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All Journal HAYATI Journal of Biosciences Jurnal Teknologi Dan Industri Pangan Jurnal Ilmu dan Teknologi Kelautan Tropis Buletin Kimia VALENSI CAKRA KIMIA (Indonesian E-Journal of Applied Chemistry) JURNAL KIMIA SAINS DAN APLIKASI Microbiology Indonesia Current Biochemistry The Journal of Pure and Applied Chemistry Research Jurnal Riset Kimia Indonesian Journal of Pharmaceutical Science and Technology Jurnal Sumberdaya Hayati SC (Savana Cendana) : Jurnal Pertanian Konservasi Lahan Kering BERITA BIOLOGI BIOMA Indonesian Journal of Chemistry QARDHUL HASAN: MEDIA PENGABDIAN KEPADA MASYARAKAT EKOLOGIA : Jurnal Ilmiah Ilmu Dasar dan Lingkungan Hidup Menara Perkebunan Jurnal Ilmu Kefarmasian Indonesia Jurnal Jamu Indonesia Pharma Xplore : Jurnal Sains dan Ilmu Farmasi Indonesian Journal of Applied Research (IJAR) Jurnal Pusat Inovasi Masyarakat Makara Journal of Science Molekul: Jurnal Ilmiah Kimia Indonesian Journal of Jamu
LAKSMI AMBARSARI
Departemen Biokimia, Fakultas Matematika Dan Ilmu Pengetahuan Alam, IPB University Bogor 16680, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Decision Sciences, Operations Research & Management Earth & Planetary Sciences Education Electrical & Electronics Engineering Engineering Environmental Science Health Professions Immunology & microbiology Industrial & Manufacturing Engineering Languange, Linguistic, Communication & Media Library & Information Science Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Public Health Social Sciences Other

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Journal : Menara Perkebunan

 1 
Evaluasi varietas, sumber eksplan dan strain Agrobacterium terhadap keberhasilan transformasi tebu dengan gen P5CS Evaluation of varieties, explant sources, and Agrobacterium strains for successful sugarcane transformation using P5CS gene Hayati MINARSIH; Dwi SUBIYARTI; Imron RIYADI; Soekarno Mismana PUTRA; Laksmi AMBARSARI
E-Journal Menara Perkebunan Vol 83, No 1: Juni 2015
Publisher : INDONESIAN RESEARCH INSTITUTE FOR BIOTECHNOLOGY AND BIOINDUSTRY

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (190.979 KB) | DOI: 10.22302/iribb.jur.mp.v83i1.7

