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Haq SAU, Bashir T, Roberts TH, Husaini AM. Ameliorating the effects of multiple stresses on agronomic traits in crops: modern biotechnological and omics approaches. Mol Biol Rep 2023; 51:41. [PMID: 38158512 DOI: 10.1007/s11033-023-09042-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 10/13/2023] [Indexed: 01/03/2024]
Abstract
While global climate change poses a significant environmental threat to agriculture, the increasing population is another big challenge to food security. To address this, developing crop varieties with increased productivity and tolerance to biotic and abiotic stresses is crucial. Breeders must identify traits to ensure higher and consistent yields under inconsistent environmental challenges, possess resilience against emerging biotic and abiotic stresses and satisfy customer demands for safer and more nutritious meals. With the advent of omics-based technologies, molecular tools are now integrated with breeding to understand the molecular genetics of genotype-based traits and develop better climate-smart crops. The rapid development of omics technologies offers an opportunity to generate novel datasets for crop species. Identifying genes and pathways responsible for significant agronomic traits has been made possible by integrating omics data with genetic and phenotypic information. This paper discusses the importance and use of omics-based strategies, including genomics, transcriptomics, proteomics and phenomics, for agricultural and horticultural crop improvement, which aligns with developing better adaptability in these crop species to the changing climate conditions.
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Affiliation(s)
- Syed Anam Ul Haq
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Tanzeel Bashir
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Thomas H Roberts
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, Sydney Institute of Agriculture, The University of Sydney, Eveleigh, Australia
| | - Amjad M Husaini
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, 190025, India.
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Liu Z, Fan S, Liu H, Yu J, Qiao R, Zhou M, Yang Y, Zhou J, Xie P. Enhanced Detection of Low-Abundance Human Plasma Proteins by Integrating Polyethylene Glycol Fractionation and Immunoaffinity Depletion. PLoS One 2016; 11:e0166306. [PMID: 27832179 PMCID: PMC5104378 DOI: 10.1371/journal.pone.0166306] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/26/2016] [Indexed: 01/27/2023] Open
Abstract
The enormous depth complexity of the human plasma proteome poses a significant challenge for current mass spectrometry-based proteomic technologies in terms of detecting low-level proteins in plasma, which is essential for successful biomarker discovery efforts. Typically, a single-step analytical approach cannot reduce this intrinsic complexity. Current simplex immunodepletion techniques offer limited capacity for detecting low-abundance proteins, and integrated strategies are thus desirable. In this respect, we developed an improved strategy for analyzing the human plasma proteome by integrating polyethylene glycol (PEG) fractionation with immunoaffinity depletion. PEG fractionation of plasma proteins is simple, rapid, efficient, and compatible with a downstream immunodepletion step. Compared with immunodepletion alone, our integrated strategy substantially improved the proteome coverage afforded by PEG fractionation. Coupling this new protocol with liquid chromatography-tandem mass spectrometry, 135 proteins with reported normal concentrations below 100 ng/mL were confidently identified as common low-abundance proteins. A side-by-side comparison indicated that our integrated strategy was increased by average 43.0% in the identification rate of low-abundance proteins, relying on an average 65.8% increase of the corresponding unique peptides. Further investigation demonstrated that this combined strategy could effectively alleviate the signal-suppressive effects of the major high-abundance proteins by affinity depletion, especially with moderate-abundance proteins after incorporating PEG fractionation, thereby greatly enhancing the detection of low-abundance proteins. In sum, the newly developed strategy of incorporating PEG fractionation to immunodepletion methods can potentially aid in the discovery of plasma biomarkers of therapeutic and clinical interest.
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Affiliation(s)
- Zhao Liu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Songhua Fan
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Haipeng Liu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Jia Yu
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Rui Qiao
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Mi Zhou
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Yongtao Yang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Jian Zhou
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
- * E-mail: (JZ); (PX)
| | - Peng Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
- Department of Neurology, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
- * E-mail: (JZ); (PX)
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Lin TE, Cortés-Salazar F, Lesch A, Qiao L, Bondarenko A, Girault HH. Multiple scanning electrochemical microscopy mapping of tyrosinase in micro-contact printed fruit samples on polyvinylidene fluoride membrane. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.03.224] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Sharmin SA, Alam I, Rahman MA, Kim KH, Kim YG, Lee BH. Mapping the leaf proteome of Miscanthus sinensis and its application to the identification of heat-responsive proteins. PLANTA 2013; 238:459-74. [PMID: 23728367 DOI: 10.1007/s00425-013-1900-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 05/14/2013] [Indexed: 05/13/2023]
Abstract
Miscanthus sinensis is a promising bioenergy crop; however, its genome is poorly represented in sequence databases. As an initial step in the comprehensive analysis of the M. sinensis proteome, we report a reference 2-DE protein map of the leaf. A total of 316 protein spots were excised from the gels, digested with trypsin and subjected to matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) or MALDI-TOF/TOF MS. Two hundred and thirty-two protein spots were identified, which are involved in a variety of cellular functions through distinct metabolic pathways. Functional annotation of the proteins revealed a nearly complete C3 and C4 cycle, starch and sugar synthesis pathway, glycolysis pathway, a significant portion of the pentose phosphate pathway, and many enzymes involved in secondary metabolism such as flavonoid/isoflavonoid, kaurene, chalcone, sesquiterpene and lignin biosynthesis. Other proteins belong to primary metabolism, transcription, protein synthesis, protein destination/storage, disease/defense, cell growth/division, transportation and signal transduction. To test the applicability of the constructed map, we studied the effect of heat stress on M. sinensis leaf proteome. Twenty-five protein spots were upregulated, five were newly induced and twenty-five spots were downregulated by heat treatment. The differentially accumulated proteins were involved in photosynthesis, energy metabolism, gene transcription, protein kinases and phosphatases, signal transduction, protein synthesis and heat shock responses. C4-specific pyruvate orthophosphate dikinase, Rubisco large subunit, Rubisco activase and some associated proteins were upregulated during heat stress and tend to restore upon recovery. Identification of these proteins provides some important clues regarding the way M. sinensis copes with hot climate. This work represents the first extensive proteomic description of M. sinensis and provides a reference map and heat-responsive candidates for future molecular and physiological studies of this bioenergy crop.
