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Han Y, Zhou Y, Li H, Gong Z, Liu Z, Wang H, Wang B, Ye X, Liu Y. Identification of diagnostic mRNA biomarkers in whole blood for ankylosing spondylitis using WGCNA and machine learning feature selection. Front Immunol 2022; 13:956027. [PMID: 36172367 PMCID: PMC9510835 DOI: 10.3389/fimmu.2022.956027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/24/2022] [Indexed: 11/28/2022] Open
Abstract
Ankylosing spondylitis (AS) is a common inflammatory spondyloarthritis affecting the spine and sacroiliac joint that finally results in sclerosis of the axial skeleton. Aside from human leukocyte antigen B27, transcriptomic biomarkers in blood for AS diagnosis still remain unknown. Hence, this study aimed to investigate credible AS-specific mRNA biomarkers from the whole blood of AS patients by analyzing an mRNA expression profile (GSE73754) downloaded Gene Expression Omnibus, which includes AS and healthy control blood samples. Weighted gene co-expression network analysis was performed and revealed three mRNA modules associated with AS. By performing gene set enrichment analysis, the functional annotations of these modules revealed immune biological processes that occur in AS. Several feature mRNAs were identified by analyzing the hubs of the protein-protein interaction network, which was based on the intersection between differentially expressed mRNAs and mRNA modules. A machine learning-based feature selection method, SVM-RFE, was used to further screen out 13 key feature mRNAs. After verifying by qPCR, IL17RA, Sqstm1, Picalm, Eif4e, Srrt, Lrrfip1, Synj1 and Cxcr6 were found to be significant for AS diagnosis. Among them, Cxcr6, IL17RA and Lrrfip1 were correlated with severity of AS symptoms. In conclusion, our findings provide a framework for identifying the key mRNAs in whole blood of AS that is conducive for the development of novel diagnostic markers for AS.
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Affiliation(s)
- Yaguang Han
- Department of Orthopaedics, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yiqin Zhou
- Department of Orthopaedics, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
- Department of Radiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Haobo Li
- Department of Orthopaedics, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Zhenyu Gong
- Department of Neurosurgery, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Ziye Liu
- Department of Orthopaedics, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Huan Wang
- Department of Orthopaedics, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Bo Wang
- Department of Orthopaedics, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
- *Correspondence: Bo Wang, ; Xiaojian Ye, ; Yi Liu,
| | - Xiaojian Ye
- Department of Orthopaedics, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Bo Wang, ; Xiaojian Ye, ; Yi Liu,
| | - Yi Liu
- Department of Orthopaedics, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
- Department of Orthopaedics, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Bo Wang, ; Xiaojian Ye, ; Yi Liu,
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Yu W, Xue Z, Zhao X, Zhang R, Liu J, Guo S. Glyphosate-induced GhAG2 is involved in resistance to salt stress in cotton. PLANT CELL REPORTS 2022; 41:1131-1145. [PMID: 35243542 DOI: 10.1007/s00299-022-02844-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 02/05/2022] [Indexed: 06/14/2023]
Abstract
KEY MESSAGE The transcription of GhAG2 was strongly enhanced by glyphosate treatment. Overexpression of GhAG2 could improve plant tolerance to salt and salicylic acid stress. Although glyphosate has been widely used as an herbicide over the past decade owing to its high efficacy on weed controls and worldwide commercialization of glyphosate-resistant crops, little is known about the glyphosate-induced responses and transcriptional changes in cotton plants. Here, we report the identification of 26 differentially expressed genes after glyphosate treatment, among which, six highly up-regulated sequences share homology to cotton expressed sequence tags (ESTs) responsive to abiotic stresses. In addition, we cloned GhAG2, a gene whose transcription was strongly enhanced by glyphosate treatment and other abiotic stresses. Transgenic GhAG2 plants showed improved tolerance to salt, and salicylic acid (SA) stress. The results could open the door to exploring the function of the GhAG2 proteins, the glyphosate-induced transcriptional profiles, and the physiological biochemical responses in cotton and other crops. GhAG2 could also be used to improve salt stress tolerance through breeding and biotechnology in crops. Furthermore, these results could provide guidelines to develop a glyphosate-inducible system for controlled expression of targeted genes in plants.
