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All Journal HAYATI Journal of Biosciences Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vegetalika Jurnal Ilmu Pertanian Agroland : Jurnal Ilmu-Ilmu Pertanian Agrotrop : Journal on Agriculture Science International Journal of Biosciences and Biotechnology International Journal of Renewable Energy Development Microbiology Indonesia BIOTROPIA - The Southeast Asian Journal of Tropical Biology Journal of Tropical Soils Journal of the Medical Sciences (Berkala Ilmu Kedokteran) Berkala Ilmiah Pertanian Jurnal Agro Teknologi Tropika Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Sains Tanah AGRIVITA, Journal of Agricultural Science agriTECH Indonesian Journal of Biotechnology Jurnal Tanah dan Air Planta Tropika Pharmacon Jurnal Pengabdian Kepada Masyarakat (Indonesian Journal of Community Engagement) Jurnal Perlindungan Tanaman Indonesia INDONESIAN JOURNAL OF PHARMACY JURNAL HAMA DAN PENYAKIT TUMBUHAN TROPIKA Jurnal Bioteknologi & Biosains Indonesia (JBBI) Caraka Tani: Journal of Sustainable Agriculture Squalen Bulletin of Marine and Fisheries Postharvest and Biotechnology Indonesian Food and Nutrition Progress OLDI (Oseanologi dan Limnologi di Indonesia) JURNAL PERTANIAN jurnal Ilmu Pertanian (Agricultural Science) Jurnal Tanah dan Air (Soil and Water Journal) Kaunia: Integration and Interconnection of Islam and Science Journal Engagement: Jurnal Pengabdian Kepada Masyarakat Indonesian Journal of Pharmacology and Therapy

JAKA WIDADA

Departemen Mikrobiologi Pertanian, Fakultas Pertanian, Universitas Gadjah Mada

Author-ID : 414939

Religion Agriculture, Biological Sciences & Forestry Arts Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Decision Sciences, Operations Research & Management Earth & Planetary Sciences Economics, Econometrics & Finance Education Energy Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Neuroscience Physics Social Sciences Veterinary

Published : 85 Documents Claim Missing Document

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Cloning of Thermostable DNA Polymerase Gene from a Thermophilic Brevibacillus sp. Isolated from Sikidang Crater, Dieng Plateu, Central Java Lucia Dhiantika Witasari; Irfan Dwidya Prijambada; Jaka Widada; Dionysius Andang Arif Wibawa
Indonesian Journal of Biotechnology Vol 15, No 2 (2010)
Publisher : Universitas Gadjah Mada

Thermostable DNA polymerase has an important role for amplifying small amount of DNA through polymerase chain reaction (PCR). Thermophillic bacteria Brevibacillus sp. was isolated from Sikidang Crater, Dieng Plateu, Central Java. Previous study showed that crude protein of the isolate could be used in PCR. Unfortunately, like most native thermostable enzymes, the thermostable DNA polymerase of the isolate is synthesized in a very low level and therefore is cumbersome to purify. The purpose of this research is to clone thermostable DNA polymerase gene of the isolate. The DNA polymerase gene was amplified by means of PCR using spesific primers. The amplified fragment was then isolated, purified, and ligated into the pGEM-T cloning vector. The recombinant plasmid was then transformed to competent E. coli JM109 cells using heat shock method. The cloned thermostable DNA polymerase gene from the thermophilic isolate was then characterized for its nucleotide base sequence. The result showed that the DNA Pol I gene was successfully be amplified from the isolate DNA genom, resulting in ± 2,7 kb DNA fragment in length. Sequence analysis of segment of targeted gene showed high similarity to that of thermostable DNA polymerase genes from other Bacillus.Key words : Thermostable DNA Pol I, Brevibacillus sp., PCR, cloning

Antifungal Production of a Strain of Actinomycetes spp Isolated from the Rhizosphere of Cajuput Plant: Selection and Detection of Exhibiting Activity Against Tested Fungi A. Alimuddin; Jaka Widada; Widya Asmara; M. Mustofa
Indonesian Journal of Biotechnology Vol 16, No 1 (2011)
Publisher : Universitas Gadjah Mada

Actinomycetes are bacteria known to constitute a large part of the rhizosphere microbiota. Their isolation is an important step for screening of new bioactive compounds. Culturable actinomycetes populations from cajuput plant rhizosphere soils in Wanagama I Forest UGM Yogyakarta were collected to study about their antifungal activity. Among 17 of a total 43 isolates that showed activity were screened for producing antifungi substances. Screening for antifungal activity of isolates were performed with dual culture bioassay in vitro. One isolate that was designated as Streptomyces sp.GMR-22 was the strongest against all tested fungi and appeared promising for a sources of antifungal. Culture’s supernatant and mycelia were extracted with chloroform, ethyl acetate and methanol, respectively. Antifungal activity of crude extracts was tested by diffusion method against tested fungi. The result indicates that isolates of actinomycetes from cajuput plant rhizosphere could be an interesting sources of antifungal bioactive substances.