Abstract

Abstract Genetic transformation can be used as an alter-native to develop sugarcane (Saccharum officinarum L.) tolerant to drought stress. P5CS gene has a role in biosynthesis of proline, an amino acid that accumulated under drought stress conditions. Transfer of a P5CS gene construct into plant cells in conjunction with regeneration of transgenic plantlets may develop sugarcane tolerant to drought stress. The aim of this research was to obtain an optimal transformation method which includes a suitable strain of Agrobacterium tumefaciens, and the best sugarcane explant and variety. The results showed that transfer of P5CS gene has been successfully carried out on sugarcane explants from solid media-derived calli, embryogenic calli and somatic embryos derived from temporary immersion system (TIS) culture. Whilst Agrobacterium strain LBA4404 was indicated as the most effective transformation vector. The regeneration of Kidang Kencana variety transformants from calli and somatic embryos was better than those of PS 881 and PS 891. The best performance of transformants based on the source of explants obtained from somatic embryos from TIS culture. Moreover, a succesfull Agrobacterium mediated transformation on sugarcane was indicated by transient expression of Gus gene and the ability of the transformants grew in a selection medium containing 50 ppm of kanamycin.Abstrak Transformasi genetik dapat digunakan sebagai upaya untuk merakit tebu (Saccharum officinarum L.) toleran terhadap cekaman kekeringan. Gen P5CS diketahui  berperan  dalam  biosintesis  prolin,  yaitu asam amino yang umumnya terakumulasi ketika tanaman mengalami cekaman kekeringan. Transfor-masi gen P5CS dan regenerasi transgeniknya mungkin dapat menghasilkan tanaman tebu trans-genik yang toleran terhadap cekaman kekeringan. Tujuan penelitian ini adalah untuk mendapatkan metode transformasi yang optimum yang mencakup strain Agrobacterium tumefaciens yang sesuai, sumber eksplan dan varietas tebu terbaik sebagai target transformasi. Hasil penelitian menunjukkan bahwa transformasi gen P5CS telah berhasil dilakukan ke eksplan tebu baik yang berupa kalus asal media padat maupun kalus embriogenik dan embrio somatik asal kultur sistem perendaman sesaat (SPS). Sementara itu strain A. tumefaciens LBA4404 menunjukkan hasil yang paling efektif sebagai vektor transformasi. Pertumbuhan transforman baik pada kalus maupun embrio somatik pada varietas Kidang Kencana terlihat paling baik dibandingkan dengan varietas PS 881 dan PS 891. Sumber eksplan yang paling efektif adalah embrio somatik yang diperoleh dari  kultur SPS. Keberhasilan transformasi tebu me-lalui Agrobacterium ditunjukkan oleh ekspresi transien dari gen GUS dan kemampuan dari trans-forman untuk tumbuh di media yang mengandung    50 ppm kanamisin.
Evaluasi varietas, sumber eksplan dan strain Agrobacterium terhadap keberhasilan transformasi tebu dengan gen P5CS Evaluation of varieties, explant sources, and Agrobacterium strains for successful sugarcane transformation using P5CS gene Hayati MINARSIH; Dwi SUBIYARTI; Imron RIYADI; Soekarno Mismana PUTRA; Laksmi AMBARSARI
Menara Perkebunan Vol. 83 No. 1: 83 (1), 2015
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v83i1.7

Abstract

Abstract Genetic transformation can be used as an alter-native to develop sugarcane (Saccharum officinarum L.) tolerant to drought stress. P5CS gene has a role in biosynthesis of proline, an amino acid that accumulated under drought stress conditions. Transfer of a P5CS gene construct into plant cells in conjunction with regeneration of transgenic plantlets may develop sugarcane tolerant to drought stress. The aim of this research was to obtain an optimal transformation method which includes a suitable strain of Agrobacterium tumefaciens, and the best sugarcane explant and variety. The results showed that transfer of P5CS gene has been successfully carried out on sugarcane explants from solid media-derived calli, embryogenic calli and somatic embryos derived from temporary immersion system (TIS) culture. Whilst Agrobacterium strain LBA4404 was indicated as the most effective transformation vector. The regeneration of Kidang Kencana variety transformants from calli and somatic embryos was better than those of PS 881 and PS 891. The best performance of transformants based on the source of explants obtained from somatic embryos from TIS culture. Moreover, a succesfull Agrobacterium mediated transformation on sugarcane was indicated by transient expression of Gus gene and the ability of the transformants grew in a selection medium containing 50 ppm of kanamycin.Abstrak Transformasi genetik dapat digunakan sebagai upaya untuk merakit tebu (Saccharum officinarum L.) toleran terhadap cekaman kekeringan. Gen P5CS diketahui  berperan  dalam  biosintesis  prolin,  yaitu asam amino yang umumnya terakumulasi ketika tanaman mengalami cekaman kekeringan. Transfor-masi gen P5CS dan regenerasi transgeniknya mungkin dapat menghasilkan tanaman tebu trans-genik yang toleran terhadap cekaman kekeringan. Tujuan penelitian ini adalah untuk mendapatkan metode transformasi yang optimum yang mencakup strain Agrobacterium tumefaciens yang sesuai, sumber eksplan dan varietas tebu terbaik sebagai target transformasi. Hasil penelitian menunjukkan bahwa transformasi gen P5CS telah berhasil dilakukan ke eksplan tebu baik yang berupa kalus asal media padat maupun kalus embriogenik dan embrio somatik asal kultur sistem perendaman sesaat (SPS). Sementara itu strain A. tumefaciens LBA4404 menunjukkan hasil yang paling efektif sebagai vektor transformasi. Pertumbuhan transforman baik pada kalus maupun embrio somatik pada varietas Kidang Kencana terlihat paling baik dibandingkan dengan varietas PS 881 dan PS 891. Sumber eksplan yang paling efektif adalah embrio somatik yang diperoleh dari  kultur SPS. Keberhasilan transformasi tebu me-lalui Agrobacterium ditunjukkan oleh ekspresi transien dari gen GUS dan kemampuan dari trans-forman untuk tumbuh di media yang mengandung    50 ppm kanamisin.
Pemodelan protein dan analisis molecular docking enzim β-glukanase solat Bacillus subtilis W3.15: Ainia Hanifitri; Laksmi Ambarsari; Nisa Rachmania Mubarik
Menara Perkebunan Vol. 91 No. 1 (2023): 91 (1), 2023
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v91i1.523