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Affiliation(s)
- Wancong Yu
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhaohui Xue
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Xianzheng Zhao
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jiping Liu
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture, Agricultural Research Service, Ithaca, NY, 14853, USA.
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Vemanna RS, Vennapusa AR, Easwaran M, Chandrashekar BK, Rao H, Ghanti K, Sudhakar C, Mysore KS, Makarla U. Aldo-keto reductase enzymes detoxify glyphosate and improve herbicide resistance in plants. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:794-804. [PMID: 27611904 PMCID: PMC5466437 DOI: 10.1111/pbi.12632] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 08/31/2016] [Indexed: 05/19/2023]
Abstract
In recent years, concerns about the use of glyphosate-resistant crops have increased because of glyphosate residual levels in plants and development of herbicide-resistant weeds. In spite of identifying glyphosate-detoxifying genes from microorganisms, the plant mechanism to detoxify glyphosate has not been studied. We characterized an aldo-keto reductase gene from Pseudomonas (PsAKR1) and rice (OsAKR1) and showed, by docking studies, both PsAKR1 and OsAKR1 can efficiently bind to glyphosate. Silencing AKR1 homologues in rice and Nicotiana benthamiana or mutation of AKR1 in yeast and Arabidopsis showed increased sensitivity to glyphosate. External application of AKR proteins rescued glyphosate-mediated cucumber seedling growth inhibition. Regeneration of tobacco transgenic lines expressing PsAKR1 or OsAKRI on glyphosate suggests that AKR can be used as selectable marker to develop transgenic crops. PsAKR1- or OsAKRI-expressing tobacco and rice transgenic plants showed improved tolerance to glyphosate with reduced accumulation of shikimic acid without affecting the normal photosynthetic rates. These results suggested that AKR1 when overexpressed detoxifies glyphosate in planta.
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Affiliation(s)
- Ramu S. Vemanna
- Department of Crop PhysiologyUniversity of Agricultural SciencesGKVKBangaloreIndia
- Plant Biology DivisionThe Samuel Roberts Noble FoundationArdmoreOKUSA
| | - Amaranatha Reddy Vennapusa
- Department of Crop PhysiologyUniversity of Agricultural SciencesGKVKBangaloreIndia
- Department of BotanySri Krishnadevaraya UniversityAnantapurIndia
| | - Murugesh Easwaran
- Department of BioinformaticsCentre for BioinformaticsBharathiar UniversityCoimbatoreIndia
| | - Babitha K. Chandrashekar
- Department of Crop PhysiologyUniversity of Agricultural SciencesGKVKBangaloreIndia
- Plant Biology DivisionThe Samuel Roberts Noble FoundationArdmoreOKUSA
| | - Hanumantha Rao
- Department of Crop PhysiologyUniversity of Agricultural SciencesGKVKBangaloreIndia
- Present address: Orris Life SciencesBangaloreIndia
| | - Kirankumar Ghanti
- Department of Crop PhysiologyUniversity of Agricultural SciencesGKVKBangaloreIndia
- Present address: Monsanto Research CenterBangaloreIndia
| | - Chinta Sudhakar
- Department of BotanySri Krishnadevaraya UniversityAnantapurIndia
| | | | - Udayakumar Makarla
- Department of Crop PhysiologyUniversity of Agricultural SciencesGKVKBangaloreIndia
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4
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Doğramacı M, Foley ME, Horvath DP, Hernandez AG, Khetani RS, Fields CJ, Keating KM, Mikel MA, Anderson JV. Glyphosate's impact on vegetative growth in leafy spurge identifies molecular processes and hormone cross-talk associated with increased branching. BMC Genomics 2015; 16:395. [PMID: 25986459 PMCID: PMC4437557 DOI: 10.1186/s12864-015-1627-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 05/11/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Leafy spurge (Euphorbia esula) is a perennial weed that is considered glyphosate tolerant, which is partially attributed to escape through establishment of new vegetative shoots from an abundance of underground adventitious buds. Leafy spurge plants treated with sub-lethal concentrations of foliar-applied glyphosate produce new vegetative shoots with reduced main stem elongation and increased branching. Processes associated with the glyphosate-induced phenotype were determined by RNAseq using aerial shoots derived from crown buds of glyphosate-treated and -untreated plants. Comparison between transcript abundance and accumulation of shikimate or phytohormones (abscisic acid, auxin, cytokinins, and gibberellins) from these same samples was also done to reveal correlations. RESULTS Transcriptome assembly and analyses confirmed differential abundance