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All Journal Vegetalika Indonesian Journal of Agricultural Science Agro Bali: Agricultural Journal Makara Journal of Science Buitenzorg: Journal of Tropical Science
Toto Hadiarto
Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian, Jl. Tentara Pelajar 3A, Bogor 16111 Telp. (0251) 8337975
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Environmental Science Health Professions

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MULTIFUNCTIONAL MUTANTS OF Azospirillum sp. WITH ENHANCED CAPABILITY OF SOLUBILIZING PHOSPHORUS, FIXING NITROGEN AND PRODUCING INDOLE ACETIC ACID Riyanti, Eny Ida; Hadiarto, Toto; Susilowati, D.N.
Indonesian Journal of Agricultural Science Vol 13, No 1 (2012): April 2012
Publisher : Indonesian Agency for Agricultural Research and Development - MOA

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Abstract

Azospirillum sp. have long been known as biofertilizer for plant growth because of its capability to produce phytohormones and fix nitrogen from the atmosphere. Multifunctional Azospirillum strain Aj Bandung 6.4.1.2 isolated in 2009 from cauliflower (Brassica oleracea) rhizosphere in Lembang, Bandung, West Java, was capable of fixing nitrogen, solubilizing tricalcium-phosphate, and producing phytohormone indole acetic acid (IAA). The study aimed to modify the multifunctions of Azos-pirillum sp. for better capability of fixing N2, solubilizing P, and producing IAA using ethyl methanesulfonate and 1-methyl-3-nitro-1-nitrosoguanidine (EMS) mutagen. The study was conducted at Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD) in 2010. The results showed that this strain was genetically mutagenized using EMS for better performance in solubilizing P, fixing N2 (nitrogenase activity), and producing phytohormone (IAA). The optimum concentration and the length of incubation time for the process have been determined. Nine selected mutants with increasing capability to solubilize P (determined by clear-zone formation on Pikovskaya’s medium) have been characterized for nitrogenase activities and IAA production compared to wild type Aj Bandung 6.4.1.2. The effect of mutagenesis on IAA produc-tion and nitrogenase activities varied among the mutans. Two mutants, AzM 3.7.1.16 and AzM 1.7.2.12, showed superiority in the production of IAA, while two mutants, AzM 1.5.1.14 and AzM 3.7.1.15, were superior in nitrogenase activities. The EMS mutagenesis of Azospirillum sp. showed enhanced dissolving capa-bility of unsoluble phosphate (tricalciumphosphate) and increased IAA production and nitrogenase activity.  
Bioinformatics Toxicity Assessment of RB Protein from Transgenic Potato Resistant to Phytophthora infestans Hadiarto, Toto; Ambarwati, Alberta Dinar
Makara Journal of Science Vol. 23, No. 1
Publisher : UI Scholars Hub

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Abstract

The genetically engineered potato cultivar Katahdin SP951 is resistant to late blight disease, which is caused by Phytophthora infestans. The biosafety and food safety of this cultivar should be assessed prior to its commercialization. Toxicity is one of the parameters tested in the food safety evaluation of transgenics. Toxicity testing includes the bioinformatics analysis of the homology of the RB protein of Katahdin SP951 with known proteins. Therefore, this study aimed to perform the bioinformatics analysis of Katahdin SP951 RB protein against homologous toxin proteins. Bioinformatics analysis was conducted by first translating the RB gene into an amino acid sequence by using the Emboss Transeq program from the EMBL-EBI website. The Shuffle Protein Program was then applied to obtain the randomized amino acid sequences of the RB protein. The Basic Local Alignment Search Tool (BLAST) Protein search program was utilized to identify proteins with high similarity and homology. Moreover, BLAST Suite-2 was used to analyze the homology between two or more sequence alignments. Results showed high homology between the sequences of the RB protein and those of known resistance (R) proteins with an E value of less than 0.22. This result may be attributed to the presence of numerous R proteins in plants. Further analysis indicated that the sequence of the RB protein had extremely nonsignificant homology with sequences of proteins known to be toxic in the Entrez protein database of National Center for Biotechnology Information. Therefore, the RB protein is nontoxic.
Performance Test of Vegetative Characteristics of Crossed Rice (Oryza sativa L.) Lines of Ciherang Variety X B11143D Line in Telagasari, Karawang Regency, Indonesia Damayanti, Utari; Lestari, Ani; Subardja, Vera Oktavia; Hadiarto, Toto; Enggarini, Wening
Agro Bali : Agricultural Journal Vol 7, No 2 (2024)
Publisher : Universitas Panji Sakti

