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All Journal Journal of Food and Pharmaceutical Science Vegetalika Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Jurnal Ilmu Dasar AL KAUNIYAH AGRICOLA Indonesian Journal of Biotechnology Bioeksperimen: Jurnal Penelitian Biologi Journal of Tropical Biodiversity and Biotechnology Omni-Akuatika Jurnal Biologi Tropis Biosaintifika: Journal of Biology & Biology Education Journal of Multidisciplinary Applied Natural Science Proceeding Biology Education Conference Berkala Penelitian Hayati Asia Pacific Journal of Sustainable Agriculture, Food and Energy (APJSAFE) Journal of Food and Pharmaceutical Sciences
Yekti Asih Purwestri
Faculty Of Biology, Universitas Gadjah Mada
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Control & Systems Engineering Education Energy Environmental Science Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Neuroscience Physics Public Health Veterinary

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Extract of Black Rice (Oryza sativa L. ‘Sembada Hitam’) Bran Protect Cytotoxicity of Hydrogen Peroxide on Vero Cells in a Short Time Incubation: Black rice bran ‘Sembada Hitam’ protect cytotoxicity of H2O2 Aprilianti, Suci Hari; Purwestri, Yekti Asih; Saragih, Hendry T.S.S.G; Nuriliani, Ardaning
Journal of Tropical Life Science Vol. 14 No. 1 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.01.01

Abstract

Oxidative stress induced by hydrogen peroxide (H2O2) can lead to cellular damage, contributing to degenerative diseases and aging. Black rice bran is a functional food known for its antioxidant properties, which are crucial in reducing the adverse effects of oxidative stress and maintaining redox balance. In this study, we aimed to investigate the protective effect of the extract of black rice bran (EBRB) 'Sembada Hitam' on Vero cells against H2O2 toxicity. To evaluate the protective effect, a co-culture method was employed, and cell viability was assessed using the MTT assay. Additionally, cell growth was examined through trypan blue staining. Vero cells were exposed to different concentrations of H2O2 and EBRB for a 24-hour period. The results demonstrated that EBRB at concentrations of 15.625, 250, and 500 μg/mL exhibited a protective effect on Vero cells exposed to H2O2 at concentrations of 100, 200, and 400 μM, respectively. Notably, when Vero cells were treated with EBRB at concentrations of 250 or 500 μg/mL for five days in conjunction with H2O2 exposure at concentrations of 200 or 400 μM for 24 hours, a significant decrease in cell viability was observed on day 3. Based on the collective findings, it can be concluded that EBRB has the potential to protect Vero cells against H2O2 -induced toxicity, but primarily during a short-term incubation period. Overall, this study highlights the protective properties of EBRB against H2O2 -induced cellular damage and emphasizes the importance of further investigations to fully elucidate the underlying mechanisms and potential long-term effects of EBRB on cell viability.
Scanning Electron Microscopy Analysis of Tea’s Embryo Axis Explant Cultured on Murashige and Skoog Medium Containing 2,4-Dichlorophenoxyacetic acid Eskundari, Ratna Dewi; Taryono, Taryono; Indradewa, Didik; 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.76451

Abstract

Camellia sinensis L. is an important crop in Indonesia as healthy beverage that contains several secondary metabolism compounds, such as polyphenols and catechins. Tissue culture including somatic embryogenesis and organogenesis has been used for propagating plant for various needs. In this present short-communication, scanning electron microscopic (SEM) analysis of tea was conducted and discussed. This study aimed to investigate surface ultrastructure of TRI2025 embryo axis tea clone cultured on Murashige and Skoog (MS) medium containing 2,4-Dichlorophenoxyacetic acid (2,4-D). The results revealed two different forms of explant’s development, i.e. somatic embryo and transitional form between somatic embryogenesis and organogenesis; or called by “Globular-like Structure” (GLS). Surface ultrastructure analysis of somatic embryo and GLS revealed respectively many stages of somatic embryo development i.e. globular, torpedo, and cotyledon stage, and leaf development form GLS regeneration. 
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. 
Therapeutic Effects of BRC Functional Food from Indonesian Black Rice on Body Weight and Haematological Parameters in Obese Rats Sofyantoro, Fajar; Syam, Adi Mazdi; Adania, Baik Aisyah; Almunawar, Muhammad Fikri; Nasution, Nurlita Putri Bela; Hidayat, Rheina Faticha Asyamsa; Mataram, Made Bagus Auriva; Maharesi, Chesa Ekani; Nurhidayah, Septika; Purwestri, Yekti Asih; Nuriliani, Ardaning; Hidayati, Lisna; Pratiwi, Rarastoeti
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.85847

