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Hekmati Z, Solouki M, Emamjomeh A, Zahiri J, Mirzaie-Asl A. Transcriptomic Analysis of Cyclamen persicum to Identify Invovled Genes in Triterpene Secondary Metabolites Pathway. Biochem Genet 2024:10.1007/s10528-024-10745-1. [PMID: 38578589 DOI: 10.1007/s10528-024-10745-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/16/2024] [Indexed: 04/06/2024]
Abstract
Saponins are considered as a diverse group of natural active compounds, which are widely found in crops. Mevalonate pathway (MVA) is regarded as the main pathway for synthesis of saponins in crops. This study aims to compare transcriptome of the leaf with tuber of crop including tubers and roots. First, more than 166 million reads were generated. The existence of 36,678 unigenes in the two samples out of 48,936 assembled ones showed a significant difference in expression. Finally, 310 and 290 highly up-regulated genes in leaf and tuber were selected for the next analysis. In addition, the expression profiles of 13 key genes in the MVA pathway were compared in RNA sequencing and reverse transcription-quantitative polymerase chain reaction analysis. The results indicated that cyclamen tuber has a higher level of expression of MVA pathway genes. The topological analysis for gene co-expression network involved in triterpenoid synthesis represented that the genes at the beginning of such pathway play a critical role so that the reduction of their expression challenges triterpenoid synthesis severely. The tuber of the cyclamen appears to be the major site of triterpene synthesis, and transfer of excess Isopentenyl pyrophosphate (IPP) from tuber to leaf activates downstream genes in leaf of crop.
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Affiliation(s)
- Zahra Hekmati
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Daneshgah Blvd., Zabol, Iran
| | - Mahmood Solouki
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Daneshgah Blvd., Zabol, Iran.
| | - Abbasali Emamjomeh
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Daneshgah Blvd., Zabol, Iran.
- Laboratory of Computational Biotechnology and Bioinformatics (CBB Lab), Department of Bioinformatics, University of Zabol, Zabol, Iran.
| | - Javad Zahiri
- Department of Neuroscience, University of California, San Diego, San Diego, CA, USA
| | - Asghar Mirzaie-Asl
- Department of Agricultural Biotechnology, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
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Chang W, Lee W, Lin Y, Shih J, Hong C, Chen Z, Chu C, Hsu C. Transpulmonary Expression of Exosomal microRNAs in Idiopathic and Congenital Heart Disease-Related Pulmonary Arterial Hypertension. J Am Heart Assoc 2023; 12:e031435. [PMID: 38014665 PMCID: PMC10727351 DOI: 10.1161/jaha.123.031435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/31/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Pulmonary artery hypertension (PAH) is a fatal disease characterized by a complex pathogenesis. Exosomes containing microRNAs (miRs) have emerged as a novel biomarker. Transpulmonary exosomal miRs offer valuable insights into pulmonary circulation microenvironments. Hereby, we aimed to explore the potentials of transpulmonary exosomal miRs as differentiating factors between idiopathic PAH and congenital heart disease (CHD)-related PAH. METHODS AND RESULTS During right heart catheterization, we collected exosomes at pulmonary arteries in 25 patients diagnosed with idiopathic PAH and 20 patients with CHD-related PAH. Next-generation sequencing identified several candidate exosomal miRs. Using quantitative polymerase chain reaction, we validated the expressions of these miRs and revealed significantly elevated expressions of miR-21, miR-139-5p, miR-155-5p, let-7f-5p, miR-328-3p, miR-330-3p, and miR-103a-3p in patients with CHD-related PAH, in contrast to patients with idiopathic PAH. Among these miRs, miR-21 exhibited the highest expression in patients with CHD-related PAH. These findings were further corroborated in an external cohort comprising 10 patients with idiopathic PAH and 8 patients with CHD-related PAH. Using an in vitro flow model simulating the shear stress experienced by pulmonary endothelial cells, we observed a significant upregulation of miR-21. Suppressing miR-21 rescued the shear stress-induced downregulation of the RAS/phosphatidylinositol 3-kinase/protein kinase B pathway, leading to a mitigation of apoptosis. CONCLUSIONS Our study identified a pronounced expression of transpulmonary exosomal miR-21, particularly in patients with CHD-related PAH, through next-generation sequencing analysis. Further investigation is warranted to elucidate the regulatory mechanisms involving miR-21 in the pathophysiology of PAH.
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Affiliation(s)
- Wei‐Ting Chang
- School of Medicine and Doctoral Program of Clinical and Experimental Medicine, College of Medicine and Center of Excellence for Metabolic Associated Fatty Liver DiseaseNational Sun Yat‐sen UniversityKaohsiungTaiwan
- Division of Cardiology, Department of Internal MedicineChi Mei Medical CenterTainanTaiwan
| | - Wei‐Chieh Lee
- Division of Cardiology, Department of Internal MedicineChi Mei Medical CenterTainanTaiwan
- School of Medicine, College of MedicineNational Sun Yat‐sen UniversityKaohsiungTaiwan
| | - Yu‐Wen Lin
- Division of Cardiology, Department of Internal MedicineChi Mei Medical CenterTainanTaiwan
| | - Jhih‐Yuan Shih
- Division of Cardiology, Department of Internal MedicineChi Mei Medical CenterTainanTaiwan
- School of Medicine, College of MedicineNational Sun Yat‐sen UniversityKaohsiungTaiwan
| | - Chon‐Seng Hong
- Division of Cardiology, Department of Internal MedicineChi Mei Medical CenterTainanTaiwan
- Department of Health and NutritionChia Nan University of Pharmacy and ScienceTainanTaiwan
| | - Zhih‐Cherng Chen
- Division of Cardiology, Department of Internal MedicineChi Mei Medical CenterTainanTaiwan
- School of Medicine, College of MedicineNational Sun Yat‐sen UniversityKaohsiungTaiwan
| | - Chun‐Yuan Chu
- Division of Cardiology, Department of Internal MedicineKaohsiung Medical University HospitalKaohsiungTaiwan
| | - Chih‐Hsin Hsu
- Division of Critical Care, Department of Internal MedicineNational Cheng Kung University Hospital, College of Medicine, National Cheng Kung UniversityTainanTaiwan
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Rather MA, Agarwal D, Bhat TA, Khan IA, Zafar I, Kumar S, Amin A, Sundaray JK, Qadri T. Bioinformatics approaches and big data analytics opportunities in improving fisheries and aquaculture. Int J Biol Macromol 2023; 233:123549. [PMID: 36740117 DOI: 10.1016/j.ijbiomac.2023.123549] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Aquaculture has witnessed an excellent growth rate during the last two decades and offers huge potential to provide nutritional as well as livelihood security. Genomic research has contributed significantly toward the development of beneficial technologies for aquaculture. The existing high throughput technologies like next-generation technologies generate oceanic data which requires extensive analysis using appropriate tools. Bioinformatics is a rapidly evolving science that involves integrating gene based information and computational technology to produce new knowledge for the benefit of aquaculture. Bioinformatics provides new opportunities as well as challenges for information and data processing in new generation aquaculture. Rapid technical advancements have opened up a world of possibilities for using current genomics to improve aquaculture performance. Understanding the genes that govern economically relevant characteristics, necessitates a significant amount of additional research. The various dimensions of data sources includes next-generation DNA sequencing, protein sequencing, RNA sequencing gene expression profiles, metabolic pathways, molecular markers, and so on. Appropriate bioinformatics tools are developed to mine the biologically relevant and commercially useful results. The purpose of this scoping review is to present various arms of diverse bioinformatics tools with special emphasis on practical translation to the aquaculture industry.
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Affiliation(s)
- Mohd Ashraf Rather
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries Ganderbal, Sher-e- Kashmir University of Agricultural Science and Technology, Kashmir, India.
| | - Deepak Agarwal
- Institute of Fisheries Post Graduation Studies OMR Campus, Vaniyanchavadi, Chennai, India
| | | | - Irfan Ahamd Khan
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries Ganderbal, Sher-e- Kashmir University of Agricultural Science and Technology, Kashmir, India
| | - Imran Zafar
- Department of Bioinformatics and Computational Biology, Virtual University Punjab, Pakistan
| | - Sujit Kumar
- Department of Bioinformatics and Computational Biology, Virtual University Punjab, Pakistan
| | - Adnan Amin
- Postgraduate Institute of Fisheries Education and Research Kamdhenu University, Gandhinagar-India University of Kurasthra, India; Department of Aquatic Environmental Management, Faculty of Fisheries Rangil- Ganderbel -SKUAST-K, India
| | - Jitendra Kumar Sundaray
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002, India
| | - Tahiya Qadri
- Division of Food Science and Technology, SKUAST-K, Shalimar, India
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Pons S, Frapy E, Sereme Y, Gaultier C, Lebreton F, Kropec A, Danilchanka O, Schlemmer L, Schrimpf C, Allain M, Angoulvant F, Lecuyer H, Bonacorsi S, Aschard H, Sokol H, Cywes-Bentley C, Mekalanos JJ, Guillard T, Pier GB, Roux D, Skurnik D. A high-throughput sequencing approach identifies immunotherapeutic targets for bacterial meningitis in neonates. EBioMedicine 2023; 88:104439. [PMID: 36709579 PMCID: PMC9900374 DOI: 10.1016/j.ebiom.2023.104439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Worldwide, Escherichia coli is the leading cause of neonatal Gram-negative bacterial meningitis, but full understanding of the pathogenesis of this disease is not yet achieved. Moreover, to date, no vaccine is available against bacterial neonatal meningitis. METHODS Here, we used Transposon Sequencing of saturated banks of mutants (TnSeq) to evaluate E. coli K1 genetic fitness in murine neonatal meningitis. We identified E. coli K1 genes encoding for factors important for systemic dissemination and brain infection, and focused on products with a likely outer-membrane or extra-cellular localization, as these are potential vaccine candidates. We used in vitro and in vivo models to study the efficacy of active and passive immunization. RESULTS We selected for further study the conserved surface polysaccharide Poly-β-(1-6)-N-Acetyl Glucosamine (PNAG), as a strong candidate for vaccine development. We found that PNAG was a virulence factor in our animal model. We showed that both passive and active immunization successfully prevented and/or treated meningitis caused by E. coli K1 in neonatal mice. We found an excellent opsonophagocytic killing activity of the antibodies to PNAG and in vitro these antibodies were also able to decrease binding, invasion and crossing of E. coli K1 through two blood brain barrier cell lines. Finally, to reinforce the potential of PNAG as a vaccine candidate in bacterial neonatal meningitis, we demonstrated that Group B Streptococcus, the main cause of neonatal meningitis in developed countries, also produced PNAG and that antibodies to PNAG could protect in vitro and in vivo against this major neonatal pathogen. INTERPRETATION Altogether, these results indicate the utility of a high-throughput DNA sequencing method to identify potential immunotherapy targets for a pathogen, including in this study a potential broad-spectrum target for prevention of neonatal bacterial infections. FUNDINGS ANR Seq-N-Vaq, Charles Hood Foundation, Hearst Foundation, and Groupe Pasteur Mutualité.