Diversity of Dibenzofuran-Utilizing Bacteria Isolated by Direct-Plating and Enrichment Methods Irfan Dwidya Prijambada; Jaka Widada; Pintaka Kusumaningtyas; Dhani Suryawan
Indonesian Journal of Biotechnology Vol 17, No 1 (2012)
Publisher : Universitas Gadjah Mada

The effect of enrichment bias on the diversity of Dibenzofuran (DBF)-degrading bacteria recovered from soil was evaluated by direct plating, plating after in-soil adaptation, and plating after batch culture enrichment. Among colonies appeared on Bushnell Haas agar with DBF as the sole carbon source, 119 colonies (49, 38, and 32 from direct plating, plating after in-soil adaptation, and plating after batch culture enrichment, respectively) were arbitrarily selected based on the appearance of the colonies. Total DNA were then extracted from the rest of the colonies and analyzed for their diversity using Ribosomal Intergenic Spacer Analysis (RISA). Number of DNA bands obtained from direct plating was higher than the ones obtained after in-soil enrichment and batch culture enrichment. The RISA bands obtained from direct plating were also found to be distributed more evenly than the ones obtained after in-soil enrichment and batch culture enrichment. Dominant bands were observed on RISA from samples obtained after in-soil enrichment and batch culture enrichment. Out of 119, only 9 isolates were consistently able to grow on Bushnell-Haas broth with DBF as the sole carbon source as indicated by broth turbidity. All of the isolates were obtained from soil samples which were enriched in a batch culture. Some of the isolates were able to degrade more then 80 % DBF in the minimal medium.

The Diversity of Legume-Nodulating Bacteria from Several Agroecosystems in Sumberjaya, Lampung Sri Wedhastri; Yuliana Prahastiwi; Jaka Widada; Donny Widianto; Siti Kabirun
Indonesian Journal of Biotechnology Vol 18, No 1 (2013)
Publisher : Universitas Gadjah Mada

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

Legume Nodulating Bacterium, Achromobacter xylosoxidans Found in Tropical Shrub Agroecosystem, Sumatera, Indonesia Sri Wedhastri; Dinar Mindrati Fardhani; Siti Kabirun; Jaka Widada; Donny Widianto; Rusdi Evizal; Irfan Dwidya Prijambada
Indonesian Journal of Biotechnology Vol 18, No 2 (2013)
Publisher : Universitas Gadjah Mada

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

Molecular Identification of Phenol-Degrading and Biofi lm-Forming Bacteria from Wastewater and Peat Soil Arifah Khusnuryani; Erni Martani; Tri Wibawa; Jaka Widada
Indonesian Journal of Biotechnology Vol 19, No 2 (2014)
Publisher : Universitas Gadjah Mada

Phenol is hazardous aromatic pollutant which needs to be treated to reduce its hazardous effects.Bioremediation using bacteria which can form biofi lm offer an alternative wastewater treatment that is cheaperand environmentally safe. Eighteen strains of phenol-degrading and biofi lm-forming bacteria were isolatedfrom peat soil, also hospital and textile wastewater. Screening for phenol degradation ability of isolates wereperformed using Folin-ciocalteau reagent, while for biofi lm formation ability were performed using microtiterplate and crystal violet dye. Based on the ability to degrade phenol and to form biofi lm, four isolates (HP3,DOK135, DL120, andATA6) were choosen as phenol-degrading bacteria as well as biofi lm-forming bacteria.Based on phenotypic and genotypic characterization, isolate HP3 was highly similar to Rhodococcus equi strainDSM20307T, while DOK135 was highly similar to Enterobacter mori strain R18-2.The results also suggested thatDL120 and ATA6 could be classifi ed to the genus of Micrococcus and Bacillus respectively