Abstract

Obesity increases the risk of various diseases. Black rice, renowned for its high anthocyanin content, is considered a potential functional food for preventing metabolic disorders. The current study investigated the effects of black rice crunch (BRC) on body weight and haematological profiles in obese rats. Rats were fed with high-fat diet to induce obesity and supplemented with different concentrations of BRC for 4 and 8 weeks. The results showed that high-fat diet effectively induced obesity, as evidenced by significant increase in body weight. Importantly, 75% BRC supplementation resulted in significant weight reduction in obese rats. Further analysis revealed an increase in erythrocyte numbers in obese groups supplemented with 75% BRC, but no significant changes in haemoglobin concentration or haematocrit percentage. Further investigation showed that 75% BRC led to a decrease in mean corpuscular haemoglobin (MCH), mean corpuscular haemoglobin concentration (MCHC), and mean corpuscular volume (MCV), potentially affecting the size and concentration of haemoglobin within erythrocytes. The total leucocytes count increased with the high-fat diet, while BRC supplementation alone did not have significant impact. Lymphocyte percentage remained stable across the groups, indicating minimal influence of the dietary interventions. Neutrophil percentage varied initially but was not specific to BRC or the high-fat diet. Platelet count and distribution width were not significantly influenced, but mean platelet volume (MPV) increased after 8 weeks of BRC treatment, suggesting larger platelet sizes associated with obesity. Overall, the study provides important insights into the effects of BRC supplementation on body weight and haematological parameters related to obesity. 
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.
Expression of Rice Resistance Gene OsNPR1 Against Bacterial Leaf Blight on Black Rice Cempo Ireng Cultivar after Salicylic Acid Treatment Ikhsan Maulana; Triyaningsih; Tri Rini Nuringtyas; Yekti Asih Purwestri
Asia Pacific Journal of Sustainable Agriculture, Food and Energy Vol. 9 No. 1 (2021): June 2021
Publisher : Asia Pacific Network for Sustainable Agriculture, Food and Energy Network (SAFE Network)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.36782/apjsafe.v9i1.78

Abstract

Black rice is an alternative staple food better than white rice. It has lower carbs, but higher antocyanin compared to white rice. Nowadays, black rice consumption has increased, production needs to be increased to accomodate the demand. But, to our knowledge, there is lack of information about black rice resistance against biotic stresses, one of black rice cultivar is Cempo Ireng. This information needed for optimal Cempo Ireng cultivation. In this research, we determined chlorophyl content and analyzed OsNPR1 expression of three cultivars: Java14 (resistant control), Cempo Ireng, and IR64 (susceptible control), against Xanthomonas oryzae (Xoo). All of them were sprayed with salicylic acid (SA) before inoculated with Xoo. IR64 24h had the lowest chlorophyll content (0,576 ± 0,066 mg/g), meanwhile Java14 72h had the highest content (2,358 ± 1,301 mg/g). However, all the cultivars did not show any correlation between them and time after Xoo inoculation. OsNPR1 expression did not show any significant change in Java14 and Cempo Ireng after being inoculation. However, IR64 showed increasing OsNPR1 in 72h and did not change in 96h after inoculation. It indicated that OsNPR1 played important role in IR64 resistance against Xoo, but not in Cempo Ireng and Java14.
Expression, Characterisation and Structural Homology Modelling of Recombinant Mercuric Reductase of Streptomyces sp. AS2 Khasanah, Anis Uswatun; Putri, Wahyu Aristyaning; Rahayu, Hanum Mukti; Sembiring, Langkah; Purwestri, Yekti Asih
Journal of Tropical Biodiversity and Biotechnology Vol 9, No 4 (2024): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.88773