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Affiliation(s)
- Stéphanie Pons
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA,Department of Anesthesiology and Critical Care, Sorbonne University, GRC 29, AP-HP, DMU DREAM, Pitié-Salpêtrière, Paris, France
| | - Eric Frapy
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, F-75015 Paris, France,Faculté de Médecine, University of Paris City, Paris, France
| | - Youssouf Sereme
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, F-75015 Paris, France,Faculté de Médecine, University of Paris City, Paris, France
| | - Charlotte Gaultier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - François Lebreton
- Department of Ophthalmology and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02114, USA
| | - Andrea Kropec
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Olga Danilchanka
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Laura Schlemmer
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, F-75015 Paris, France
| | - Cécile Schrimpf
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, F-75015 Paris, France
| | - Margaux Allain
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, F-75015 Paris, France
| | - François Angoulvant
- Assistance Publique - Hôpitaux de Paris, Pediatric Emergency Department, Necker-Enfants Malades University Hospital, University of Paris City, Paris, France,INSERM, Centre de Recherche des Cordeliers, UMRS 1138, Sorbonne Université, Université de Paris, Paris, France
| | - Hervé Lecuyer
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, F-75015 Paris, France,Faculté de Médecine, University of Paris City, Paris, France,Department of Clinical Microbiology, Fédération Hospitalo-Universitaire Prématurité (FHU PREMA), Necker-Enfants Malades University Hospital, University of Paris City, Paris, France
| | - Stéphane Bonacorsi
- E IAME, UMR 1137, INSERM, Université de Paris, AP-HP, Paris, France,Laboratoire de Microbiologie, Hôpital Robert Debré, AP-HP, Paris, France
| | - Hugues Aschard
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France,Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Harry Sokol
- Gastroenterology Department, Sorbonne University, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, F-75012 Paris, France,INRA, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France,Paris Centre for Microbiome Medicine FHU, Paris, France
| | - Colette Cywes-Bentley
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - John J. Mekalanos
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Guillard
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA,Université de Reims Champagne-Ardenne, SFR CAP-Santé, Inserm UMR-S 1250 P3Cell, Reims, France,Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière-Parasitologie-Mycologie, CHU, Reims, France
| | - Gerald B. Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Damien Roux
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA,Université de Paris, INSERM, UMR 1137 IAME, F-75018 Paris, France,AP-HP, Médecine Intensive Réanimation, Hôpital Louis Mourier, F-92700 Colombes, France
| | - David Skurnik
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; CNRS, INSERM, Institut Necker Enfants Malades-INEM, F-75015 Paris, France; Faculté de Médecine, University of Paris City, Paris, France; Department of Clinical Microbiology, Fédération Hospitalo-Universitaire Prématurité (FHU PREMA), Necker-Enfants Malades University Hospital, University of Paris City, Paris, France.
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Khodavirdipour A, Safaralizadeh R, Haghi M, Hosseinpourfeizi MA. Comparative de novo transcriptome analysis of flower and root of Oliveria decumbens Vent. to identify putative genes in terpenes biosynthesis pathway. Front Genet 2022; 13:916183. [PMID: 35991569 PMCID: PMC9386285 DOI: 10.3389/fgene.2022.916183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
The Oliveria decumbens Vent. is a wild, rare, annual medicinal plant and endemic plant of Iran that has metabolites (mostly terpenes) which make it a precious plant in Persian Traditional Medicine and also a potential chemotherapeutic agent. The lack of genetic resources has slowed the discovery of genes involved in the terpenes biosynthesis pathway. It is a wild relative of Daucus carota. In this research, we performed the transcriptomic differences between two samples, flower and root of Oliveria decumbens, and also analyze the expression value of the genes involved in terpenoid biosynthesis by RNA-seq and its essential oil’s phytochemicals analyzed by GC/MS. In total, 136,031,188 reads from two samples of flower and root have been produced. The result shows that the MEP pathway is mostly active in the flower and the MVA in the root. Three genes of GPP, FPPS, and GGPP that are the precursors in the synthesis of mono, di, and triterpenes are upregulated in root and 23 key genes were identified that are involved in the biosynthesis of terpenes. Three genes had the highest upregulation in the root including, and on the other hand, another three genes had the expression only in the flower. Meanwhile, 191 and 185 upregulated genes in the flower and root of the plant, respectively, were selected for the gene ontology analysis and reconstruction of co-expression networks. The current research is the first of its kind on Oliveria decumbens transcriptome and discussed 67 genes that have been deposited into the NCBI database. Collectively, the information obtained in this study unveils the new insights into characterizing the genetic blueprint of Oliveria decumbens Vent. which paved the way for medical/plant biotechnology and the pharmaceutical industry in the future.
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Díaz-Silva M, Maldonado J, Veloso P, Delgado N, Silva H, Gallardo JA. RNA-Seq analysis and transcriptome assembly of Salicornia neei reveals a powerful system for ammonium detoxification. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Gao C, Cai X, Cao M, Fu Q, Yang N, Liu X, Wang B, Li C. Comparative analysis of the miRNA-mRNA regulation networks in turbot (Scophthalmus maximus L.) following Vibrio anguillarum infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 124:104164. [PMID: 34129850 DOI: 10.1016/j.dci.2021.104164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/06/2021] [Accepted: 06/06/2021] [Indexed: 06/12/2023]
Abstract
MicroRNAs could not only regulate posttranscriptional silencing of target genes in eukaryotic organisms, but also have positive effect on their target genes as well. These microRNAs have been reported to be involved in mucosal immune responses to pathogen infection in teleost. Therefore, we constructed the immune-related miRNA-mRNA networks in turbot intestine following Vibrio anguillarum infection. In our results, 1550 differentially expressed (DE) genes and 167 DE miRNAs were identified. 113 DE miRNAs targeting 89 DE mRNAs related to immune response were used to construct miRNA-mRNA interaction networks. Functional analysis showed that target genes were associated with synthesis and degradation of ketone bodies, mucin type O-Glycan biosynthesis, homologous recombination, biotin metabolism, and intestinal immune network for IgA production that were equivalent to the function of IgT and IgM in fish intestine. Finally, 10 DE miRNAs and 7 DE mRNAs were selected for validating the accuracy of high-throughput sequencing results by qRT-PCR. The results of this study will provide valuable information for the elucidation of the regulation mechanisms of miRNA-mRNA interactions involved in disease resistance in teleost mucosal immune system.
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Affiliation(s)
- Chengbin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China; Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, 90 South St, Murdoch, Perth, 6150, Australia
| | - Xin Cai
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China; Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, 90 South St, Murdoch, Perth, 6150, Australia
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiaoli Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Beibei Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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Transcriptome Analysis Reveals Potential Mechanisms for Ethylene-Inducible Pedicel–Fruit Abscission Zone Activation in Non-Climacteric Sweet Cherry (Prunus avium L.). HORTICULTURAE 2021; 7. [PMID: 36313595 PMCID: PMC9608358 DOI: 10.3390/horticulturae7090270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The harvesting of sweet cherry (Prunus avium L.) fruit is a labor-intensive process. The mechanical harvesting of sweet cherry fruit is feasible; however, it is dependent on the formation of an abscission zone at the fruit–pedicel junction. The natural propensity for pedicel—fruit abscission zone (PFAZ) activation varies by cultivar, and the general molecular basis for PFAZ activation is not well characterized. In this study, ethylene-inducible change in pedicel fruit retention force (PFRF) was recorded in a developmental time-course with a concomitant analysis of the PFAZ transcriptome from three sweet cherry cultivars. In ‘Skeena’, mean PFRF for both control and treatment fruit dropped below the 0.40 kg-force (3.92 N) threshold for mechanical harvesting, indicating the activation of a discrete PFAZ. In ‘Bing’, mean PFRF for both control and treatment groups decreased over time. However, a mean PFRF conducive to mechanical harvesting was achieved only in the ethylene-treated fruit. While in ‘Chelan’ the mean PFRF of the control and treatment groups did not meet the threshold required for efficient mechanical harvesting. Transcriptome analysis of the PFAZ region followed by the functional annotation, differential expression analysis, and gene ontology (GO) enrichment analyses of the data facilitated the identification of phytohormone-responsive and abscission-related transcripts, as well as processes that exhibited differential expression and enrichment in a cultivar-dependent manner over the developmental time-course. Additionally, read alignment-based variant calling revealed several short variants in differentially expressed genes, associated with enriched gene ontologies and associated metabolic processes, lending potential insight into the genetic basis for different abscission responses between the cultivars. These results provide genetic targets for the induction or inhibition of PFAZ activation, depending on the desire to harvest the fruit with or without the stem attached. Understanding the genetic mechanisms underlying the development of the PFAZ will inform future cultivar development while laying a foundation for mechanized sweet cherry harvest.
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Buckley AM, Moura IB, Arai N, Spittal W, Clark E, Nishida Y, Harris HC, Bentley K, Davis G, Wang D, Mitra S, Higashiyama T, Wilcox MH. Trehalose-Induced Remodelling of the Human Microbiota Affects Clostridioides difficile Infection Outcome in an In Vitro Colonic Model: A Pilot Study. Front Cell Infect Microbiol 2021; 11:670935. [PMID: 34277467 PMCID: PMC8284250 DOI: 10.3389/fcimb.2021.670935] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/02/2021] [Indexed: 12/19/2022] Open
Abstract
Within the human intestinal tract, dietary, microbial- and host-derived compounds are used as signals by many pathogenic organisms, including Clostridioides difficile. Trehalose has been reported to enhance virulence of certain C. difficile ribotypes; however, such variants are widespread and not correlated with clinical outcomes for patients suffering from C. difficile infection (CDI). Here, we make preliminary observations on how trehalose supplementation affects the microbiota in an in vitro model and show that trehalose-induced changes can reduce the outgrowth of C. difficile, preventing simulated CDI. Three clinically reflective human gut models simulated the effects of sugar (trehalose or glucose) or saline ingestion on the microbiota. Models were instilled with sugar or saline and further exposed to C. difficile spores. The recovery of the microbiota following antibiotic treatment and CDI induction was monitored in each model. The human microbiota remodelled to utilise the bioavailable trehalose. Clindamycin induction caused simulated CDI in models supplemented with either glucose or saline; however, trehalose supplementation did not result in CDI, although limited spore germination did occur. The absence of CDI in trehalose model was associated with enhanced abundances of Finegoldia, Faecalibacterium and Oscillospira, and reduced abundances of Klebsiella and Clostridium spp., compared with the other models. Functional analysis of the microbiota in the trehalose model revealed differences in the metabolic pathways, such as amino acid metabolism, which could be attributed to prevention of CDI. Our data show that trehalose supplementation remodelled the microbiota, which prevented simulated CDI, potentially due to enhanced recovery of nutritionally competitive microbiota against C. difficile.