among 12,918 transcripts (FDR ≤ 0.05) and highlighted numerous processes associated with shoot apical meristem maintenance and stem growth, which is consistent with the increased number of actively growing meristems in response to glyphosate. Foliar applied glyphosate increased shikimate abundance in crown buds prior to decapitation of aboveground shoots, which induces growth from these buds, indicating that 5-enolpyruvylshikimate 3-phosphate (EPSPS) the target site of glyphosate was inhibited. However, abundance of shikimate was similar in a subsequent generation of aerial shoots derived from crown buds of treated and untreated plants, suggesting EPSPS is no longer inhibited or abundance of shikimate initially observed in crown buds dissipated over time. Overall, auxins, gibberellins (precursors and catabolites of bioactive gibberellins), and cytokinins (precursors and bioactive cytokinins) were more abundant in the aboveground shoots derived from glyphosate-treated plants. CONCLUSION Based on the overall data, we propose that the glyphosate-induced phenotype resulted from complex interactions involving shoot apical meristem maintenance, hormone biosynthesis and signaling (auxin, cytokinins, gibberellins, and strigolactones), cellular transport, and detoxification mechanisms.
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Affiliation(s)
- Münevver Doğramacı
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Michael E Foley
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - David P Horvath
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Alvaro G Hernandez
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Radhika S Khetani
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Christopher J Fields
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Kathleen M Keating
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Mark A Mikel
- Department of Crop Sciences, 2608 Institute for Genomic Biology, and Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL, 61801, USA.
| | - James V Anderson
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
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5
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Doğramacı M, Foley ME, Horvath DP, Hernandez AG, Khetani RS, Fields CJ, Keating KM, Mikel MA, Anderson JV. Glyphosate's impact on vegetative growth in leafy spurge identifies molecular processes and hormone cross-talk associated with increased branching. BMC Genomics 2015. [PMID: 25986459 DOI: 10.1186/s12864‐015‐1627‐9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Leafy spurge (Euphorbia esula) is a perennial weed that is considered glyphosate tolerant, which is partially attributed to escape through establishment of new vegetative shoots from an abundance of underground adventitious buds. Leafy spurge plants treated with sub-lethal concentrations of foliar-applied glyphosate produce new vegetative shoots with reduced main stem elongation and increased branching. Processes associated with the glyphosate-induced phenotype were determined by RNAseq using aerial shoots derived from crown buds of glyphosate-treated and -untreated plants. Comparison between transcript abundance and accumulation of shikimate or phytohormones (abscisic acid, auxin, cytokinins, and gibberellins) from these same samples was also done to reveal correlations. RESULTS Transcriptome assembly and analyses confirmed differential abundance among 12,918 transcripts (FDR ≤ 0.05) and highlighted numerous processes associated with shoot apical meristem maintenance and stem growth, which is consistent with the increased number of actively growing meristems in response to glyphosate. Foliar applied glyphosate increased shikimate abundance in crown buds prior to decapitation of aboveground shoots, which induces growth from these buds, indicating that 5-enolpyruvylshikimate 3-phosphate (EPSPS) the target site of glyphosate was inhibited. However, abundance of shikimate was similar in a subsequent generation of aerial shoots derived from crown buds of treated and untreated plants, suggesting EPSPS is no longer inhibited or abundance of shikimate initially observed in crown buds dissipated over time. Overall, auxins, gibberellins (precursors and catabolites of bioactive gibberellins), and cytokinins (precursors and bioactive cytokinins) were more abundant in the aboveground shoots derived from glyphosate-treated plants. CONCLUSION Based on the overall data, we propose that the glyphosate-induced phenotype resulted from complex interactions involving shoot apical meristem maintenance, hormone biosynthesis and signaling (auxin, cytokinins, gibberellins, and strigolactones), cellular transport, and detoxification mechanisms.