Abstract

Mercury pollution poses a significant environmental challenge worldwide, prompting extensive efforts over the past two decades to combat its detrimental effects. Cloning merA from Streptomyces sp. AS2 (Accession numbers LC026157) into the expression vector pET-28c (+) marks a critical advancement in this field, necessitating further investigation into the expression and structural analysis of the resulting recombinant mercuric reductase protein. This study aimed to optimise the expression and characterise the structural MerA protein. The study involved the expression of merA from AS2 isolate in the host Escherichia coli BL21 and the measurement of mercuric reductase using SDS-PAGE. Induction of E. coli BL21 was optimized by adding IPTG concentration and incubation time. Purification of mercuric reductase was attempted using ammonium sulphate precipitation, dialysis, and column chromatography. Protein structural characterisation was conducted using computational modelling tools Swiss-Model and Phyre2. Expression of merA from AS2 isolate was successfully performed in E. coli BL21, with SDS-PAGE showing a dominant band in the 55-70 kDa range using IPTG concentration 1 and 1,2 mM and 18-hour incubation time. The specific activity of mercuric reductase was obtained at an enzyme concentration of 294.07 Unit/mg. Protein structural characterisation revealed homology with Lysinibacillus sphaericus (Swiss-Model) and similar folding to c5c1Yc, a known mercuric reductase from the same species using Phyre2. The successful expression of recombinant pET-28c (+)-MerA in E. coli BL21 offers new opportunities for bioremediation efforts targeting mercury contamination. 
Characterization of Lactic Acid Bacteria Isolated from Soymilk and Its Growth in Soymilk By-product Medium for the Application in Soymilk Fermentation Retnowati, Faizah Diah; Purwestri, Yekti Asih; Sine, Yuni
Journal of Tropical Biodiversity and Biotechnology Vol 9, No 4 (2024): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.89003

Abstract

The separation phase of soy-product manufacturing, especially of soymilk production, involves using the liquid portion of soy while disposing primarily of the solid portion, known as soymilk by-product (SMB). The improper disposal of SMB can contribute to environmental concerns. As SMB contains many beneficial nutrients, this could serve as a valuable culture medium for lactic acid bacteria (LAB), especially considering the expense of the standard de Man, Rogosa, and Sharpe (MRS) medium. This study aimed to isolate and identify LAB from soymilk through 16S rRNA sequencing, assess the potential of SMB as a culture medium for LAB, and ferment soymilk with LAB cultured from SMB to demonstrate the probiotic capacity. The research identified a potential LAB as Weissella confusa. Effective cultivation of LAB was demonstrated at 2% SMB concentration, although LAB cultured with MRS medium yielded a higher colony count. Furthermore, fermentation of soymilk by the LAB isolates from SMB exhibited a positive probiotic ability, reaching 5.5 × 109 CFU/mL, with a lactic acid content of 0.27%. 
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.
Extract of Black Rice (Oryza sativa L. ‘Sembada Hitam’) Bran Protect Cytotoxicity of Hydrogen Peroxide on Vero Cells in a Short Time Incubation: Black rice bran ‘Sembada Hitam’ protect cytotoxicity of H2O2 Aprilianti, Suci Hari; Purwestri, Yekti Asih; Saragih, Hendry T.S.S.G; Nuriliani, Ardaning
Journal of Tropical Life Science Vol. 14 No. 1 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.01.01