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Affiliation(s)
- Anthony M. Buckley
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Ines B. Moura
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Norie Arai
- R&D Division, Hayashibara Co. Ltd./NAGASE Group, Okayama, Japan
| | - William Spittal
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Emma Clark
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | | | - Hannah C. Harris
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Karen Bentley
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Georgina Davis
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Dapeng Wang
- LeedsOmics, University of Leeds, Leeds, United Kingdom
| | - Suparna Mitra
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | | | - Mark H. Wilcox
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
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Transcriptional and Metabolic Response of Wine-Related Lactiplantibacillus plantarum to Different Conditions of Aeration and Nitrogen Availability. FERMENTATION 2021. [DOI: 10.3390/fermentation7020068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Lactic acid bacteria (LAB) perform the process of malolactic fermentation (MLF) in wine. Availability of oxygen and nitrogen nutrients could influence LAB growth, malolactic activity, and other metabolic pathways, impacting the subsequent wine quality. The impact of these two factors has received limited investigation within LAB, especially on a transcriptome level. The aim of this study was to evaluate metabolic changes in the strain Lactiplantibacillus plantarum IWBT B063, growing in synthetic grape juice medium (GJM) under different oxygen exposure conditions, and with low availability of nitrogen-based nutrients. Next-generation sequencing was used to analyze expression across the transcriptome (RNA-seq), in combination with conventional microbiological and chemical analysis. L. plantarum consumed the malic acid present in all the conditions evaluated, with a slight delay and impaired growth for nitrogen limitation and for anaerobiosis. Comparison of L. plantarum transcriptome during growth in GJM with and without O2 revealed differential expression of 148 functionally annotated genes, which were mostly involved in carbohydrate metabolism, genetic information processing, and signaling and cellular processes. In particular, genes with a protective role against oxidative stress and genes related to amino acid metabolism were differentially expressed. This study confirms the suitability of L. plantarum IWBT B063 to carry out MLF in different environmental conditions due to its potential adaption to the stress conditions tested and provides a better understanding of the genetic background of an industrially relevant strain.
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11
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Landi M, Agati G, Fini A, Guidi L, Sebastiani F, Tattini M. Unveiling the shade nature of cyanic leaves: A view from the "blue absorbing side" of anthocyanins. PLANT, CELL & ENVIRONMENT 2021; 44:1119-1129. [PMID: 32515010 DOI: 10.1111/pce.13818] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 06/01/2020] [Indexed: 05/02/2023]
Abstract
Anthocyanins have long been suggested as having great potential in offering photoprotection to plants facing high light irradiance. Nonetheless, their effective ability in protecting the photosynthetic apparatus from supernumerary photons has been questioned by some authors, based upon the inexact belief that anthocyanins almost exclusively absorb green photons, which are poorly absorbed by chlorophylls. Here we focus on the blue light absorbing features of anthocyanins, a neglected issue in anthocyanin research. Anthocyanins effectively absorb blue photons: the absorbance of blue relative to green photons increases from tri- to mono-hydroxy B-ring substituted structures, reaching up to 50% of green photons absorption. We offer a comprehensive picture of the molecular events activated by low blue-light availability, extending our previous analysis in purple and green basil, which we suggest to be responsible for the "shade syndrome" displayed by cyanic leaves. While purple leaves display overexpression of genes promoting chlorophyll biosynthesis and light harvesting, in green leaves it is the genes involved in the stability/repair of photosystems that are largely overexpressed. As a corollary, this adds further support to the view of an effective photoprotective role of anthocyanins. We discuss the profound morpho-anatomical adjustments imposed by the epidermal anthocyanin shield, which reflect adjustments in light harvesting capacity under imposed shade and make complex the analysis of the photosynthetic performance of cyanic versus acyanic leaves.
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Affiliation(s)
- Marco Landi
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Giovanni Agati
- Institute of Applied Physics 'Nello Carrara', Florence, Italy
| | - Alessio Fini
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy University of Milan, Milan, Italy
| | - Lucia Guidi
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Federico Sebastiani
- Institute for Sustainable Plant Protection, National Research Council of Italy, Florence, Italy
| | - Massimiliano Tattini
- Institute for Sustainable Plant Protection, National Research Council of Italy, Florence, Italy
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Hickey TE, Selth LA, Chia KM, Laven-Law G, Milioli HH, Roden D, Jindal S, Hui M, Finlay-Schultz J, Ebrahimie E, Birrell SN, Stelloo S, Iggo R, Alexandrou S, Caldon CE, Abdel-Fatah TM, Ellis IO, Zwart W, Palmieri C, Sartorius CA, Swarbrick A, Lim E, Carroll JS, Tilley WD. The androgen receptor is a tumor suppressor in estrogen receptor-positive breast cancer. Nat Med 2021; 27:310-320. [PMID: 33462444 DOI: 10.1038/s41591-020-01168-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/03/2020] [Indexed: 01/28/2023]
Abstract
The role of the androgen receptor (AR) in estrogen receptor (ER)-α-positive breast cancer is controversial, constraining implementation of AR-directed therapies. Using a diverse, clinically relevant panel of cell-line and patient-derived models, we demonstrate that AR activation, not suppression, exerts potent antitumor activity in multiple disease contexts, including resistance to standard-of-care ER and CDK4/6 inhibitors. Notably, AR agonists combined with standard-of-care agents enhanced therapeutic responses. Mechanistically, agonist activation of AR altered the genomic distribution of ER and essential co-activators (p300, SRC-3), resulting in repression of ER-regulated cell cycle genes and upregulation of AR target genes, including known tumor suppressors. A gene signature of AR activity positively predicted disease survival in multiple clinical ER-positive breast cancer cohorts. These findings provide unambiguous evidence that AR has a tumor suppressor role in ER-positive breast cancer and support AR agonism as the optimal AR-directed treatment strategy, revealing a rational therapeutic opportunity.
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Affiliation(s)
- Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
- Freemason's Foundation Centre for Men's Health, University of Adelaide, Adelaide, South Australia, Australia
| | - Kee Ming Chia
- Garvan Institute of Medical Research & St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Geraldine Laven-Law
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Heloisa H Milioli
- Garvan Institute of Medical Research & St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Daniel Roden
- Garvan Institute of Medical Research & St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Shalini Jindal
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Mun Hui
- Garvan Institute of Medical Research & St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Esmaeil Ebrahimie
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Stephen N Birrell
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Suzan Stelloo
- Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Richard Iggo
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Institut Bergonié, University of Bordeaux, Bordeaux, France
| | - Sarah Alexandrou
- Garvan Institute of Medical Research & St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - C Elizabeth Caldon
- Garvan Institute of Medical Research & St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | | | | | - Wilbert Zwart
- Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Carlo Palmieri
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool & Clatterbridge Centre NHS Foundation Trust, Liverpool, UK
| | | | - Alex Swarbrick
- Garvan Institute of Medical Research & St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Elgene Lim
- Garvan Institute of Medical Research & St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia.
- Freemason's Foundation Centre for Men's Health, University of Adelaide, Adelaide, South Australia, Australia.
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Gabay-Maskit S, Cruz-Zaragoza LD, Shai N, Eisenstein M, Bibi C, Cohen N, Hansen T, Yifrach E, Harpaz N, Belostotsky R, Schliebs W, Schuldiner M, Erdmann R, Zalckvar E. A piggybacking mechanism enables peroxisomal localization of the glyoxylate cycle enzyme Mdh2 in yeast. J Cell Sci 2020; 133:jcs244376. [PMID: 33177075 PMCID: PMC7758625 DOI: 10.1242/jcs.244376] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 10/26/2020] [Indexed: 01/25/2023] Open
Abstract
Eukaryotic cells have evolved organelles that allow the compartmentalization and regulation of metabolic processes. Knowledge of molecular mechanisms that allow temporal and spatial organization of enzymes within organelles is therefore crucial for understanding eukaryotic metabolism. Here, we show that the yeast malate dehydrogenase 2 (Mdh2) is dually localized to the cytosol and to peroxisomes and is targeted to peroxisomes via association with Mdh3 and a Pex5-dependent piggybacking mechanism. This dual localization of Mdh2 contributes to our understanding of the glyoxylate cycle and provides a new perspective on compartmentalization of cellular metabolism, which is critical for the perception of metabolic disorders and aging.
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Affiliation(s)
- Shiran Gabay-Maskit
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Luis Daniel Cruz-Zaragoza
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, Bochum D-44780, Germany
| | - Nadav Shai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miriam Eisenstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Chen Bibi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nir Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tobias Hansen
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, Bochum D-44780, Germany
| | - Eden Yifrach
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nofar Harpaz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ruth Belostotsky
- Division of Pediatric Nephrology, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Wolfgang Schliebs
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, Bochum D-44780, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ralf Erdmann
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, Bochum D-44780, Germany
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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Tayengwa R, Sharma Koirala P, Pierce CF, Werner BE, Neff MM. Overexpression of AtAHL20 causes delayed flowering in Arabidopsis via repression of FT expression. BMC PLANT BIOLOGY 2020; 20:559. [PMID: 33308168 PMCID: PMC7731500 DOI: 10.1186/s12870-020-02733-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/09/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND The 29-member Arabidopsis AHL gene family is classified into three main classes based on nucleotide and protein sequence evolutionary differences. These differences include the presence or absence of introns, type and/or number of conserved AT-hook and PPC domains. AHL gene family members are divided into two phylogenetic clades, Clade-A and Clade-B. A majority of the 29 members remain functionally uncharacterized. Furthermore, the biological significance of the DNA and peptide sequence diversity, observed in the conserved motifs and domains found in the different AHL types, is a subject area that remains largely unexplored. RESULTS Transgenic plants overexpressing AtAHL20 flowered later than the wild type under both short and long days. Transcript accumulation analyses showed that 35S:AtAHL20 plants contained reduced FT, TSF, AGL8 and SPL3 mRNA levels. Similarly, overexpression of AtAHL20's orthologue in Camelina sativa, Arabidopsis' closely related Brassicaceae family member species, conferred a late-flowering phenotype via suppression of CsFT expression. However, overexpression of an aberrant AtAHL20 gene harboring a missense mutation in the AT-hook domain's highly conserved R-G-R core motif abolished the late-flowering phenotype. Data from targeted yeast-two-hybrid assays showed that AtAHL20 interacted with itself and several other Clade-A Type-I AHLs which have been previously implicated in flowering-time regulation: AtAHL19, AtAHL22 and AtAHL29. CONCLUSION We showed via gain-of-function analysis that AtAHL20 is a negative regulator of FT expression, as well as other downstream flowering time regulating genes. A similar outcome in Camelina sativa transgenic plants overexpressing CsAHL20 suggest that this is a conserved function. Our results demonstrate that AtAHL20 acts as a photoperiod-independent negative regulator of transition to flowering.
