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All Journal Bioscience Jurnal Penelitian Pendidikan IPA (JPPIPA) Jurnal Biologi Tropis EKSAKTA : Jurnal Penelitian dan Pembelajaran MIPA Indonesian Food Science and TechnologyJournal Martabe : Jurnal Pengabdian Kepada Masyarakat 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
Religion Agriculture, Biological Sciences & Forestry Arts Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Computer Science & IT Decision Sciences, Operations Research & Management Dentistry Economics, Econometrics & Finance Education Engineering Environmental Science Immunology & microbiology Languange, Linguistic, Communication & Media Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Neuroscience Nursing Physics Public Health Social Sciences Veterinary Other

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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.
Training Simple Analysis For Lake Water Pollution For The Nagari Community Of Kampung Batu Dalam Solok District, West Sumatra Yusni Atifah; Violita Violita; Afifatul Achyar; Irma Leilani Eka Putri
Pelita Eksakta Vol 4 No 2 (2021): Pelita Eksakta Vol. 4 No. 2
Publisher : Fakultas MIPA Universitas Negeri Padang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/pelitaeksakta/vol4-iss2/158

Abstract

The Nagari community of Kampung Batu Dalam as a community that lives around Lake Talang is a community that will get a direct impact from the existence of Lake Talang as a tourist destination in Solok City. In order to prepare for the Tourism Village, Nagari Kampung Batu Dalam needs to be equipped with knowledge and skills that will be useful for the Nagari Kampung community. Therefore, it is necessary to provide assistance to the people of Nagari Kampung Batu Dalam to increase public knowledge regarding pollution of lake waters, the impact of pollution and how to simply detect the presence of pollution in the lake. This activity was carried out in September 2021, and was attended by 15 participants from 10 youths representing the Batu Dalam community and 5 students from SMAN Batu Dalam. The results of the activity evaluation showed an increase in the knowledge of the Batu community regarding the conservation of Talang Lake and an increase in community skills in detecting simply the presence of pollution in Talang Lake water. In conclusion, this activity has been effectively carried out and can help the Batu Dalam community as an initial preparation towards Batu Dalam village as a tourist village
Design of primer Ipomoea batatas chloroplast gene matK S. Syamsurizal; Ardi Ardi; Des M; Resti Fevria; Yusni Atifah; Elsa Badriyya; Afifatul Achyar
Tropical Genetics Vol. 1 No. 1 (2021)
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (911.191 KB)

Abstract

Sweet potato varieties (Ipomoea batatas) Pucuk Hitam Panyalaian and Madu Pucuk Hitam Panyalaian have the potential to be a superior commodity in West Sumatra, but the information of genetic diversity is very limited. Data on the diversity of sweet potato germplasm is beneficial in the selection of plants to obtain superior cultivars in plant breeding. Aim: The aim of the study was to find specific primers for the study of sweet potato genetic markers using Ipomoea batatas chloroplast genes matK. Methods: DNA extraction from sweet potato young leaves; designing forward and reverse primers Ipomoea batatas chloroplast genes matK; PCR; sequencing; bioinformatics analysis and species identification by comparing the NCBI database. Results: Plant DNA barcoding PCR using designed primers matK were successfully resulting single DNA band in different amplicon size in some samples. This indicating that the designed primers used were able to distinguish variation in one species.
Primer design, in silico PCR and optimum annealing temperature for Escherichia coli detection in refillable drinking water samples Afifatul Achyar; Annisa Irna Putri; Dwi Hilda Putri; Yuni Ahda
Tropical Genetics Vol. 1 No. 2 (2021)
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1092.036 KB)

