Article Per Year (5 Year)
p-Index From 2021 - 2026
1.116
P-Index
This Author published in this journals
All Journal JURNAL PEMULIAAN TANAMAN HUTAN Indonesian Journal of Biotechnology Journal of Tropical Biodiversity and Biotechnology Agrin : Jurnal Penelitian Pertanian Journal of Tropical Crop Science Menara Perkebunan Nusantara Science and Technology Proceedings
Riza Arief Putranto
Unknown Affiliation
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Economics, Econometrics & Finance Engineering Environmental Science Immunology & microbiology Law, Crime, Criminology & Criminal Justice Materials Science & Nanotechnology Medicine & Pharmacology

Published : 36 Documents Claim Missing Document
Claim Missing Document
Check
Articles

Found 36 Documents
Search

 1   2   3   4 
Structure-based virtual screening of bioherbicide candidates for weeds in sugarcane plantation using in silico approaches Galuh Wening PERMATASARI; Riza Arief PUTRANTO; Happy WIDIASTUTI
Menara Perkebunan Vol. 88 No. 2 (2020): 88 (2), 2020
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v88i2.379

Abstract

Weeds in sugarcane have negatively affected the sugar yield rate. Several approaches have been carried out to overcome the weeds, including the usage of diuron as synthetic herbicide. However, the long-term usage of diuron is known to have a negative effect leads to the production of 3,4- Dichloroaniline responsible for soil leach and bioaccumulation. Therefore, this study aimed to find a potential natural herbicide. By mimicking the diuron's mode of action which inhibits the process of photosynthesis through blocking the Photosystem II protein D1 (psbA) of the weeds, fourteen compounds as potential candidate bioherbicides were virtually docked by PyRx v0.9.5 software to the specific site. Three important species of the weeds were chosen including Eleusine indica, Praxelis clematidea, and Momordica charantia. The binding affinity score was further calculated and ranked to screen the top six compounds as bioherbicide candidates. Interaction of each complex and the biological activity prediction were then performed by Discovery Studio software and PASS server, respectively. Aurachin P, Aurachin A, and Cyanobacterin were placed in the top ranked compounds with high binding affinity score around -6 to -9 kcal mol-1 toward the psbA. The amino acid interaction involved in the complex shows 50-90% similar to the control, psbA and diuron complex. Besides, the biological activity prediction of Aurachin P, Aurachin A, and Cyanobacterin exhibits the terms related to the inhibition of photosynthesis process via enzymatic pathway. Thus, the active compounds might have inhibition action in the photosynthesis process and control  the weeds in sugarcane.
Analisis ko-ekspresi gen-gen regulasi upstream dari gen Dehydrin di tanaman tebu (Saccharum officinarum L.) pada kondisi cekaman kekeringan Hayati MINARSIH; Jembar PAMBUDI; Riza Arief PUTRANTO
Menara Perkebunan Vol. 88 No. 2 (2020): 88 (2), 2020
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v88i2.396

Abstract

Sugarcane plantations in Indonesia have been expanded and shifted to the marginal land characterized by long drought period, therefore, an attempt has been initiated to generate drought tolerance varieties through genetic engineering. It could be conducted by inserting the gene that involve in plant adaptation response to drought stress such as dehydrin (DHN) into sugarcane genome. The promoter of sugarcane DHN gene was isolated and transformed into sugarcane in the previous research. This study aimed to demonstrate the functionality of sugarcane DHN promoter through expression analysis of DHN regulatory genes that play a role in response to drought stress. Expression analyses using RT-qPCR were also conducted on regulatory genes of sugarcane that inserted by Pr-1DHNSo construct treated with drought stress. The results showed that the expressions of  SoMYB, SoWRKY, SoNAC, and SoDHN genes were escalated on sugarcane 16 days after stress treatment ranging from 353 to 4067 folds relatively to untreated samples in which SoNAC gene showed the highest expression. On the other hand, the analysis on transgenic sugarcane carrying DHNpromoter construct showed SoNAC and SoDREB expression increased after 72 hours under drought stress. The expression values of SoNAC in transgenic and non-transgenic plants under drought condition were 4.79 and 4.99, respectively. Meanwhile, the expression values of SoDREB in transgenic and non-transgenic plants under drought condition were 13.2 and 13.3, respectively. The results of these experiments showed that the promoter construct of Pr-1DHNSo was induced by drought stress treatments highlighting the regulation of several upstream genes of SoDHN.
The in silico study of the COBRA gene family in sugarcane related to potential biomass content Riza Arief PUTRANTO; Galuh Wening PERMATASARI; Rizka Tamania SAPTARI
Menara Perkebunan Vol. 90 No. 1 (2022): 90 (1), 2022
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v90i1.486