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Affiliation(s)
- Münevver Doğramacı
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Michael E Foley
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - David P Horvath
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Alvaro G Hernandez
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Radhika S Khetani
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Christopher J Fields
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Kathleen M Keating
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Mark A Mikel
- Department of Crop Sciences, 2608 Institute for Genomic Biology, and Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL, 61801, USA.
| | - James V Anderson
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
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Samsel A, Seneff S. Glyphosate, pathways to modern diseases III: Manganese, neurological diseases, and associated pathologies. Surg Neurol Int 2015; 6:45. [PMID: 25883837 PMCID: PMC4392553 DOI: 10.4103/2152-7806.153876] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/21/2015] [Indexed: 12/20/2022] Open
Abstract
Manganese (Mn) is an often overlooked but important nutrient, required in small amounts for multiple essential functions in the body. A recent study on cows fed genetically modified Roundup(®)-Ready feed revealed a severe depletion of serum Mn. Glyphosate, the active ingredient in Roundup(®), has also been shown to severely deplete Mn levels in plants. Here, we investigate the impact of Mn on physiology, and its association with gut dysbiosis as well as neuropathologies such as autism, Alzheimer's disease (AD), depression, anxiety syndrome, Parkinson's disease (PD), and prion diseases. Glutamate overexpression in the brain in association with autism, AD, and other neurological diseases can be explained by Mn deficiency. Mn superoxide dismutase protects mitochondria from oxidative damage, and mitochondrial dysfunction is a key feature of autism and Alzheimer's. Chondroitin sulfate synthesis depends on Mn, and its deficiency leads to osteoporosis and osteomalacia. Lactobacillus, depleted in autism, depend critically on Mn for antioxidant protection. Lactobacillus probiotics can treat anxiety, which is a comorbidity of autism and chronic fatigue syndrome. Reduced gut Lactobacillus leads to overgrowth of the pathogen, Salmonella, which is resistant to glyphosate toxicity, and Mn plays a role here as well. Sperm motility depends on Mn, and this may partially explain increased rates of infertility and birth defects. We further reason that, under conditions of adequate Mn in the diet, glyphosate, through its disruption of bile acid homeostasis, ironically promotes toxic accumulation of Mn in the brainstem, leading to conditions such as PD and prion diseases.
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Affiliation(s)
- Anthony Samsel
- Research Scientist and Consultant, Deerfield, NH 03037, USA
| | - Stephanie Seneff
- Spoken Language Systems Group, Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge MA 02139, USA
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Faus I, Zabalza A, Santiago J, Nebauer SG, Royuela M, Serrano R, Gadea J. Protein kinase GCN2 mediates responses to glyphosate in Arabidopsis. BMC PLANT BIOLOGY 2015; 15:14. [PMID: 25603772 PMCID: PMC4312595 DOI: 10.1186/s12870-014-0378-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 12/10/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND The increased selection pressure of the herbicide glyphosate has played a role in the evolution of glyphosate-resistance in weedy species, an issue that is becoming a threat to global agriculture. The molecular components involved in the cellular toxicity response to this herbicide at the expression level are still unidentified. RESULTS In this study, we identify the protein kinase GCN2 as a cellular component that fosters the action of glyphosate in the model plant Arabidopsis thaliana. Comparative studies using wild-type and gcn2 knock-out mutant seedlings show that the molecular programme that the plant deploys after the treatment with the herbicide, is compromised in gcn2. Moreover, gcn2 adult plants show a lower inhibition of photosynthesis, and both seedlings and adult gcn2 plants accumulate less shikimic acid than wild-type after treatment with glyphosate. CONCLUSIONS These results points to an unknown GCN2-dependent factor involved in the cascade of events triggered by glyphosate in plants. Data suggest either that the herbicide does not equally reach the target-enzyme in a gcn2 background, or that a decreased flux in the shikimate pathway in a gcn2 plants minimize the impact of enzyme inhibition.
