Article
Agriculture, Multidisciplinary
Duan Yao-ke, Su Yen, Han Rong, Sun Hao, Gong Hai-jun
Summary: This study reports the functional characteristics of CsNIP2;2 in cucumber, which was found to be a tandem repeat of CsNIP2;1 with different subcellular localization and selectivity filter compared to previously characterized silicon influx transporters in other plants.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
Article
Multidisciplinary Sciences
Yuxiang Zhang, Shihong Fei, Yunmin Xu, Yong He, Zhujun Zhu, Yuanyuan Liu
Summary: The study identified 43 putative aquaporins in tomato, including 12 NIPs, with some potentially involved in Si transportation, water, ammonia, urea, and boron transport, contributing to pollen development, while others might function as boron facilitators affecting plant growth and anther development. This research offers valuable candidates for further exploration of Si transporters and NIP proteins in tomato regarding uptake and transport of silicon, boron, and other substrates.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Yuqi Wang, Shaohua Yang, Chune Li, Taijiao Hu, Siyu Hou, Qing Bai, Xiyue Ji, Feng Xu, Chongdai Guo, Min Huang, Yanfei Cai, Jiping Liu
Summary: In this study, the function of OsNIP1;2, a gene in rice, in aluminum detoxification was characterized. OsNIP1;2 was found to be specifically induced by aluminum stress in the roots and played a role in internal aluminum detoxification by regulating aluminum accumulation in the cell wall, cytosol, and distribution between roots and above-ground tissues.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Plant Sciences
Yasunori Saitoh, Michihiro Suga
Summary: Silicon is beneficial for plant growth and production, particularly in rice. Plant roots take up silicon in the form of silicic acid through silicic acid channels. Understanding the crystal structures of these channels and their mechanism of silicic acid permeation is crucial for the development of secure and sustainable crops.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Maroua Ben Amira, Mohamed Faize, Magnus Karlsson, Mukesh Dubey, Magdalena Frac, Jacek Panek, Boris Fumanal, Aurelie Gousset-Dupont, Jean-Louis Julien, Hatem Chaar, Daniel Auguin, Robin Mom, Philippe Label, Jean-Stephane Venisse
Summary: The study focuses on the diversity and structure of the fungal uncharacterized X-Intrinsic Protein (XIP) subfamily in Trichoderma atroviride, exploring their roles in development, biomass accumulation, and mycoparasitic activities. The research sheds light on the function of the XIP subfamily and their impact on the physiological integrity of the fungus.
Article
Biotechnology & Applied Microbiology
Md Mahmudul Hassan, Samir Martin, Kai Feng, Timothy B. Yates, Guoliang Yuan, Madhavi Z. Martin, Stanton Martin, Wellington Muchero, Natalie A. Griffiths, David J. Weston, Xiaohan Yang
Summary: Silicon enhances plant tolerance to stressors and contributes to carbon sequestration. In this study, Si transporters and proteins related to silicification were identified in the bioenergy crop poplar. These findings have implications for improving Si accumulation, enhancing plant stress tolerance, and carbon sequestration in poplar.
PLANT BIOTECHNOLOGY REPORTS
(2023)
Article
Agronomy
Yanru Du, Jun Li, Shaopeng Chen, Yuxian Xia, Kai Jin
Summary: The comparative study highlighted the different infection strategies between M. anisopliae and M. acridum, providing new insights into their pathogenicity. Differences in virulence-related secreted proteins, carbon source utilization, cell wall surface epitopes, and secondary metabolite gene clusters were identified as key factors contributing to the distinctive pathogenesis of these two Metarhizium species.
PEST MANAGEMENT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Nitika Rajora, Vandana Thakral, Geetika, Sanskriti Vats, Gunashri Padalkar, Sreeja Sudhakaran, Surbhi Kumawat, Humira Sonah, Rupesh Deshmukh
Summary: NIP2-1 in carrot plants was predicted to be a silicon transporter, but the plants showed low silicon accumulation and minimal benefits from silicon supplementation, as confirmed by pot-experiments.
JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Guy W. W. Dayhoff, Vladimir N. N. Uversky
Summary: This article presents RIDAO, a high-efficiency web-based disorder predictor for protein intrinsic disorder analysis. RIDAO integrates six disorder predictors into a unified platform, offering high accuracy and processing efficiency.
Article
Biochemistry & Molecular Biology
Nikhil R. Gandasi, Vasiliki Arapi, Michel E. Mickael, Prajakta A. Belekar, Louise Granlund, Lakshmi Kothegala, Robert Fredriksson, Sonchita Bagchi
Summary: SLC38A6 (SNAT6) is a transporter expressed exclusively in excitatory neurons of the brain, with high specificity for glutamine and glutamate. It forms complexes with caveolin on the plasma membrane to aid in its sodium dependent trafficking. Potential interacting partners identified include CTP synthase 2, phosphate activated glutaminase, and glutamate metabotropic receptor 2.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Lotus A. Lofgren, Nhu H. Nguyen, Rytas Vilgalys, Joske Ruytinx, Hui-Ling Liao, Sara Branco, Alan Kuo, Kurt LaButti, Anna Lipzen, William Andreopoulos, Jasmyn Pangilinan, Robert Riley, Hope Hundley, Hyunsoo Na, Kerrie Barry, Igor V. Grigoriev, Jason E. Stajich, Peter G. Kennedy
Summary: This study conducted a comparative genomic analysis of ectomycorrhizal (ECM) fungi, particularly focusing on the specialist genus Suillus, and found that Suillus has highly dynamic genomes with many rapidly evolving gene families, indicating that host specificity is a dynamic process at the genome level which is mainly influenced by secondary metabolites.
Article
Biochemistry & Molecular Biology
Bi Zhao, Sina Ghadermarzi, Lukasz Kurgan
Summary: This study expands the research on AlphaFold2 (AF2) in the field of intrinsic disorder prediction by comparing it with other accurate, popular, and recently released disorder predictors. The results show that AF2-based disorder predictions are relatively accurate, with an AUC of 0.77, but are outperformed by several modern disorder predictors with AUCs around 0.8 and shorter runtime. AF2 also shows moderate accuracy in predicting fully disordered proteins and disorder content compared to the best disorder predictor. Interestingly, both AF2 and the most accurate disorder predictors rely on deep neural networks, indicating their usefulness in protein structure and disorder predictions.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Chuanfeng Ju, Zhenqian Zhang, Jinping Deng, Cuicui Miao, Zhangqing Wang, Lukas Wallrad, Laiba Javed, Dali Fu, Ting Zhang, Jorg Kudla, Zhizhong Gong, Cun Wang
Summary: Manganese is an essential micronutrient for plants, but excess supply can be toxic. This study reveals a two-tiered calcium-controlled mechanism that regulates plant manganese homeostasis.
Article
Materials Science, Multidisciplinary
Hitoshi Sai, Hung-Jung Hsu, Po-Wei Chen, Pei-Ling Chen, Takuya Matsui
Summary: The impact of intrinsic amorphous silicon bilayers on surface passivation in a-Si:H/c-Si heterojunction solar cells was investigated. By controlling the microstructure factor R* of the interfacial layer, high-efficiency solar cells can be achieved through the optimization of intrinsic bilayers. Various PECVD process parameters can be utilized to grow interfacial layers with good surface passivation capabilities.
