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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 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 Computer Science & IT Decision Sciences, Operations Research & Management Dentistry Economics, Econometrics & Finance Education 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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Journal : tropical genetics

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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

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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

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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.
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

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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.
Analisis Filogenetik Bakteri Escherichia coli Berdasarkan DNA Genomik Gen BlaTEM Dari Data Sekuens NCBI: Pendekatan Bioinformatika terhadap Variasi Gen BlaTEM pada Escherichia coli Tahun 2016–2025 Indria Palupi; Afifatul Achyar
Tropical Genetics Vol. 5 No. 2 (2025): Genetics
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v5i2.102

Abstract

Resistensi antibiotik yang disebabkan oleh bakteri penghasil β-laktamase, seperti Escherichia coli, menjadi permasalahan global yang serius. Gen blaTEM merupakan salah satu gen utama yang berkontribusi terhadap resistensi tersebut. Penelitian ini bertujuan untuk menganalisis hubungan filogenetik antar isolat Escherichia coli berdasarkan sekuens DNA gen blaTEM yang diambil dari database NCBI dalam rentang waktu 2016 hingga 2025. Data sekuens diselaraskan menggunakan metode ClustalW dalam perangkat lunak MEGA X, kemudian dianalisis menggunakan metode Neighbor-Joining dan 1000 bootstrap. Hasil analisis menunjukkan pembentukan beberapa klade utama dengan tingkat kedekatan genetik yang bervariasi. Kelompok isolat tahun 2021–2024 memiliki kedekatan genetik tinggi, sedangkan isolat tahun 2020 dan 2025 menunjukkan divergensi yang signifikan. Temuan ini mengindikasikan adanya variasi evolusioner dalam gen blaTEM yang penting untuk dipantau sebagai bagian dari strategi pengendalian resistensi antibiotik.
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.
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 has local varieties of citrus that are no less than imported citrus, especially in terms of fruit freshness. However, people are more interested in the color of citrus peel so people prefer imported citrus to local citrus, especially in Sumatera. Therefore, it is necessary to carry out efforts to conserve and improve the characteristics of these citrus to improve their quality through plant breeding. This study aims to optimize DNA isolation methods for citrus fruit samples with Chelex-TE and to determine the genetic profile of local Sumatera citrus and imported citrus using the genotyping RAPD. The samples used were several local citrus in Sumatera (Citrus Siam Mountain Omeh, Citrus Madu, Citrus Keprok Maga, Citrus Keprok Brastepu and Citrus Pasaman) and imported Citrus (Citrus Sunkist, Citrus Clemengold, Citrus Murkot and Citrus Wokam). DNA was isolated using the 10% Chelex-TE method which was optimized for several parameters such as grain size, fruit skin and leaves. RAPD was performed using 10 RAPD primers. The results showed that the optimum 10% Chelex Chelex-TE isolation method was a sample size of 1 grain. The amplification of local Sumatran citrus and imported citrus using 10 single primers produced polymorphic bands. The value of jaccard's similarity indicates that the five samples of Sumatera local variety of citrus and imported citrus have high genetic variation. Indonesia has local varieties of citrus that are no less than imported citrus, especially in terms of fruit freshness. However, people are more interested in the color of citrus peel so people prefer imported citrus to local citrus, especially in Sumatera. Therefore, it is necessary to carry out efforts to conserve and improve the characteristics of these citrus to improve their quality through plant breeding. This study aims to optimize DNA isolation methods for citrus fruit samples with Chelex-TE and to determine the genetic profile of local Sumatera citrus and imported citrus using the genotyping RAPD. The samples used were several local citrus in Sumatera (Citrus Siam Mountain Omeh, Citrus Madu, Citrus Keprok Maga, Citrus Keprok Brastepu and Citrus Pasaman) and imported Citrus (Citrus Sunkist, Citrus Clemengold, Citrus Murkot and Citrus Wokam). DNA was isolated using the 10% Chelex-TE method which was optimized for several parameters such as grain size, fruit skin and leaves. RAPD was performed using 10 RAPD primers. The results showed that the optimum 10% Chelex Chelex-TE isolation method was a sample size of 1 grain. The amplification of local Sumatran citrus and imported citrus using 10 single primers produced polymorphic bands. The value of jaccard's similarity indicates that the five samples of Sumatera local variety of citrus and imported citrus have high genetic variation.
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.
Analysis of VNTRs (variable number tandem repeat) D1S80 in Biology students class Sari Rahma Pinta; Andini Novalia Pradila; Afifatul Achyar
Tropical Genetics Vol. 3 No. 1 (2023):
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v3i1.39