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Affiliation(s)
- Reuben Tayengwa
- Program in Molecular Plant Sciences, Washington State University, Pullman, WA, 99164, USA.
- Department Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
- Present address: Plant Sciences and Horticultural Landscape Department, University of Maryland, College Park, MD, 20742, USA.
| | - Pushpa Sharma Koirala
- Department Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Present address: Washington State Department of Fish and Wildlife, Olympia, WA, 987501, USA
| | - Courtney F Pierce
- Department Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Present address: United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, 80521, USA
| | - Breanna E Werner
- Department Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Present address: Washington State University College of Nursing, Spokane, WA, 99202, USA
| | - Michael M Neff
- Program in Molecular Plant Sciences, Washington State University, Pullman, WA, 99164, USA
- Department Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
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15
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Chandra S, Satapathy L, Basu S, Jha SK, Kumar M, Mukhopadhyay K. Characterization of the leaf rust responsive ARF genes in wheat (Triticum aestivum L.). PLANT CELL REPORTS 2020; 39:1639-1654. [PMID: 32892289 DOI: 10.1007/s00299-020-02591-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/26/2020] [Indexed: 05/09/2023]
Abstract
Genome-wide identification, classification, functional characterization and expression analysis of Auxin Responsive Factor (ARF) gene family in wheat reveal their attributes and role during leaf rust infection. Auxins are important plant growth regulators that also impact plant-pathogen interaction. Auxin responsive factors (ARF) are plant specific transcription factors that control responses to auxins. Whole genome investigation of ARF gene family is limited in allohexaploid wheat (Triticum aestivum L.). Comprehensive study of this gene family was carried out by employing the currently available reference genome sequence of wheat. In total, 27 ARF genes were identified and located on the wheat genome as well as were positioned on wheat chromosome arms. Additionally, examination of the predicted genes unveiled a decent degree of relatedness within and among the phylogenetic clades. Leaf rust, caused by the obligate biotrophic fungal pathogen Puccinia triticina, is responsible for drastic loss of wheat crop worldwide reducing grain yield by 10-90%. Expression profiling of ARF genes in retort to leaf rust infection indicated their differential regulation during this plant-pathogen interaction. Highest expression of ARF genes were observed at 12 hpi that was maintained up to 72 hpi during incompatible interaction, whereas the high expression levels receded at 48 hpi during compatible interactions. Few of the identified ARF genes were likely to be post-transcriptionally regulated by microRNAs. Many light and stress responsive elements were detected in the promoter regions of ARF genes. Microsynteny analysis showed the conservation of ARF genes within the members of the Poaceae family. This study provides fundamental details for understanding the different types of ARF genes in wheat and there putative roles during leaf rust-wheat interaction.
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Affiliation(s)
- Saket Chandra
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Lopamudra Satapathy
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- Faculty of Agriculture, Usha Martin University, Angara, Ranchi, Jharkhand, 835103, India
| | - Srirupa Basu
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | | | - Manish Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Kunal Mukhopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
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Chen SD, Pan HY, Huang JB, Liu XP, Li JH, Ho CJ, Tsai MH, Yang JL, Chen SF, Chen NC, Chuang YC. Circulating MicroRNAs from Serum Exosomes May Serve as a Putative Biomarker in the Diagnosis and Treatment of Patients with Focal Cortical Dysplasia. Cells 2020; 9:cells9081867. [PMID: 32785072 PMCID: PMC7465068 DOI: 10.3390/cells9081867] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/03/2020] [Accepted: 08/08/2020] [Indexed: 12/12/2022] Open
Abstract
Focal cortical dysplasia (FCD) is a congenital malformation of cortical development where the cortical neurons located in the brain area fail to migrate in the proper formation. Epilepsy, particularly medically refractory epilepsy, is the most common clinical presentation for all types of FCD. This study aimed to explore the expression change of circulating miRNAs in patients with FCD from serum exosomes. A total of nine patients with FCD and four healthy volunteers were enrolled in this study. The serum exosomes were isolated from the peripheral blood of the subjects. Transmission electron microscopy (TEM) was used to identify the exosomes. Both exosomal markers and neuronal markers were detected by Western blotting analysis to prove that we could obtain central nervous system-derived exosomes from the circulation. The expression profiles of circulating exosomal miRNAs were assessed using next-generation sequencing analysis (NGS). We obtained a total of 107 miRNAs with dominant fold change (>2-fold) from both the annotated 5p-arm and 3p-arm of 2780 mature miRNAs. Based on the integrated platform of HMDD v3.2, miRway DB and DIANA-miRPath v3.0 online tools, and confirmed by MiRBase analysis, four potentially predicted miRNAs from serum exosomes in patients with FCD were identified, including miR194-2-5p, miR15a-5p, miR-132-3p, and miR-145-5p. All four miRNAs presented upregulated expression in patients with FCD compared with controls. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and pathway category of four target miRNAs, we found eight possible signaling pathways that may be related to FCD. Among them, we suggest that the mTOR signaling pathway, PI3K-Akt signaling pathway, p53 signaling pathway, and cell cycle regulation and TGF-beta signaling pathway are high-risk pathways that play a crucial role in the pathogenesis of FCD and refractory epilepsy. Our results suggest that the circulating miRNAs from exosomes may provide a potential biomarker for diagnostic, prognostic, and therapeutic adjuncts in patients with FCD and refractory epilepsy.
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Affiliation(s)
- Shang-Der Chen
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (S.-D.C.); (C.-J.H.); (M.-H.T.); (S.-F.C.); (N.-C.C.)
- Institute for Translation Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (X.-P.L.); (J.-H.L.); (J.-L.Y.)
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Hsiu-Yung Pan
- Department of Emergency Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (H.-Y.P.); (J.-B.H.)
| | - Jyun-Bin Huang
- Department of Emergency Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (H.-Y.P.); (J.-B.H.)
| | - Xuan-Ping Liu
- Institute for Translation Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (X.-P.L.); (J.-H.L.); (J.-L.Y.)
| | - Jie-Hau Li
- Institute for Translation Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (X.-P.L.); (J.-H.L.); (J.-L.Y.)
| | - Chen-Jui Ho
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (S.-D.C.); (C.-J.H.); (M.-H.T.); (S.-F.C.); (N.-C.C.)
| | - Meng-Han Tsai
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (S.-D.C.); (C.-J.H.); (M.-H.T.); (S.-F.C.); (N.-C.C.)
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Jenq-Lin Yang
- Institute for Translation Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (X.-P.L.); (J.-H.L.); (J.-L.Y.)
| | - Shu-Fang Chen
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (S.-D.C.); (C.-J.H.); (M.-H.T.); (S.-F.C.); (N.-C.C.)
| | - Nai-Ching Chen
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (S.-D.C.); (C.-J.H.); (M.-H.T.); (S.-F.C.); (N.-C.C.)
| | - Yao-Chung Chuang
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (S.-D.C.); (C.-J.H.); (M.-H.T.); (S.-F.C.); (N.-C.C.)
- Institute for Translation Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; (X.-P.L.); (J.-H.L.); (J.-L.Y.)
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Neurology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Biological Science, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
- Correspondence:
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Zhou H, He Y, Zhu Y, Li M, Song S, Bo W, Li Y, Pang X. Comparative transcriptome profiling reveals cold stress responsiveness in two contrasting Chinese jujube cultivars. BMC PLANT BIOLOGY 2020; 20:240. [PMID: 32460709 PMCID: PMC7254757 DOI: 10.1186/s12870-020-02450-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/19/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Low temperature is a major factor influencing the growth and development of Chinese jujube (Ziziphus jujuba Mill.) in cold winter and spring. Little is known about the molecular mechanisms enabling jujube to cope with different freezing stress conditions. To elucidate the freezing-related molecular mechanism, we conducted comparative transcriptome analysis between 'Dongzao' (low freezing tolerance cultivar) and 'Jinsixiaozao' (high freezing tolerance cultivar) using RNA-Seq. RESULTS More than 20,000 genes were detected at chilling (4 °C) and freezing (- 10 °C, - 20 °C, - 30 °C and - 40 °C) stress between the two cultivars. The numbers of differentially expressed genes (DEGs) between the two cultivars were 1831, 2030, 1993, 1845 and 2137 under the five treatments. Functional enrichment analysis suggested that the metabolic pathway, response to stimulus and catalytic activity were significantly enriched under stronger freezing stress. Among the DEGs, nine participated in the Ca2+ signal pathway, thirty-two were identified to participate in sucrose metabolism, and others were identified to participate in the regulation of ROS, plant hormones and antifreeze proteins. In addition, important transcription factors (WRKY, AP2/ERF, NAC and bZIP) participating in freezing stress were activated under different degrees of freezing stress. CONCLUSIONS Our research first provides a more comprehensive understanding of DEGs involved in freezing stress at the transcriptome level in two Z. jujuba cultivars with different freezing tolerances. These results may help to elucidate the molecular mechanism of freezing tolerance in jujube and also provides new insights and candidate genes for genetically enhancing freezing stress tolerance.
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Affiliation(s)
- Heying Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Ying He
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yongsheng Zhu
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan, 430074, China
| | - Meiyu Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Shuang Song
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Wenhao Bo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yingyue Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaoming Pang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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18
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Bicker A, Nauth T, Gerst D, Aboouf MA, Fandrey J, Kristiansen G, Gorr TA, Hankeln T. The role of myoglobin in epithelial cancers: Insights from transcriptomics. Int J Mol Med 2019; 45:385-400. [PMID: 31894249 PMCID: PMC6984796 DOI: 10.3892/ijmm.2019.4433] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/08/2019] [Indexed: 12/25/2022] Open
Abstract
The muscle-associated respiratory protein myoglobin (MB) is expressed in multiple types of cancer, including breast and prostate tumors. In Kaplan-Meier analyses of the two tumor types, MB positivity is associated with favorable prognoses. Despite its well-characterized function in myocytes, the role of MB in cancer remains unclear. To study the impact of endogenous MB expression, small interfering RNA MB-knockdown cells were engineered using breast, prostate and colon cancer cell lines (MDA-MB468, LNCaP, DLD-1), and their transcriptomes were investigated using RNA-Seq at different oxygen levels. In MB-positive cells, increased expression of glycolytic genes was observed, which was possibly mediated by a higher activity of hypoxia-inducible factor 1α. In addition, the results of the gene set enrichment analysis suggested that MB contributed to fatty acid transport and turnover. MB-positive, wild-type-p53 LNCaP cells also exhibited increased expression of p53 target genes involved in cell cycle checkpoint control and prevention of cell migration. MB-positive cells expressing mutant p53 exhibited upregulation of genes associated with prolonged cancer cell viability and motility. Therefore, it was hypothesized that these transcriptomic differences may result from MB-mediated generation of nitric oxide or reactive oxygen species, thus employing established enzymatic activities of the globin. In summary, the transcriptome comparisons identified potential molecular functions of MB in carcinogenesis by highlighting the interaction of MB with key metabolic and regulatory processes.