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Affiliation(s)
- Shamima Akhtar Sharmin
- Division of Applied Life Sciences (BK21 program), IALS, PMBBRC, Gyeongsang National University, Jinju, 660-701, Korea,
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Slattery M, Ankisetty S, Corrales J, Marsh-Hunkin KE, Gochfeld DJ, Willett KL, Rimoldi JM. Marine proteomics: a critical assessment of an emerging technology. JOURNAL OF NATURAL PRODUCTS 2012; 75:1833-1877. [PMID: 23009278 DOI: 10.1021/np300366a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The application of proteomics to marine sciences has increased in recent years because the proteome represents the interface between genotypic and phenotypic variability and, thus, corresponds to the broadest possible biomarker for eco-physiological responses and adaptations. Likewise, proteomics can provide important functional information regarding biosynthetic pathways, as well as insights into mechanism of action, of novel marine natural products. The goal of this review is to (1) explore the application of proteomics methodologies to marine systems, (2) assess the technical approaches that have been used, and (3) evaluate the pros and cons of this proteomic research, with the intent of providing a critical analysis of its future roles in marine sciences. To date, proteomics techniques have been utilized to investigate marine microbe, plant, invertebrate, and vertebrate physiology, developmental biology, seafood safety, susceptibility to disease, and responses to environmental change. However, marine proteomics studies often suffer from poor experimental design, sample processing/optimization difficulties, and data analysis/interpretation issues. Moreover, a major limitation is the lack of available annotated genomes and proteomes for most marine organisms, including several "model species". Even with these challenges in mind, there is no doubt that marine proteomics is a rapidly expanding and powerful integrative molecular research tool from which our knowledge of the marine environment, and the natural products from this resource, will be significantly expanded.
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Affiliation(s)
- Marc Slattery
- Department of Pharmacognosy, School of Pharmacy, The University of Mississippi, University, Mississippi 38677, USA.
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In vivo assessment and potential diagnosis of xenobiotics that perturb the thyroid pathway: Proteomic analysis of Xenopus laevis brain tissue following exposure to model T4 inhibitors. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2010; 5:138-50. [PMID: 20452843 DOI: 10.1016/j.cbd.2010.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 03/24/2010] [Accepted: 03/25/2010] [Indexed: 02/08/2023]
Abstract
As part of a multi-endpoint systems approach to develop comprehensive methods for assessing endocrine stressors in vertebrates, differential protein profiling was used to investigate expression patterns in the brain of the amphibian model (Xenopus laevis) following in vivo exposure to a suite of T4 synthesis inhibitors. We specifically address the application of Two Dimensional Polyacrylamide Gel Electrophoresis (2D PAGE), Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) and LC-MS/MS to assess changes in relative protein expression levels. 2D PAGE and iTRAQ proved to be effective complementary techniques for distinguishing protein changes in the developing amphibian brain in response to T4 synthesis inhibition. This information served to evaluate the use of distinctive protein profiles as a potential mechanism to screen chemicals for endocrine activity in anurans. Regulatory pathways associated with proteins expressed as a result of chemical effect are reported. To our knowledge, this is also the first account of the anuran larvae brain proteome characterization using proteomic technologies. Correlation of protein changes to other cellular and organism-level responses will aid in the development of a more rapid and cost-effective, non-mammalian screening assay for thyroid axis-disrupting chemicals.
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Sveinsdóttir H, Vilhelmsson O, Gudmundsdóttir Á. Proteome analysis of abundant proteins in two age groups of early Atlantic cod (Gadus morhua) larvae. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2008; 3:243-50. [DOI: 10.1016/j.cbd.2008.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 06/04/2008] [Accepted: 06/07/2008] [Indexed: 12/15/2022]
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Chang MS, Ji Q, Zhang J, El-Shourbagy TA. Historical review of sample preparation for chromatographic bioanalysis: pros and cons. Drug Dev Res 2007. [DOI: 10.1002/ddr.20173] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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