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Sekuen Penyandi 18S Ribosomal RNA dan Ubiquitin pada Pandanus sp. Asal Riau (Sequences Encoding 18S Ribosomal RNA and Ubiquitin on Pandanus sp. from Riau) Dewi Indriyani Roslim; Nurin Nuryani; Herman Herman
JURNAL BIOS LOGOS Vol 8, No 1 (2018): JURNAL BIOSLOGOS
Publisher : Universitas Sam Ratulangi

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.35799/jbl.8.1.2018.20590

Abstrak Gen penyandi 18S ribosomal RNA (18S rRNA) dan ubiquitin merupakan anggota dari housekeeping genes yang sering digunakan sebagai kontrol internal pada analisis ekspresi. Penelitian bertujuan mengisolasi kedua gen tersebut pada tanaman Pandanus sp asal Riau. Metode penelitian meliputi isolasi DNA total, elektroforesis, PCR, purifikasi gel, sekuensing, dan analisis data sekuen DNA menggunakan program BioEdit version 7.0.0, BLASTn, dan MEGA6. Sekuen DNA penyandi 18S rRNA (420 bp) dan ubiquitin (493 bp) telah diperoleh. Sekuen 18S rRNA Pandanus sp memiliki kemiripan sebesar 99% dengan beberapa spesies Pandanus. Sekuen ubiquitin Pandanus sp memiliki kemiripan sebesar 87%-89% dengan sekuen ubiquitin dari beberapa tanaman dan alga hijau. Dendrogram yang diturunkan dari kedua sekuen juga mendukung hasil tersebut bahwa sekuen 18S rRNA dari Pandanus sp. membentuk satu kelompok dengan sesama sekuen 18S rRNA, begitu pula dengan sekuen ubiquitin Pandanus sp. membentuk satu kelompok dengan sesama sekuen ubiquitin. Kedua gen berpotensi dijadikan kontrol internal setelah dilakukan validasi.Kata kunci: RNA ribosom 18S, housekeeping gene, Pandanus sp., Riau, ubiquitin. Abstrak This research aimed to isolate genes encoding 18S rRNA and ubiquitin in Pandanus sp. from Riau. The research method included total DNA extraction, polymerase chain reaction, electrophoresis, gel purification, sequencing, and DNA sequence analysis using BioEdit version 7.0.0, BLASTn, and MEGA6 programs. Sequences encoding 18S rRNA (420 bp) and ubiquitin (493 bp) had been obtained. The BLASTn analysis showed that 18S rRNA of Pandanus sp. had 99% similarity to some species of Pandanus. Ubiquitin sequence in Pandanus sp. had 87%-89% similarity to ubiquitin sequences of some plants and green algae. Dendrograms generated from both sequences also supported the results that 18S rRNA sequence of Pandanus sp. was the same group as 18S rRNA on Pandanus genus. Similarly, ubiquitin sequence of Pandanus sp was the same cluster as other plants. Both genes were potentially used as internal control in gene expression studies after their validation.Keywords: 18S ribosomal RNA, housekeeping gene, Pandanus sp., Riau, ubiquitin.

The DNA Sequence Encoding Actin (ACT1) of Pandan (Benstonea sp.) Dewi Indriyani Roslim; Herman Herman
Journal of Tropical Life Science Vol. 9 No. 3 (2019)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.09.03.06