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Affiliation(s)
- Isabel Faus
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politécnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC). Ciudad Politécnica de la Innovación (CPI), Ed. 8E. C/ Ingeniero Fausto Elio s/n, 46022, Valencia, Spain.
| | - Ana Zabalza
- Departamento de Ciencias del Medio Natural, Universidad Pública de Navarra, Campus Arrosadía, 31006, Pamplona, Spain.
| | - Julia Santiago
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politécnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC). Ciudad Politécnica de la Innovación (CPI), Ed. 8E. C/ Ingeniero Fausto Elio s/n, 46022, Valencia, Spain.
| | - Sergio G Nebauer
- Departamento de Producción Vegetal, Universitat Politécnica de València (UPV), Camino de Vera s/n, 46022, Valencia, Spain.
| | - Mercedes Royuela
- Departamento de Ciencias del Medio Natural, Universidad Pública de Navarra, Campus Arrosadía, 31006, Pamplona, Spain.
| | - Ramon Serrano
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politécnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC). Ciudad Politécnica de la Innovación (CPI), Ed. 8E. C/ Ingeniero Fausto Elio s/n, 46022, Valencia, Spain.
| | - Jose Gadea
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politécnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC). Ciudad Politécnica de la Innovación (CPI), Ed. 8E. C/ Ingeniero Fausto Elio s/n, 46022, Valencia, Spain.
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Seneff S, Swanson N, Li C. Aluminum and Glyphosate Can Synergistically Induce Pineal Gland Pathology: Connection to Gut Dysbiosis and Neurological Disease. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/as.2015.61005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Kuzuoglu-Ozturk D, Cebeci Yalcinkaya O, Akpinar BA, Mitou G, Korkmaz G, Gozuacik D, Budak H. Autophagy-related gene, TdAtg8, in wild emmer wheat plays a role in drought and osmotic stress response. PLANTA 2012; 236:1081-92. [PMID: 22569921 DOI: 10.1007/s00425-012-1657-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 04/16/2012] [Indexed: 05/02/2023]
Abstract
An autophagy-related gene Atg8 was cloned for the first time from wild emmer wheat, named as TdAtg8, and its role on autophagy under abiotic stress conditions was investigated. Examination of TdAtg8 expression patterns indicated that Atg8 expression was strongly upregulated under drought stress, especially in the roots when compared to leaves. LysoTracker(®) red marker, utilized to observe autophagosomes, revealed that autophagy is constitutively active in Triticum dicoccoides. Moreover, autophagy was determined to be induced in plants exposed to osmotic stress when compared to plants grown under normal conditions. Functional studies were executed in yeast to confirm that the TdATG8 protein is functional, and showed that the TdAtg8 gene complements the atg8∆::kan MX yeast mutant strain grown under nitrogen deficiency. For further functional analysis, TdATG8 protein was expressed in yeast and analyzed using Western immunoblotting. Atg8-silenced plants were exposed to drought stress and chlorophyll and malondialdehyde (MDA) content measurements demonstrated that Atg8 plays a key role on drought stress tolerance. In addition, Atg8-silenced plants exposed to osmotic stress were found to have decreased Atg8 expression level in comparison to controls. Hence, Atg8 is a positive regulator in osmotic and drought stress response.