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Affiliation(s)
- Anne Bicker
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University, D‑55099 Mainz, Germany
| | - Theresa Nauth
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University, D‑55099 Mainz, Germany
| | - Daniela Gerst
- Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, CH‑8057 Zurich, Switzerland
| | - Mostafa Ahmed Aboouf
- Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, CH‑8057 Zurich, Switzerland
| | - Joachim Fandrey
- Institute of Physiology, University of Duisburg‑Essen, D‑45147 Essen, Germany
| | - Glen Kristiansen
- Institute of Pathology, Center for Integrated Oncology, University Hospital Bonn, University of Bonn, D‑53127 Bonn, Germany
| | - Thomas Alexander Gorr
- Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, CH‑8057 Zurich, Switzerland
| | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University, D‑55099 Mainz, Germany
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RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49. Genes (Basel) 2019; 10:genes10121042. [PMID: 31888133 PMCID: PMC6947843 DOI: 10.3390/genes10121042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/26/2019] [Accepted: 12/07/2019] [Indexed: 12/16/2022] Open
Abstract
Quinoa (Chenopodium quinoa Willd.), a model halophytic crop species, was used to shed light on salt tolerance mechanisms at the transcriptomic level. An RNA-sequencing analysis of genotype R49 at an early vegetative stage was performed by Illumina paired-ends method comparing high salinity and control conditions in a time-course pot experiment. Genome-wide transcriptional salt-induced changes and expression profiling of relevant salt-responsive genes in plants treated or not with 300 mM NaCl were analyzed after 1 h and 5 days. We obtained up to 49 million pairs of short reads with an average length of 101 bp, identifying a total of 2416 differentially expressed genes (DEGs) based on the treatment and time of sampling. In salt-treated vs. control plants, the total number of up-regulated and down-regulated genes was 945 and 1471, respectively. The number of DEGs was higher at 5 days than at 1 h after salt treatment, as reflected in the number of transcription factors, which increased with time. We report a strong transcriptional reprogramming of genes involved in biological processes like oxidation-reduction, response to stress and response to abscisic acid (ABA), and cell wall organization. Transcript analyses by real-time RT- qPCR supported the RNA-seq results and shed light on the contribution of roots and shoots to the overall transcriptional response. In addition, it revealed a time-dependent response in the expression of the analyzed DEGs, including a quick (within 1 h) response for some genes, suggesting a "stress-anticipatory preparedness" in this highly salt-tolerant genotype.
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20
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Hill SR, Ghaninia M, Ignell R. Blood Meal Induced Regulation of Gene Expression in the Maxillary Palps, a Chemosensory Organ of the Mosquito Aedes aegypti. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00336] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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Balestrini R, Rosso LC, Veronico P, Melillo MT, De Luca F, Fanelli E, Colagiero M, di Fossalunga AS, Ciancio A, Pentimone I. Transcriptomic Responses to Water Deficit and Nematode Infection in Mycorrhizal Tomato Roots. Front Microbiol 2019; 10:1807. [PMID: 31456765 PMCID: PMC6700261 DOI: 10.3389/fmicb.2019.01807] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/22/2019] [Indexed: 11/13/2022] Open
Abstract
Climate changes include the intensification of drought in many parts of the world, increasing its frequency, severity and duration. However, under natural conditions, environmental stresses do not occur alone, and, in addition, more stressed plants may become more susceptible to attacks by pests and pathogens. Studies on the impact of the arbuscular mycorrhizal (AM) symbiosis on tomato response to water deficit showed that several drought-responsive genes are differentially regulated in AM-colonized tomato plants (roots and leaves) during water deficit. To date, global changes in mycorrhizal tomato root transcripts under water stress conditions have not been yet investigated. Here, changes in root transcriptome in the presence of an AM fungus, with or without water stress (WS) application, have been evaluated in a commercial tomato cultivar already investigated for the water stress response during AM symbiosis. Since root-knot nematodes (RKNs, Meloidogyne incognita) are obligate endoparasites and cause severe yield losses in tomato, the impact of the AM fungal colonization on RKN infection at 7 days post-inoculation was also evaluated. Results offer new information about the response to AM symbiosis, highlighting a functional redundancy for several tomato gene families, as well as on the tomato and fungal genes involved in WS response during symbiosis, underlying the role of the AM fungus. Changes in the expression of tomato genes related to nematode infection during AM symbiosis highlight a role of AM colonization in triggering defense responses against RKN in tomato. Overall, new datasets on the tomato response to an abiotic and biotic stress during AM symbiosis have been obtained, providing useful data for further researches.
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Affiliation(s)
- Raffaella Balestrini
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Turin, Italy
| | - Laura C Rosso
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Turin, Italy
| | - Pasqua Veronico
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Turin, Italy
| | - Maria Teresa Melillo
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Turin, Italy
| | - Francesca De Luca
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Turin, Italy
| | - Elena Fanelli
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Turin, Italy
| | - Mariantonietta Colagiero
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Turin, Italy
| | | | - Aurelio Ciancio
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Turin, Italy
| | - Isabella Pentimone
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Turin, Italy
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22
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Gao C, Cai X, Fu Q, Yang N, Song L, Su B, Tan F, Liu B, Li C. Dynamics of MiRNA Transcriptome in Turbot (Scophthalmus maximus L.) Intestine Following Vibrio anguillarum Infection. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:550-564. [PMID: 31111338 DOI: 10.1007/s10126-019-09903-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
MicroRNAs (miRNAs) are a group of small non-coding RNAs, which could bind to the 3'-untranslated regions of their target mRNAs to regulate gene expression in various biological processes, including immune-regulated signaling pathways. Turbot (Scophthalmus maximus L.), an important commercial fish species in China, has been suffering with Vibrio anguillarum infection resulted in dramatic economic loss. Therefore, we investigated the expression profiles of miRNAs, as well as the immune-related miRNA-mRNA pairs in turbot intestine at 1 h, 4 h, and 12 h following V. anguillarum infection. As a result, 266 predicted novel miRNAs and 283 conserved miRNAs belonging to 92 miRNA families were detected. A total of 44 miRNAs were differentially expressed in the intestine following V. anguillarum infection. Following prediction, the potential target genes of differentially expressed miRNAs were grouped into a wide range of functional categories, including immune defense/evasion, inflammatory responses, RIG-I signaling pathway, and Toll-like receptor signaling pathway. Moreover, we selected 15 differentially expressed immune genes and their related differentially expressed miRNAs to construct an interaction network for V. anguillarum infection in turbot. These results suggested that in teleost, as in higher vertebrates, miRNAs prominently contribute to immune responses, protecting the host against infection. In addition, this is the first report of comprehensive identification of turbot miRNAs being differentially regulated in the intestine related to V. anguillarum infection. Our results provided an opportunity for further understanding of the molecular mechanisms of miRNA regulation in turbot host-pathogen interactions.
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Affiliation(s)
- Chengbin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xin Cai
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lin Song
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Fenghua Tan
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Baining Liu
- Menaul School Qingdao, Qingdao, 266200, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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23
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Sebastiani F, Torre S, Gori A, Brunetti C, Centritto M, Ferrini F, Tattini M. Dissecting Adaptation Mechanisms to Contrasting Solar Irradiance in the Mediterranean Shrub Cistus incanus. Int J Mol Sci 2019; 20:E3599. [PMID: 31340536 PMCID: PMC6678608 DOI: 10.3390/ijms20143599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/08/2019] [Accepted: 07/16/2019] [Indexed: 01/25/2023] Open
Abstract
Molecular mechanisms that are the base of the strategies adopted by Mediterranean plants to cope with the challenges imposed by limited or excessive solar radiation during the summer season have received limited attention. In our study, conducted on C. incanus plants growing in the shade or in full sunlight, we performed measurements of relevant physiological traits, such as leaf water potential, gas exchange and PSII photochemistry, RNA-Seq with de-novo assembly, and the analysis of differentially expressed genes. We also identified and quantified photosynthetic pigments, abscisic acid, and flavonoids. Here, we show major mechanisms regulating light perception and signaling which, in turn, sustain the shade avoidance syndrome displayed by the 'sun loving' C. incanus. We offer clear evidence of the detrimental effects of excessive light on both the assembly and the stability of PSII, and the activation of a suite of both repair and effective antioxidant mechanisms in sun-adapted leaves. For instance, our study supports the view of major antioxidant functions of zeaxanthin in sunny plants concomitantly challenged by severe drought stress. Finally, our study confirms the multiple functions served by flavonoids, both flavonols and flavanols, in the adaptive mechanisms of plants to the environmental pressures associated to Mediterranean climate.
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Affiliation(s)
- Federico Sebastiani
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), 50019 Sesto Fiorentino (Florence), Italy
| | - Sara Torre
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), 50019 Sesto Fiorentino (Florence), Italy
| | - Antonella Gori
- Department of Agriculture, Food, Environment and Forestry, University of Florence, 50019 Sesto Fiorentino (Florence), Italy
| | - Cecilia Brunetti
- Institute of BioEconomy, The National Research Council of Italy (CNR), 50019 Sesto Fiorentino (Florence), Italy
| | - Mauro Centritto
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), 50019 Sesto Fiorentino (Florence), Italy
| | - Francesco Ferrini
- Department of Agriculture, Food, Environment and Forestry, University of Florence, 50019 Sesto Fiorentino (Florence), Italy
| | - Massimiliano Tattini
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), 50019 Sesto Fiorentino (Florence), Italy.
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24
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Muñoz-Galindo L, Melendez-Zajgla J, Pacheco-Fernández T, Rodriguez-Sosa M, Mandujano-Tinoco EA, Vazquez-Santillan K, Castro-Oropeza R, Lizarraga F, Sanchez-Lopez JM, Maldonado V. Changes in the transcriptome profile of breast cancer cells grown as spheroids. Biochem Biophys Res Commun 2019; 516:1258-1264. [PMID: 31301772 DOI: 10.1016/j.bbrc.2019.06.155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 06/27/2019] [Indexed: 01/02/2023]
Abstract
BACKGROUND Multicellular tumor spheroids mimic the functional organization of tumors in vivo, providing biological readouts that predict the behavior of cancer cells more accurately. The current study aimed to evaluate the transcriptome (mRNAs and long non-coding RNAs) of multicellular tumor spheroids from breast cancer cells. METHODS MCF-7 cell spheroids were used; the transcriptome was analyzed using RNAseq and RNA microarrays; the secretion of macrophage migration inhibitor (MIF), a cytokine exported by the cholesterol efflux regulatory protein, was measured by ELISA. Linc00052 was inhibited using short-hairpin RNAs (shRNAs). RESULTS We found several differentially regulated mRNAs and lncRNAs in MCF-7 cell spheroids. We also found significant enrichment of the Wnt/B-catenin death receptor and the cholesterol metabolic processes. Interestingly, we also found an increased concentration of MIF. Further, at 12 and 20 days of 3D culture we found 221 and 1146 dysregulated lncRNAs, respectively; including linc00052 (long intergenic non-protein coding RNA 52), which has been involved in breast cancer. Linc00052 knock-down experiments suggest that it could be a key regulator of cholesterol pathways in breast cancer. CONCLUSIONS Our data shows that tumor spheroids can induce changes in the transcriptome of the cultured cells, including both mRNAs and ncRNA. One of the major changes included the deregulation of cholesterol pathways, of which linc00052 is apparently a key regulator.