Abstract

The β-glucanase enzyme is an enzyme protein that can hydrolyze β-glucan, one of the main components of the fungal cell wall. This enzyme protein is produced by several bacteria, one of which is B. subtilis. The three-dimensional (3D) structure of proteins is necessary to understand their properties and functions of proteins. Enzyme proteins can be analyzed for their structure and function using in silico method. This study aims to detect the β-glucanase gene from B. subtilis W3.15 and analyze it using the in silico method. The methods in this research are homology modeling and molecular docking analyses. Modeling was carried out using the SWISS-MODEL server and docking analysis using the PLANTS 1.1 program. Modeling the β-glucanase enzyme is based on the template of the β-glucanase enzyme protein model with PDB code 3o5s. The results of sequence alignment and model visualization were quite good as indicated by the model having a Ramachandran Plot value in the favored area of 91.10 %, a MolProbity score of 0.95, and a QMEAN value of 0.90 ± 0.06. The β-glucanase enzyme model was then docked using the PLANTS1.1 program with native ligand B3P, 1,4-β-D-Glucan, D-glucose, β-D-Glucan from oats, and N-Acetyl glucosamine. The results of docking analysis showed that the β-glucan ligand (β-D-glucan from oats) used as a substrate in the cultivation of isolate B. subtilis W3.15 had a better binding energy prediction value compared to the B3P ligand, which is a natural ligand in the template proteins.   [Keywords: β-Glucan, β-D-Glucan from oat, ligand, PLANTS 1.1, 3D structure, SWISS-MODEL]
In silico study: molecular docking of SARS-Cov-2 endoribonuclease on active compounds of Gmelina arborea Roxb. bark Shobiroh Nuur'Alimah; Agnia Nurul Jannati; Laksmi Ambarsari; Syamsul Falah
Menara Perkebunan Vol. 92 No. 1 (2024): 92(1), 2024
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v92i1.561