Abstract

AbstractSugarcane (Saccharum sp.) is potential as a biofuel and biomaterial source for its high cellulose content. Cellulose is the main constituent of the plant cell wall, as a linear chain arranged in a polysaccharide bundle, called cellulose microfibril. A gene named COBRA has been revealed to play role in the orientation of microfibril and cellulose crystallization. The COBRA gene in the Saccharum spp is under-explored. Therefore, the in silico study was conducted to explore the COBRA gene in Saccharum sp. By comparative genomics methods, the COBRA genes from Arabidopsis sp. (AtCOBLs) were compared to the Saccharum sp. (SoCOBLs). The conserved domain was then identified and the cluster system was constructed under a phylogenetic tree. Furthermore, each SoCOBLs protein was modelled to analyze its structure. According to the analysis, eleven of Saccharum sp. genomic scaffolds were successfully identified. Moreover, conserved domain identification resulted in nine SoCOBLs proteins. The phylogenetic tree showed two main clusters: I and II, differentiating those COBLs families based on the protein sequence, domain motif and amino acid properties. It leads to the variation of SoCOBLs protein structure as the results of the amino acid properties. Overall, the COBRA gene has been identified genomically in Saccharum sp. Yet, the function and tissue-specific expression are still unclear. It was predicted to act as the regulator of microfibril orientation and the cellulose synthesis process. Hence, further analyses by in vitro and in vivo are indispensable.[Keywords: cellulose, comparative genomic, Saccharum sp.]AbstrakTanaman tebu (Saccharum sp.) berpotensi sebagai sumber bahan bakar nabati dan biomaterial karena kandungan selulosanya yang tinggi. Selulosa merupakan komponen utama penyusun dinding sel tanaman, sebagai rantai lurus yang tersusun dalam gugusan polisakarida, yang disebut mikrofibril selulosa. Sebuah gen bernama COBRA telah diketahui berperan dalam menentukan arah mikrofibril dan kristalisasi selulosa. Gen COBRA pada spesies Saccharum spp. belum banyak dipelajari. Oleh karena itu, kajian in silico dilakukan untuk mempelajari gen COBRA pada Saccharum sp. Melalui metode perbandingan genomika, gen COBRA dari Arabidopsis sp. (AtCOBLs) dibandingkan dengan gen COBRA dari Saccharum sp. (SoCOBLs). Domain conserve pada gen kemudian diidentifikasi dan sistem klaster disusun dalam sebuah pohon filogeni. Setelah itu, dibuat model untuk menganalisis struktur dari protein SoCOBL. Dari hasil analisis, sebelas perancah genom Saccharum sp. berhasil diidentifikasi. Kemudian, identifikasi daerah lestari menghasilkan sembilan protein SoCOBL. Pohon filogeni menggambarkan dua klaster utama: I dan II, yang membedakan famili SoCOBLs tersebut berdasarkan sekuens protein, motif domain, dan karakteristik asam amino. Karakteristik asam amino menyebabkan variasi pada struktur protein-protein SoCOBL. Secara umum, gen COBRA telah teridentifikasi pada Saccharum sp., meskipun fungsi dan ekspresi spesifiknya pada jaringan masih belum diketahui. Diperkirakan gen tersebut berperan sebagai pengatur arah mikrofibril dan proses sintesis selulosa. Oleh karena itu, perlu adanya analisis lebih lanjut pada level in vitro dan in vivo.[Kata kunci: selulosa, genomika komparatif, Saccharum sp.] 
Sterilization method of contaminated oil palm plantlets affects the survival rate during acclimatization Masna Maya Sinta; Lailia Zubaidah; Rizka Tamania Saptari; Imron Riyadi; Galuh Wening Permatasari; Riza Arief Putranto; Annisa A Aksa; Larasati D Mahardhika; Yuli Setiawati; Hayati Minarsih; Ernayunita Ernayunita
Menara Perkebunan Vol. 91 No. 2 (2023): 91 (2), 2023
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v91i2.551