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Affiliation(s)
- Duygu Kuzuoglu-Ozturk
- Biological Sciences and Bioengineering Program, Sabanci University, Tuzla, Istanbul, Turkey
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10
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Li S, Ran XQ, Xu L, Wang JF. microRNA and mRNA Expression Profiling Analysis of Dichlorvos Cytotoxicity in Porcine Kidney Epithelial PK15 Cells. DNA Cell Biol 2011; 30:1073-83. [DOI: 10.1089/dna.2011.1267] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Sheng Li
- Key Laboratory of Green Pesticide and Agriculture Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Xue Qin Ran
- Faculty of Animal Science and Veterinary Medicine, Guizhou University, Guiyang, China
| | - Lin Xu
- Key Laboratory of Green Pesticide and Agriculture Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Jia Fu Wang
- Key Laboratory of Green Pesticide and Agriculture Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
- Faculty of Animal Science and Veterinary Medicine, Guizhou University, Guiyang, China
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11
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Kantar M, Lucas SJ, Budak H. miRNA expression patterns of Triticum dicoccoides in response to shock drought stress. PLANTA 2011; 233:471-84. [PMID: 21069383 DOI: 10.1007/s00425-010-1309-4] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Accepted: 10/25/2010] [Indexed: 05/18/2023]
Abstract
Drought is a major environmental stress factor that affects plant growth and development worldwide. Wild emmer wheat (Triticum turgidum ssp. dicoccoides), the ancestor of domesticated durum wheat (Triticum turgidum ssp. durum), has great potential for improving the understanding of the wheat drought response. MicroRNAs (miRNAs) are a recently discovered class of gene expression regulators that have also been linked to several plant stress responses; however, this relationship is just beginning to be understood. miRNA expression patterns of drought-resistant wild emmer wheat in response to drought stress were investigated using a plant miRNA microarray platform. Expression was detected to be 205 miRNAs in control and 438 miRNAs in drought-stressed leaf and root tissues. Of these miRNAs, the following 13 were differentially regulated in response to drought: miR1867, miR896, miR398, miR528, miR474, miR1450, miR396, miR1881, miR894, miR156, miR1432, miR166 and miR171. Regulation of miRNAs upon 4 and 8 h drought stress applications observed by qRT-PCR. Target transcripts of differentially regulated miRNAs were computationally predicted. In addition to miRNA microarray study, five new conserved T. turgidum miRNAs were identified through a homology-based approach, and their secondary structures and putative targets were predicted. These findings both computationally and experimentally highlight the presence of miRNAs in T. dicoccoides and further extend the role of miRNAs under shock drought stress conditions.
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Affiliation(s)
- Melda Kantar
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
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12
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Jin K, Zheng X, Xia Y. Gene Expression Profiling via Multigene Concatemers. PLoS One 2011; 6:e15711. [PMID: 21267445 PMCID: PMC3022625 DOI: 10.1371/journal.pone.0015711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 11/23/2010] [Indexed: 12/26/2022] Open
Abstract
We established a novel method, Gene Expression Profiling via Multigene Concatemers (MgC-GEP), to study multigene expression patterns simultaneously. This method consists of the following steps: (1) cDNA was obtained using specific reverse primers containing an adaptor. (2) During the initial 1-3 cycles of polymerase chain reaction (PCR), the products containing universal adaptors with digestion sites at both termini were amplified using specific forward and reverse primers containing the adaptors. (3) In the subsequent 4-28 cycles, the universal adaptors were used as primers to yield products. (4) The products were digested and ligated to produce concatemers. (5) The concatemers were cloned into the vector and sequenced. Then, the occurrence of each gene tag was determined. To validate MgC-GEP, we analyzed 20 genes in Saccharomyces cerevisiae induced by weak acid using MgC-GEP combined with real-time reverse transcription (RT)-PCR. Compared with the results of real-time RT-PCR and the previous reports of microarray analysis, MgC-GEP can precisely determine the transcript levels of multigenes simultaneously. Importantly, MgC-GEP is a cost effective strategy that can be widely used in most laboratories without specific equipment. MgC-GEP is a potentially powerful tool for multigene expression profiling, particularly for moderate-throughput analysis.