Abstract

Refill Drinking Water Depots (DAMIU) in the community are easy to find at affordable prices, which is a concern in the feasibility of refill drinking water quality. E.coli is one of the pathogenic bacteria present in drinking water that has poor quality. When it enters the body it can cause symptoms of diarrhea, fever, vomiting and others. The purpose of this study was to create a specific primer for E.coli that can be used to detect E.coli and determine the optimum temperature of primer annealing. Researchers do a new primer design because the existing design does not necessarily produce the same results due to various factors of different experimental conditions. The primer design was carried out on an in silico-based and had to meet the criteria for a good primer because it would be used in vitro. E.coli gene sequences was aligned with Shigella sp. using Pairwise Alignment. Primer candidates were analyzed using NCBI's Primer3 and Geneious Prime tools. The result is that the first primer pair is forward 5'–ATGCAGTGGTTCCTTATCTCACA-3' reverse 5'- ATCCTTAATGGCACTGCGCT-3', amplifying the amplicons along 417 bp in the yraJ gene. The second primer pair, forward 5'-CAGAACGTTTTTCATTCAGCAGG-3' reverse 5'-GCCACTACCAGATCGAGTCA-3' amplifies the 573 bp amplicon in the rne gene. The optimum annealing temperature for both pairs of primers was 59.5oC.
Snack Safety Identification through Information on Snack Packaging to Elementary Students Yusni Atifah; Afifatul Achyar
Pelita Eksakta Vol 5 No 2 (2022): Pelita Eksakta Vol. 5 No. 2
Publisher : Fakultas MIPA Universitas Negeri Padang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/pelitaeksakta/vol5-iss2/187

Abstract

Snack types of chips, biscuits are sold using packaging. The snack packaging contains important information related to the nutritional component of the snack, expiration date, product halalness and other important information that is important for buyers to know. Elementary school students have insufficient attention and knowledge related to the information on snack packaging so that it can result in adverse conditions for elementary school students if they consume snacks that are not good for health. As a preventive step, it is necessary to educate elementary school children, one of which is knowledge of how to identify the meaning of symbols and information found on snack packages. The methods used in this activity are lectures and discussions by conveying information to elementary school students about the information found on snack packages and demonstrating several pictures and ways to identify symbols found on snack packages. The results of the evaluation showed that the students enthusiastically participated in this activity. In addition, there is also an increase in students' knowledge and ability to explain the symbols and information found on snack packaging.
Optimization of DNA Isolation Dried Leaf Samples of Endangered Plants Dipterocarpus cinereus Ruri Fitriyani; Iyan Robiansyah; Afifatul Achyar
Tropical Genetics Vol. 2 No. 1 (2022):
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v2i1.19

Abstract

Dipterocarpus cinereus (Lagan bras) is an endemic tree of Mursala, a small island in Central Tapanuli, North Sumatra. Lagan bras is a tree that has good quality for shipbuilding or construction materials. This plant has a critical status by the IUCN Red List 2020 so that conservation efforts need to be carried out. Conservation efforts are still limited to the status of conservation, ecology and distribution as well as vegetative propagation while molecular studies have never been carried out. Therefore, it is necessary to know the optimum DNA isolation method because DNA quality is very important as a determinant of the success of molecular analyzes such as PCR. Various techniques can be used to isolate DNA, depending on the type of plant used. Each type of plant contains different secondary metabolite compounds that require an optimum isolation method. This study aims to obtain the optimum DNA isolation method and produce good quality genomic DNA from the dried plant Dipterocarpus cinereus from the LIPI Plant Conservation Research Center and Botanical Gardens collection. This research was conducted at the Genetics and Biotechnology Laboratory, State University of Padang in October 2021. The DNA isolation method used was the modified CTAB method with variations in leaf size, the use of PVP, and grinding with and without liquid nitrogen as well as the Promega and Qiagen isolation kit methods. The results showed that a large quantity of DNA and high quality DNA could be produced in plant samples by modifying DNA isolation using the Cetyl Trimethyl Ammonium Bromide (CTAB) method as well as the addition of polyvinylpolypyrrolidone (PVP) antioxidants and the use of liquid nitrogen with a leaf size of 2x2 cm.
Optimization of Specific PCR Conditions for Cows (Bos taurus) in Rendang Samples for Molecular-Based Halal Tests Nurfadillatun Nisa Wijaya; Sisca Alicia Farma; Dwi Hilda Putri; Afifatul Achyar
Tropical Genetics Vol. 2 No. 1 (2022):
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Rendang is one of the popular foods in Indonesia made from beef as the main ingredient, which has great potential in tourism development. As a country that has a Muslim majority population, this is very influential for the halal tourism industry. Halal tourism is the parent of tourism in accordance with Islamic principles. The issue of halal food is a sensitive issue for the community. The rise of mixing of non-halal ingredients such as pork in processed food products has worried the public, especially for adherents of the Islamic religion. However, this can be detected molecularly using the Polymerase Chain Reaction (PCR) technique which will amplify the DNA of the target gene of the species to be identified. Each gene has a primer with a different concentration and annealing temperature, so that prior to PCR with research samples, it is necessary to optimize the primer concentration and annealing temperature in order to obtain the appropriate PCR composition and conditions so as to obtain optimal PCR results. In this study, optimization of bovine-specific BOS primers that amplify the ND5 gene in mitochondrial DNA was carried out, namely ND5 (NADH dehydrogenase subunit 5). The results showed that the optimum annealing temperature was 48.2ºC, the optimum primary concentration was 0.5 μM.
Genotyping Of Sumatera Local Variety Of Citrus Using Random Amplified Polymorphism DNA (RAPD) Technique Rinti Mutiara Sari; Afifatul A Achyar; Yuni Ahda; Dwi Hilda Putri
Tropical Genetics Vol. 2 No. 2 (2022):
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v2i2.29