One of housekeeping genes is actin gene. This gene is frequently used in gene expression studies as an internal control. The DNA sequence encoding actin from Pandan (Benstonea sp.) clone Riau has not been reported, therefore, this study investigated the DNA sequence encoding actin isolated from Benstonea sp. clone Riau. Total DNA isolation was performed in fresh leaves, total RNA isolation from stem, total cDNA synthesis, polymerase chain reaction using degenerate actin primer, electrophoresis, cloning, transformation, blue white colony selection, colony PCR, sequencing, data analysis using BioEdit and MEGA6 softwares and BLASTn program. The partial DNA sequence encoding actin from Benstonea sp. clone Riau obtained was 1,403 bp. The sequence was grouped as part of actin1 (ACT1) and it was consisted of two exons and one intron. The predicted coding and peptide sequences were 616 bp and 205 amino acids, respectively.Â The predicted coding sequence had 90% similarity to some ACT1 mRNA from some plants species but none of which belongs to Benstonea genus or Pandanaceae family. The deduced peptide sequence had similarity to some ACT1 peptide from some plant species of up to 99% and also none of them belongs to Benstonea genus or Pandanaceae family. Thus, the partial ACT1 gene obtained in this study was the first sequence reported from Benstonea genus. Furthermore, this sequence can be used as a reference to isolate actin genes from other species within Benstonea genus for gene expression analysis purposes.

Analisis Empat Sekuen Barkode DNA Pada Pandan (Benstonea sp.) Asal Danau Kajuik, Riau Dewi Indriyani Roslim; Intan Sari Nuraini; Siti Nurhayati; Ciska Vivian Sianturi; At-Thahirah At-Thahirah; Herman Herman
Al-Kauniyah: Jurnal Biologi Vol 16, No 1 (2023): AL-KAUNIYAH JURNAL BIOLOGI
Publisher : Department of Biology, Faculty of Science and Technology, Syarif Hidayatullah State Islami

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/kauniyah.v16i1.21697

Barkode DNA merupakan sekuen DNA berukuran pendek yang digunakan untuk identifikasi organisme secara molekuler. Penelitian bertujuan menganalisis empat barkode DNA pada tumbuhan pandan (Benstonea sp.) asal Danau Kajuik, Riau. Metode meliputi isolasi DNA, PCR, elektroforesis, purifikasi, sekuesing, serta analisis bioinformatika. Pada penelitian ini telah diperoleh sekuen DNA untuk atpB-rbcL IGS, trnV-ndhC IGS, ndhF-rpl32 IGS, dan trnQ-5’rps16 IGS sepanjang 812 pb, 924 pb, 952 pb, dan 886 pb, secara berturut-turut. Aksesi yang muncul paling atas pada analisis BLASTn pada keempat sekuen tersebut tidak ada yang memiliki kemiripan 100% dengan Benstonea sp. asal Danau Kajuik, Riau. Walaupun nilai query cover tinggi (93–100%) dan E-value sebesar 0,00. Pada keempat barkode DNA yang diteliti, terdapat beberapa perbedaan nukleotida yang disebabkan oleh mutasi insersi-delesi (indel) (6,99%) maupun subtitusi (4,96%). Mutasi indel paling banyak dijumpai pada sekuen trnV-ndhC IGS dan mutasi subtitusi paling banyak terjadi pada sekuen ndhF-rpl32 IGS. Nukleotida kritis yang menjadi penciri bagi Benstonea sp. asal Danau Kajuik, Riau, dijumpai pada sekuen ndhF-rpl32 IGS dan trnQ-5’rps16 IGS. Simpulan, dua sekuen DNA yaitu ndhF-rpl32 IGS dan trnQ-5’rps16 IGS berpotensi menjadi barkode DNA untuk identifikasi tumbuhan ini secara molekuler. Ketersediaan barkode DNA pada database publik sangat diperlukan untuk menunjang identifikasi organisme secara molekuler.AbstractDNA barcode is a piece of short DNA that is developed for molecular identification of organisms. This study aims to analyze four DNA barcodes in pandan plant (Benstonea sp.) from Kajuik Lake, Riau. Methods included DNA extraction, PCR, electrophoresis, purification, sequencing, and bioinformatics analysis. The DNA sequences of atpB-rbcL IGS, trnV-ndhC IGS, ndhF-rpl32 IGS, and trnQ-5’rps16 IGS have been obtained with the length of 812 pb, 924 pb, 952 pb, and 886 pb, respectively. The top accession in BLASTn analysis results showed that there was no accession that had 100% similarity to Benstonea sp. from Kajuik Lake, Riau even though the query cover high (93–100%) and E-value of 0,00. There were some nucleotide variations caused by insertion-deletion (indel) mutation (6,99%) and subtitution (4,96%). Indel was most occur in trnV-ndhC IGS and subtitution in ndhF-rpl32 IGS. Critical nucleotides that were be a characteristic for Benstonea sp. from Kajuik Lake, Riau were seen in ndhF-rpl32 IGS and trnQ-5’rps16 IGS. Conclusion, both of ndhF-rpl32 IGS and trnQ-5’rps16 IGS are potentially as DNA barcodes for molecular identification of this plant. The avaibility of the DNA barcodes is very important to support of organisms molecular identifications.

