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Analysis of flowering gene in palm oil (Elaeis guineensis) FAIZAL, IRVAN; EMDI, AXEL
Asian Journal of Agriculture Vol 1 No 02 (2017)
Publisher : Society for Indonesian Biodiversity & Universitas Mulawarman, Samarinda, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/asianjagric/g010201

Faizal I, Emdi A. 2017. Analysis of flowering gene in palm oil (Elaeis guineensis). Asian J Agric 1: 53-58. Palm oil has always been an important commodity in Indonesia. The most common species is palm oil, Elaeis guineensis. Palm oil is a monoecious plant with a tendency to be a temporal dioecious. Female flower will be the one that produces palm oil fruit, that later is treated with palm oil while male flower only takes part in the fertilization process. In order to know the ratio between female and male flower tree in a plantation, this study was performed to detect a distinction between female and male flowering gene sequences from DNA sample of E. guineensis. Based on previous study which managed to characterize MADS-box gene of palm oil, a primer was designed and named GmG (Globosa-male-Gaps). The result shows that the primer has the ability to differentiate DNA sequence female and male flower of E.guineensis, Palm oil. However, further studies with full sequence and more samples are needed to find distinctive results between female and male flower sequences as the GmG primer could be used to design a specific marker or primer to detect the presence of female or male flower within a tree.

Identification of MADS-box Gene in Oil Palm (Elaeis guineensis Jacq.) Nawfetrias, Winda; Sobir,; Faizal, Irvan
Makara Journal of Science Vol. 20, No. 3
Publisher : UI Scholars Hub

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The bunch size represented by the fruit number is the main parameter of oil palm (Elaeis guineensis Jacq.) yield. The fruit number, which is determined during the initial phase of development, is related to various factors, including the genetic properties of the trees. Trees that have more pistillate flowers have more fruit. The diversity of MADS-box genes assumed can be used as a marker for trees that have a higher number of pistillate flowers. Therefore, the aims of this research were to isolate and identify the MADS-box genes from flowers of tenera oil palm using PCR techniques. The SQUAMOSA (SQUA) gene and the GLOBOSA (GLO) gene are members of the MADS-box genes family that are responsible for sepal, petal and stamen organ development. The genomic DNA of the staminate flowers of trees that have more staminate flowers (P1) and the genomic DNA of the pistillate flowers of trees that have more pistillate flowers (P2) were isolated using the CTAB+ PVP method. The CTAB+PVP method was more efficient for isolating pistillate flower genomic DNA than staminate flower genomic DNA. The genomic DNA of P1 and P2 was amplified with two primers: BMS and BMG. The BMS primers gave a PCR product size of 1250 bp for the genomic DNA of P1 and P2. Meanwhile, the BMG primers gave a PCR product size of 1250 bp and 1300 bp for P1 and P2, respectively. The PCR products were sequenced and analyzed for homology using the GenBank database. BLAST analysis showed the PCR products have high homology with the SQUA1 gene and the GLO2 gene. Alignment analysis showed that the DNA fragments amplified with the BMS primers of the P1 and P2 sequences have variations in the exons and introns, and the variations were observed only in the introns of the DNA fragments amplified with the BMG primers.

Development and Optimization of SARS-CoV-2-Specific Primers for Accurate Diagnosis: A Case Study in West Sumatra - Indonesia Aulia, Ony Nattasha; Putri, Dwi Hilda; Faizal, Irvan
Althea Medical Journal Vol 11, No 4 (2024)
Publisher : Faculty of Medicine Universitas Padjadjaran