Abstract

Indonesia memiliki varietas jeruk lokal yang tidak kalah dengan jeruk impor, terutama dalam hal kesegaran buah. Namun, masyarakat lebih tertarik dengan warna kulit jeruk sehingga masyarakat lebih memilih jeruk impor ketimbang jeruk lokal, khususnya di Sumatera. Oleh karena itu, perlu dilakukan upaya pelestarian dan peningkatan karakteristik jeruk ini untuk meningkatkan kualitasnya melalui pemuliaan tanaman. Penelitian ini bertujuan untuk mengoptimalkan metode isolasi DNA sampel buah jeruk dengan Chelex-TE dan untuk mengetahui profil genetik jeruk lokal Sumatera dan jeruk impor menggunakan genotipe RAPD. Sampel yang digunakan adalah beberapa jeruk lokal di Sumatera (Citrus Siam Gunung Omeh, Citrus Madu, Citrus Keprok Maga, Citrus Keprok Brastepu dan Citrus Pasaman) dan Citrus impor (Citrus Sunkist, Citrus Clemengold, Citrus Murkot dan Citrus Wokam). DNA diisolasi menggunakan metode Chelex-TE 10% yang dioptimalkan untuk beberapa parameter seperti ukuran butir, kulit buah dan daun. RAPD dilakukan dengan menggunakan 10 primer RAPD. Hasil penelitian menunjukkan bahwa metode isolasi Chelex Chelex-TE 10% yang optimal adalah ukuran sampel 1 butir. Amplifikasi jeruk lokal Sumatera dan jeruk impor menggunakan 10 primer tunggal menghasilkan pita polimorfik. Nilai kesamaan jaccard menunjukkan bahwa kelima sampel jeruk tersebut merupakan varietas lokal Sumatera yang diamati memiliki variasi genetik yang tinggi dibandingkan dengan keempat jeruk impor tersebut. Indonesia memiliki varietas jeruk lokal yang tidak kalah dengan jeruk impor, terutama dalam hal kesegaran buah. Namun, masyarakat lebih tertarik dengan warna kulit jeruk sehingga masyarakat lebih memilih jeruk impor ketimbang jeruk lokal, khususnya di Sumatera. Oleh karena itu, perlu dilakukan upaya pelestarian dan peningkatan karakteristik jeruk ini untuk meningkatkan kualitasnya melalui pemuliaan tanaman. Penelitian ini bertujuan untuk mengoptimalkan metode isolasi DNA sampel buah jeruk dengan Chelex-TE dan untuk mengetahui profil genetik jeruk lokal Sumatera dan jeruk impor menggunakan genotipe RAPD. Sampel yang digunakan adalah beberapa jeruk lokal di Sumatera (Citrus Siam Gunung Omeh, Citrus Madu, Citrus Keprok Maga, Citrus Keprok Brastepu dan Citrus Pasaman) dan Citrus impor (Citrus Sunkist, Citrus Clemengold, Citrus Murkot dan Citrus Wokam). DNA diisolasi menggunakan metode Chelex-TE 10% yang dioptimalkan untuk beberapa parameter seperti ukuran butir, kulit buah dan daun. RAPD dilakukan dengan menggunakan 10 primer RAPD. Hasil penelitian menunjukkan bahwa metode isolasi Chelex Chelex-TE 10% yang optimal adalah ukuran sampel 1 butir. Amplifikasi jeruk lokal Sumatera dan jeruk impor menggunakan 10 primer tunggal menghasilkan pita polimorfik. Nilai kesamaan jaccard menunjukkan bahwa kelima sampel jeruk tersebut merupakan varietas lokal Sumatera yang diamati memiliki variasi genetik yang tinggi dibandingkan dengan keempat jeruk impor tersebut.
Dermatoglyphic Analysis of Asthma Sufferers in a Population Of Students At The Faculty of Mathematics and Science, Universitas Negeri Padang Velina Salsabil; Afifatul Achyar; Yuni Ahda
Tropical Genetics Vol. 2 No. 2 (2022):
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v2i2.30

