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All Journal Bioscience AL KAUNIYAH Jurnal Penelitian Pendidikan IPA (JPPIPA) Jurnal Biologi Tropis EKSAKTA : Jurnal Penelitian dan Pembelajaran MIPA Indonesian Food Science and TechnologyJournal Martabe : Jurnal Pengabdian Kepada Masyarakat JURNAL PENDIDIKAN TAMBUSAI Pelita Eksakta Jurnal Biogenerasi Journal of halal product and research (JHPR) 3BIO: Journal of Biological Science, Technology and Management Jurnal Jeumpa Halal Research Journal TROPICAL GENETICS MASALIQ: Jurnal Pendidikan dan Sains Promotor: Jurnal Mahasiswa Kesehatan Masyarakat Tropical Genetics Symbiotic: Journal of Biological Education and Science Jurnal Serambi Biologi
Achyar, Afifatul
Departemen Biologi, Fakultas Matematika Dan Ilmu Pengetahuan Alam, Universitas Negeri Padang, Padang Indonesia
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Journal : Bioscience

 1 
Primer Construction to detect SNP rs11196205 Transcription Factor 7 Like 2 (TCF7L2) Using Amplification Refractory Mutation System (ARMS) PCR to detect Type-2 Diabetes Mellitus Elsa Badriyya; Afifatul Achyar
Bioscience Vol 4, No 2 (2020): Biology
Publisher : UNIVERSITAS NEGERI PADANG

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/0202042108497-0-00

Abstract

Type-2 Diabetes Mellitus (T2DM) is a metabolic disease characterized by an increase in blood glucose levels. The macrovascular and microvascular complications of T2DM can increase the risk of death in patient. SNP rs11196205 Transcription Factor 7 Like 2 (TCF7L2) gene has been associated with T2DM in several regions like Iceland, Denmark, the United State, and Thailand. SNP rs11196205 is characterized by polymorphism at position 113.047.288 from nucleotide Guanine to Cytosine. Amplification Refractory Mutation System Polymerase Chain Reaction (ARMS PCR) is a method that can be used to detect mutation or polymorphism in a DNA. The aim of this research was to design a specific primer to detect SNP rs11196205 TCF7L2 gene using ARMS PCR. The design of study was a descriptive study to determine the specific primer. The method of the research includes DNA isolation, primer design using Geneious software, amplification of targeted area using ARMS PCR, and DNA sequencing method for bioinformatics study. Based on the research, four primers to detect SNP rs11196205 TCF7L2 gene have been successfully constructed. The primers were rs11196205-F, rs11196205-R, rs11196205-F(C) as a specific primer for C allele, and rs11196205- R(G) to detect G allele, the reaction produced 3 fragments of 856bp, 559bp, and 339bp.  
Analysis of Genetic Variations in Poly Gene Sequences in Dengue Virus 2 Using In-Silico RFLP Afifatul Achyar; Alvenaya Hindayageni; Fadhila Humaira; Nurfadillatun Nisa Wijaya; Nur Aqsha; Zultsatunni’mah Zultsatunni’mah
Bioscience Vol 5, No 1 (2021): Biology
Publisher : UNIVERSITAS NEGERI PADANG

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/0202151111916-0-00

Abstract

Dengue hemorrhagic fever (DHF) is a disease caused by Dengue virus  transmitted to humans through infected Aedes aegypti and Ae. Albopictus. Dengue virus classified into 4 serotypes, including DEN-1, DEN-2, DEN-3, and DEN-4. The genomes of the four dengue viruses share about 65% similarities, the rest is a genetic variation that differentiates between serotypes. Genetic variations also occur even within one serotype. This study aimed to analyse genetic variation in envelope protein E (POLY) gene sequences in Dengue Virus 2 NCBI PopSet 1760494694 using in-silico RFLP by free bioinformatic tools on internet. The restriction enzymes used were AfeI and ApaLI. The results of the in-silico RFLP in this study showed that there were genetic variations in the recognition site of the AfeI enzymes (A1 allele and A2 allele) and ApaLI (B1 allele and B2 allele) in 18 DNA sequences of the POLY gene for Dengue 2 virus NCBI PopSet 1760494694.
Polymerase chain reaction (PCR) primer design to identify SNP rs7901695 transcription factor 7 like 2 (TCF7L2) Elsa Badriyya; Afifatul Achyar
Bioscience Vol 7, No 1 (2023): Biology
Publisher : UNIVERSITAS NEGERI PADANG