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Affiliation(s)
- Kai Jin
- Genetic Engineering Research Center, School of Bioengineering, Chongqing University, Chongqing, People's Republic of China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, People's Republic of China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, People's Republic of China
| | - Xiaoli Zheng
- Genetic Engineering Research Center, School of Bioengineering, Chongqing University, Chongqing, People's Republic of China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, People's Republic of China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, People's Republic of China
| | - Yuxian Xia
- Genetic Engineering Research Center, School of Bioengineering, Chongqing University, Chongqing, People's Republic of China
- Chongqing Engineering Research Center for Fungal Insecticide, Chongqing, People's Republic of China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission, Chongqing, People's Republic of China
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Chong WPK, Yusufi FNK, Lee DY, Reddy SG, Wong NSC, Heng CK, Yap MGS, Ho YS. Metabolomics-based identification of apoptosis-inducing metabolites in recombinant fed-batch CHO culture media. J Biotechnol 2010; 151:218-24. [PMID: 21167884 DOI: 10.1016/j.jbiotec.2010.12.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 12/03/2010] [Accepted: 12/08/2010] [Indexed: 10/18/2022]
Abstract
A liquid chromatography-mass spectrometry (LC-MS) based metabolomics platform was previously established to identify and profile extracellular metabolites in culture media of mammalian cells. This presented an opportunity to isolate novel apoptosis-inducing metabolites accumulating in the media of antibody-producing Chinese hamster ovary (CHO mAb) fed-batch bioreactor cultures. Media from triplicate cultures were collected daily for the metabolomics analysis. Concurrently, cell pellets were obtained for determination of intracellular caspase activity. Metabolite profiles from the LC-MS data were subsequently examined for their degree of correlation with the caspase activity. A panel of extracellular metabolites, the majority of which were nucleotides/nucleosides and amino acid derivatives, exhibited good (R² > 0.8) and reproducible correlation. Some of these metabolites, such as oxidized glutathione, AMP and GMP, were later shown to induce apoptosis when introduced to fresh CHO mAb cultures. Finally, metabolic engineering targets were proposed to potentially counter the harmful effects of these metabolites.
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Affiliation(s)
- William P K Chong
- Bioprocessing Technology Institute, A*STAR (Agency for Science, Technology and Research), 20 Biopolis Way, #06-01, Singapore 138668, Singapore. william
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14
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Unver T, Bakar M, Shearman RC, Budak H. Genome-wide profiling and analysis of Festuca arundinacea miRNAs and transcriptomes in response to foliar glyphosate application. Mol Genet Genomics 2010; 283:397-413. [PMID: 20213187 DOI: 10.1007/s00438-010-0526-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2009] [Accepted: 02/10/2010] [Indexed: 12/14/2022]
Abstract
Glyphosate is a broad spectrum herbicide which has been widely used for non-selective weed control in turfgrass management. Festuca arundinacea cv. Falcon was shown to be one of the tolerant turfgrass species in response to varying levels of glyphosate [5% (1.58 mM), 20% (6.32 mM)] recommended for weed control. However, there is a lack of knowledge on the mRNA expression patterns and miRNA, critical regulators of gene expression, in response to varying levels of glyphosate treatments. Here, we investigate the transcriptome and miRNA-guided post-transcriptional networks using plant miRNA microarray and Affymetrix GeneChip Wheat Genome Array platforms. Transcriptome analysis revealed 93 up-regulated and 78 down-regulated genes, whereas a smaller number showed inverse differential expressions. miRNA chip analysis indicated a number of (34 out of the 853) plant miRNAs were differentially regulated in response to glyphosate treatments. Target transcripts of differentially regulated miRNAs were predicted and nine of them were quantified by quantitative real-time PCR (qRT-PCR). Target transcripts of miRNAs validate the expression level change of miRNAs detected by miRNA microarray analysis. Down-regulation of miRNAs upon 5 and 20% glyphosate applications led to the up-regulation of their target observed by qRT-PCR or vice versa. Quantification of F. arundinacea miRNA, homologous of osa-miR1436, revealed the agreement between the Affymetrix and miRNA microarray analyses. In addition to miRNA microarray experiment, 25 conserved F. arundinacea miRNAs were identified through homology-based approach and their secondary structures were predicted. The results presented serve as analyses of genome-wide expression profiling of miRNAs and target mRNAs in response to foliar glyphosate treatment in grass species.
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Affiliation(s)
- Turgay Unver
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
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