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.37637/ab.v7i2.1721

Abstract

One way to increase the genetic diversity of Ciherang as the superior variety is to cross Ciherang with the donor B11143D line as a New Plant Type (NPT) rice. This study aimed to obtain Ciherang X B11143D lines with the best vegetative characteristics in the field. The research was conducted in rice fields in Talagasari Village, Telagasari District, Karawang Regency, from May to September 2023. This experiment used a single-factor Randomized Block Design (RBD) with three replications of 22 treatments, consisting of 19 Ciherang X B11143D lines and three comparison varieties. The effect of treatment was studied using analysis of variance. The results showed that the rice lines significantly influenced the vegetative characters of Ciherang X B11143D lines in Telagasari, Karawang Regency. Based on the observed characters, several lines were selected i.e. 124.2.3, 94.3.3, and 20.4.4 lines. Those three lines chosen as backcrossing lines performed similarly compared to Ciherang as recurrent parent and inherited several important traits for rising productivity from the B11143D line as donor parent, namely the length and area of flag leaf, the total number of tillers, and the number of productive tillers, which were significantly higher than Ciherang.
Optimasi Ekstraksi RNA dan Teknik Kloning: Studi Kasus Kloning Gen Heading Date 3a pada Kelapa Sawit Polosoro, Aqwin; Enggarini, Wening; Kusumanegara, Kusumawaty; Hadiarto, Toto; Miftahudin, Miftahudin; Supena, Ence Darmo Jaya
Vegetalika Vol 13, No 2 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/veg.92085

Abstract

Pembungaan memegang peranan penting bagi tumbuhan karena memfasilitasi rekombinasi genetik, sehingga mendukung perkembangan keragaman genetik yang penting. Keluarga protein phosphatidylethanolamine binding proteins (PEBP) memainkan peran penting dalam mengatur waktu pembungaan dan dormansi benih di beragam spesies tanaman. Penelitian ini bertujuan untuk merancang vektor biner dengan membangun pCAMBIA1300 yang menggabungkan rangkaian gen EgHd3a dari kelapa sawit. Proses konstruksi gen meliputi ekstraksi RNA, sintesis cDNA, amplifikasi gen EgHd3a, kloning gen menjadi vektor kloning, subkloning ke dalam vektor biner pCAMBIA1300, dan diakhiri dengan validasi gen melalui analisis sekuens. Pada ekstraksi RNA, metode PCL-Chisam telah terbukti efektif melalui ekstraksi berulang, meningkatkan kualitas dan kuantitas total RNA. Dalam proses kloaning, metode konvensional menghadapi tantangan dalam memilih lokasi pembelahan yang tepat. Untuk mengatasi kendala ini, penggunaan enzim dengan overhang yang kompatibel diusulkan sebagai solusi potensial. Secara khusus, penggantian BamHI dari BglII telah secara efektif mengatasi tantangan ini. Konfirmasi integrasi fragmen gen ke dalam plasmid pCAMBIA1300 dicapai melalui pengurutan. Meskipun perbedaan diidentifikasi dalam rangkaian EgHd3a-2, perubahan ini tidak berdampak pada asam amino yang dikodekan, sehingga menjaga integritas rangkaian protein
Perbandingan Metode Ekstraksi DNA pada Tanaman Ulin (Eusideroxylon zwageri) Ridzqya, Salsabila Al Alya; Polosoro, Aqwin; Enggarini, Wening; Kusumanegara, Kusumawaty; Helmanto, Hendra; Magandhi, Mahat; Satyawan, Dani; Hadiarto, Toto; Yuniaty, Alice
Buitenzorg: Journal of Tropical Science Vol 1 No 1 (2024): Buitenzorg: Journal of Tropical Science
Publisher : Innovation Centre for Tropical Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.70158/buitenzorg.v1i1.7

Abstract

DNA isolation is a routine procedure in molecular analysis. The method of plant genome DNA extraction has been widely available throughout global laboratories. Several labs made some modifications to obtain optimal results. This research was aimed to analyse two types of DNA extraction methods for ironwood plant (Eusideroxylon zwageri), one tropical rain forest woody plant known for its high strength and durability. The results indicate that isolation DNA kit produced high DNA purity with lower concentrations while CTAB methods generated lower DNA purity with higher concentrations. This may be used as consideration of DNA isolation for downstream molecular analyses.   Keywords: DNA extraction, ironwood, CTAB, genomic DNA
Co-Authors Alberta Dinar Ambarwati Alice Yuniaty Ani Lestari D.N. Susilowati Damayanti, Utari Dani Satyawan Eny Ida Riyanti Helmanto, Hendra Kusumanegara, Kusumawaty Mahat Magandhi Miftahudin . Polosoro, Aqwin Ridzqya, Salsabila Al Alya Supena, Ence Darmo Jaya Vera Oktavia Subardja Wening Enggarini