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/0202371122575-0-00

Abstract

ABSTRACT. Transcription Factor 7 Like 2 (TCF7L2) is a gene that produces a protein that controls the expression and function of several incretin hormones. One of the primary activities of incretin hormones is to increase insulin production, which is important in glucose and energy homeostasis. Single Nucleotide Polymorphism (SNP) in the TCF7L2 gene is reported to be association with Type II Diabetes Mellitus (T2DM). T2DM is featured by persistent hyperglycemia because of the decrease in insulin production, insulin resistance, or both. In patients with diabetes mellitus, chronic hyperglycemia can damage organ systems and cause metabolic abnormalities. SNP rs7901695 TCF7L2 gene has been linked to T2DM in a number of places, including South Asia, Iceland, and the United States. The polymorphism at location 112.994.329 from nucleotide Timine (T) to Cytosine (C) enables the recognition of SNP rs7901695. Polymerase Chain Reaction (PCR) was used to identify the polymorphism. The objective of this research was to generate a precise primer for the PCR recognition of the SNP rs7901695 in the TCF7L2 gene. The research's methodology comprises DNA isolation, primer designing with Geneious, target amplification with PCR, and DNA sequencing for bioinformatic analysis. As a result of the study, four primers for the SNP rs7901695 TCF7L2 gene have been developed. The reaction obtained two fragments, sized 177 and 367 bp. The primers used were rs7901695-F, rs7901695-R, rs7901695-F(C), and rs7901695-R(T), which were used to detect the T allele.  ABSTRAK. Transcription Factor 7 Like 2 (TCF7L2) adalah gen yang menghasilkan protein yang mengontrol ekspresi dan fungsi beberapa hormon inkretin. Salah satu aktivitas utama hormon inkretin adalah meningkatkan produksi insulin, yang penting dalam homeostasis glukosa dan energi. Single Nucleotide Polymorphism (SNP) pada TCF7L2 gene dilaporkan adanya hubungan dengan Diabetes Mellitus Tipe II (DMT2). DMT2 ditandai dengan hiperglikemia persisten karena penurunan produksi insulin, resistensi insulin, atau keduanya. Pada penderita diabetes melitus, hiperglikemia kronis dapat merusak sistem organ dan kelainan metabolisme. Gen SNP rs7901695 TCF7L2 dilaporkan memiliki asosiasi dengan DMT2 di sejumlah daerah, termasuk Asia Selatan, Islandia, dan Amerika Serikat. SNP rs7901695 ditandai dengan polimorfisme pada lokasi 112.994.329 dari nukleotida Timin (T) menjadi Sitosin (C). Metode yang digunakan untuk mengidentifikasi polimorfisme adalah Polymerase Chain Reaction (PCR). Penelitian ini bertujuan untuk menghasilkan primer yang tepat untuk pengenalan PCR terhadap SNP rs7901695 pada gen TCF7L2. Metodologi penelitian meliputi isolasi DNA, perancangan primer dengan aplikasi Geneious, amplifikasi target dengan PCR, dan sekuensing DNA untuk analisis bioinformatik. Sebagai hasil penelitian, empat primer untuk deteksi gen SNP rs7901695 TCF7L2 telah dikembangkan. Dua fragmen, berukuran 177 dan 367 bp, diperoleh dari reaksi tersebut. Primer yang digunakan adalah rs7901695-F, rs7901695-R, rs7901695-F(C), dan rs7901695-R(T), yang digunakan untuk mendeteksi alel T.
Specific primer design and optimization of annealing temperature for amplification gene peroxidase (POD) in Oryza sativa L. Nella Fauziah; Afifatul Achyar; Zulyusri Zulyusri; Yusni Atifah; Linda Advinda; Violita Violita
Bioscience Vol 7, No 2 (2023): Biology
Publisher : UNIVERSITAS NEGERI PADANG

