid production were determined using high performance liquid chromatography (HPLC). The results indicated that A. niger YD 17 was able to secrete organic acid when it was grown with phosphate rock. The level of organic acid in the Pikovskaya liquid medium reached 255.7 g.ml-1, whereas in the soil reached 2992.5 g.g-1. Malate dominated organic acid in the Pikovskaya liquid medium, while in the soils dominated by oxalate. The type and level of organic acid secreted by A. niger YD 17 were influenced by carbon and phosphorus sources, concentration of inoculums, and characteristic of the soils.
Soil Bacterial Diversity and Productivity of Coffee - Shade Tree Agro-ecosystems Evizal, Rusdi; Tohari, .; Prijambada, Irfan Dwidja; Widada, Jaka; Widianto, Donny
JOURNAL OF TROPICAL SOILS Vol 17, No 2: May 2012
Publisher : UNIVERSITY OF LAMPUNG

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5400/jts.2012.v17i2.181-187

Abstract

Coffee productions should have environmental value such as providing high soil microbial diversity while producing high yield. To examine that purposes, two experimental plots were constucted at benchmark site of Conservation and Sustainable Management of Below-Ground Biodiversity (CSM-BGBD), in Sumberjaya Subdistrict, West Lampung, Indonesia, during 2007-2010. Types of coffee agro-ecosystem to be examined were Coffea canephora with shade trees of Gliricidia sepium, Erythrina sububrams, Michelia champaca, and no shade. Two plots were constructed at 5-years-coffee and 15-years-coffee. Diversity of soil bacteria was determined based on DNA finger printing of total soil bacteria using Ribosomal Intergenic Spacer Analysis (RISA) method. The results showed that: (1) For mature coffee (15 years old), shade-grown coffee agro-ecosystems had higher soil bacterial diversity than those of no shade coffee agro-ecosystem, (2) Shaded coffee agro-ecosystems were able to conserve soil bacterial diversity better than no-shade coffee agro-ecosystem. Soil organic C and total litter biomass had positive effect on soil bacterial diversity, (3) Types of agro-ecosystem significantly affect the bean yield of 15 years coffee. Coffee agro-ecosystems shaded by legume trees had higher yield than those of non-legume shade and no shade coffee agro-ecosystem, (4) Shannon-Weaver indices of soil bacterial diversity together with weed biomass and N content of coffee leaf had positive effect on coffee bean yield.
Reforming the Limits of Discretion and Strengthening the Police Code of Ethics in Achieving Justice in Law Enforcement Widianto, Donny; Budianto, Azis
Jurnal Impresi Indonesia Vol. 3 No. 12 (2024): Indonesian Impression Journal (JII)
Publisher : Riviera Publishing

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.58344/jii.v3i12.5731

Abstract

Effective law enforcement requires clear regulations and high accountability. However, the use of discretion by law enforcement officers often poses a dilemma in maintaining a balance between flexibility and legal certainty. This study aims to analyze the legal regulations governing police discretion and code of ethics in Indonesia and to formulate a reform model to improve justice in law enforcement. This study uses a normative legal method with a legislative and conceptual approach, which examines written legal regulations and the underlying legal concepts. Data were collected from various relevant legal and scientific literature sources. The results of the study indicate that the use of undirected discretion can create injustice and reduce public trust in law enforcement officers. Reforms are needed to limit discretion by strengthening the police code of ethics and implementing clearer legal guidelines. The implications of this study include the development of policies that are more transparent, accountable, and in accordance with the principles of social justice. This reform is expected to increase the professionalism and legitimacy of the police in the eyes of the public.
Keragaman Jamur Mikoriza Arbuskular pada Rizosfer Tiga Varietas Tanaman Tebu Fatmawati, Zulfa; Widada, Jaka; Widianto, Donny; Cahyaningtyas, Anjar; Putri, Devanda Ayu Lidya Permata
Acta Solum Vol 3 No 2 (2025): Maret 2025
Publisher : Department of Soil, Faculty of Agriculture, Lambung Mangkurat University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20527/actasolum.v3i2.3293

Abstract

Jamur Mikoriza Arbuskular (JMA) merupakan kelompok jamur yang dapat bersimbiosis dengan lebih dari 80% akar tanaman. Hubungan simbisosis ini mampu meningkatan serapan hara dan ketahanan tanaman terhadap cekaman lingkungan. Macam dan jumlah JMA sebagai simbion sangat dipengaruhi oleh tanaman inangnya. Penelitian ini bertujuan untuk mengidentifikasi jenis-jenis JMA pada berbagai varietas tebu (Bululawang, Kidang Kencana, dan Pasuruan Jengkol 922) yang ditanam pada lokasi dan tanah yang sama. Spora JMA diisolasi dengan metode penyaringan basah secara bertingkat. Proses identifikasi dilakukan dengan pengamatan mikroskopik terhadap morfologi spora yang telah diberi pewarna PVLG dan reagen Melzer. Identifikasi molekuler melalui analisis sekuens gen rRNA menggunakan metode nested PCR dengan pasangan primer NS1 dan NS4 dilanjutkan dengan pasangan primer AML1-AML2. Berdasarkan hasil penelitian menunjukkan keanekaragaman spora terbesar genus JMA ditemukan pada tanah varietas Kidang Kencana yaitu 269 spora (berbeda nyata dengan uji DMRT, p<0.05) diikuti varietas Bululawang dengan jumlah spora 191 dan Pasuruang Jengkol 922 dengan jumlah spora 142. Angka keanekaragaman JMA pada tanaman tebu tergolong sedang, dan terdapat empat spesies JMA yang berhasil diidentifikasi secara morfologi dan molekuler, yaitu Glomus flavisporum, Acaulospora koskei, Gigaspora Margarita, dan Scutellospora savannicola. Temuan ini menunjukkan bahwa jumlah dan jenis JMA yang berasosiasi dengan akar tanaman tebu dipengaruhi oleh varietas tanaman, dan Glomus sp. merupakan kelompok yang mendominasi tiga varietas tanaman tebu yang diteliti.
Co-Authors . Tohari Arofatullah, Nur Akbar Budianto, Azis Cahyaningtyas, Anjar Chusnul Hidayat Devanda Ayu Lidya Permata Putri Dinar Mindrati Fardhani Fatmawati, Zulfa Hiroyuki Araki, Hiroyuki Irfan Dwidya Prijambada JAKA WIDADA Jasman . Kenji Irie, Kenji Kurniasari, Irianti Maharani, Rina Prijambada, Irfan Dwidja Rinda Fajrin Aldina, Rinda Fajrin Rusdi Evizal Shiddieq, Dja'far SITI KABIRUN Siwi Indarti Sri Wedhastri Triwibowo Yuwono Waele, Dirk De Yasuji Oshima, Yasuji Yudi Sastro Yukio Mukai, Yukio Yuliana Yuliana Prahastiwi, Yuliana