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Affiliation(s)
- Laura Muñoz-Galindo
- Laboratorio de Epigenética, CDMX, México; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México (UNAM). CDMX, Mexico
| | - Jorge Melendez-Zajgla
- Genómica Functional. Instituto Nacional de Medicina Genómica (INMEGEN). CDMX, Mexico
| | - Thalia Pacheco-Fernández
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México (UNAM), Estado de Mexico, Mexico
| | - Miriam Rodriguez-Sosa
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México (UNAM), Estado de Mexico, Mexico
| | - Edna Ayerim Mandujano-Tinoco
- Laboratorio de Epigenética, CDMX, México; Laboratorio de Tejido Conjuntivo. Instituto Nacional de Rehabilitación (INR) "Luis Guillermo Ibarra Ibarra". CDMX, Mexico
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25
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Neupane S, Varenhorst AJ, Nepal MP. Transcriptome profiling of induced susceptibility effects on soybean-soybean aphid (Hemiptera: Aphididae) interaction. BMC Res Notes 2019; 12:325. [PMID: 31182145 PMCID: PMC6558899 DOI: 10.1186/s13104-019-4372-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/05/2019] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVES Soybean aphid (Aphis glycines Matsumura; SBA) is the most economically damaging insect of soybean (Glycine max) in the United States. One previous study demonstrated that avirulent (biotype 1) and virulent (biotype 2) biotypes could co-occur and interact on resistant (i.e., Rag1) and susceptible soybean resulting in induced susceptibility after 11 days of feeding. The main objective of this research was to employ RNA sequencing (RNA-seq) technique to compare the induced susceptibility effect of biotype 2 on susceptible and resistant soybean at day 1 and day 11 (i.e., both susceptible and resistant soybean were initially challenged by biotype 2 and the effect was monitored through biotype 1 populations). DATA DESCRIPTION We investigated susceptible and Rag1 transcriptome response to SBA feeding in soybean plants colonized by biotype 1 in the presence or absence of an inducer population (i.e., biotype 2). Ten RNA datasets are reported with 266,535,654 sequence reads (55.2 GB) obtained from pooled samples derived from the leaves collected at day 1 and day 11 post SBA infestation. A comprehensive understanding of these transcriptome data will enhance our understanding of interactions among soybean and two different biotypes of soybean aphids at the molecular level.
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Affiliation(s)
- Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007 USA
| | - Adam J. Varenhorst
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007 USA
| | - Madhav P. Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007 USA
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26
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Shiri Y, Solouki M, Ebrahimie E, Emamjomeh A, Zahiri J. Gibberellin causes wide transcriptional modifications in the early stage of grape cluster development. Genomics 2019; 112:820-830. [PMID: 31136791 DOI: 10.1016/j.ygeno.2019.05.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/01/2019] [Accepted: 05/24/2019] [Indexed: 10/26/2022]
Abstract
Yaghooti grape of Sistan is seedless, early ripening but has compact clusters. To study gibberellin effect on cluster compactness of Yaghooti grape, it has been studied transcriptomic changes in three developmental stages (cluster formation, berry formation and final size of cluster). We found out that 5409 of 22,756 genes in cluster tissue showed significant changes under gibberellin. Finally, it was showed that 2855, 2862 and 497 genes have critically important role on above developmental stages, respectively. GO enrichment analysis showed that gibberellin enhances biochemical pathways activity. Moreover, genes involved in ribosomal structure and photosynthesis rate in cluster tissue were up- and down- regulated, respectively. In addition, we observed location of metabolomic activities was transferred from nucleus to cytoplasm and from cytoplasm to cell wall and intercellular spaces during cluster development; but there is not such situation in gibberellin treated samples.
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Affiliation(s)
- Yasoub Shiri
- Department of Agronomy and Plant Breeding, Agriculture Research Center, University of Zabol, Zabol, Iran
| | - Mahmood Solouki
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran.
| | - Esmaeil Ebrahimie
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia; Genomics Research Platform, School of Life Sciences, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Abbasali Emamjomeh
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran.
| | - Javad Zahiri
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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27
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Berral-Gonzalez A, Riffo-Campos AL, Ayala G. OMICfpp: a fuzzy approach for paired RNA-Seq counts. BMC Genomics 2019; 20:259. [PMID: 30940089 PMCID: PMC6444640 DOI: 10.1186/s12864-019-5496-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 01/29/2019] [Indexed: 12/16/2022] Open
Abstract
Background RNA sequencing is a widely used technology for differential expression analysis. However, the RNA-Seq do not provide accurate absolute measurements and the results can be different for each pipeline used. The major problem in statistical analysis of RNA-Seq and in the omics data in general, is the small sample size with respect to the large number of variables. In addition, experimental design must be taken into account and few tools consider it. Results We propose OMICfpp, a method for the statistical analysis of RNA-Seq paired design data. First, we obtain a p-value for each case-control pair using a binomial test. These p-values are aggregated using an ordered weighted average (OWA) with a given orness previously chosen. The aggregated p-value from the original data is compared with the aggregated p-value obtained using the same method applied to random pairs. These new pairs are generated using between-pairs and complete randomization distributions. This randomization p-value is used as a raw p-value to test the differential expression of each gene. The OMICfpp method is evaluated using public data sets of 68 sample pairs from patients with colorectal cancer. We validate our results through bibliographic search of the reported genes and using simulated data set. Furthermore, we compared our results with those obtained by the methods edgeR and DESeq2 for paired samples. Finally, we propose new target genes to validate these as gene expression signatures in colorectal cancer. OMICfpp is available at http://www.uv.es/ayala/software/OMICfpp_0.2.tar.gz. Conclusions Our study shows that OMICfpp is an accurate method for differential expression analysis in RNA-Seq data with paired design. In addition, we propose the use of randomized p-values pattern graphic as a powerful and robust method to select the target genes for experimental validation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5496-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alberto Berral-Gonzalez
- Grupo de Investigación Bioinformática y Genómica Funcional. Laboratorio 19. Centro de Investigación del Cáncer (CiC-IBMCC, Universidad de Salamanca-CSIC, Campus Universitario Miguel de Unamuno s/n, Salamanca, 37007, Spain
| | - Angela L Riffo-Campos
- Universidad de La Frontera. Centro De Excelencia de Modelación y Computación Científica, C/ Montevideo 740, Temuco, Chile.
| | - Guillermo Ayala
- Universidad de Valencia. Departamento de Estadística e Investigación Operativa, Avda. Vicent Andrés Estellés, 1, Burjasot, 46100, Spain
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Maldonado J, Dhingra A, Carrasco B, Meisel L, Silva H. Transcriptome datasets from leaves and fruits of the sweet cherry cultivars ‘Bing’, ‘Lapins’ and ‘Rainier’. Data Brief 2019; 23:103696. [PMID: 30788404 PMCID: PMC6369327 DOI: 10.1016/j.dib.2019.01.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/08/2019] [Accepted: 01/18/2019] [Indexed: 11/05/2022] Open
Abstract
Sweet cherry fruits from different cultivars have different pre- and post-harvest qualities. Here we present the transcriptome profile datasets of leaves and mature fruits of three sweet cherry cultivars (‘Bing’, ‘Lapin’ and ‘Rainier’). Using 454 GS-FLX technology (454 Life Sciences, Roche), transcriptomes of leaves and mature fruits were obtained from these cultivars. These transcriptome data sets are reported here.
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Xiberras J, Klein M, Nevoigt E. Glycerol as a substrate for Saccharomyces cerevisiae based bioprocesses - Knowledge gaps regarding the central carbon catabolism of this 'non-fermentable' carbon source. Biotechnol Adv 2019; 37:107378. [PMID: 30930107 DOI: 10.1016/j.biotechadv.2019.03.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 12/14/2022]
Abstract
Glycerol is an interesting alternative carbon source in industrial bioprocesses due to its higher degree of reduction per carbon atom compared to sugars. During the last few years, significant progress has been made in improving the well-known industrial platform organism Saccharomyces cerevisiae with regard to its glycerol utilization capability, particularly in synthetic medium. This provided a basis for future metabolic engineering focusing on the production of valuable chemicals from glycerol. However, profound knowledge about the central carbon catabolism in synthetic glycerol medium is a prerequisite for such incentives. As a matter of fact, the current assumptions about the actual in vivo fluxes active on glycerol as the sole carbon source have mainly been based on omics data collected in complex media or were even deduced from studies with other non-fermentable carbon sources, such as ethanol or acetate. A number of uncertainties have been identified which particularly regard the role of the glyoxylate cycle, the subcellular localization of the respective enzymes, the contributions of mitochondrial transporters and the active anaplerotic reactions under these conditions. The review scrutinizes the current knowledge, highlights the necessity to collect novel experimental data using cells growing in synthetic glycerol medium and summarizes the current state of the art with regard to the production of valuable fermentation products from a carbon source that has been considered so far as 'non-fermentable' for the yeast S. cerevisiae.
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Affiliation(s)
- Joeline Xiberras
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Campus Ring 1, 28759 Bremen, Germany.
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Chicken Embryonic-Stem Cells Are Permissive to Poxvirus Recombinant Vaccine Vectors. Genes (Basel) 2019; 10:genes10030237. [PMID: 30897824 PMCID: PMC6471371 DOI: 10.3390/genes10030237] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 12/17/2022] Open
Abstract
The discovery of mammalian pluripotent embryonic stem cells (ESC) has revolutionised cell research and regenerative medicine. More recently discovered chicken ESC (cESC), though less intensively studied, are increasingly popular as vaccine substrates due to a dearth of avian cell lines. Information on the comparative performance of cESC with common vaccine viruses is limited. Using RNA-sequencing, we compared cESC transcriptional programmes elicited by stimulation with chicken type I interferon or infection with vaccine viruses routinely propagated in primary chicken embryo fibroblasts (CEF). We used poxviruses (fowlpox virus (FWPV) FP9, canarypox virus (CNPV), and modified vaccinia virus Ankara (MVA)) and a birnavirus (infectious bursal disease virus (IBDV) PBG98). Interferon-stimulated genes (ISGs) were induced in cESC to levels comparable to those in CEF and immortalised chicken fibroblast DF-1 cells. cESC are permissive (with distinct host transcriptional responses) to MVA, FP9, and CNPV but, surprisingly, not to PBG98. MVA, CNPV, and FP9 suppressed innate immune responses, while PBG98 induced a subset of ISGs. Dysregulation of signalling pathways (i.e., NFκB, TRAF) was observed, which might affect immune responses and viral replication. In conclusion, we show that cESC are an attractive alternative substrate to study and propagate poxvirus recombinant vaccine vectors.