Abstract

Infection by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) triggers COVID-19 disease of the respiratory tract similar to pneumonia. The virus encodes four structural proteins and 16 non-structural proteins (nsp), one of which includes nsp15 or endoribonuclease (NendoU). NendoU plays an important role in viral replication and transcription and reduces the stimulation of immune cell responses. Active compounds in Gmelina arborea Roxb. bark have antioxidant properties that can inhibit the NendoU activity of SARS-CoV-2. This study aims to analyze the potential of compounds from Gmelina arborea Roxb. bark in inhibiting SARS-CoV-2 NendoU within in silico using the YASARA structure application. Balnophonin is the best test ligand based on binding ΔG value, dissociation constant (Kd), prediction of physicochemical characteristics, pharmacokinetics, and toxicity. Therefore, balanophonin can be developed as an effective alternative drug to inhibit SARS CoV-2 NendoU.
Co-Authors -, Suryani . SURYANI A.E. Zainal Hasan Ade Heri Mulyati Adrian Adiva Adriansyah Nanda Putra Aghnia, Diya Agnia Nurul Jannati Agung Isnanto Agustina L.N. Aminin Ahmad Irvan Pratama Ainia Hanifitri Aisyah Girindra Akbar, Nadhira Fathiaz Akhiruddin Maddu Akhmad Endang Zainal Hasan Alifia Mutiara Annisa Alimah, Shobiroh Nuur Ambarsavitri, Rahmadhani ANINDA INDRIANI Anja Meryandini Annisa Dhiya Athiyyah Khanza Aqilah, Rifany Fairuz Aris Tri Wahyudi Arwansyah Arwansyah Aryani, Hanifah Asrul Muhamad Fuad, Asrul Muhamad Assifah Eryandini AYU LESTARI Azhari, Muhammad Alwin Azzara Putri Elvaza Chelsea Chelsea, Chelsea Chelsy Narita Choirunnisa Miftahul Jannah Deki Geraldi Dewi Seswita Zilda Diana Widiastuti DIMAS ANDRIANTO Djarot Sasongko Hami Seno DWI NINGSIH SUSILOWATI DWI NINGSIH SUSILOWATI Dwi SUBIYARTI Dwicesaria, Maheswari Alfira Dwiningsih Susilowati Edy Djauhari Purwakusumah Edy Djauhari Purwakusumah Efi Sanfitri Harahap Faliha Arinda Lestari Farhan Azhwin Maulana Fathin, Muhammad Faris Fatriani, Rizka Febrianti, Riska G Jeni christi A Genta Asvarhoza GIA PERMASKU Giovanny, Lisa Gustini Syahbirin H. M. Mochtar Hanhan Dianhar Harahap, Efi Sanfitri HARTUTIK EKA SUSANTI Hasim - Hasim Hasim Hayati Minarsih Heri Purwoto Hidayat, Radika Evita Hudayanti, Martini Husnawati Husnawati Husnawati, . I MADE ARTIKA I Made Samudera I Made Samudera, I Made I MADE SAMUDRA Ifa Manzila Ifa Manzila Ika Yuni Astutik Ika Yuni Astutik, Ika Yuni Ike Wahyuni Putri Ilham Kurniawan Ilham Kurniawan Imelia Dewi Imron RIYADI Inayah, Mazidah Noer Inda Setyawati, Inda Irma Rahmayani Isnanto, Agung Jaya Hardi Kandi, Rizky Putra Kapitan, Origenes Boy Karichsa Hariana Komalasari, Nurma Angeliani Latifah K Darusman Lestari, Faliha Arinda Liliyani , Ni Putu Peggy Lisa Giovanny Made Suhandana Madyastuti, Rini Marfira, Nurul Mega Safithri Miantika, Shafillah Muhamad Rifai Muhamad Rifai Muhammad Alwin Azhari Muhammad Farhan Muhammad Faris Fathin Muhammad Halim Mustika Luthfia Mustika Permatasari Mustopa, Syahrul Nabila Nur Nafiati Natalia Marbun, Natalia NISA RACHMANIA MUBARIK Novia Winarti Nur Qadri Rasyid Nurhidayat Nurhidayat Nurul Marfira Nuur'Alimah, Shobiroh Nuur’Alimah, Shobiroh Okta Vino Pratama, Ahmad Irvan Pratiwi, Anggita Aziz Purwantiningsih Sugita Purwanto, Ukhradiya Magharaniq Safira Purwatiningsih Sugita Puspa Julistia Puspita Putri, Ike Wahyuni Radika Evita Hidayah Rahayu, Dyah Utami Cahyaning Rahman, Syabilla Aulia Rasyid, Nur Qadri Ridho Pratama Rifany Fairuz Aqilah Riki Riki Riksa Nur Wahyuni Rini Kurniasih, Rini Rini Novita Riska Febrianti Rosyidah, Rara Annisaur Rury Eryna Putri Sanro Tachibana Sarmila Sarmila Setyanto Tri Wahyudi Shobiroh Nuur' Alimah Shobiroh Nuur'Alimah Siti Nur'aeni Siti Nurjanah Siti Warnasih Slameut, Fitria Soekarno Mismana Putra Steffanus Gozales Suryani - Suryani Suryani Syamsul Falah TATI NURHAYATI Tirta Setiawan Tony Sumaryada Trah Yudha Tri Puji Priyatno Tri Puji Priyatno Uswatun Hasanah Wahyuni, Riksa Nur Wanda Hamidah Waras Nurcholis Yadi Suryadi Yadi Suryadi Zahra Silmi Muscifa Zuniar Subastian