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All Journal HAYATI Journal of Biosciences Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Jurnal Ilmu Pertanian Indonesia Jurnal Fitopatologi Indonesia Jurnal Teknologi Industri Pertanian Jurnal Pengolahan Hasil Perikanan Indonesia Jurnal Akuatika Microbiology Indonesia Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Agrointek Jurnal Hortikultura Current Biochemistry BIOTIK: Jurnal Ilmiah Biologi Teknologi dan Kependidikan Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (Journal of Natural Resources and Environmental Management) Indonesian Journal of Biotechnology Agrokreatif Jurnal Ilmiah Pengabdian kepada Masyarakat Jurnal Sumberdaya Hayati Journal of Tropical Biodiversity and Biotechnology Jurnal Bioteknologi & Biosains Indonesia (JBBI) Squalen Bulletin of Marine and Fisheries Postharvest and Biotechnology Majalah Ilmiah Biologi BIOSFERA: A Scientific Journal Biosaintifika: Journal of Biology & Biology Education Jurnal Purifikasi Jurnal Pascapanen dan Bioteknologi Kelautan dan Perikanan Menara Perkebunan Jurnal Mangifera Edu Journal of Microbial Systematics and Biotechnology Konservasi Hayati Prosiding Seminar Nasional Biologi, Teknologi dan Kependidikan (Biotik) MADURANCH: JURNAL ILMU PETERNAKAN Makara Journal of Science International Journal of Oil Palm
NISA RACHMANIA MUBARIK
Bogor Agricultural University
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Decision Sciences, Operations Research & Management Dentistry Earth & Planetary Sciences Economics, Econometrics & Finance Education Energy Engineering Environmental Science Immunology & microbiology Industrial & Manufacturing Engineering Languange, Linguistic, Communication & Media Library & Information Science Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience Nursing Public Health Social Sciences Other

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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]
ISOLASI DAN KARAKTERISASI BAKTERI PENAMBAT NITROGEN INDIGENOUS POTENSIAL SEBAGAI PUPUK HAYATI DALAM REMEDIASI LAHAN BEKAS TAMBANG BATU KAPUR Mashudi, Mashudi; Mubarik, Nisa Rachmania
Purifikasi Vol 22 No 1 (2023): Jurnal Purifikasi
Publisher : Department of Environmental Engineering-Faculty of Civil, Planning, and Geo Engineering. Institut Teknologi Sepuluh Nopember, Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.12962/j25983806.v22.i1.452

Abstract

Lahan bekas pertambangan umumnya memiliki struktur fisik dan kimia yang kurang optimum untuk pertumbuhan tanaman. Bakteri tanah indigenous dapat digunakan untuk membantu proses remediasi lahan bekas pertambangan dengan cara dimanfaaatkan sebagai pupuk hayati. Bakteri penambat nitrogen merupakan salah satu bakteri yang dapat membantu mempercepat remediasi tanah karena memiliki kemampuan memperkaya kandungan nitrogen dalam tanah. Penelitian ini bertujuan untuk mengisolasi dan melakukan karakterisasi bakteri penambat nitrogen dari tanah bekas tambang batu kapur di wilayah Cirebon, Jawa Barat. Isolasi bakteri dilakukan terhadap 13 sampel yang berasal dari area sekitar lahan bekas tambang batu kapur. Hasil isolasi diperoleh 6 isolat bakteri penambat nitrogen hidup bebas dan 2 isolat bakteri penambat nitrogen simbiosis. Seluruh isolat memiliki kemampuan menghasilkan Indole-3-acetic acid (IAA) jika ditambahkan 1 mM L-triptofan. Dua isolat dipilih (7B21Y dan 5A22) berdasarkan ciri morfologi sel dan koloni untuk dilakukan pengujian fisiologis. Aktivitas nitrogenase isolat 7B21Y dan 5A22 diukur dengan menggunakan Pengujian Reduksi Asetilen dan diperoleh masing-masing 7.09 ppm dan 5.59 ppm. Isolat 7B21Y kemudian diidentifikasi secara fisiologi menggunakan kit API dan diketahui memiliki kemiripan 99.9% dengan Rhizobium radiobacter.
Interaksi Molekuler Senyawa Kuersetin dan Eugenol terhadap Protein Regulator Lintasan Penuaan SIR2, pada Khamir Saccharomyces cerevisiae Alfaridza, Annisa Nourma; Astuti, Rika Indri; Mubarik, Nisa Rachmania
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 10, No 1 (2025): February 2025
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24002/biota.v10i1.6819