Diversity of Nonribosomal Peptide Synthetase Genes in the AnticancerProducing Actinomycetes Isolated from Marine Sediment in Indonesia Camelia Herdini; Shinta Hartanto; Sofia Mubarika; Bambang Hariwiyanto; Nastiti Wijayanti; Akira Hosoyama; Atsushi Yamazoe; Hideaki Nojiri; Jaka Widada
Indonesian Journal of Biotechnology Vol 20, No 1 (2015)
Publisher : Universitas Gadjah Mada

Marine actinomycetes is a group of bacteria that is highly potential in producing novel bioactivecompound. It has unique characteristics and is different from other terrestrial ones. Extreme environmentalcondition is suspected to lead marine actinomycetes produce different types of bioactive compoundfound previously. The aim of this study was to explore the presence and diversity of NRPS genes in 14anticancer-producing actinomycetes isolated from marine sediment in Indonesia. PCR amplificationand restriction fragment analysis of NRPS genes with HaeIII from 14 marine actinomycetes were doneto assess the diversity of NRPS genes. Genome mining of one species of marine actinomycetes (strainGMY01) also was employed towards this goal. The result showed that NRPS gene sequence diversity in 14marine actinomycetes could be divided into 4 groups based on NRPS gene restriction patterns. Analysisof 16S rRNA gene sequences of representatives from each group showed that all isolates belong to genusof Streptomyces. Genome mining result showed that strain GMY01 harboring 10 different NRPS geneclusters that encode secondary metabolites, as pure NRPS or hybrid between NRPS and other compounds.These results indicated that marine actinomycetes having a high potential to be developed as source ofanticancer drugs development.

Application of CRISPR/Cas9 genome editing system for molecular breeding of orchids Endang Semiarti; Sri Nopitasari; Yuli Setiawati; Muhammad Dylan Lawrie; Aziz Purwantoro; Jaka Widada; Yasushi Yoshioka; Shogo Matsumoto; Kana Ninomiya; Yuuki Asano
Indonesian Journal of Biotechnology Vol 25, No 1 (2020)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.39485

Orchid is an important ornamental plant in Indonesia due to their natural beauty of flowers. In the tropical forest, orchids are being acquired for trading and commercial market. Thus, the effort is required to proliferate orchid in large quantities for conservation and improve the floral variation for plant breeding. The purpose of this study is to develop a firmed methodology of molecular breeding of orchids using CRISPR/Cas9 KO system. The plant material used was Phalaenopsis amabilis protocorms growth on NP medium+pepton (2 g/L). Protocorm were submerged in the culture of Agrobacterium tumefaciens that Ti‐plasmid had been filled with a T‐DNA construct of a pRGEB32 vector harboring sgRNA with PDS3 sequence. Detection for transformants was confirmed by PCR using HPT primers (545 bp), Cas9 primers (402 bp), PDS primers (280 bp) and trnL‐F (1200 bp) as an internal control. The results showed that 0.96% PDS transformants were obtained from PDS3T2 lines. Several transformant showed pale leaf color compared to non‐transformant plants. This study suggests that the target gene has successfully edited by CRISPR/Cas9 system and could be applied for that functional gene editing in orchids.

Karakterisasi asam humat dan asam fulvat pada ultisol dengan pemberian limbah segar organik dan pengalengan nenas Susila Herlambang; Azwar Maas; Sri Nuryani Hidayah Utami; Jaka Widada
Jurnal Ilmu Tanah dan Air Vol 14, No 2 (2017)
Publisher : Universitas Pembangunan Nasional Veteran Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31315/jta.v14i2.2574

The purpose of the study to know characterization of humic and fulvic acids after three months decomposition by fresh organic waste and canning pineapples treatment at Ultisol Lampung. The research was designed with a completely randomized factorial design with three factors in the plot pots 165 cm x 165 cm x 55 cm. The first is fresh organic waste (200 ton.ha-1 chopper pineapple crops, 40 ton.ha-1 cattle manure, 40 ton.ha-1 cassava waste, 40 ton.ha-1 waste pump pineapple, 2 ton.ha-1 mill juice pineapple), and the second is depth on the soil (i.e. 0 - 15 cm, 0 - 30 cm and 0 - 45 cm), the each repeated three replication so total treatments are 24 plot pots. The results showed ameliorant treatment fresh organic waste and canning pineapples can increase the levels of C-organic from <1% to >1.5%. On the control (K0) in two months decomposition did not significantly different at 5%, but the decomposition of humic acid for three months showed significant differences in the treatment of K0, K1 and K2. Utilization of combinations of fresh organic waste and canning pineapples treatment at the depths (0 - 15, 0 - 30 and 0 – 45 cm) can increase the humic acid content about >1.5% in three months decomposition waste. The combination treatment of fresh organic waste and canning pineapples on Ultisol for three months decomposition, able to provide sufficient nutrients especially the availability of C-organic, humic acid and fulvic acid for growth pineapples.