Abstract

Asthma is a disease defined as chronic inflammation of the airways which is characterized by recurrent coughing and shortness of breath. Dermatoglyphs are the appearance of tendrils and tendril patterns on the fingers, palms, toes and soles. Dermatoglyph is used as an aid in the detection of a number of diseases that have a strong heritable basis and is also used to detect abnormalities. This study aims to analyze and compare the patterns of dermatoglyphics in asthma sufferers and non-asthmatics on the fingertips. This type of research is descriptive research with cross sectional sampling method. Samples were taken from the student population of the Faculty of Mathematics and Natural Sciences, Padang State University as many as 100 samples of fingerprint patterns. The results obtained showed that there was a significant difference in the number of arch fingerprint patterns of asthmatics compared to normal individuals. Seeing this significant difference in numbers indicates a possible link between fingerprint patterns and asthma phenotypes.
Co-Authors Afionita, Santi Ahmad Hambali, Ahmad Ahmad Wibisana, Ahmad Alvenaya Hindayageni Ananda Putri, Ananda Annisa Irna Putri Annisa Khaira Annisa Khaira Annisa, Silvy Ara, Farrah Azzahra Ardi Ardi Atifah, Yusni Aura Zahra Nafisah Bintang Fadhil Ramadhan Cici Mustika cynthia perdana putri Dara Suci Amini, Dara Suci Des M Dezi Handayani Dwi Hilda Putri Dwi Hilda Putri Dwi Hilda Putri Edwin Edwin Edwin Edwin Elsa Badriyya Elsa Yuniarti Elviana, Alifah Hazelia Fadhila Humaira Fatiha, Fathma Dwi Fevria, Resti Fitri, Afifah Ismu Gilang Amanda Hafizah Fadhilah Hafizh Alza Afra Helsa Rahmatika Herisanti, Dini Indiastri P Monica Irma Leilani Eka Putri Iyan Robiansyah Iyan Robiansyah Jalilah Azizah Jumatul Hafsah Khairani, Fidia Aura Linda Advinda Marten, Threo Wanda Moralita Chatri Muhammad Farikh Muharani, Silvia Mutia Andini, Tri Nadira Nafisa Arini Nella Fauziah Nur Aqsha Nurfadillatun Nisa Wijaya Nurul Hasanah NURUL HIDAYAH Oliv Nurul Kanaya Nurul Kanaya Pinta, Sari Rahma Pradila, Andini Novalia Pramila, Cindy Pratama, Chelsylia Dara Pryatna, Muhamad Zacky Putri, Isna Aryunita Putri Putri, Santi Diana Putrizalda, Hafizhah Rahmad Wanizal Pastha Rahmawati, Atika Ayu Rezeki Rival Alridho Rezi Nabilah Rijal Satria Rijal Satria Rini Wulandari Rinti Mutiara Sari Ruri Fitriyani Ruri Fitriyani S. Syamsurizal safitri, fira Salsabil, Velina Salsabilla, Vishtari Sari Rahma Pinta Sari, Rinti Mutiara Satria, Rijal Sefina, Nadia Sisca Alicia Farma Suryani, Elisa Vauzia Vauzia 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