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All Journal Jurnal Penelitian Sains BIOEDUSAINS: Jurnal Pendidikan Biologi dan Sains Life Science and Biotechnology
Afidah, Yusfi
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemistry Education Immunology & microbiology Mathematics Physics

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Metode Direct PCR yang Cepat dan Hemat Biaya untuk DNA Barcoding Anggrek Obat Dendrobium crumenatum Sw. Afidah, Yusfi; Su'udi, Mukhamad
BIOEDUSAINS:Jurnal Pendidikan Biologi dan Sains Vol 7 No 2 (2024): Bioedusains: Jurnal Pendidikan Biologi dan Sains
Publisher : Institut Penelitian Matematika, Komputer, Keperawatan, Pendidikan dan Ekonomi (IPM2KPE)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31539/bioedusains.v7i2.12893

Abstract

This study aims to develop a rapid and cost-effective Direct PCR method for amplifying the rbcL gene without requiring DNA isolation, particularly for Dendrobium crumenatum Sw., an orchid species known for its traditional medicinal uses. The method involved soaking fresh leaves of D. crumenatum in TE buffer, followed by incubation at 55ºC. The incubation product was Directly used as a PCR template. The results showed a clear DNA band of 600 bp, corresponding to the target rbcL gene. BLAST analysis confirmed that the DNA sequence shared 84-85% identity with other species in GenBank. In conclusion, the Direct PCR method proved to be effective for DNA barcoding applications, offering advantages in speed and cost-efficiency over conventional DNA isolation methods. Keywords: Medicinal Orchids, Dendrobium crumenatum Sw., Direct PCR, DNA Barcoding
Adaptasi Morfologi Trikoma pada Tillandsia sp. dalam Penyerapan Air Afidah, Yusfi; Noviyani, Anis; Munawaroh, Putri Aisiyya Qutlana; Su'udi, Mukhamad
Jurnal Penelitian Sains Vol 26, No 1 (2024)
Publisher : Faculty of Mathtmatics and Natural Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.56064/jps.v26i1.920

Abstract

Tillandsia sp. merupakan tanaman hijau sepanjang tahun yang berasal dari Amerika Latin. Tanaman ini tergolong tanaman epifit dengan ciri khusus tidak memiliki akar tanah yang kokoh seperti tanaman pada umumnya. Bentuk adaptasi yang dilakukan dengan adanya trikoma yang berfungsi sebagai penyerapan air dan nutrisi sehingga Tillandsia sp. dapat tumbuh dengan baik. Berbagai macam bentuk trikoma dapat menyesuaikan dengan kondisi lingkungan yang ada, sehingga morfologi setiap jenisnya berbeda sebagai bentuk adaptasi. Melalui berbagai sumber ditemukan adanya perbedaan pada kerapatan trikoma serta panjang sel sayap “wing cells” yang dimiliki oleh beberapa jenis Tillandsia sp. Ciri khusus yang dimiliki tanaman ini yaitu pada trikoma dan sel sayap berfungsi sebagai sistem penyerapan air untuk menggantikan fungsi dan peran akar.
The matK Mini-barcode as a Potential Molecular Identification Tool for Medicinal Orchids Su'udi, Mukhamad; Setyati, Dwi; Khoirunnisa, Gita Ayu; Afidah, Yusfi; Ulum, Fuad Bahrul
Life Science and Biotechnology Vol. 1 No. 1 (2023): May
Publisher : Department of Biology, Faculty Mahematics and Natural Sciences, University of Jember

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19184/lsb.v1i1.39851

Abstract

matK is one of the universal loci which is commonly used as a barcode in the molecular identification of plants. Up to now, the problem of matK as a single locus is the use of the entire gene region as barcodes. The long amplicon size of matK raises several problems in DNA barcoding. The aim of this study is to uncover a small region of the matK gene as a potential mini-barcode region for alternative sites to get more efficient and effective results. In silico studies performed include the collection of matK sequence of medicinal orchid from GenBank, the amplicon size from matK primer sets that are commonly used in the Orchidaceae family, and PCR analysis. Data analysis was done by comparing the results of PCR amplification from several primer sets: matK 390F-1326R, 743F-R2, 712F-1154R and 712F-1216R. The results show that all primer pairs are able to amplify the DNA template isolated from Dendrobium purpureum. However, the shorter DNA band obtained from matK 743F-R2, 712F-1154R and 712F-1216R primers sets were visualized more thick than the longer amplicon band produced from matK primer 390F-1326R. This indicates that short matK sequence for DNA barcoding (mini-barcode) is more efficient in amplifying DNA templates compared to generally applied barcoding using full length sequences.
in-silico PASS prediction for medicinal potency of antioxidant from Ranunculus japonicus Thunb. Amalini, Yusrina Risky; Afidah, Yusfi
Life Science and Biotechnology Vol. 1 No. 2 (2023): November 2023
Publisher : Department of Biology, Faculty Mahematics and Natural Sciences, University of Jember

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19184/lsb.v1i2.45078

Abstract

Ranunculus japonicus has been traditionally used to treat various ailments, including malaria, jaundice, gastric problems, toothache, and eye inflammation. Recent studies reported that the plant extract effectively treat rheumatoid arthritis due to its secondary metabolites with antioxidant activities, such as flavonoids and phenols. In this study, we analyzed the flavonoids and phenols from R. japonicus using in silico methods. The study determined the flavonoid and phenol contents based on existing literature. The antioxidant potential analysis was conducted using PASS (Prediction of Activity Spectra for Substances). The results indicate the presence of two flavonoid compounds, namely Apigenin 6,8-di-C-|A-L-Arabinopyranoside and 3-Methylquercetin, and three phenol compounds, namely 3-Hydroxytrisol 3-O-glucoside, 4-Hydroxy-3-methoxyacetate, and Hydroxytrisol. Two compounds exhibited high bioactive potential (Pa value > 0.7), two compounds showed medium bioactive potential (Pa value > 0.5), and one compound exhibited low bioactive potential (Pa value < 0.5). The most bioactive compounds were Apigenin 6,8-di-C-|A-L-Arabinopyranoside and 3-Methylquercetin. The compounds with medium bioactivity were 3-Hydroxytrysol 3-O-glucoside and 4-Hydroxy-3-methoxycinnamic. The PASS online analysis revealed the potential of antioxidants for medicinal potencies
Co-Authors Amalini, Yusrina Risky Dwi Setyati Farrennina, Tasya Preira Fuad Bahrul Ulum Khoirunnisa, Gita Ayu Mukhamad Su'udi Munawaroh, Putri Aisiyya Qutlana Mustafidah, Qori’atul Noviyani, Anis Putri, Aura Balqis Nicheta Sani, Luthfiana Mutiara Su'udi, Mukhamad Yang, Haoling