Abstract

Proses penuaan dapat dipengaruhi oleh beberapa faktor, seperti peningkatan cekaman oksidatif dan inflamasi di mana senyawa antioksidan seperti kuersetin dan eugenol dapat mengatasi hal tersebut. Kuersetin dan eugenol merupakan senyawa antioksidan yang dapat ditemukan di alam. Kuersetin dan eugenol memiliki aktivitas antioksidan pada sel khamir maupun sel mamalia. Namun, mekanisme kedua senyawa ini dalam meregulasi penuaan di level molekuler belum tersedia. Oleh karena itu, penelitian ini dilakukan dengan tujuan untuk mengetahui interaksi senyawa kuersetin dan eugenol pada protein Sir2 pada Saccharomyces cerevisiae yang memiliki peran sebagai regulator sistem penuaan. Penelitian menggunakan studi penambatan molekular dengan senyawa kuersetin dan eugenol sebagai ligan uji, sedangkan reseptornya menggunakan Sir2 asal Saccharomyces cerevisiae dengan kode PDB, 2HJH. Hasil penelitian menunjukkan bahwa senyawa kuersetin dan eugenol dapat berikatan secara molekuler dengan protein Sir2. Parameter afinitas ikatan (ΔG) dilihat dengan nilai negatif yang tinggi. Senyawa kuersetin memiliki afinitas ikatan (ΔG) sebesar -8.5 kkal/mol, sedangkan pada senyawa eugenol memiliki afinitas ikatan (ΔG) sebesar -6.5 kkal/mol. Selain itu, adanya ikatan kimia dan residu asam amino menunjukkan bahwa senyawa ligan uji memiliki potensi untuk bersaing dengan ligan alami. Namun, penelitian lebih lanjut diperlukan untuk menentukan efek ligan uji terhadap lintasan penuaan, in vivo.
Respon Pertumbunan Tanaman Kedelai terhadap Bradyrhizobium japonicum Toleran Masam dan Pemberian Pupuk di Tanah Masam Triadiati, ,; Mubarik, Nisa Rachmania; Ramasita, Yoan
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 41 No. 1 (2013): Jurnal Agronomi Indonesia
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (318.229 KB) | DOI: 10.24831/jai.v41i1.7072

Abstract

The use of acid tolerant rhizobacteria such as Bradyrhizobium japonicum is one effort for increasing soybeanproductivity in acid soil. B. japonicum is a N-fixing bacteria that can promote soybean growth through symbiosis with thehost plants. The objective of this study was to investigate the growth and production of soybean var. Wilis inoculated by B.japonicum and NPK inorganic fertilizer application in acid soil. Two isolates of B. japonicum that were BJ 11(19) and BJ11(wt) were used as inoculant for soybean. BJ 11(19) was resulted by transposons mutagenesis, whereas BJ 11(wt) is a wild type of bacteria. Both isolates of B. japonicum were acid tolerant. Soybean was inoculated with BJ 11(19) and BJ 11(wt)combined with compost and nitrogen fertilizer (with two rates). The field experiment was conducted at Cikabayan, Darmaga,in a randomized complete block design with 12 treatments and 3 replicates. The results showed that application of the acidtolerant B. japonicum BJ 11(wt), compost, and nitrogen fertilizer (10 g m-2) increased the plant height, dry weight of shootsand roots, nodule number, dry weight of nodules, nitrogenase activity, number of pod and seed, seed weight, and nitrogencontent of seeds in acid soil.Keywords: acid soil, acid tolerant rhizobia, Bradyrhizobium japonicum, compost, nitrogen fertilizer
Peningkatan akumulasi tiamin pada kultur Escherichia coli melalui peningkatan oksigenasi dan penghilangan rpoS Nuraliah Rusman; Prayoga Suryadarma; Nisa Rachmania Mubarik
AGROINTEK Vol 19, No 1 (2025)
Publisher : Agroindustrial Technology, University of Trunojoyo Madura

