Article
Plant Sciences
Jannik Hornbergs, Karolin Montag, Jennifer Loschwitz, Inga Mohr, Gereon Poschmann, Anika Schnake, Regina Gratz, Tzvetina Brumbarova, Monique Eutebach, Kalina Angrand, Claudia Fink-Straube, Kai Stuehler, Juergen Zeier, Laura Hartmann, Birgit Strodel, Rumen Ivanov, Petra Bauer
Summary: This study reveals a significant connection between vitamin E, metal ion transport, and antioxidant activities in response to iron in root cells.
Article
Plant Sciences
Maribela Pestana, Pedro Garcia-Caparros, Teresa Saavedra, Florinda Gama, Javier Abadia, Amarilis de Varennes, Pedro Jose Correia
Summary: This study evaluated the tolerance to iron deficiency of five citrus rootstocks and found that micronutrient homeostasis in roots and shoots of all rootstocks were affected by iron stress conditions. Additionally, the Fe/Cu ratio was significantly related to total leaf chlorophyll, which may be used to assess rootstock performance.
Article
Biochemistry & Molecular Biology
Jie Xiao, Yoo Gyeong Park, Ge Guo, Byoung Ryong Jeong
Summary: The growth and development of S. commixta in vitro was affected by both the Fe source and pH, with plantlets showing greener leaves under pH 4.70 and 5.70. Despite higher Fe absorption at pH 4.70, Fe-EDTA combined with pH 5.70 was found to be the most beneficial for the overall growth and development of S. commixta.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Chandan Kumar Gautam, Huei-Hsuan Tsai, Wolfgang Schmidt
Summary: The study reveals that ectopic expression of peptides IMA1 and IMA2 improves plant growth on calcareous soil by enhancing iron uptake, which is mediated by the biosynthesis and secretion of the compound fraxetin. This response is dependent on elevated environmental pH and involves the regulation of gene expression to adapt to different soil conditions.
Article
Plant Sciences
Qingguo Du, Wenshuai Lv, Yu Guo, Juan Yang, Shanhong Wang, Wen-Xue Li
Summary: This study reveals the importance of miR164 in plant responses to iron deficiency and its role in regulating the NAC5-NFYA8 module. The NAC domain transcription factor5 protein plays a crucial role in Arabidopsis tolerance to iron deficiency by promoting the expression of Nuclear Factor Y, Subunit A8.
Article
Agronomy
Florinda Gama, Teresa Saavedra, Susana Dandlen, Pedro Garcia-Caparros, Amarilis de Varennes, Gustavo Nolasco, Pedro Jose Correia, Maribela Pestana
Summary: This study used the VIGS method to investigate the role of the FRO1 gene in tomato plants and its impact on the regulation of root FCR activity and nutritional homeostasis.
JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE
(2023)
Article
Horticulture
Fabian Perez-Labrada, Adalberto Benavides-Mendoza, Antonio Juarez-Maldonado, Susana Solis-Gaona, Susana Gonzalez-Morales
Summary: Iron deficiency is a common abiotic stress for plants in calcareous soils. The application of citric acid (CA) and humic-like substances (HLS) can improve iron nutrition by inducing temporal alterations in enzyme activity and gene expression.
Article
Plant Sciences
Tirthankar Bandyopadhyay, Manoj Prasad
Summary: Iron is essential for plant growth and different plants employ different iron uptake strategies to maintain iron homeostasis through a series of physiological processes. Recent research has led to a better understanding of the ecophysiology of iron transport.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Biochemistry & Molecular Biology
Alasteir Ong, Mark R. O'Brian
Summary: In Bradyrhizobium japonicum, iron uptake involves selective outer membrane proteins and non-selective periplasmic and cytoplasmic membrane components. FsrB is identified as an iron-regulated gene required for growth on catecholate- and hydroxymate-type siderophores. The activity of FsrB occurs in the periplasm and is involved in the reduction and dissociation of iron from the siderophore.
MOLECULAR MICROBIOLOGY
(2023)
Article
Agronomy
Takanori Kobayashi, Keisuke Maeda, Yutaro Suzuki, Naoko K. Nishizawa
Summary: Iron is an essential micronutrient with low solubility under alkaline conditions. Iron deficiency in calcareous soils affects plant productivity, while iron deficiency anemia is a common problem in humans, especially in Asian and African populations. Transgenic manipulation of genes involved in iron uptake and storage has shown improvements in iron deficiency tolerance and accumulation in plants. This study introduces the simultaneous expression of OsHRZ knockdown and OsIRT1 promoter-Refre1/372 genes, resulting in enhanced iron deficiency tolerance and accumulation in rice plants.
Article
Plant Sciences
DurreShahwar Muhammad, Natalie M. Clark, Samiul Haque, Cranos M. Williams, Rosangela Sozzani, Terri A. Long
Summary: POPEYE is a transcription factor in Arabidopsis roots that regulates iron deficiency responses. It moves between different cells and its function depends on transcript abundance. Proper localization of POPEYE is necessary for managing iron availability, but excessive localization exacerbates deficiencies and disrupts iron mobilization.