PHYSICA STATUS SOLIDI A-APPLICATIONS AND MATERIALS SCIENCE
(2021)
Article
Physiology
Cong Huang, Xue Zhang, Dongfeng He, Qiang Wu, Rui Tang, Longsheng Xing, Wanxue Liu, Wenkai Wang, Bo Liu, Yu Xi, Nianwan Yang, Fanghao Wan, Wanqiang Qian
Summary: In this study, 40 OBPs were identified in C. pomonella through genomic and transcriptomic analysis, with the majority being classic OBPs. It was found that two OBP genes were lost in C. pomonella relative to a possible distant ancestor in the Lepidoptera lineage based on analysis of gene gains and losses. The expansion of OBP genes in C. pomonella was mainly due to tandem duplications.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Plant Sciences
Shivani Sharma, Amit Kumar, Priyanka Dhakte, Gaurav Raturi, Gautam Vishwakarma, Kalyani M. Barbadikar, B. K. Das, S. M. Shivaraj, Humira Sonah, Rupesh Deshmukh
Summary: Crop improvement is a major concern for researchers due to climate change and increasing population. Current progress is not sufficient to meet food demand, hence the need for speed breeding to reduce generation time and enhance efficiency. By combining modern breeding and genetic engineering technologies, speed breeding shows promising potential in achieving nutritional security and sustainable agriculture.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Plant Sciences
Ruchi Bansal, Surbhi Kumawat, Pallavi Dhiman, Sreeja Sudhakaran, Nitika Rana, Rajdeep Jaswal, Akshay Singh, Humira Sonah, Tilak Raj Sharma, Rupesh Deshmukh
Summary: In this study, we identified eight BAG genes in the rice genome and 78 BAG homologs in nine other Oryza species. We predicted the haplotype diversity and functional effect of variations in BAG genes based on whole genome resequencing data. Transcriptomic analyses revealed the multifunctional roles of BAG genes in both developmental and defense response in rice.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Plant Sciences
Gaurav Raturi, Surbhi Kumawat, Rushil Mandlik, Deepak Duhan, Vandana Thakral, Sreeja Sudhakaran, Chet Ram, Humira Sonah, Rupesh Deshmukh
Summary: In this study, AQPs in the watermelon genome were identified and analyzed to understand their role and regulation during various abiotic stress conditions. The expression of certain AQPs, particularly ClaPIP1-2 and ClaPIP2-4, was found to be significantly increased under stress. This information provides a fundamental basis for understanding AQP-mediated transport in watermelon and related species.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Cell Biology
Virender Kumar, Vinod Goyal, Rushil Mandlik, Surbhi Kumawat, Sreeja Sudhakaran, Gunashri Padalkar, Nitika Rana, Rupesh Deshmukh, Joy Roy, Tilak Raj Sharma, Humira Sonah
Summary: In this study, a meta-analysis incorporating QTL information, region-specific association, and transcriptomic analysis was performed. The results identified 14 meta-QTLs for oil and 16 meta-QTLs for protein content in soybean. Further analysis using whole genome re-sequenced data revealed a haplotypic association of certain genes with oil and protein content. The transcriptomic analysis provided insights into the tissue-specific expression of candidate genes. This study provides valuable information for map-based cloning of regulatory genes and marker-assisted breeding in soybean.
Article
Microbiology
Sagar Yadav, Zarrine Raazi, Sheelavanta Matha Shivaraj, Deepika Somani, Ramya Prashant, Abhijeet Kulkarni, Rajeev Kumar, Suma Biradar, Shreenivas Desai, Narendra Kadoo
Summary: This study compared the genomes of 12 isolates of Bipolaris sorokiniana collected from wheat fields in India and found that the isolate D2 had the highest virulence and a larger genome with an expanded arsenal of pathogenicity genes, which may contribute to its higher virulence among the tested isolates.
Review
Plant Sciences
Deepmala Sehgal, Priyanka Dhakate, Heena Ambreen, Khasim Hussain Baji Shaik, Nagenahalli Dharmegowda Rathan, Nayanahalli Munireddy Anusha, Rupesh Deshmukh, Prashant Vikram
Summary: Plant omics has played a crucial role in discovering new genes and biomolecules that can improve crops, and has made significant progress in wheat research on both qualitative and quantitative traits. Combining various omics approaches has led to advances in gene discovery, pathway investigation, and understanding stress responses and yields. The development of a Wheat Omics database further aids functional genomics studies in wheat.