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15850/amj.v11n4.3348

Background: In 2022, new cases of Covid-19 emerged, including the Omicron variant which is classified as a variant of concern (VOC). West Sumatra is one of the top ten provinces with the highest number of cases in Indonesia. This study aimed to design specific primers and optimize the PCR method that can be used for accurate detection, specifically for SARS-CoV-2 circulating in West Sumatra.Methods: This study used an in silico approach, using whole genome sequencing (WGS) data available at the global initiative on sharing avian influenza data (GISAID), and employing the Geneious Prime application which confirmed samples collected from Padang, West Sumatra, and from Jakarta, Bogor, Depok, Tangerang, Bekasi (Jabodetabek) serving as comparative sample tests. Technology development was supported by bioinformatics testing, laboratory testing, and validation methods, involving gene mining, sequence alignment, and primer design. Laboratory tests and validation included viral genomes extraction and cDNA synthesis, polymerase chain reaction (PCR) testing, and results analysis. Results: Three sets of optimal primer candidates amplified the coveted target gene was discovered, specifically, the S gene of the receptor binding domain (RBD) region.Conclusions: The primers designed through a consensus between the complete genome of the SARS-CoV-2 isolate Wuhan-Hu-1 and the WGS of the Omicron variant in Padang, West Sumatra, have successfully detected the SARS-CoV-2 virus variant in the region. The most effective temperature optimization results were achieved by testing three primer products on samples from Padang and Jabodetabek. It has significance as a valuable diagnostic tool in the primer form.

Production and bioactivity test of recombinant protein common carp growth hormone Utomo, Deny Sapto Chondro; Alimuddin, .; Sudrajat, Agus Oman; Faizal, Irvan
Jurnal Akuakultur Indonesia Vol. 10 No. 1 (2011): Jurnal Akuakultur Indonesia
Publisher : Indonesian Society of Scientific Aquaculture (ISSA)

This study aimed to produce recombinant growth hormone (rGH) protein of common carp (Cyprinus carpio) and evaluate its bioactivity. DNA fragment encoding mature GH protein of common carp (mCcGH) was amplified by polymerase chain reaction (PCR) method and PCR products were then ligated into pCold I to generate pCold I-mCcGH protein expression vector. Escherichia coli BL21 (DE3) harboring pCold I-mCcGH was cultured in the 2xYT medium at 15 °C for 24 hours and protein production was induced by isopropyl-beta-thio galactopyranoside (IPTG). The inclusion bodies containing rGH protein from E. coli transformants were isolated by sonication method and analyzed by SDS-PAGE. The result showed that rGH with molecular weight of about 25 kDa was obtained. Common carp juveniles with average body weight of 5.2±0.4 g were intramuscularly injected once a week for 4 weeks with rGH protein solution from 1 μg bacterial cells per gram fish body weight. The result showed that juveniles fish injected with rGH grew 106.56% higher than control. This result indicated that rGH produced in E. coli BL21 possessed biological activity and it may be useful to improve growth of aquaculture species.Key words: growth hormone, recombinant protein, common carp ABSTRAKPenelitian ini bertujuan menghasilkan protein rekombinan hormon pertumbuhan (growth hormone, GH) dari ikan mas (Cyprinus carpio) dan menguji bioaktivitasnya. Fragmen DNA penyandi protein matang (mature) GH ikan mas (mCcGH) diamplifikasi dengan menggunakan metode PCR dan hasilnya kemudian diligasi ke dalam pCold-I untuk menghasilkan konstruksi vektor ekspresi pCold-I-mCcGH. Plasmid pCold-I-mCcGH ditransformasi ke bakteri Escherichia coli BL21 (DE3), dikultur dalam media 2xYT cair pada suhu 15°C selama 24 jam dan produksi protein diinduksi dengan menggunakan isopropyl-beta-thio galactopyranoside (IPTG). Badan inklusi yang mengandung protein rekombinan GH (rGH) dari bakteri E. coli transforman diisolasi menggunakan metode sonikasi dan dianalisis dengan menggunakan SDS-PAGE. Hasil penelitian menunjukkan bahwa rGH dengan bobot molekul sekitar 25 kDa berhasil diproduksi. Benih ikan mas dengan bobot rata-rata 5,15±0,4 g diinjeksi secara intramuskular satu kali per minggu selama 4 minggu dengan larutan rGH hasil ekstraksi dari 1 µg pelet bakteri/g bobot ikan. Benih yang disuntik dengan rGH tumbuh sekitar 100% lebih cepat bila dibandingkan dengan kontrol yang tidak diinjeksi rGH. Hasil ini mengindikasikan bahwa rGH yang diproduksi dalam bakteri E. coli memiliki bioaktivitas dan dapat bermanfaat untuk memacu pertumbuhan spesies ikan-ikan budidaya.Kata kunci: hormon pertumbuhan, protein rekombinan, ikan mas

