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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
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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Analysis of Genetic Variations in PHT1 Gene Sequences in Rice (Oryza sativa) NCBI Popset 240028097 Using In-Silico RFLP Oliv Nurul Kanaya Nurul Kanaya; Afifatul Achyar
Jurnal Serambi Biologi Vol. 8 No. 1 (2023): Jurnal Serambi Biologi
Publisher : Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Padang

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Abstract

Abstract Rice is a plant that has high economic value. According to FAO, Indonesia is the third largest rice consuming country in the world. However, rice will become stunted and its growth will be stunted if there is a lack of phosphorus. The PHT1 gene plays an important role in plant growth and development, because this gene plays a role in taking phosphate from the soil. The PHT1 gene is transcribed when there is drought, salt stress, and nutrition in plants. Genetic variation in a population will affect the survival of an individual. This study used the restriction enzyme ScaI. This study aims to analyze genetic variation in the PHT1 gene sequence in NCBI Popset 2400280979 rice using RFLP in silico. The results showed that there was genetic variation in the rice PHT1 gene sequence and two allele variations present in 24 rice gene sequences using the restriction enzyme ScaI.
Specific Primer Design and Optimization of Monodehydroascorbate reductase (MDHAR) Gene Amplification in Rice (Oryza sativa L.) Jumatul Hafsah; Afifatul Achyar; Zulyusri; Yusni Atifah; Linda Advinda; Violita
Jurnal Serambi Biologi Vol. 8 No. 3 (2023): Jurnal Serambi Biologi
Publisher : Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Padang

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Abstract

Monodehydroascorbate reductase (MDHAR) is an enzyme responsible for growth and response to biotic and abiotic stress. MDHAR in rice shows a higher sensitivity to stress compared to other plants. This study aims to obtain specific primers for the MDHAR gene in rice to be used in PCR amplification so that it can amplify the MDHAR gene. Primers are designed using the Pickprimer and Geneious Primer tools. Optimization of annealing temperature was carried out using the gradient PCR method and then an in vitro primary specification test was carried out using the Touchdown PCR method. The results of the primary design obtained one candidate primer that met the ideal primer requirements, namely a pair of primers (5'-AAAAACACTGCATGGGTCGTC-3' and 5'-CGCCTACCGTTTCCCAAGTT-3') with an amplicon length of 160 bp. The visualization results of PCR products using 1.5% agarose showed that 6 samples were able to amplify the MDHAR gene at 160 bp in size. However, in each lane there is a non-specific DNA band (Primer dimer). In vitro primer specification testing with Touchdown succeeded in increasing product formation specifications and was able to reduce non-specific DNA bands (Primer dimers).
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.
Training of Halal Product Process Assistant for Alumni of the UNP Biology Department to Assist Micro and Middle Class Businessman in Self-Declare Halal Certification Afifatul Achyar; Violita Violita; Rijal Satria; Vauzia Vauzia; Yusni atifah
Pelita Eksakta Vol 6 No 2 (2023): Pelita Eksakta, Vol. 6, No. 2
Publisher : Fakultas MIPA Universitas Negeri Padang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/pelitaeksakta/vol6-iss2/228

Abstract

The Halal Product Guarantee Organizing Agency (BPJPH) of the Indonesian Ministry of Religion requires human resources as qualified Halal Product Process Assistants (PPH) to help accelerate the halal certification process for MSE products in Indonesia. On the other hand, there are not many alumni of the Biology Department, FMIPA UNP who got jobs in less than 6 months after graduating. Therefore, the solution offered to the problems faced by partners is to conduct halal product process assistance (PPH) training for alumni of the Biology Department, FMIPA UNP so that they have the capacity and competence to assist MSE business actors in halal certification of their products through a self-declaration scheme. Community service activities consist of two main activities, namely the delivery of material about the halal certification self-declaration scheme and the practice of halal product process assistance (PPH) simulations. The competency of PPH assistants is evaluated and used as an indicator of graduation.
The Primer Design and Optimization of Annealing Temperature for Analysis of Glutathione Reductase Gene Expression in Rice (Oryza sativa L.) Annisa Khaira; Afifatul Achyar; Zulyusri Zulyusri; Yusni Atifah; Dwi Hilda Putri; Violita Violita
3BIO: Journal of Biological Science, Technology and Management Vol. 5 No. 1 (2023)
Publisher : School of Life Sciences and Technology, Institut Teknologi Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/3bio.2023.5.1.3

