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All Journal Bioscientist : Jurnal Ilmiah Biologi Journal of Biology Science and Education
Messe, Yunita
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Education Immunology & microbiology Social Sciences

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Desain Primer Polymerase Chain Reaction (PCR) secara In Silico untuk Amplifikasi Gen gyrA Extensively Drug Resistant Tuberculosis (XDR-TB) Messe, Yunita; Budiarsa, I Made; Laenggeng, Abd Hakim
Journal of Biology Science and Education Vol. 8 No. 2 (2020): Desember
Publisher : Universitas Tadulako

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22487/jbse.v8i2.1169

Abstract

Perubahan asam amino di area pengikatan fluorokuinolon pada gen gyrA Mycobacterium tuberculosis menyebabkan penanganan dan pengendalian penyakit tuberkulosis menjadi semakin sulit. Teknik PCR dapat dipergunakan untuk mendeteksi adanya resistensi terhadap obat fluorokuinolon dan keberhasilan cara ini tergantung pada primer yang digunakan. Penelitian ini bertujuan untuk mendesain kandidat primer gen gyrA XDR-TB secara in silico. Data yang digunakan dalam penelitian ini diperoleh melalui pencarian dalam situs GeneBank NCBI (https://www.ncbi.nlm.nih.gov). Desain primer ini dilakukan dengan menggunakan beberapa software dan situs bioinformatika, seperti software BioEdit versi 7.2.6, FastPCR 6.6 dan OligoAnalyzer (https://sg.idtdna.com/calc/analyzer). Studi ini berhasil mendesain sepasang kandidat primer dengan suhu Tm 57,8ºC dan telah memenuhi karakter primer yang baik yaitu primer-forward (5’-AACATTGAGGACCAGTCTAGCGA-3’) memiliki panjang 23 bp dan GC content 47,8%, sedangkan primer-reverse (5’-CCAGCAGATAGGTGCCTTCAC-3’) dengan panjang 21 bp dan GC content 57,1% serta terdapat peluang terbentuknya self-dimer sebanyak 1 bentuk.
Phylogenetic Investigation of Megapodius cumingii from Kabetan, Central Sulawesi, Based on the RDP1 Gene Akram; Budiarsa, I Made; Messe, Yunita
Bioscientist : Jurnal Ilmiah Biologi Vol. 14 No. 1 (2026): March
Publisher : Department of Biology Education, FSTT, Mandalika University of Education, Indonesia.

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33394/bioscientist.v14i1.20024

Abstract

This study investigated the phylogenetic relationships of Megapodius cumingii using bioinformatic analyses. Blood samples were collected from the Kabetan Island population, followed by DNA extraction using the QIAamp DNA Blood Mini Kit, PCR amplification with Takara Ex Taq™ and RDP1.U1/RDP1.L1 primers, and sequencing with BigDye Terminator v3.1 ABI PRISM 3100. Chromatograms were converted into nucleotide sequences using BioEdit, and sequence similarity was assessed using NCBI BLAST. Multiple sequence alignment, model selection, nucleotide composition analysis, and phylogenetic reconstruction were performed in MEGA 12. The RDP1 gene of M. cumingii from Kabetan showed a consistent nucleotide composition with high GC content (55.27%) and high similarity to M. cumingii sequence KF834037.1, with substitutions dominated by transitions (A↔G, T↔C). Maximum likelihood analysis under the T92+G model (1.03) revealed three major clades, with clades 1 and 2 strongly supported (bootstrap = 100). The Kabetan population formed a monophyletic subclade with KF834037.1 (bootstrap = 86) and showed a very short branch length (~0.05 substitutions/site), indicating low intraspecific divergence, with Megapodius tenimberensis as the closest sister taxon. These findings support the utility of RDP1 for phylogenetic resolution within Megapodiidae and provide a preliminary basis for conservation planning and population connectivity assessment of M. cumingii in Wallacea.
Co-Authors Abd Hakim Laenggeng, Abd Hakim Akram I Made Budiarsa