Article
Biochemistry & Molecular Biology
Angela Roman, Joaquin Montenegro, Laura Fraile, Marina Urra, Javier Buezo, Alfonso Cornejo, Jose Fernando Moran, Yolanda Gogorcena
Summary: Iron is an essential micronutrient for plants and is usually limited in calcareous soils. This study investigates the effects of the auxin-precursor IAOx on iron deficiency responses in Medicago truncatula plants. The results show that exogenous IAOx promotes lateral roots growth, decreases chlorosis, and delays the decline in pH and increase in FCR activity and flavins in iron-deficient plants. Gene expression levels are consistent with the physiological responses, suggesting that IAOx plays an active role in iron homeostasis.
Article
Plant Sciences
Teresa Saavedra, Florinda Gama, Maria A. Rodrigues, Javier Abadia, Amarilis de Varennes, Maribela Pestana, Jose Paulo Da Silva, Pedro Jose Correia
Summary: The economic costs and environmental impacts of iron-chelate treatments have led researchers to explore alternative methods for controlling iron deficiency chlorosis. This study examined the effects of applying malic acid, citric acid, and succinic acid to strawberry plants and found that succinic acid improved chlorophyll levels and altered the overall nutritional balance in the plants.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Article
Plant Sciences
Mate Sagi-Kazar, Eva Sarvari, Barnabas Cseh, Levente Illes, Zoltan May, Csaba Hegedus, Attila Barocsi, Sandor Lenk, Katalin Solymosi, Adam Solti
Summary: The uptake of iron by chloroplasts does not solely rely on photosynthetic functions, as demonstrated by the ability of etioplasts to acquire iron even in the absence of photosynthetic activity. This likely occurs through the internal reducing capacity of etioplasts supporting the reduction-based iron uptake.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Cell Biology
Barbara Peracino, Valentina Monica, Luca Primo, Enrico Bracco, Salvatore Bozzaro
Summary: Iron is essential for cellular activities and defense mechanisms against intracellular pathogens. Dictyostelium cells express iron transporter proteins and ferric reductase enzymes for iron transport and reduction.
EUROPEAN JOURNAL OF CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jagesh Kumar Tiwari, Shashi Rawat, Satish K. Luthra, Rasna Zinta, Sarika Sahu, Shivangi Varshney, Vinod Kumar, Dalamu Dalamu, Nagesh Mandadi, Manoj Kumar, Swarup K. Chakrabarti, Atmakuri R. Rao, Anil Rai
Summary: This study decoded draft genome sequences of different potato genotypes and identified common late blight resistance genes among them. Analysis included structural variations, sequence diversity, and differential expression of these resistance genes, providing valuable insights for future research on potato improvement.
MOLECULAR BIOLOGY REPORTS
(2021)
Correction
Multidisciplinary Sciences
Prabina Kumar Meher, Subhrajit Satpathy, Atmakuri Ramakrishna Rao
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Prabina Kumar Meher, Shbana Begam, Tanmaya Kumar Sahu, Ajit Gupta, Anuj Kumar, Upendra Kumar, Atmakuri Ramakrishna Rao, Krishna Pal Singh, Om Parkash Dhankher
Summary: In this study, a machine learning-based computational method was developed to predict abiotic stress-responsive miRNAs in plants. By using support vector machine and generating pseudo K-tuple nucleotide compositional features, high prediction accuracy was achieved, and an online prediction server was developed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Mallana Gowdra Mallikarjuna, Rinku Sharma, Palanisamy Veeraya, Akshita Tyagi, Atmakuri Ramakrishna Rao, Lohithaswa Hirenallur Chandappa, Viswanathan Chinnusamy
Summary: This study investigated maize GPXs using evolutionary and functional analyses, identifying seven GPX genes with splice variants and examining their role in stress tolerance.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Kuldeep Kumar, Priyanka Anjoy, Sarika Sahu, Kumar Durgesh, Antara Das, Kishor U. Tribhuvan, Amitha Mithra Sevanthi, Rekha Joshi, Pradeep Kumar Jain, Nagendra Kumar Singh, Atmakuri Ramakrishna Rao, Kishor Gaikwad
Summary: This study used a genome-wide association strategy to discover the genes that regulate flowering time in pigeonpea. The results revealed a set of 22 SNPs associated with flowering time, some of which are located near genes involved in auxin signaling pathways. The study also showed that principal component analysis is a more robust method for identifying genes in GWAS, and FarmCPU is a better choice for controlling false positive and negative associations.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Rashmi Aggarwal, Shweta Agarwal, Sapna Sharma, Malkhan Singh Gurjar, Bishnu Maya Bashyal, Atmakuri Ramakrishna Rao, Sarika Sahu, Prachi Jain, Mahender Singh Saharan
Summary: Spot blotch disease of wheat caused by Bipolaris sorokiniana is an emerging problem in South Asian countries. The ToxA gene and its interaction with the Tsn1 gene play important roles in the development and severity of the disease.