The Effect of Colchicine Concentration and Immersion Time on Growth and Morphological Characters of Acacia crassicarpa A. Cunn. Ex Benth In-vitro Explants Frederika Sinuraya; Dewi Indriyani Roslim; Deviona Deviona; Suharyanto Suharyanto
Jurnal Biologi Tropis Vol. 23 No. 3 (2023): July - September
Publisher : Biology Education Study Program, Faculty of Teacher Training and Education, University of Mataram, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29303/jbt.v23i3.4955

The production of polyploidy with a chemical mutagen such as colchicine is one strategy that can be applied to improve the genetic traits and wood properties of acacia trees. The aim of this study was to determine the effects of colchicine at various concentrations and immersion times on the percentage of surviving explants, percentage of rooted explants, and morphological traits of shoot and root A. crassicarpa in-vitro. A completely randomized design (CRD) with two factors was used in this study. The first factor was the concentration of colchicine solution with five levels (0,00%, 0,02%, 0,04%, 0,06%, and 0,08%), and the second factor was the immersion time with three levels (24, 48, and 72 hours). There were fifteen treatment combinations with each treatment repeated three times. Data were analyzed by ANOVA and Duncan’s multiple range test at 5% significance level. The results showed that the treatment combination of colchicine concentration with immersion time showed a significant effect on the percentage of surviving explants, number of leaves, number of shoots and height of A. crassicarpa explants, but did not significantly affect on the number of roots, length of the root and percentage of rooted A. crassicarpa explants.

Analisis Empat Sekuen Barkode DNA Pada Pandan (Benstonea sp.) Asal Danau Kajuik, Riau Dewi Indriyani Roslim; Intan Sari Nuraini; Siti Nurhayati; Ciska Vivian Sianturi; At-Thahirah At-Thahirah; Herman Herman
Al-Kauniyah: Jurnal Biologi Vol 16, No 1 (2023): AL-KAUNIYAH JURNAL BIOLOGI
Publisher : Department of Biology, Faculty of Science and Technology, Syarif Hidayatullah State Islami