Abstract

DNA can be obtained from all parts of the body with the same profile in each person. The oral mucosal epithelium is one of the DNA sources that is often used for individual identification because of taking it using a swab method that does not hurt the volunteers. The purpose of this study was to determine DNA polymorphism in Biology students of Class of 2022. The sample used in this study were 49 people with details, 34 female and 15 male students. After cheek mucosa was sampling, the PCR and electrophoresis was performed to see the DNA bands formed. The visible band was measured in length and calculated using a formula to see the repeatability of the D1S80 locus on the DNA band. From the 49 samples which were collected, the DNA bands were seen in 27 samples with DNA band lengths ranging from 400-600 bp. The number of bands in each sample were also different. The highest frequency of locus repetitions was 26 repetitions and the lowest was 14 repetitions.
Dermatoglyphic analysis of left-handed individuals in the student population of the Faculty of Mathematics and Natural Sciences Universitas Negeri Padang Dini Herisanti; Afifatul Achyar; Yuni Ahda
Tropical Genetics Vol. 3 No. 1 (2023):
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v3i1.41

Abstract

Dermatoglyphics is a science that studies fingerprint patterns that can be inherited genetically. Fingerprint patterns can be divided into three patterns, arch, loop, and whorl. Observation of fingerprints is used to determine fingerprint patterns and the relationship between these patterns and the fields of health, education, and criminology. Left-handed is a term for people who predominantly use their left hand as their main hand to carry out daily activities. This research aims to determine the relationship between fingerprint patterns and individuals who tend to carry out activities with the left side of their body (left-handed). The type of research carried out was descriptive research with a cross-sectional sample collection method. The sample was taken from the 2019-2022 student population of the Faculty of Mathematics and Natural Sciences, Padang State University, totaling 100 individuals. The samples were taken in November and December. This research was carried out at the Genetics and Biotechnology Laboratory, Faculty of Mathematics and Natural Sciences, Padang State University. The results of this study show that the dominant fingerprint pattern found in the left-handed individual phenotype is 16 fingerprint patterns, while normal individuals have 5 arch fingerprint patterns. This shows that there is a link between the phenotype of left-handed individuals and dermatoglyphics.
Analysis of genetic sequence variation in Formicidae NCBI popset 1871743971 using in silico RFLP Muhamad Zacky Pryatna; Rijal Satria; Afifatul Achyar
Tropical Genetics Vol. 4 No. 1 (2024): Genetics
Publisher : Genetikawan Muda Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/tg.v4i1.43

Abstract

In practically every region of the world, with the exception of the poles, ants are a common form of insect. This one organism lives in colonies and cooperates, therefore these insects are referred to as social insects. In an ant colony, three types of castes have their respective roles and functions, namely, there are queen ants, worker ants, and male ants. In one ant species, many colonies live scattered and each of them has different genes that are influenced by environmental factors and other factors. The purpose of this study was to determine and analyze the genetic variation of ants with the WNT-1 gene sequence in NCBI popset 1871743971. This research was conducted in May-June 2023 using the RFLP method in silico. Based on the results of the study, it was found that there were genetic variations in the WNT-1 gene sequence in Formicidae available at NCBI in PopSet 1871743971.
Co-Authors Afionita, Santi Ahmad Hambali Ahmad Wibisana, Ahmad Alifah Hazelia Elviana Alvenaya Hindayageni Ananda Putri, Ananda Andini Novalia Pradila Annisa Irna Putri Annisa Khaira Annisa Khaira Aprilia, Amanda Ardi Ardi Atifah, Yusni Aura Zahra Nafisah Bintang Fadhil Ramadhan Cici Mustika cynthia perdana putri Dara Suci Amini Des M Dezi Handayani Dezi Handayani Dina Sukma Dini Herisanti Dwi Hilda Putri Dwi Hilda Putri Dwi Hilda Putri Edwin Edwin Edwin Edwin Elisa Suryani Elsa Badriyya Elsa Yuniarti Fadhila Humaira Fardilla, Midratul Farrah Azzahra Ara Fatiha, Fathma Dwi Fevria, Resti Fitri, Afifah Ismu Fronica, Imelda Gilang Amanda Hafizah Fadhilah Hafizh Alza Afra Hafizhah Putrizalda Helsa Rahmatika Indiastri P Monica Indria Palupi Irma Leilani Eka Putri Iyan Robiansyah Jalilah Azizah Jumatul Hafsah Kardiman, Reki Khairani, Fidia Aura Linda Advinda Marten, Threo Wanda Moralita Chatri Muhamad Zacky Pryatna 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 Pinta, Sari Rahma Pramila, Cindy Pratama, Chelsylia Dara Pratama, Sandi Fransisco Putri, Aulia Devani Putri, Irma Leilani Putri, Isna Aryunita Putri Putri, Santi Diana 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 S. Syamsurizal Salsabilla, Vishtari Sari Rahma Pinta Satria, Rijal Sefina, Nadia Selaras, Ganda Hijrah Silvy Annisa Sisca Alicia Farma 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