Pengaruh Inokulasi Mikoriza Arbuskula Terhadap Pertumbuhan dan Hasil Kedelai (Glycine max (L.) Merrill) pada Berbagai Interval Penyiraman Asmary Muis, Didik Indradewa, Jaka Widada
Vegetalika Vol 2, No 2 (2013)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/veg.2411

Pada umumnya kedelai ditanam di sawah dan tegalan (lahan kering). Kedua jenis lahan ini berpotensi mengalami keterbatasan air. Kekurangan air dapat menghambat pertumbuhan tanaman dan menurunkan hasil. Aplikasi mikoriza pada tanaman merupakan salah satu upaya untuk mengatasi terhambatnya pertumbuhan karena cekaman kekeringan. Penelitian bertujuan untuk mengetahui pengaruh inokulasi mikoriza arbuskula terhadap pertumbuhan dan hasil kedelai pada kondisi air yang terbatas. Penelitian dilaksanakan di rumah kaca Kebun Percobaan Fakultas Pertanian UGM, Banguntapan, Bantul, Yogyakarta dari bulan Juni hingga September 2012. Penelitian menggunakan Rancangan Acak Lengkap 2 faktor. Faktor pertama dengan 2 aras yaitu tanpa inokulasi mikoriza dan inokulasi mikoriza. Faktor kedua dengan 3 aras interval penyiraman yakni setiap hari, 3 hari, dan 6 hari. Inokulasi mikoriza dilakukan sebelum benih ditanam sedangkan perbedaan interval penyiraman setelah tanaman berumur 4 mst. Kadar lengas tanah diukur sebelum dan setelah penyiraman. Infeksi mikoriza pada akar diamati pada vegetatif maksimum. Pengamatan terhadap sistem perakaran dan tajuk pada 8 mst serta pengamatan komponen hasil dan hasil tanaman pada saat panen. Hasil penelitian menunjukkan tidak terdapat interaksi antara mikoriza dengan interval penyiraman. Inokulasi mikoriza dapat meningkatkan jumlah bintil akar dan tidak mendukung pertumbuhan akar dan tajuk serta tidak meningkatkan komponen hasil dan hasil tanaman kedelai. Peningkatan interval penyiraman menjadi 6 hari menurunkan kadar lengas tanah, menghambat pertumbuhan akar dan tajuk, menurunkan bobot kering total serta komponen hasil dan hasil tanaman