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/bsc.v7i2.122972

Abstract

Peroksidase (POD) merupakan enzim antioksidan yang memiliki beragam fungsi dalam siklus hidup tanaman, salah satunya adalah sebagai pertahanan dalam melawan ROS dengan mengkatalisis konversi H2O2 menjadi udara dan O2 . Kemampuan aktifitas enzim POD dalam mengatur kandungan H2O2 memungkinkan enzim tersebut dapat mempertahankan tanaman dari cekaman. Metode yang dapat digunakan untuk amplifikasi gen POD salah satunya yaitu kuantitatif reverse transcription- PCR (qRT-PCR). Metode ini memerlukan beberapa komponen penting salah satunya yaitu primer ( forward dan reverse ). Primer yang digunakan dalam amplifikasi gen harus spesifik terhadap gen target sehingga dapat mengenali dan menempel pada gen target yang diinginkan. Penelitian ini bertujuan untuk mendesain primer yang sesuai untuk amplifikasi gen POD menggunakan teknik qRT-PCR. Primer dirancang menggunakan perangkat PrimerQuest. Primer yang telah dirancang kemudian dianalisis untuk spesifikasinya dengan geneious prime . Kemudian spesifikasi primer di cek menggugakan primer BLAST. Hasil desain primer dengan kriteria terbaik untuk amplifikasi gen POD yaitu Forward POD 5'-AAATGCGTCGATCTACTGTACCT-3' dan Reverse POD 5'-GTGTTGAAAATGGCAATAAACCGG-3'
Rice Growth Response to Drought Simulation Treatment Using PEG Annisa Khaira; Zulyusri Zulyusri; Afifatul Achyar; Dwi Hilda Putri; Yusni Atifah; Violita Violita
Bioscience Vol 7, No 2 (2023): Biology
Publisher : UNIVERSITAS NEGERI PADANG

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/bsc.v7i2.122674

Abstract

Rice is the main food source for Indonesians. The demand for rice to meet people's needs increases every year due to population growth and efforts to improve nutrition by the community. One of the problems that can affect rice production is drought. Drought is an environmental condition when plants do not get enough water to grow and develop optimally, which can cause a decrease in rice production. To find out how rice growth responds to drought, a study was carried out by giving drought simulation treatments using polyethylene glycol (PEG) on several rice varieties. This study used a completely randomized design that was arranged in a factorial manner with two factors. The first factor was the rice varieties (Harum, Situbagendit, Rosna) the second factor was 0% and 20% PEG concentration. The data obtained were then analyzed statistically using a two-way ANOVA test, and if the results were significantly different, then proceed with Duncan's test at the 5% level.The results showed that the drought simulation treatment had a negative effect on rice growth. Drought simulation treatment using 20% PEG resulted in a decrease in Kadar air relatif (KAR), root length, plant height, and root dry weight of rice. The highest decrease in KAR was found in the sensitive rice variety (Rosna), which was 43.42%. The highest average root length (7.99 cm) was on the sitabaendit variety, and the lowest (5.61) was on the rosna variety. The highest average crown height (17.32 cm) and the lowest (6.61) were on the rosna variety.
Multiple Alignment and Primer Design for Groups of Barnacle Organisms and Amphibalanus amphitrite as Biofouling Markers Muhammad Farikh; Rahmad Wanizal Pastha; Rezeki Rival Alridho; Aura Zahra Nafisah; Bintang Fadhil Ramadhan; Afifatul Achyar
Bioscience Vol 7, No 2 (2023): Biology
Publisher : UNIVERSITAS NEGERI PADANG