Article
Biochemical Research Methods
Sanskriti Vats, S. M. Shivaraj, Humira Sonah, Gunvant Patil, Joy Roy, Tilak Raj Sharma, Rupesh Deshmukh
Summary: In this study, a highly efficient protocol for tomato transformation was developed and optimized. Different factors affecting regeneration and transformation were evaluated, and the best conditions were determined. This standardized protocol can be applied to transform any tomato variety.
PLANT MOLECULAR BIOLOGY REPORTER
(2023)
Review
Environmental Sciences
Gaurav Raturi, Anchal Chaudhary, Varnika Rana, Rushil Mandlik, Yogesh Sharma, Vitthal Barvkar, Prafull Salvi, Durgesh Kumar Tripathi, Jagdeep Kaur, Rupesh Deshmukh, Hena Dhar
Summary: Arsenic contamination is a serious environmental issue in aquatic and terrestrial ecosystems. Microbial approaches, such as oxidation of arsenite, methylation of arsenic, biosorption, bioprecipitation, and bioaccumulation, are promising strategies for arsenic remediation. Genetic engineering of bacteria also plays a significant role in bioremediation strategies.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Genetics & Heredity
Sanskriti Vats, Virender Kumar, Rushil Mandlik, Gunvant Patil, Humira Sonah, Joy Roy, Tilak Raj Sharma, Rupesh Deshmukh
Summary: We reported a reference-guided genome assembly of the superior tomato cultivar Solanum lycopersicum cv. Pusa Ruby (PR), which covers 97.6% of the single-copy genes in the solanales order. The PR genome contains 34,075 genes and 423,288 variants, with 127,131 intragenic variants and 1232 high impact variants. PR shows the lowest affinity towards Fla.8924 among the compared tomato varieties. The high regeneration rate (45.51%) of PR was analyzed and only AGAMOUS-LIKE15 was found to have a null mutation.
Article
Biochemistry & Molecular Biology
Prasanta K. Dash, Rhitu Rai, Sharat Kumar Pradhan, Sheelavanta Matha Shivaraj, Rupesh Deshmukh, Rohini Sreevathsa, Nagendra K. Singh
Summary: Flax is a crop grown for its oil, bast fiber, and industrial solvent, but it is affected by climate changes, such as high temperature and drought, which hinder its growth and productivity. In this study, gene expression profiling was conducted to analyze the effects of drought-induced oxidative stress on flax, and a stable reference gene for normalization of qRT-PCR data was identified. The results suggest that EF1a alone or in combination with ETIF5A is suitable for real-time visualization of the cellular impact of drought and oxidative stress on flax.
Article
Plant Sciences
Vandana Thakral, Yogesh Sharma, Rushil Mandlik, Surbhi Kumawat, Gunvant Patil, Humira Sonah, Paul Isenring, Richard Belanger, Tilak Raj Sharma, Rupesh Deshmukh
Summary: In this study, VrNIP2-1 was identified as a metalloid transporter in mungbean through a comprehensive evaluation of AQPs in the mungbean genome. Molecular dynamics simulation revealed the pore-morphology of VrNIP2-1. The study also found that VrNIP2-1 has a unique aromatic/arginine selectivity filter, different from other metalloid transporters in higher plants. The metalloid transport activity of VrNIP2-1 with its unique structural features provides insights into the solute specificity of NIP2s in mungbean and related pulses.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Plant Sciences
Hemant B. Kardile, Suhas Gorakh Karkute, Clarissa Challam, Nirmal Kant Sharma, Rahul Mahadev Shelake, Prashant Govindrao Kawar, Virupaksh U. Patil, Rupesh Deshmukh, Vinay Bhardwaj, Kumar Nishant Chourasia, Srikar Duttasai Valluri
Summary: This study identified and characterized 37 putative SWEET genes in potato and investigated their response to the late blight disease caused by Phytophthora infestans. Nine transporter genes were found to be responsive to P. infestans, with their expression levels correlating with the life cycle of the pathogen.