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Gonçalves AT, Núñez-Acuña G, Détrée C, Gallardo-Escárate C. Coding/non-coding cross-talk in intestinal epithelium transcriptome gives insights on how fish respond to stocking density. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 29:14-23. [DOI: 10.1016/j.cbd.2018.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 10/15/2018] [Indexed: 02/04/2023]
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Singh R, Junghare V, Hazra S, Singh U, Sengar GS, Raja TV, Kumar S, Tyagi S, Das AK, Kumar A, Koringa P, Jakhesara S, Joshi CJ, Deb R. Database on spermatozoa transcriptogram of catagorised Frieswal crossbred (Holstein Friesian X Sahiwal) bulls. Theriogenology 2019; 129:130-145. [PMID: 30844654 DOI: 10.1016/j.theriogenology.2019.01.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 01/11/2019] [Accepted: 01/31/2019] [Indexed: 12/22/2022]
Abstract
Bull spermatozoa contain different functional genes and many of them plays important roles in different stages of spermatogenesis, spermatozoa kinetics, fertilization as well as embryonic development. RNA deep sequencing is one of the preferred tools for absolute quantification of messenger RNA. The intention of the current study was to investigate the abundance of spermatozoal transcripts in categorized Frieswal (Holstein-Friesian X Sahiwal) crossbred bull semen through RNA deep sequencing. A total 1546561 and 1019308 numbers of reads were identified among good and poor quality bull spermatozoa based on their conception rate. Post mapping with Bos taurus reference genome identified 1,321,236 and 842,022 number of transcripts among good and poor quality RNA libraries, respectively. However, a total number of 3510 and 6759 functional transcripts were identified among good and poor quality bull spermatozoa, respectively. Most of the identified transcripts were related to spermatozoa functions, embryonic development and other functional aspects of fertilization. Wet laboratory validation of the top five selected transcripts (AKAP4, PRM1, ATP2B4, TRIM71 and SLC9B2) illustrated the significant (p < 0.01) level of expression in the good quality crossbred bull semen than the poor quality counterparts. The present study with comprehensive profiling of spermatozoal transcripts provides a useful non-invasive tool to understand the causes of as well as an effective way to predict male infertility in crossbred bulls.
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Affiliation(s)
- Rani Singh
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India.
| | - Vivek Junghare
- Department of Biotechnology, Center of Nanotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Saugata Hazra
- Department of Biotechnology, Center of Nanotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Umesh Singh
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - Gyanendra Singh Sengar
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - T V Raja
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - Sushil Kumar
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - Shrikant Tyagi
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - A K Das
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - Ashish Kumar
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - Prakash Koringa
- Ome Research Laboratory, Anand Agricultural University, Anand, Gujarat, India
| | - Subhash Jakhesara
- Ome Research Laboratory, Anand Agricultural University, Anand, Gujarat, India
| | - C J Joshi
- Ome Research Laboratory, Anand Agricultural University, Anand, Gujarat, India
| | - Rajib Deb
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India.
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Briem E, Budkova Z, Sigurdardottir AK, Hilmarsdottir B, Kricker J, Timp W, Magnusson MK, Traustadottir GA, Gudjonsson T. MiR-203a is differentially expressed during branching morphogenesis and EMT in breast progenitor cells and is a repressor of peroxidasin. Mech Dev 2019; 155:34-47. [PMID: 30508578 DOI: 10.1016/j.mod.2018.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 11/01/2018] [Accepted: 11/23/2018] [Indexed: 12/12/2022]
Abstract
MicroRNAs regulate developmental events such as branching morphogenesis, epithelial to mesenchymal transition (EMT) and its reverse process mesenchymal to epithelial transition (MET). In this study, we performed small RNA sequencing of a breast epithelial progenitor cell line (D492), and its mesenchymal derivative (D492M) cultured in three-dimensional microenvironment. Among the most downregulated miRNAs in D492M was miR-203a, a miRNA that plays an important role in epithelial differentiation. Increased expression of miR-203a was seen in D492, concomitant with increased complexity of branching. When miR-203a was overexpressed in D492M, a partial reversion towards epithelial phenotype was seen. Gene expression analysis of D492M and D492MmiR-203a revealed peroxidasin, a collagen IV cross-linker, as the most significantly downregulated gene in D492MmiR-203a. Collectively, we demonstrate that miR-203a expression temporally correlates with branching morphogenesis and is suppressed in D492M. Overexpression of miR-203a in D492M induces a partial MET and reduces the expression of peroxidasin. Furthermore, we demonstrate that miR-203a is a novel repressor of peroxidasin. MiR-203-peroxidasin axis may be an important regulator in branching morphogenesis, EMT/MET and basement membrane remodeling.
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Affiliation(s)
- Eirikur Briem
- Stem Cell Research Unit, Biomedical Center, Department of Anatomy, Faculty of Medicine, School of Health Sciences, University of Iceland, Iceland
| | - Zuzana Budkova
- Stem Cell Research Unit, Biomedical Center, Department of Anatomy, Faculty of Medicine, School of Health Sciences, University of Iceland, Iceland
| | - Anna Karen Sigurdardottir
- Stem Cell Research Unit, Biomedical Center, Department of Anatomy, Faculty of Medicine, School of Health Sciences, University of Iceland, Iceland
| | - Bylgja Hilmarsdottir
- Stem Cell Research Unit, Biomedical Center, Department of Anatomy, Faculty of Medicine, School of Health Sciences, University of Iceland, Iceland; Department of Tumor Biology, The Norwegian Radium Hospital, Oslo, Norway
| | - Jennifer Kricker
- Stem Cell Research Unit, Biomedical Center, Department of Anatomy, Faculty of Medicine, School of Health Sciences, University of Iceland, Iceland
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, USA
| | - Magnus Karl Magnusson
- Department of Laboratory Hematology, Landspitali - University Hospital, Iceland; Department of Pharmacology and Toxicology, Faculty of Medicine, School of Health Sciences, University of Iceland, Iceland
| | - Gunnhildur Asta Traustadottir
- Stem Cell Research Unit, Biomedical Center, Department of Anatomy, Faculty of Medicine, School of Health Sciences, University of Iceland, Iceland
| | - Thorarinn Gudjonsson
- Stem Cell Research Unit, Biomedical Center, Department of Anatomy, Faculty of Medicine, School of Health Sciences, University of Iceland, Iceland; Department of Laboratory Hematology, Landspitali - University Hospital, Iceland.
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Li N, Bao L, Zhou T, Yuan Z, Liu S, Dunham R, Li Y, Wang K, Xu X, Jin Y, Zeng Q, Gao S, Fu Q, Liu Y, Yang Y, Li Q, Meyer A, Gao D, Liu Z. Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation. BMC Genomics 2018; 19:952. [PMID: 30572844 PMCID: PMC6302426 DOI: 10.1186/s12864-018-5355-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 12/09/2018] [Indexed: 11/22/2022] Open
Abstract
Background Walking catfish (Clarias batrachus) is a freshwater fish capable of air-breathing and locomotion on land. It usually inhabits various low-oxygen habitats, burrows inside the mudflat, and sometimes “walks” to search for suitable environments during summer. It has evolved accessory air-breathing organs for respiring air and corresponding mechanisms to survive in such challenging environments. Thereby, it serves as a great model for understanding adaptations to terrestrial life. Results Comparative genomics with channel catfish (Ictalurus punctatus) revealed specific adaptations of C. batrachus in DNA repair, enzyme activator activity, and small GTPase regulator activity. Comparative analysis with 11 non-air-breathing fish species suggested adaptive evolution in gene expression and nitrogenous waste metabolic processes. Further, myoglobin, olfactory receptor related to class A G protein-coupled receptor 1, and sulfotransferase 6b1 genes were found to be expanded in the air-breathing walking catfish genome, with 15, 15, and 12 copies, respectively, compared to non-air-breathing fishes that possess only 1–2 copies of these genes. Additionally, we sequenced and compared the transcriptomes of the gill and the air-breathing organ to characterize the mechanism of aerial respiration involved in elastic fiber formation, oxygen binding and transport, angiogenesis, ion homeostasis and acid-base balance. The hemoglobin genes were expressed dramatically higher in the air-breathing organ than in the gill of walking catfish. Conclusions This study provides an important genomic resource for understanding the adaptive mechanisms of walking catfish to terrestrial environments. It is possible that the coupling of enhanced abilities for oxygen storage and oxygen transport through genomic expansion of myoglobin genes and transcriptomic up-regulation of hemoglobin and angiogenesis-related genes are important components of the molecular basis for adaptation of this aquatic species to terrestrial life. Electronic supplementary material The online version of this article (10.1186/s12864-018-5355-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ning Li
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Lisui Bao
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zihao Yuan
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shikai Liu
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Rex Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yuanning Li
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA
| | - Kun Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xiaoyan Xu
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yulin Jin
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qifan Zeng
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Sen Gao
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qiang Fu
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yang Liu
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yujia Yang
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qi Li
- Shellfish Genetics and Breeding Laboratory, Fisheries College, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78464, Konstanz, Germany
| | - Dongya Gao
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, 13244, USA.