Abstract

Glutathione Reductase (GR) belongs to the NADPH-dependent flavoprotein oxidoreductase family and is found in both prokaryotes and eukaryotes. The GR gene is considered to play a key role in the elimination of oxidative reaction products by looking at the level of gene expression of GR rice in dealing with  drought stress using qPCR. One of the important steps to develop a specific, effective and efficient qPCR is the primer design. Several studies analyzing GR gene expression in rice have also designed primers. However, the primer still lacks an ideal characteristic of primer, as it still has a secondary structure. This studies aims to design rice GR specific primers and optimize the annealing temperature for GR gene expression analysis on rice. Primers were designed using the  Primer3 and Geneious Prime and checked for specificity using the Primer-BLAST tool. The selected primer pairs were then optimized for annealing  temperature using gradient PCR. The best primer design results were GR-Forward 5’-ACGATTGCAGCCAGTGAAGA-3’ and GR-Reverse 5’-TGCGGCAATACTATCAACATCC-3’, with an amplicon length of 204 bp, primer base lengths of 20 and 22 nucleotides, Tm values of 60°C and 58.9°C, %GC of 50% and 45.5%, respectively. This primer pair had no secondary structure, both hairpin and self dimer. Gradient PCR showed the optimum annealing temperature for this primer pair was 52.2oC so that the primer can be used as a specific primer to analyze  the GR gene expression in rice using qPCR.
Variasi Genetik Prion Protein Gene pada Kucing Domestik (Felis catus) Menggunakan Metode RFLP In Silico Pinta, Sari Rahma; Pratama, Chelsylia Dara; Fatiha, Fathma Dwi; Muharani, Silvia; Achyar, Afifatul
Jurnal Jeumpa Vol 11 No 1 (2024): Jurnal Jeumpa
Publisher : Department of Biology Education, Faculty of Teacher Training and Education, Samudra University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33059/jj.v11i1.9933

Abstract

FSE adalah penyakit neurodegeneratif yang disebabkan oleh prion yang mempengaruhi semua keluarga kucing. Penelitian ini bertujuan untuk mengidentifikasi variasi genetik dalam prion protein gene pada kucing domestik (Felis catus) menggunakan RFLP In silico. Penelitian ini merupakan penelitian deskriptif yang menyajikan karakteristik dari sampel yang diuji. Sampel yang digunakan yaitu sekuen prion protein gene dalam format fasta dari NCBI, dengan nomor identitas NCBI Popset 2445476754. Skrining enzim restriksi dilakukan menggunakan situs insilico.ehu.es. Metode RFLP in silico ini dilakukan menggunakan tools pada situs benchling.com dengan enzim restriksi yang diperoleh selama tahap skrining. Data yang telah didapatkan dianalisis secara deskriptif. Enzim restriksi yang digunakan yaitu enzim HhaI dengan sisi pemotongan pada basa G_CG'C dan enzim DpnI dengan sisi pemotongan pada GA'TC. Hasil restriksi dengan enzim HhaI pada 25 isolat prion protein gene Felis catus menghasilkan 4 variasi alel yaitu alel A1 (frekuensi alel 0,08), alel A2 (frekuensi alel 0,16), alel A3 (frekuensi alel 0,68) dan alel A4 (frekuensi alel 0,08). Restriksi yang dilakukan oleh enzim DpnI menghasilkan 2 alel yaitu alel B1(frekensi alel 0,84) dan alel B2 (frekuensi alel 0,16). Hasil penelitian ini dapat digunakan sebagai rujukan awal penelitian tentang gen Prion kucing domestik pada tahap yang lebih kompleks seperti bioinformatika, maupun pada tahap kerja laboratorium.
Optimization of DNA Isolation Dried Leaf Samples of Endangered Plants Dipterocarpus cinereus Ruri Fitriyani; Robiansyah, Iyan; Achyar, Afifatul
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 Sari, Rinti Mutiara; Achyar, Afifatul A; Ahda, Yuni; Hilda Putri, Dwi
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 Salsabil, Velina; Achyar, Afifatul; Ahda, Yuni
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 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