Abstract

Contamination in the in vitro culture is a critical problem causing the failure of seed production. Contamination in the oil palm plantlet is detrimental, considering that oil palm propagation is difficult and takes a long time. This research aimed to study the effect of sterilization during acclimatization of the contaminated oil palm plantlets by fungi on viability and to determine the optimum viability achieved from the contaminated materials. The materials used were contaminated plantlets of oil palm with roots, four leaves, and a height of about 17 cm. The plantlets were removed from the tube and cleaned with running tap water, then were sterilized, with treatments P1: soaking in benomyl-mancozeb-sodium hypochlorite and mannitol and rinsing with aquadest, P2: soaking in benomyl-mancozeb, P3: soaking in mancozeb. Cleaning plantlets under running tap water was carried out as a control treatment. The results showed that at 10 weeks after acclimatization, the survival rate of plantlets in each treatment (P1, P2, and P3) was significantly higher than that of the control. Sterilization methods affect the time new leaves emerge, leaf condition after sterilization treatment, and shoot height. The lowest fungal contamination after treatments was found in P2, followed by P3. After 3 months, plantlet survival rate decreased, with the highest survival rate in treatment P3 (32.3%) followed by treatment P2 (22.5%). In conclusion, acclimatization of contaminated oil palm plantlets can be carried out using a suitable sterilization treatment. Sterilization affects the survival rate and growth of in vitro-contaminated oil palm plantlets during acclimatization.
Characterization and morphological development of oil palm transformed-callus on modified culture media Yuli Setiawati; Imron Riyadi; Dini Astika Sari; Rizka Tamania Saptari; Masna Maya Sinta; Hayati Minarsih; Turhadi; Riza Arief Putranto
Menara Perkebunan Vol. 92 No. 2 (2024): 92(2), 2024
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v92i2.576

Abstract

Genome editing through cisgenesis develops into scientific breakthroughs in accelerating oil palm breeding programs. However, one remaining problem is the low success of transformed-calli regeneration, while its scientific explanation is still underexplored. This study aimed to characterize and regenerate transformed-calli using various amino acids and antioxidants.  Transformed callus that did not regenerate (un-regenerated transformed callus or UTC) after the transformation process was taken, then T-DNA integration was detected using the NPTII gene. Furthermore, the UTC was divided into four types based on morphological characteristics. The four types of UTCs were regenerated on media enriched with glutamine (for Type-1 callus), cysteine and putrescine (for Type-2 callus), and a combination of cysteine and ascorbic acid (for Type-3 and Type-4 callus). The research results obtained NPTII successfully amplified with a band size of 700bp. The results showed that on Type-1 callus, enrichment media with 10 mg L-1 L-glutamine could induce the formation of new nodular structures on UTC Type-1. On Type-2, media enriched with 5 mg L-1 L-cysteine + 20 mg L-1 putrescine increased the density of callus structures. Media enriched with 25 mg L-1 ascorbic acid + 25 mg L-1 L-cysteine could prevent the spread of brown callus on Type-3 callus, while Type-4 callus did not show any response and became dry. Our new findings will facilitate the basic research and unregenerated transformed callus and morphological callus development behavior in oil palm.
OPTIMASI DAN EFISIENSI TEKNIK ISOLASI RNA DAUN DAN AKAR KELAPA SAWIT (Elaeis guineensis Jacq) Sari, Dini Astika; Martiansyah, Irfan; Mukmin, Restu Prasetya; Hadi, Sapto Nugroho; Syahputra, Indra; Afandi, Dadang; Putranto, Riza Arief
Agrin Vol 23, No 2 (2019): Agrin
Publisher : Jenderal Soedirman University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (191.431 KB) | DOI: 10.20884/1.agrin.2019.23.2.500