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/kauniyah.v16i1.21697

Barkode DNA merupakan sekuen DNA berukuran pendek yang digunakan untuk identifikasi organisme secara molekuler. Penelitian bertujuan menganalisis empat barkode DNA pada tumbuhan pandan (Benstonea sp.) asal Danau Kajuik, Riau. Metode meliputi isolasi DNA, PCR, elektroforesis, purifikasi, sekuesing, serta analisis bioinformatika. Pada penelitian ini telah diperoleh sekuen DNA untuk atpB-rbcL IGS, trnV-ndhC IGS, ndhF-rpl32 IGS, dan trnQ-5’rps16 IGS sepanjang 812 pb, 924 pb, 952 pb, dan 886 pb, secara berturut-turut. Aksesi yang muncul paling atas pada analisis BLASTn pada keempat sekuen tersebut tidak ada yang memiliki kemiripan 100% dengan Benstonea sp. asal Danau Kajuik, Riau. Walaupun nilai query cover tinggi (93–100%) dan E-value sebesar 0,00. Pada keempat barkode DNA yang diteliti, terdapat beberapa perbedaan nukleotida yang disebabkan oleh mutasi insersi-delesi (indel) (6,99%) maupun subtitusi (4,96%). Mutasi indel paling banyak dijumpai pada sekuen trnV-ndhC IGS dan mutasi subtitusi paling banyak terjadi pada sekuen ndhF-rpl32 IGS. Nukleotida kritis yang menjadi penciri bagi Benstonea sp. asal Danau Kajuik, Riau, dijumpai pada sekuen ndhF-rpl32 IGS dan trnQ-5’rps16 IGS. Simpulan, dua sekuen DNA yaitu ndhF-rpl32 IGS dan trnQ-5’rps16 IGS berpotensi menjadi barkode DNA untuk identifikasi tumbuhan ini secara molekuler. Ketersediaan barkode DNA pada database publik sangat diperlukan untuk menunjang identifikasi organisme secara molekuler.AbstractDNA barcode is a piece of short DNA that is developed for molecular identification of organisms. This study aims to analyze four DNA barcodes in pandan plant (Benstonea sp.) from Kajuik Lake, Riau. Methods included DNA extraction, PCR, electrophoresis, purification, sequencing, and bioinformatics analysis. The DNA sequences of atpB-rbcL IGS, trnV-ndhC IGS, ndhF-rpl32 IGS, and trnQ-5’rps16 IGS have been obtained with the length of 812 pb, 924 pb, 952 pb, and 886 pb, respectively. The top accession in BLASTn analysis results showed that there was no accession that had 100% similarity to Benstonea sp. from Kajuik Lake, Riau even though the query cover high (93–100%) and E-value of 0,00. There were some nucleotide variations caused by insertion-deletion (indel) mutation (6,99%) and subtitution (4,96%). Indel was most occur in trnV-ndhC IGS and subtitution in ndhF-rpl32 IGS. Critical nucleotides that were be a characteristic for Benstonea sp. from Kajuik Lake, Riau were seen in ndhF-rpl32 IGS and trnQ-5’rps16 IGS. Conclusion, both of ndhF-rpl32 IGS and trnQ-5’rps16 IGS are potentially as DNA barcodes for molecular identification of this plant. The avaibility of the DNA barcodes is very important to support of organisms molecular identifications.

Isolation of Partial Housekeeping Genes on Tuntun Angin (Elaeocarpus floribundu) Dewi Indriyani Roslim; Ashfira Ashfira; Dilla Mutiarawati; Tio Fanny Rosmeilinda; Nur Aisyah; Herman Herman; Wahyu Lestari
Biosaintifika: Journal of Biology & Biology Education Vol 11, No 2 (2019): August 2019
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v11i2.19052

Some genes like 18S rRNA, 26S rRNA, elongation factor 1-alpha (EF1a), and beta-tubulin (TUB) are members of housekeeping genes group that are commonly used as internal control in gene expression study. This study aimed to isolate those four housekeeping genes of tuntun angin (Elaeocarpus floribundus). The research material included fresh leaves of E. floribundus that were picked up from Kajuik Lake in Riau Province and four primer pairs. The procedures consisted of total DNA isolation using Genomic DNA Mini Kit Plant (Geneaid), polymerase chain reaction (PCR), electrophoresis on 1% agarose gel, sequencing, and bioinformatic analysis. This study has been isolated 18S rRNA, 26S rRNA, EF1a, and TUB genes with the size of 422 bp, 922 bp, 856 bp, and 877 bp, respectively. The EF1a and TUB genes has never been reported in Elaeocarpaceae family. Thus, those partial DNA sequences are the first sequences reported from this species and can be used as reference genes in this plant after validation.

Analisis Sebagian Sekuen Gen Ferritin2 pada Padi (Oryza sativa L.) Indragiri Hilir, Riau Fadel Nugraha; Dewi Indriyani Roslim; Yolla Putri Ardilla; Herman -
Biosaintifika: Journal of Biology & Biology Education Vol 6, No 2 (2014): September 2014
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v6i2.3102