Kloning gen virulen Streptococcus agalactiae sebagai bahan dasar vaksin rekombinan Sutanti, ,; Soejoedono, Retno Damayanti; Faizal, Irvan
Jurnal Akuakultur Indonesia Vol. 15 No. 2 (2016): Jurnal Akuakultur Indonesia
Publisher : Indonesian Society of Scientific Aquaculture (ISSA)

ABSTRACT Streptococcus agalactiae has emerged as an important pathogen that affects Nile tilapia in Indonesia aquaculture. Vaccination is one of the most effective tools for enhancing host defense and protecting fish from pathogens. DNA vaccine is a third generation of vaccines based on the gene encoding a vaccine antigen rather than the antigen itself. Mga is DNA-binding protein that activates expression of several important virulence gene, including those encoding M protein (emm), C5a peptidase (SCPA) and mga. The goals of this study were to isolate and molecular characterize the mga gene of local isolate of S. agalactiae to support the development of DNA vaccine. Local bacterial strain was isolated from Nile tilapia farming in West Java, Indonesia. Bacterial identification was accomplished by PCR, using 16S rRNA primers, which revealed the 1,500 bp PCR product. Mga gene isolation was accomplished by PCR using mga gene S. agalactiae SAF and SAR- specific primers, which revealed the 1,494 bp PCR product. Mga gene was cloned into pGEM T-easy and sequenced using M13 primers. SalI and NotI restriction enzymes were used to digest the pGEM T-easy vector containing mga gene. Mga gene was cloned into pMBA containing beta actin promoter of Japanese medaka. The 16S rRNA sequence analyses confirmed that the local bacteria was 97% similarity with S. agalactiae strain 15-92MPnew. The nucleotide sequence analyses confirmed that the clones were contained 98% similarity with M protein mga S. agalactiae. The mga gene controlled by MBA promoter has constructed successfully as a candidate of DNA vaccine to against S. agalactiae infection in Nile tilapia. Keywords: DNA Vaccine, Streptococcus agalactiae, mga gene, Oreochromis niloticus, recombinant DNA ABSTRAK Streptococcus agalactiae merupakan patogen penting yang mempengaruhi budidaya ikan nila di Indonesia. Vaksinasi merupakan salah satu metode yang paling efektif untuk meningkatkan pertahanan dan melindungi ikan dari patogen. Vaksin DNA adalah vaksin generasi ketiga yang mengandung gen penyandi antigen vaksin. Mga adalah protein DNA-binding yang mengaktifkan ekspresi beberapa gen virulensi, termasuk M protein (emm), C5a peptidase (SCPA) dan mga. Tujuan dari penelitian ini adalah untuk mengisolasi dan karakterisasi secara molekuler gen mga dari isolat lokal S. agalactiae untuk mendukung pengembangan vaksin DNA. Identifikasi bakteri dilakukan dengan PCR, menggunakan primer 16S rRNA dengan produk PCR 1.500 bp. Isolasi gen mga dilakukan dengan metode PCR menggunakan primer SAF dan SAR dengan ukuran target 1.494 bp. Gen mga dikloning ke vektor pGEMT–easy dan disekuensing menggunakan primer M13. Enzim Sal I dan Not I digunakan untuk memotong gen mga dari vektor pGEMT- easy, selanjutnya gen mga dikloning ke vektor pMBA yang mengandung promoter beta-aktin ikan medaka Jepang. Berdasarkan analisis menggunakan gen 16S rRNA diperoleh bahwa sampel memiliki kesamaan 97% sebagai S. agalactiae. Analisis sekuen nukleotida menunjukkan bahwa klon mengandung gen mga dengan 98% kesamaan dengan M protein mga S. agalactiae. Konstruksi mga gene yang dikendalikan oleh promoter MBA telah berhasil dibuat dan ini merupakan kandidat vaksin DNA untuk mengendalikan infeksi S. agalactiae pada ikan nila. Kata kunci: Vaksin DNA, Streptococcus agalactiae, gen mga, Oreochromis niloticus, DNA rekombinan

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