Co-Authors , Tamad . Tohari A. Alimuddin Achmad Dinoto Adi Laksono Ahmad Romdhon Akira Hosoyama Akira Hosoyama Ali Ikhwan Alim Isnansetyo Amekan, Yumechris Angga Prasetya Anna Safarrida Anna Safarrida, Anna Annisa Yusuf, Wahida Ariani Hatmanti Arif Muliawan Arifah Khusnuryani Arifah Khusnuryani Ariyanti, Nur Fitriana Asrul Asrul Asrul Asrul Atsushi Yamazoe Atsushi Yamazoe Aziz Purwantoro Azwar Maas Bambang Hadisutrisno Bambang Hadisutrisno Bambang Hadisutrisno Bambang HADISUTRISNO Bambang Hariwiyanto Bambang Hariwiyanto Bambang Hendro Sunarminto Bambang Hendro sunarminto Bostang Radjagukguk Camelia Herdini Christanti Sumardiyono Denny Irawati Dewi Seswita Zilda DEWI SESWITA ZILDA Dhani Suryawan Dhani Suryawan, Dhani Diani Mentari Diannastiti, Fani Aulia Didik Indradewa Didik Indradewa Didik Indradewa Dinar Mindrati Fardhani Dionysius Andang Arif Wibawa Dionysius Andang Arif Wibawa, Dionysius Andang Dody Kastono Dolly Iriani Damarjaya Dolly Iriani Damarjaya, Dolly Iriani Donny Widianto Donny Widianto Donny Widianto Donny Widianto Dyah Weny Respatie Edy Meiyanto Eka Tarwaca Susila Putra Eko Hanudin Eko Hanudin EKO IRIANTO Ema Damayanti Ema Damayanti Endang Semiarti Endang Sutriswati Rahayu Eni Harmayani ENI HARMAYANI Erni Martani Erni Martani Eti Nurwening Sholikhah Fatturahman Ridwan, Nur Febriansah , Rifki Galang Indra Jaya Ganis Lukmandaru Gintung Patantis Gintung Patantis GINTUNG PATANTIS Hadi, Ismanurrahman Hari Eko Irianto Hartono Hartono H, Hartono Hera Nirwati Hideaki Nojiri Hideaki Nojiri Indun Dewi Puspita IRFAN D. PRIJAMBADA Irfan Dwidya Prijambada Irwan Suluk Padang Jauhari Syamsiyah Joko Sulistyo Kana Ninomiya Keishi Senoo Keishi Senoo, Keishi Khoirun Nisa Lucia Dhiantika Witasari Lucia Dhiantika Witasari, Lucia Dhiantika M. Mustofa Maria Gratias Mariyatun Mariyatun, Mariyatun Masagus Muhammad Prima Putra Masaya Nishiyama Masaya Nishiyama, Masaya Ma’as, Azwar Melki Melki Mirtani Naima Mohamad Aji Ikhrami Muhammad Dylan Lawrie Muhammad Nur Cahyanto Muhammad Saifur Rohman Mujiyo Mujiyo Mukhlissul Faatih Mukhlissul Faatih1, Mukhlissul Mulyadi Mulyadi Mulyadi Mulyadi Mulyono Mulyono Murwantoko . Mustofa M, Mustofa Mustofa Mustofa Mustofa Mustofa N. Ngadiman Naima, Mirtani Nastiti Wijayanti Nastiti Wijayanti Nastiti Wijayanti Ngadiman Ngadiman . Ngadiman ., Ngadiman Ngadiman N, Ngadiman Noviyanto, Amir Nunuk Supriyatno Nur Edy Nur Prihatiningsih Nurfiani, Sri Ocky Karna Radjasa Oedjijono Oedjijono, Oedjijono Pintaka Kusumaningtyas Prijambada, Irfan Dwidja PUSPITA LISDIYANTI Putra, Sukmana Siswandana Putu Sudira R. Riyanti Rahayu, Endang Sutriswati Reni Nurjasmi Reni Nurjasmi, Reni Riska Wulansari Ristiarini, Susana Riyanti Riyanti Rusdi Evizal Saipul Abbas Sarto SATRIYAS ILYAS Shigeto Otsuka Shigeto Otsuka, Shigeto Shinta Hartanto Shogo Matsumoto Sigit Sunarta, Sigit SITI KABIRUN Siti Kabirun Siti Kabirun Siti Subandiyah Sofia Mubarika Haryana Sri Hastuti Sri Nopitasari Sri Nuryani Hidayah Utami Sri Nuryani Hidayah Utami Sri Nuryani Hidayah Utami Sri Suryanti Sri Suryanti Sri Wedhastri Stalis Norma Ethica Subagus Wahyuono Sudadi Sudadi Suhartiningsih Dwi Nurcahyanti Sumarno Sumarno Sumarno Sumarno Suryanti Suryanti Suryanti Suryanti Susila Herlambang TOHARI TOHARI Tohari Tohari Tomy Listyanto Tomy Listyanto Tri Harjaka Tri Joko Raharjo Tri Rini Nuringtyas Tri Wibawa Tri Wibawa Triwibowo Yuwono Triwidodo Arwiyanto Wangi, Dyah Sekar A P Widya Asmara WIDYA ASMARA Wulansari, Riska Yani Lestari Nuraini Yani Lestari Nuraini, Yani Lestari Yasushi Yoshioka Yenny Sariasih Yose Rizal Yuli Setiawati Yuliana Prahastiwi Yuliana Yuliana Prahastiwi, Yuliana Yusro Nuri Fawzya Yusro Nuri Fawzya YUSRO NURI FAWZYA Yuuki Asano Yuyun Farida Yuyun Farida, Yuyun Zilda, Dewi Zeswita

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