Abstract

Tanaman kelapa sawit memiliki kandungan polisakarida dan polifenol yang tinggi. Kontaminasi polisakarida dan polifenol menyebabkan sulitnya proses isolasi RNA dari jaringan tanaman kelapa sawit. Penelitian ini dilakukan untuk mengoptimasi beberapa protokol isolasi RNA tanaman kelapa sawit yang efektif dan efisien. Penelitian dilaksanakan selama tiga bulan, pada bulan Oktober-Desember 2018 di Laboratorium Biokimia dan Biologi Molekuler, Pusat Penelitian Bioteknologi dan Bioindustri Indonesia (PPBBI), Jalan Taman Kencana No. 1 Bogor 16128. Penelitian dilakukan dengan melaksanakan teknik isolasi RNA menggunakan tiga protokol, yaitu modifikasi Cetyl Trimethyl Ammonium Bromide (CTAB), kit isolasi RNA RNeasy Plant Mini Kit (Qiagen), dan kit isolasi NucleoSpin RNAPlant (Macherey-Nagel). Sampel yang digunakan adalah daun dan akar tanaman kelapa sawit berumur kurang dari tiga bulan dengan bobot 0,1 gram dan 2,5 gram yang disesuaikan untuk tiap protokol. Variabel yang diamati adalah konsentrasi (ng/µl), kemurnian (rasio A260/A280 dan A260/A230), dan pita RNA pada elektroforesis gel agarosa. Hasil penelitian menunjukkan, RNA total hasil isolasi protokol NucleoSpin RNAPlant (Macherey-Nagel) memiliki kualitas paling tinggi. Konsentrasi RNA total daun dan akar kelapa sawit yang didapatkan melalui protokol NucleoSpin RNAPlant (Macherey-Nagel) sebesar 338 ng/µl dan 184,4 ng/µl dengan rasio A260/A280 RNA total daun dan akar kelapa sawit sebesar 2,13 dan 2,18 serta rasio A260/A230 sebesar 2,09 dan 2,20. Hasil elektroforesis gel agarosa menunjukkan integritas yang bagus dari RNA total hasil isolasi RNeasy Plant Mini Kit (Qiagen) dan NucleoSpin RNAPlant (Macherey-Nagel), namun terdapat kontaminasi dan smear pada RNA total hasil isolasi CTAB modifikasi 1 dan 2. Kata kunci: kelapa sawit, isolasi RNA, spektrofotometer, elektroforesis gel agarosa
Co-Authors . KUSWANHADI . NUHAIMI-HARIS . PRIYONO . SISWANTO . SUMARYONO Afandi, Dadang Agustin Sri MULYATNI Akhirta Atikana Aksa, Annisa Aulia Alfero Putra Iryanto Anggia Prasetyoputri Annisa A Aksa Asmini Budiani Asmini BUDIANI Asmini Budiani Asmini Budiani Asmini Budiani Asmini BUDIANI1 Barahima Abbas Christy Dewi Sukma Dini Astika Sari Dini Astika Sari Dini Astika Sari Ernayunita Ernayunita Ernayunita, Ernayunita Galuh Wening PERMATASARI Galuh Wening PERMATASARI Galuh Wening Permatasari Happy WIDIASTUTI Hayati Minarsih Hayati MINARSIH Hayati Minarsih Hayati Minarsih Imam Bagus Nugroho Imron Riyadi Imron Riyadi Imron RIYADI Imron Riyadi Indra Syahputra Inez Palupi Irfan MARTIANSYAH Irfan Martiansyah Iskandar, Hayati Minarsih Jembar PAMBUDI Julie LECLERCQ Lailia Zubaidah Larasati D Mahardhika Lutfi Anggadhania Mardhika, Larasati Dena MARTIANSYAH, Irfan Masna Maya Sinta Masna Maya Sinta Mose, Windi Muhammad Farrel Ewaldo Mukmin, Restu Prasetya Nurul Khumaida Nurul Khumaida Pambudi, Jembar Pascal MONTORO Pascal MONTORO Pascal MONTORO PERMATASARI, Galuh Wening pri yono Radite TISTAMA Ratih Asmana Ningrum Rizka Tamania Saptari Rizka Tamania Saptari Rizka Tamania SAPTARI Rokhana Faizah Rokhana Faizah Sapto Nugroho Hadi Sapto Nugroho Hadi Sari, Dini Astika Sekar WOELAN Sri Wening Sri Wening Sudarsono Sudarsono Suhandono, Sonny Sustiprijatno Sustiprijatno, Sustiprijatno TATI KRISTIANTI Turhadi Turhadi Vivi Restu Raharti Y.M.M Anita Nugraheni Yuli Setiawati Yuli Setiawati Yuli Setiawati, Yuli