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21107/agrointek.v19i1.11110

Abstract

Microorganisms as cell factories in producing a product are strongly influenced by their metabolism. engineering microbial metabolism by increasing coenzymes that play a role in enzyme activity. Thiamine diphosphate is one of the coenzymes that are commonly found in the metabolic pathways of microbial cells. Increasing the thiamine formation pathway as a precursor in the thiamine metabolic pathway is a strategy in this study. Enhancing thiamine accumulation in Escherichia coli culture by inducing oxygenation level and deleting rpoS was investigated. The investigation was conducted by comparing the cultivation of  Escherichia coli BW25113 (parent strain) and BW25113-∆rpoS (rpoS mutant) cultures under aerobic conditions at different shaking rotation rates of 150 and 200 rpm. The measured parameters were thiamine accumulation, dry cell weight, acetate concentration and glucose consumption of the cultures. Inducing oxygenation level of parent strain cultures through increasing shaking rotation rate from 150 to 200 rpm induced 40 % thiamine accumulation. Meanwhile, deletion of rpoS increased 9,5 % thiamine accumulation compared to parent strain culture
Biocontrol Potential of Chitinase-Producing Soil Bacteria Against Fusarium proliferatum Wulandari Antika Putri; Nisa Rachmania Mubarik; Aris Tri Wahyudi
HAYATI Journal of Biosciences Vol. 33 No. 4 (2026): July 2026
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.33.4.1136-1146

Abstract

Fusarium proliferatum, a phytopathogenic fungus, causes significant agricultural losses. Chitinase-producing bacteria from post-mining soil have potential as biocontrol agents because they degrade chitin, a major component of fungal cell walls. This study aimed to isolate, characterize, and purify bacterial chitinase and evaluate its antifungal activity against F. proliferatum. Bacterial isolates were obtained from post-mining soil in Martabe and screened for chitinase activity using chitin agar medium. The selected isolates were identified through 16S rRNA gene sequencing, and the chitinase enzyme was partially purified using ammonium sulfate precipitation. The antifungal activity against F. proliferatum was evaluated using dual-culture and food-poisoning assays. Two isolates, TSU4 and TSU5, exhibited high chitinolytic activity with hydrolytic zone indices of 2.1±0.2 cm and 1.9±0.41 cm, respectively; TSU4 (Bacillus cereus) was selected for further study. The 70% ammonium sulfate-precipitated chitinase showed a specific activity of 15.66 U/mg, and the concentrated enzyme inhibited F. proliferatum growth by 33.8±0.23%. Chitinases belong to the glycoside hydrolase family 18 (GH18), an evolutionarily widespread group of chitin-degrading enzymes with a conserved catalytic domain that hydrolyzes β-1,4 linkages in chitin, making GH18 chitinases effective for degrading fungal cell walls in biocontrol applications. These findings indicate that the chitinase produced by B. cereus TSU4 shows significant antifungal activity and has strong potential as a biocontrol agent against F. proliferatum.
Selection and Identification of Potential Hydrolytic Bacillus from Litter Composting Ika Setianingsih; Nisa Rachmania Mubarik; Iman Rusmana
Jurnal Ilmu Pertanian Indonesia Vol. 31 No. 1 (2026): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18343/jipi.31.1.107