Ion Fe bebas sangat beracun bagi tanaman, karena dapat membentuk radikal bebas di dalam sel. Walaupun demikian, tanaman memiliki mekanisme untuk mempertahankan homeostasis Fe di dalam sel yang melibatkan protein ferritin. Penelitian ini bertujuan untuk menganalisis dan membandingkan sekuen nukleotida gen ferritin2 dari dua genotipe padi lokal (Bakung dan Serei) dari Indragiri Hilir, Riau dengan varietas padi rawa unggul tahan cekaman kelebihan Fe (Siam Sintanur), padi unggul tidak tahan cekaman kelebihan Fe (IR64), dan data sekuen nukleotida kultivar Nipponbare. Metode penelitian meliputi isolasi DNA toal dari daun segar tanaman padi menggunakan metode CTAB dan amplifikasi DNA (PCR) menggunakan primer OsFer_F3 (forward) dan Gross_R (reverse). Produk PCR kemudian disekuensing dan disejajarkan. Pada penelitian ini telah diperoleh fragmen dari gen ferritin2 dari kelima genotype atau varietas padi yang diuji, yang berukuran sekitar 1200 pb. Analisis pensejajaran menunjukkan terdapat 56 SNP (single nucleotide polymorphism) pada sekuen nukleotida gen ferritin2 tersebut. Bakung menunjukkan kedekatan yang tinggi dengan Nipponbare, diikuti dengan IR64, Siam Sintanur, dan Serei. Kemungkinan Bakung merupakan genotipe padi lokal dari Indragiri Hilir, Riau yang tahan cekaman kelebihan Fe. Free Fe ions are highly toxic to plants, because it can form free radicals in the cells. However, plants have mechanisms to maintain Fe homeostasis in the cells involving ferritin proteins. This study was aimed to analyze and to compare the nucleotide sequence of ferritin2 gene in two local rice genotypes (namely Bakung and Serei) from Indragiri Hilir, Riau and in Fe overload-tolerant rice variety (Siam Sintanur), Fe overload-sensitive rice variety (IR64), as well as the nucleotide sequence of Nipponbare rice cultivar. The research methods consisted of DNA isolation from fresh leaves of rice plants using CTAB method and DNA amplification (PCR) using a couple of primers, OsFer_F3 (forward) and Gross_R (reverse). The PCR products were then sequenced and aligned. DNA fragments of ferritin2 gene with length of approx. 1200 bp were obtained from those four rice varieties or genotypes tested. Alignment revealed 56 SNPs (single nucleotide polymorphisms) in the ferritin2 gene sequences. Bakung showed close distance with Nipponbare, followed by IR64, Siam Sintanur, and Serei. It wa suggested that Bakung was Fe overload-tolerant local rice genotype from Indragiri Hilir, Riau.

Isolation of Housekeeping Genes on Durik-durik (Syzygium sp) Dewi Indriyani Roslim; Liza Aulia Yusfi; Desriani Ritawati Hutagalung; Niswah Faizah; Lestari Andriani; Azrial Azrial; Herman Herman; Wahyu Lestari
Biosaintifika: Journal of Biology & Biology Education Vol 10, No 2 (2018): August 2018
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v10i2.14234

Housekeeping gene is a gene expressed with a fixed level and in abundant amounts under various conditions. After validation, the housekeeping gene can be used as an internal control to normalize gene expression data. This study reports the isolation of several housekeeping genes in Durik-durik plant (Syzygium sp). This plant material in form of fresh leaves from Durik-durik plants are taken from Kajuik Lake, Riau Province. The next stage is total DNA isolation, polymerase chain reaction, electrophoresis, sequencing and data analysis using bioinformatic tools. The isolated housekeeping genes included 18S rRNA, actin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Beta-tubulin and Ubiquitin with sizes of 400 bp, 679 bp, 1134 bp, 836 bp, 1167 bp and 2155 bp, respectively. In addition to 18S rRNA, the five housekeeping genes are the first reported from the genus Syzygium and referable to isolate housekeeping genes in other species in this genus. The six housekeeping genes can be used as internal controls on Durik-durik plants after validation.