Review
Biochemical Research Methods
Tanmaya Kumar Sahu, Prabina Kumar Meher, Nalini Kanta Choudhury, Atmakuri Ramakrishna Rao
Summary: This study analyzes the performance of machine learning approaches with 18 different amino acid encoding schemes in the prediction of flexible length linear B-cell epitopes. Two combinations of peptide encoding schemes are identified to have improved performance over the state-of-the-art tools for flexible length linear B-cell epitope prediction.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Manimaran Balakumaran, Parameshwaran Chidambaranathan, Jagannadham Prasanth Tej J. P. Kumar, Anil Sirohi, Pradeep Kumar Jain, Kishore Gaikwad, Yuvaraj Iyyappan, Atmakuri Ramakrishna Rao, Sarika Sahu, Anil Dahuja, Sharad Mohan
Summary: The entomopathogenic nematode Heterorhabditis indica possesses genetic architecture to survive desiccation stress and undergoes anhydrobiosis. The induction of anhydrobiosis activates genes involved in antioxidant defense, detoxification pathways, signal transduction, and molecular chaperones. Differential expression of genes related to various metabolic pathways is also observed. This study provides insights into the survival strategies of anhydrobiotic nematodes and can contribute to the development of formulations with enhanced shelf-life.
Article
Agronomy
Subhrajit Satpathy, Dipendra Shahi, Brayden Blanchard, Michael Pontif, Kenneth Gravois, Collins Kimbeng, Anna Hale, James Todd, Atmakuri Rao, Niranjan Baisakh
Summary: This study assessed the prediction accuracy of ridge regression best linear unbiased prediction (rrBLUP) and various Bayesian models in the Louisiana sugarcane breeding program. The results showed that Bayesian models demonstrated higher correlation than rrBLUP, suggesting the potential implementation of genomic prediction in sugarcane variety development.
Article
Biochemistry & Molecular Biology
Sneha Murmu, Himanshushekhar Chaurasia, Sayanti Guha Majumdar, A. R. Rao, Anil Rai, Sunil Archak
Summary: The CRISPR-Cas system has revolutionized genome editing and research in animals and plants. However, uncontrolled nuclease activity of Cas protein can lead to unintended effects. Acr proteins, natural inhibitors of Cas proteins, help control off-target cleavage and improve the efficiency of CRISPR-Cas technology.
JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Upendra Kumar Pradhan, Prabina Kumar Meher, Sanchita Naha, Atmakuri Ramakrishna Rao, Upendra Kumar, Soumen Pal, Ajit Gupta
Summary: In this study, a machine learning-based computational model was developed to predict miRNAs associated with four specific abiotic stresses: cold, drought, heat, and salt. The model represented miRNAs in numeric form using pseudo K-tuple nucleotide compositional features of Kmer size 1 to 5. Support vector machine (SVM) achieved the highest cross-validation accuracy in all four abiotic stress conditions. The proposed computational model provides a new method for identifying specific abiotic stress-responsive miRNAs in plants.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
Article
Genetics & Heredity
Upendra Kumar Pradhan, Prabina Kumar Meher, Sanchita Naha, Atmakuri Ramakrishna Rao, Ajit Gupta
Summary: This study developed a machine learning-based computational model for predicting abiotic stress-responsive lncRNAs. The model achieved high accuracy in both cross-validation and independent testing using Kmer features and support vector machine algorithm. The developed model was implemented in an online prediction tool ASLncR to assist in the identification of abiotic stress-responsive lncRNAs in plants.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
Article
Genetics & Heredity
Nalinikanta Choudhury, Tanmaya Kumar Sahu, Atmakuri Ramakrishna Rao, Ajaya Kumar Rout, Bijay Kumar Behera
Summary: The high-throughput sequencing technologies can accurately classify microbial communities. This study used K-Means clustering and machine learning algorithms to classify unknown microbes. The model based on Random Forest showed superior performance and can be used for annotating genomic sequences.
Article
Plant Sciences
Priyanka Guha Majumdar, A. R. Rao, Amit Kairi, P. K. Meher, Sarika Sahu
Summary: This study evaluated the performance of different classifiers in discriminating coding and non-coding RNAs in plant species and found that Random Forest classifier had the highest accuracy.
INDIAN JOURNAL OF GENETICS AND PLANT BREEDING
(2022)
Article
Biochemistry & Molecular Biology
Saurabh Gupta, Vishal Singh, Pritish Kumar Varadwaj, Navajeet Chakravartty, A. V. S. Krishna Mohan Katta, Sivarama Prasad Lekkala, George Thomas, Srinivasan Narasimhan, Arjula R. Reddy, V. B. Reddy Lachagari
Summary: In this study, a group of natural spice and herbal secondary metabolites (SMs) were screened, and it was found that some of these substances have higher inhibitory efficacy against SARS-CoV-2 and human target proteins. These identified SMs may be useful in the development of preventive nutraceuticals, food supplements, and antiviral drugs.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)