Abstract

Microbe study on degraded trash has been widely conducted, with the intention of improving the efficiency and effectiveness of waste processing. The purpose of this study was to select and identify hydrolytic Bacillus from litter composting. The samples were the litter composting outcomes with five different treatments, namely the inclusion of nutrient broth (NB), commercial formula, molasses, tryptic soy broth (TSB), and talcum, with each formula containing a microbial consortium. Bacteria were isolated using the serial dilution method. Each isolate was evaluated for its capacity to lyse red blood cells on blood agar media. Cellulolytic, amylolytic, and proteolytic bacteria were grown on nutritional agar media containing carboxy-methyl cellulose (CMC), starch, and skim milk. The antagonistic test involved testing isolates that hydrolyze all three types of substrates. Isolates that were not antagonistic to one another were identified based on phenotypes (colony and cell morphology using Gram staining) and genotypes (16S rRNA gene). Fourteen isolates of Bacillus sp. had cellulolytic, amylolytic, and proteolytic properties. Four isolates were chosen; two of them were comparable to Bacillus stercoris, while the other two, 5.5 and 5.9R, are similar to Calidifontibacillus erzurumensis and Bacillus amyloliquefaciens. Therefore, litter can be used to determine the hydrolytic capability of Bacillus isolates. Keywords: amylolytic, Bacillus, cellulolytic, proteolytic
Co-Authors , Triadiati . QATRUNNADA Aas Ratnasari Ahmad Suryadi Ainia Hanifitri Alfan Cahyadi Alfaridza, Annisa Nourma ALINA AKHDIYA Andreas Adhi Satya Andreas Adhi Satya ANGELIA REZTY FITRIANI SITUMORANG Anggreandari, Rizky Ani Suryani Ani Suryani Anja Meryandini Antonius Suwanto Aris Tjahjoleksono Aris Tri Wahyudi Atang Sutandi Ayni, Qurrotu Bambang - Riyanto Besty Maranatha BRAMANTYO JATI PRASOJO Budiasih Wahyuntari Budiasih Wahyuntari Budiasih Wahyuntari Cahyadi, Alfan Dadang Suhendar Dadang Suhendar Delfi Trisnawati DERI YURATMOKO Desniar - - Dewi Seswita Zilda Dewi Seswita Zilda Dian Syahfitri Dinamella Wahjuningrum Dwi Ambarawati DWI ANDREAS SANTOSA Ekowati Chasanah Encah Ewi Mulyeti Esti Puspitasari ESTI PUSPITASARI Evi Damayanti Evi Damayanti, Evi Fahmi, Riziq Ilham Nur Fauzy Rachman Fauzy Rachman Fauzy Rachman Ferymon Mahulette Ferymon Mahulette Ferymon Mahulette, Ferymon Fitratul Aini Fitratul Aini, Fitratul Fitriani Idham Galih Cendana Nabilasani Galih Cendana Nabilasani Hadi Susilo Hamim Hamim Hana Nurullita Prestisia Hasrul Satria Hasrul Satria, Hasrul HENDRA PARDEDE Hirmas Fuady Putra HIRMAS FUADY PUTRA, HIRMAS FUADY Idin Abidin Ika Roostika Tambunan, Ika Roostika Ika Setianingsih Iman Rusmana Iman Rusmana Ismi Isti'anah Isna Rahma Dini Iswati, Ruma It Jamilah Ivan Permana Putra Jepri Agung Priyanto Jepri Agung Priyanto, Jepri Agung Karina Eku Dwinanda Gunawan Kusuma Handayani LAKSMI AMBARSARI Lia Siti Nur'amaliyah Lia Siti Nur'amaliyah Lisdar Idwan Sudirman Listyowati, Sri lmiah, Sitti Nur Luky Adrianto Maggy Thenawidjaya Suhartono Maherani, Vincentia Fenice Angger Maranatha, Besty Maria Dita Febriani Lumban Gaol Marini Adani Mashudi Mashudi Masrukhin Masrukhin Muhamad Azwar Syah Mulyorini Rahayuningsih Mutiha Panjaitan Nabilasani, Galih Cendana Nabilasani, Galih Cendana Ninda Ningtyas Nuraliah Rusman Nurul Hidayati Partomuan Simanjuntak Partomuan Simanjuntak Partomuan Simanjuntak Prayoga SURYADARMA Puspita Lisdiyanti Rika Indri Astuti RIMA ERNIA Risky Hadi Wibowo Risky Hadi wibowo Rizky Anggreandari Rury Eryna Putri Sarah Asih Faulina Sarah Asih Faulina, Sarah Asih Sipriyadi Sipriyadi Sipriyadi Siswa Setyahadi Siswodarsono, Trismilah Siswodarsono, Trismilah Siti Azzira Rahma Sitti Nur Ilmiah Sonya Tobing Sri Budiarti Poerwanto Sri Listyowati Suhendar, Dadang Suhendar, Dadang SYAMSUL BAHRI SYAMSUL BAHRI TEDJA IMAS Thenawidjaya, Maggy Titi Candra Sunarti TRI ASMIRA DAMAYANTI Tri Handayani Kurniati Tri Handayani Kurniati Trismilah Trismilah Siswodarsono Untung Sudadi Wahyu Widosari Wibowo, Risky Hadi Widanarni Widanarni WIDANARNI WIDANARNI Widosari, Wahyu Wulandari Antika Putri Yoan Ramasita Yusro Nuri Fawzya Zaenal Arifin, Sukarya Zulfarina Zulfarina Zulfarina,