Relationship between Seed Properties and Outcome Components for Selection Criteria of Corn (Zea Mays L.) Products at Various Dosages of Popostium Fertilizer Vera Magdaleni Manullang; Aslim Rasyad; Dewi Indriyani Roslim
JURNAL AGRONOMI TANAMAN TROPIKA (JUATIKA) Vol 5 No 2 (2023): Jurnal Agronomi Tanaman Tropika (JUATIKA) Vol. 5 No. 2 Juli 2023
Publisher : LPPM UNIVERSITAS ISLAM KUANTAN SINGINGI

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.36378/juatika.v5i2.3095

This research was conducted to determine the relationship between seed developmental characteristics and yield components in a population of maize (Zea mays L.) grown at different potassium fertilizer rates. The information could be utilized as alternative selection criteria for maize genotypes with high-yielding potential. This research was conducted at the Experimental field of the Horticulture Seed Agency, Pekanbaru. Seven maize genotypes with four potassium fertilizer rates were grown in a 350 cm x 200 cm experimental plot with three replications. The genotypes used were Bisi 228. Pertiwi 3. Bisi 2. Decoral, Bisi 18. Betras 4. and Srikandi. Potassium fertilizer rates included 30 kg, 50 kg, 70 kg, and 90 kg per ha, respectively. Traits observed were plant height, tesseling flowering date, silking date, seed dry accumulation rate, effective seed filling period, cob length, cob weight, number of seed rows, number of seeds per cob, seed weight per cob, the weight of 100 seeds and seed yield per m2. Analysis of variance was performed to the data using SAS and further tested by honesty significant difference at 5% level. Variance component, heritability, genetic correlation coefficient, and selection response were calculated for all characters and effective seed filling duration. The results indicated that the genetic variance component was significant for all characters except for the dry matter accumulation rate. All characters' heritability values were quite high except for effective seed-filling duration and the number of seeds per cob. Phenotypic correlation coefficients were positively significant between seed yield per m2 and plant height, seed development rate, cob length, ear weight, number of seeds per ear, seed weight per ear, and weight of 100 seeds. The genetic correlations was significant between seed yield per m2 and plant height, seed development rate, number of seeds per ear, and seed weight per ear. All characters' direct selection response value is higher than the indirect selection response value.

Molecular Characterization of Danau Selais Fish (Ompok hypophthalmus) and Kaporeh Selais Fish (Ompok eugeneiatus) from Riau Province of Indonesia using Mitochondrial 12S rRNA Roza Elvyra; Rio Riduan; Dewi Indriyani Roslim
Jurnal Biologi Tropis Vol. 23 No. 1 (2023): Special Issue
Publisher : Biology Education Study Program, Faculty of Teacher Training and Education, University of Mataram, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29303/jbt.v23i1.5709

The floodplain river in Riau is inhabited by various types of vertebrate animals including fish from the genus Ompok. The rapid development of species in the Ompok genus can cause ambiguity in species identity due to inaccurate identification processes. This research aims to analyze the molecular characteristics of two types of selais fish, namely danau selais fish (O. hypophthalmus) and kaporeh selais fish (O. eugeneiatus) from Riau based on 12S rRNA sequences. Methods included sampling of fishes from the Kampar, Tapung and Indragiri Rivers, the total DNA isolation, PCR, electrophoresis, sequencing and data analysis. In this study, the 12S rRNA DNA sequence of the selais fish studied was 939 bp in size. The sequences consisted of 803 bp of conserved sites (86.15%), 127 bp of variable sites (13.52%), 53 bp of parsimony sites (5.64%) and 73 bp of singleton sites (18.57%), with the composition of Adenine 31.7 %, Cytosine 26.9%, Thymine 20.9% and Guanine 20.4%. The average genetic distance between the two species was ±0.034, with the lowest genetic distance identified in the species O. hypophthalmus and O. eugeneiatus from the Indragiri River with a value of ±0.032, while the farthest genetic distance was identified in the species O. eugeneiatus from the Kampar River and the species C. gariepinus (Out group) with a value of ±0.092. Transition substitution (19.50%) occurs more frequently than transversion (10.94%). Phylogenetic reconstruction showed that the two species can be separated into distinct groups based on 12S rRNA sequences.

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