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All Journal Jurnal Ilmu Dasar Journal of Tropical Biodiversity and Biotechnology Journal of Multidisciplinary Applied Natural Science
Sebastian, Alfino
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Control & Systems Engineering Energy Environmental Science Immunology & microbiology Materials Science & Nanotechnology Mathematics Physics

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Identifying Single Nucleotide Polymorphisms (SNPs) in OsFER1 and OsFER2 Genes Linked to Iron accumulation in Pigmented Indonesian Rice (Oryza sativa L.) Pratiwi, Apriliana; Bassalamah, Rizka Fahma; Elvani, I Sabila; Sebastian, Alfino; Purwestri, Yekti Asih
Journal of Tropical Biodiversity and Biotechnology Vol 9, No 1 (2024): March
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.78019

Abstract

Iron (Fe) is an essential micronutrient for the well-being of plants, animals, and bacteria. In plants, iron plays a pivotal role in a myriad of metabolic processes, encompassing redox reaction, photosynthesis, respiration, chlorophyll synthesis, and nitrogen fixation. For humans, iron is indespensable for several metabolic functions, particularly in the synthesis of haemoglobin. Iron deficiency can lead to health issues on a global scale, therefore identifying key crops, such as rice for providing sufficient iron in diet intake is very important. In rice, the maintenance of iron homeostasis is orchestrated by various genes, with OsFER1 and OsFER2 acting as iron accumulator genes in leaves, stems, flowers, and grains. The primary objective of this study was to ascertain the single nucleotide polymorphisms (SNP) in the OsFER1 and OsFER2 and to assess the iron content in Indonesian local rice cultivars. To achieve this, we examined partial sequences of OsFER1 and OsFER2 to identify SNPs in the Indonesian rice cultivars used (Cempo Ireng, Pari Ireng, Hitam Kalsel, Merah Pari Eja, and Ciherang). Concurrently, the iron content in the seeds was quantified using Atomic Absorption Spectrophotometry (AAS). The analysis revealed that the OsFER1 gene sequence, specifically exon 5, exhibited a SNP in the form of a transition. In contrast, the OsFER2 gene sequences, specifically in intron 2 displayed SNPs in the form of insertions. Notably, the iron content in the seeds was highest in Cempo Ireng (black rice), while it was lowest in Merah Pari Eja (red rice) and Ciherang (non-pigmented rice). Importantly, the identified SNPs in these partial gene sequences did not exert any discernible influence on iron levels or the formation of ferritin protein. 
Optimization of qRT-PCR Annealing Temperature of WRKY45 Gene for Detection of Resistance Genes Against Xanthomonas oryzae pv. oryzae on Black Rice Cempo Ireng Triyaningsih, Triyaningsih; Nuringtyas, Tri Rini; Purwestri, Yekti Asih; Sebastian, Alfino
Jurnal ILMU DASAR Vol 23 No 1 (2022)
Publisher : Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Jember

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19184/jid.v23i1.24181

Abstract

Plant pathogens constrain the development of black rice farming. One of these pathogens is Xanthomonas oryzae pv. oryzae (Xoo), causing a bacterial leaf blight disease. The disease disrupts crop growth and reducing yields. Cempo ireng is a local pigmented rice cultivar from Yogyakarta, Indonesia, which is reported for its high resistance to Xoo. One of the rice resistance mechanisms to Xoo infection is a molecular defense employing plant resistance genes such as WRKY45. Comparing the expression of resistance-related genes of the resistant cultivar to the susceptible ones is needed to elucidate the resistance mechanism of the black rice to Xoo. For this purpose, the expression of WRKY45 gene at the level of mRNA can be performed using qRT-PCR. The success of qPCR analysis is greatly influenced by the accuracy of the annealing primer temperature of the corresponding gene. This study aimed to optimize the primer's annealing temperature for WRKY45 gene. The optimization was done by a temperature gradient PCR. Determination of the optimal annealing temperature was selected based on the profile of the amplification curve, melt curve, melt temperature and the Ct value obtained. The annealing temperature gradient used in this study was ranging from 52°C to 60°C. The results showed that the best annealing temperature for WRKY45 gene primers is 58.3°C based on the amplification curve, melt curve, melt peak and Ct value of 29.21.
Global Perspectives on Environmental Microbiome Research: Current Status and Future Directions Putri, Wahyu Aristyaning; Subiastuti, Aprilia Sufi; Wulandari, Cahyo; Rachman, Mifta Pratiwi; Sebastian, Alfino; Siregar, Abdul Rahman; Himawan, Tyas Ikhsan; Priyono, Dwi Sendi; Sofyana, Neng Tanty; Purwestri, Yekti Asih; Nugrahapraja, Husna; Wibowo, Anjar Tri
Journal of Multidisciplinary Applied Natural Science Vol. 5 No. 2 (2025): Journal of Multidisciplinary Applied Natural Science
Publisher : Pandawa Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47352/jmans.2774-3047.266

Abstract

The environmental microbiome plays an important role in various ecosystems around the world, influencing nutrient cycling, disease dynamics and ecosystem stability. This bibliometric analysis provides a comprehensive overview of the current state and future directions of environmental microbiome research from a global perspective from 2009–2024. Through systematic examination of Scopus publications, 2154 documents were found. The results show a significant increase in the number of publications since 2017 and a peak in 2024. The most cited document was "The hidden world within plants: Ecological and evolutionary considerations for defining functioning of microbial endophytes" with 1887 citations and “Structure and function of the global ocean microbiome” with 1843 citations. The most productive countries in environmental microbiome research are the United States (n = 748), China (n = 533), India (n = 308), Germany (n = 172) and the United Kingdom (n = 157). Microbiome, microbial community, microfolora, microbiota, microbiology, bacteria, and bacterium are the most popular topics that will continue to develop in the future. Although the United States has published the highest total number of papers, more recent studies have predominantly been published from China, indicating shift in the centre of study from the United States to China. Insights gained from this analysis contribute to a deeper understanding of the environmental microbiome research landscape, guiding future research priorities and collaborations in the field.
Co-Authors Abdul Rahman Siregar, Abdul Rahman Anjar Tri Wibowo Bassalamah, Rizka Fahma Cahyo Wulandari Elvani, I Sabila Himawan, Tyas Ikhsan Nugrahapraja, Husna Pratiwi, Apriliana Priyono, Dwi Sendi Putri, Wahyu Aristyaning Rachman, Mifta Pratiwi Sofyana, Neng Tanty Subiastuti, Aprilia Sufi Tri Rini Nuringtyas Triyaningsih Triyaningsih, Triyaningsih Yekti Asih Purwestri