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/bsc.v7i2.125392

Abstract

Biota pengotor atau biofouling adalah organisme hidup yang menempel pada suatu substrat. Dampak yang ditimbulkan oleh aktivitas biofouling biota adalah oleh karena sifatnya yang korosif sehingga dapat menyebabkan kelumpuhan pada bangunan instalasi. Untuk memfasilitasi instalasi dan kestabilan biodiversitas, peneliti mencoba menghadirkan environmental DNA (e-DNA) sebagai sampel lingkungan tanpa membunuh dan mengisolasi suatu organisme tersebut dengan memanfaatkan sampel lingkungan. Penelitian ini bertujuan untuk memperoleh primer universal dan spesifik dari COX1 yang dapat digunakan untuk mengidentifikasi biofouling kelompok Barnacle yang dirancang secara in silico. Sekuen organisme target yang digunakan dalam penelitian ini adalah DNA mitokondria dari Amphibalanus amphitrite, Amphibalanus reticulatus dan Semibalanus balanoides dengan nomor aksesi NC_024525, NC_071896 dan NC_039849.. Sekuen gen COX1 yang diperoleh disimpan dalam format FASTA untuk digunakan lebih lanjut di dalam proses desain primer menggunakan Geneious Prime. Penentuan daerah lestari ditentukan dengan Geneious Prime dalam tahapan multiple alignment. Sekuen dengan kriteria primer spesifik terbaik untuk COX1 A.amphitrite didapatkan dengan panjang 20-22 basa dan ukuran amplikon 910 bp. Urutan basa primer foward dan reverse adalah 5'-GAGCTGAACTTGGTCAACCG-3' dan 5'-GCTCAAAGAAGAGGAGGGCTAT-3'. Sekuen dengan kriteria primer universal kelompok barnacle terbaik untuk COX1 didapatkan dengan panjang masing-masing 24 basa dan ukuran amplikon 1.270 bp. Urutan basa primer foward dan reverse adalah 5'-GACTTCTACCGTTAATGTTAGGAG-3''dan 5'-CTATGGTAATGAGGAGGAGTAGTG-3'. Hasil desain memenuhi syarat kriteria primer yang baik sehingga kandidat primer hasil desain dapat digunakan untuk proses PCR.
Morphological Response of Several Rice Varieties to Drought Stress Simulation using PEG Rezi Nabilah; Afifatul Achyar; Zulyusri Zulyusri; Yusni Atifah; Dwi Hilda Putri; Violita Violita
Bioscience Vol 8, No 1 (2024): Biology
Publisher : UNIVERSITAS NEGERI PADANG

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/bsc.v8i1.122676

Abstract

Rice has become food for most of the world's population. Indonesia is the third largest producer in the world. However, in fact rice production in Indonesia has decreased by 0.43% compared to 2020. One of the factors that can cause this decline is drought. Because rice is a semi-aquatic plant that grows normally in flooded conditions, it makes drought stress very threatening. Drought stress that occurs in plants causes plants to experience oxidative stress due to excessive accumulation of ROS. PEG is a compound that is widely used to provide drought conditions in plants. Previous research has classified several varieties of rice plants based on their level of resistance to drought. However, it is not yet known how the morphological response will be in different periods of drought stress and rewatering treatment. This research was conducted by giving treatment in the form of control (Yoshida nutrient culture solution) and drought stress (Yoshida + PEG-6000 20% solution) repeated 3 times. The observed parameters were RWC which were analyzed using standard errors and morphological images of roots and leaves. The results showed that the RWC obtained during the stress period from the third to the fifth day, Harum had the highest value according to its class as tolerant rice. After rewatering Rosna has a better recovery ability. In addition, root morphology shows differences in the form of root length, small root diameter, inhibition of adventive root growth. On the leaves include a decrease in leaf area, leaf curl up, and leaf yellowing.
New Records of Proceratium deelemani Perrault, 1981 (Hymenoptera : Formicidae : Proceratiinae) in Sumatra Rini Wulandari; Dwi Hilda Putri; Dezi Handayani; Afifatul Achyar; Rijal Satria
Bioscience Vol 8, No 1 (2024): Biology
Publisher : UNIVERSITAS NEGERI PADANG