Abstract

Oxidative stress induced by hydrogen peroxide (H2O2) can lead to cellular damage, contributing to degenerative diseases and aging. Black rice bran is a functional food known for its antioxidant properties, which are crucial in reducing the adverse effects of oxidative stress and maintaining redox balance. In this study, we aimed to investigate the protective effect of the extract of black rice bran (EBRB) 'Sembada Hitam' on Vero cells against H2O2 toxicity. To evaluate the protective effect, a co-culture method was employed, and cell viability was assessed using the MTT assay. Additionally, cell growth was examined through trypan blue staining. Vero cells were exposed to different concentrations of H2O2 and EBRB for a 24-hour period. The results demonstrated that EBRB at concentrations of 15.625, 250, and 500 μg/mL exhibited a protective effect on Vero cells exposed to H2O2 at concentrations of 100, 200, and 400 μM, respectively. Notably, when Vero cells were treated with EBRB at concentrations of 250 or 500 μg/mL for five days in conjunction with H2O2 exposure at concentrations of 200 or 400 μM for 24 hours, a significant decrease in cell viability was observed on day 3. Based on the collective findings, it can be concluded that EBRB has the potential to protect Vero cells against H2O2 -induced toxicity, but primarily during a short-term incubation period. Overall, this study highlights the protective properties of EBRB against H2O2 -induced cellular damage and emphasizes the importance of further investigations to fully elucidate the underlying mechanisms and potential long-term effects of EBRB on cell viability.
Co-Authors Abdul Rahman Siregar, Abdul Rahman Adania, Baik Aisyah Agung Endro Nugroho Alfino Sebastian Alfino Sebastian Alfino Sebastian Almunawar, Muhammad Fikri Andi Setiawan Anis Uswatun Khasanah Anjar Tri Wibowo Aprilianti, Suci Hari Ardaning Nuriliani Ari Indrianto Arnia Sari Mukaromah Bassalamah, Rizka Fahma Budi Setiadi Daryono Cahyo Wulandari Caroline Dwiseptianti Charlie Ester de Fretes Diah Rachmawati Dian Resti Setyaningrum Didik Indradewa Didik Indradewa Didik Indradewa Dio N. Wijaya Donny Widianto Donny Widianto Dwiseptianti, Caroline Dyah Ismoyowati, Dyah Ekowati, Nurhening Yuni Ekris Sutiyanti Elvani, I Sabila Endang Semiarti Erni Martani Erni Martani Erwin Nur Indiarto Fajar Sofyantoro Febri Adi Susanto Febri Adi Susanto Ghea Putri Christy Hidayat, Rheina Faticha Asyamsa Himawan, Tyas Ikhsan Hiroyuki Tsuji Hiroyuki Tsuji, Hiroyuki Ikhsan Maulana Khasanah, Anis Uswatun Ko Shimamoto Ko Shimamoto, Ko Kumala Dewi Kumala Dewi Langkah Sembiring Langkah Sembiring LANGKAH SEMBIRING Latifah, Emi Lila Natasaputra Lila Natasaputra, Lila Lisna Hidayati, Lisna Maharesi, Chesa Ekani Masashi Kawaichi Mataram, Made Bagus Auriva Muhammad Rizky Ulil Albab Mulyani, Putri Dwi Nasution, Nurlita Putri Bela Nugrahapraja, Husna Nurhidayah, Septika P. Parmi Parmi P, Parmi Pratiwi Apridamayanti Pratiwi, Apriliana Priyono, Dwi Sendi Putri Dwi Mulyani Putri Dwi Mulyani Putri Wijayanti Putri, Wahyu Aristyaning Rachman, Mifta Pratiwi Radhiyah Mardhiyah Hamid Radhiyah Mardhiyah Hamid Rahayu, Hanum Mukti Rarastoeti Pratiwi Rarastoeti Pratiwi Ratna Dewi Eskundari Ratna Stia Dewi Ratna Stia Dewi Respati Tri Swasono Retnowati, Faizah Diah Rifqi Zahroh Janatunaim Rifqi Zahroh Janatunaim Rina Sri Kasiamdari Rosy Feraningsih Patigu Rumiyati Rumiyati Rumiyati Saragih, Hendry T.S.S.G Satrijo Saloko Sebastian, Alfino Sine, Yuni Siti Nurbaiti Siti Subandiyah Sofyana, Neng Tanty Sri Widyastuti Sri Widyastuti Subiastuti, Aprilia Sufi Susanto, Febri Adi Syam, Adi Mazdi Taryono Taryono Taryono, Taryono Tri Rini Nuringtyas Tri Rini Nuringtyas Triastuti Rahayu Triyaningsih Triyaningsih Triyaningsih, Triyaningsih Wahyu Aristyaning Putri Woro Anindito Sri Tunjung Yohana Theresia Maria Astuti Yohana Theresia Maria Astuti, Yohana Theresia Maria Yoshiharu Fujii Yosi Bayu Murti Yudi Pranoto Yuka Ogaki Yuka Ogaki, Yuka Yustina Carolina Febrianti Salsinha