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/bsc.v8i1.126193

Abstract

Proceratium Roger, 1863 is a genus of ants that has widely distributed throughout the world, Proceratium species rarely collected, their cryptobiotic lifestyle. This condition also occurs on the Sumatra Island, Indonesia. So far, only single species was recorded in this island, namely Proceratium papuanum Emery, 1897. We conducted a survey of leaf-litter ants in June 2021 by using Winkler’s extraction method in lowland disturbed forest near Tiga Tingkat Water fall Lubuk Hitam, Teluk Kabung Utara, Bungus Teluk Kabung, Padang, West Sumatra, Indonesia. The discovery of Proceratium deelemani Perrault, 1981 for the first time in Sumatera Island, Indonesia was increased the total ant fauna in this island. In the present study, we reports new distribution record of Proceratium deelemani Perrault, 1981 in Sumatra. Total two species of this genus was recorded in Sumatra: Proceratium deelemani Perrault, 1981 and Proceratium papuanum Emery, 1897.
Co-Authors Afionita, Santi Ahmad Hambali, Ahmad Ahmad Wibisana, Ahmad Alvenaya Hindayageni Ananda Putri, Ananda Annisa Irna Putri Annisa Khaira Annisa Khaira Annisa, Silvy Aprilia, Amanda Ara, Farrah Azzahra Ardi Ardi Atifah, Yusni Aura Zahra Nafisah Azizah, Jalilah Bintang Fadhil Ramadhan Cici Mustika cynthia perdana putri Dara Suci Amini, Dara Suci Des M Dezi Handayani Dezi Handayani Dina Sukma Dwi Hilda Putri Dwi Hilda Putri Dwi Hilda Putri Edwin Edwin Elsa Badriyya Elsa Yuniarti Elviana, Alifah Hazelia Fadhila Humaira Fardilla, Midratul Fatiha, Fathma Dwi Fevria, Resti Fitri, Afifah Ismu Fronica, Imelda Gilang Amanda Hafizah Fadhilah Hafizh Alza Afra Helsa Rahmatika Herisanti, Dini Irma Leilani Eka Putri Iyan Robiansyah Iyan Robiansyah Jalilah Azizah Jumatul Hafsah Kardiman, Reki Khairani, Fidia Aura Linda Advinda Marten, Threo Wanda Monica , Indiastri P Moralita Chatri Muhammad Farikh Muharani, Silvia Mukhlis Mukhlis Mutia Andini, Tri Nabilah, Rezi Nadira Nafisa Arini Nella Fauziah Novita, Yeni Nur Aqsha Nurfadillatun Nisa Wijaya Nurul Hasanah NURUL HIDAYAH Oliv Nurul Kanaya Nurul Kanaya Palupi, Indria Pinta, Sari Rahma Pradila, Andini Novalia Pramila, Cindy Pratama, Chelsylia Dara Pratama, Sandi Fransisco Pryatna, Muhamad Zacky Putri, Aulia Devani Putri, Irma Leilani Putri, Isna Aryunita Putri Putri, Santi Diana Putrizalda, Hafizhah Rahmad Wanizal Pastha Rahmawati, Atika Ayu Rahmi Holinesti Rezeki Rival Alridho Rezi Nabilah Ria Fernanda, Irma Rijal Satria Rijal Satria Rini Wulandari Rinti Mutiara Sari Riza Umami Roza, Sri Yenica Ruri Fitriyani Ruri Fitriyani S. Syamsurizal safitri, fira Salsabil, Velina Salsabilla, Vishtari Sari Rahma Pinta Sari, Rinti Mutiara Satria, Rijal Sefina, Nadia Selaras, Ganda Hijrah Sisca Alicia Farma Suryani, Elisa Vauzia Vauzia Vauzia, Vauzia Velina Salsabil Violita Violita Violita Violita Violita Violita Violita Yulita, Nelfi Yuni Ahda Yuni Ahda Zultsatunni’mah Zultsatunni’mah Zulyusri Zulyusri Zulyusri Zulyusri Zulyusri, Zulyusri Zulzusri, Zulzusri