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Scolari F, Attardo GM, Aksoy E, Weiss B, Savini G, Takac P, Abd-Alla A, Parker AG, Aksoy S, Malacrida AR. Symbiotic microbes affect the expression of male reproductive genes in Glossina m. morsitans. BMC Microbiol 2018; 18:169. [PMID: 30470198 PMCID: PMC6251095 DOI: 10.1186/s12866-018-1289-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background Tsetse flies (Diptera, Glossinidae) display unique reproductive biology traits. Females reproduce through adenotrophic viviparity, nourishing the growing larva into their modified uterus until parturition. Males transfer their sperm and seminal fluid, produced by both testes and male accessory glands, in a spermatophore capsule transiently formed within the female reproductive tract upon mating. Both sexes are obligate blood feeders and have evolved tight relationships with endosymbionts, already shown to provide essential nutrients lacking in their diet. However, the partnership between tsetse and its symbionts has so far been investigated, at the molecular, genomic and metabolomics level, only in females, whereas the roles of microbiota in male reproduction are still unexplored. Results Here we begin unravelling the impact of microbiota on Glossina m. morsitans (G. morsitans) male reproductive biology by generating transcriptomes from the reproductive tissues of males deprived of their endosymbionts (aposymbiotic) via maternal antibiotic treatment and dietary supplementation. We then compared the transcriptional profiles of genes expressed in the male reproductive tract of normal and these aposymbiotic flies. We showed that microbiota removal impacts several male reproductive genes by depressing the activity of genes in the male accessory glands (MAGs), including sequences encoding seminal fluid proteins, and increasing expression of genes in the testes. In the MAGs, in particular, the expression of genes related to mating, immunity and seminal fluid components’ synthesis is reduced. In the testes, the absence of symbionts activates genes involved in the metabolic apparatus at the basis of male reproduction, including sperm production, motility and function. Conclusions Our findings mirrored the complementary roles male accessory glands and testes play in supporting male reproduction and open new avenues for disentangling the interplay between male insects and endosymbionts. From an applied perspective, unravelling the metabolic and functional relationships between tsetse symbionts and male reproductive physiology will provide fundamental information useful to understanding the biology underlying improved male reproductive success in tsetse. This information is of particular importance in the context of tsetse population control via Sterile Insect Technique (SIT) and its impact on trypanosomiasis transmission. Electronic supplementary material The online version of this article (10.1186/s12866-018-1289-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesca Scolari
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Geoffrey Michael Attardo
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, 06520, USA.,Present Address: Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
| | - Emre Aksoy
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, 06520, USA
| | - Brian Weiss
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, 06520, USA
| | - Grazia Savini
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Peter Takac
- Section of Molecular and Applied Zoology, Institute of Zoology, Slovak Academy of Sciences, 845 06, Bratislava, SR, Slovakia
| | - Adly Abd-Alla
- International Atomic Energy Agency, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IPC Laboratory, A-1400, Vienna, Austria
| | - Andrew Gordon Parker
- International Atomic Energy Agency, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IPC Laboratory, A-1400, Vienna, Austria
| | - Serap Aksoy
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, 06520, USA
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Martins SDT, Kuczera D, Lötvall J, Bordignon J, Alves LR. Characterization of Dendritic Cell-Derived Extracellular Vesicles During Dengue Virus Infection. Front Microbiol 2018; 9:1792. [PMID: 30131785 PMCID: PMC6090163 DOI: 10.3389/fmicb.2018.01792] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 07/17/2018] [Indexed: 12/15/2022] Open
Abstract
The dengue virus (DENV), transmitted by Aedes spp. mosquitoes, is one of the most important arboviral infections in the world. Dengue begins as a febrile condition, and in certain patients, it can evolve severe clinical outcomes, such as dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). The reasons why certain patients develop DHF or DSS have not been thoroughly elucidated to date, and both patient and viral factors have been implicated. Previous work has shown that a severe immune dysfunction involving dendritic cells and T cells plays a key role in increasing the disease severity, especially in secondary heterologous infections. Extracellular vesicles (EVs) are membranous particles that are secreted by several cell types involved in homeostatic and pathological processes. Secretion of EVs by infected cells can enhance immune responses or favor viral evasion. In this study, we compare the molecular content of EVs that are secreted by human primary dendritic cells under different conditions: uninfected or infected with DENV3 strains isolated from patients with different infection phenotypes (a severe case involving DSS and a mild case). Human monocyte-derived dendritic cells (mdDCs) were infected with the dengue virus strains DENV3 5532 (severe) or DENV3 290 (mild), and the EVs were isolated. The presence of cup-shaped EVs was confirmed by electron microscopy and immunostaining with CD9, CD81, and CD83. The RNA content from the mdDC-infected cells contained several mRNAs and miRNAs related to immune responses compared to the EVs from mock-infected mdDCs. A number of these RNAs were detected exclusively during infection with DENV3 290 or DENV3 5532. This result suggests that the differential immune modulation of mdDCs by dengue strains can be achieved through the EV pathway. Additionally, we observed an association of EVs with DENV-infectious particles that seem to be protected from antibodies targeting the DENV envelope protein. We also showed that EVs derived from cells treated with IFN alpha have a protective effect against DENV infection in other cells. These results suggested that during DENV infection, the EV pathway could be exploited to favor viral viability, although immune mechanisms to counteract viral infection can also involve DC-derived EVs.
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Affiliation(s)
- Sharon de T Martins
- Laboratory of Gene Expression Regulation, Carlos Chagas Institute, FIOCRUZ, Curitiba, Brazil
| | - Diogo Kuczera
- Laboratory of Molecular Virology, Carlos Chagas Institute, FIOCRUZ, Curitiba, Brazil
| | - Jan Lötvall
- Krefting Research Centre, University of Gothenburg, Gothenburg, Sweden
| | - Juliano Bordignon
- Laboratory of Molecular Virology, Carlos Chagas Institute, FIOCRUZ, Curitiba, Brazil
| | - Lysangela R Alves
- Laboratory of Gene Expression Regulation, Carlos Chagas Institute, FIOCRUZ, Curitiba, Brazil
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Peruzza L, Gerdol M, Oliphant A, Wilcockson D, Pallavicini A, Hawkins L, Thatje S, Hauton C. The consequences of daily cyclic hypoxia on a European grass shrimp: From short‐term responses to long‐term effects. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13150] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Luca Peruzza
- Ocean and Earth ScienceNational Oceanography Centre SouthamptonUniversity of Southampton Southampton UK
| | - Marco Gerdol
- Department of Life SciencesUniversity of Trieste Trieste Italy
| | - Andrew Oliphant
- Institute of Biological, Environmental and Rural SciencesAberystwyth University Aberystwyth UK
| | - David Wilcockson
- Institute of Biological, Environmental and Rural SciencesAberystwyth University Aberystwyth UK
| | | | - Lawrence Hawkins
- Ocean and Earth ScienceNational Oceanography Centre SouthamptonUniversity of Southampton Southampton UK
| | - Sven Thatje
- Ocean and Earth ScienceNational Oceanography Centre SouthamptonUniversity of Southampton Southampton UK
| | - Chris Hauton
- Ocean and Earth ScienceNational Oceanography Centre SouthamptonUniversity of Southampton Southampton UK
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Shiri Y, Solouki M, Ebrahimie E, Emamjomeh A, Zahiri J. Unraveling the transcriptional complexity of compactness in sistan grape cluster. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 270:198-208. [PMID: 29576073 DOI: 10.1016/j.plantsci.2018.02.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 02/06/2018] [Accepted: 02/10/2018] [Indexed: 06/08/2023]
Abstract
Yaghooti grape of Sistan is the earliest ripening grape in Iran, harvested every May annually. It is adapted to dry conditions in Sistan region and its water requirement is less than the other grape cultivars. The transcriptional complexity of this grape was studied in three stages of cluster development. Totally, 24121 genes were expressed in different cluster development steps (step 1: cluster formation, step 2: berry formation, step 3: final size of cluster) of which 3040 genes in the first stage, 2381 genes in the second stage and 2400 genes in the third stage showed a significant increase in expression. GO analysis showed that when the clusters are ripening, the activity of the nucleus, cytoplasmic, cytosol, membrane and chloroplast genes in the cluster architecture cells decreases. In contrast, the activity of the endoplasmic reticulum, vacuole and extracellular region genes enhances. When Yaghooti grape is growing and developing, some of metabolic pathways were activated in the response to biotic and abiotic stresses. Gene co-expression network reconstruction showed that AGAMOUS is a key gene in compactness of Sistan grape cluster, because it influences on expression of GA gene which leads to increase cluster length and berries size.
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Affiliation(s)
- Yasoub Shiri
- PhD student of biotechnology, Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Mahmood Solouki
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran.
| | - Esmaeil Ebrahimie
- School of Medicine, The University of Adelaide, SA, Australia; School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, University of South Australia, Adelaide, Australia; Institute of Biotechnology, Shiraz University, Shiraz, Iran; School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, Australia
| | - Abbasali Emamjomeh
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Javad Zahiri
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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Zhu J, Gan X, Ao Q, Shen X, Tan Y, Chen M, Luo Y, Wang H, Jiang H, Li C. Basal polarization of the immune responses to Streptococcus agalactiae susceptible and resistant tilapia (Oreochromis niloticus). FISH & SHELLFISH IMMUNOLOGY 2018; 75:336-345. [PMID: 29454032 DOI: 10.1016/j.fsi.2018.01.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 06/08/2023]
Abstract
One of the highest priority areas for improvement is the development of effective strategies for decreasing disease mortality levels in aquaculture production, a better understanding of the components of the fish immune system and their functions in the context of pathogen invasion is needed. Tilapia is the most common fish in South China, and Streptococcus agalactiae has become the most serious disease problem for tilapia industry in China. Here, we profiled gene expression differences between tilapia differing in their susceptibility to S. agalactiae both basally (before infection) and at three early timepoints post-infection (5 h, 50 h, and 7 d). Between group comparisons revealed 5756 unique genes differentially expressed greater than 2-fold at one or more timepoints. And the resistant fish showed much more strong ability in pathogen recognition, antigen presentation, immune activation, while the susceptible fish showed fast activation of apoptosis. Taken together, the immune profiles expand our knowledge for molecular mechanisms for disease resistance, as well as provide solid molecular resources for further identification of the candidate markers for disease-resistant selection and evaluation of disease prevention and treatment options for tilapia industry.
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Affiliation(s)
- Jiajie Zhu
- Guangxi Academy of Fishery Sciences, Guangxi 530021, China; Guangxi University, Nanning, Guangxi 530004, China
| | - Xi Gan
- Guangxi Academy of Fishery Sciences, Guangxi 530021, China
| | - Qiuwei Ao
- Guangxi Academy of Fishery Sciences, Guangxi 530021, China
| | - Xiashuang Shen
- Guangxi Academy of Fishery Sciences, Guangxi 530021, China
| | - Yun Tan
- Guangxi Academy of Fishery Sciences, Guangxi 530021, China
| | - Ming Chen
- Guangxi Academy of Fishery Sciences, Guangxi 530021, China
| | - Yongju Luo
- Guangxi Academy of Fishery Sciences, Guangxi 530021, China
| | - Hui Wang
- Guangxi Academy of Fishery Sciences, Guangxi 530021, China
| | | | - Chao Li
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao 266109, China.
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Leonova K, Safina A, Nesher E, Sandlesh P, Pratt R, Burkhart C, Lipchick B, Gitlin I, Frangou C, Koman I, Wang J, Kirsanov K, Yakubovskaya MG, Gudkov AV, Gurova K. TRAIN (Transcription of Repeats Activates INterferon) in response to chromatin destabilization induced by small molecules in mammalian cells. eLife 2018; 7:e30842. [PMID: 29400649 PMCID: PMC5815852 DOI: 10.7554/elife.30842] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 02/04/2018] [Indexed: 12/13/2022] Open
Abstract
Cellular responses to the loss of genomic stability are well-established, while how mammalian cells respond to chromatin destabilization is largely unknown. We previously found that DNA demethylation on p53-deficient background leads to transcription of repetitive heterochromatin elements, followed by an interferon response, a phenomenon we named TRAIN (Transcription of Repeats Activates INterferon). Here, we report that curaxin, an anticancer small molecule, destabilizing nucleosomes via disruption of histone/DNA interactions, also induces TRAIN. Furthermore, curaxin inhibits oncogene-induced transformation and tumor growth in mice in an interferon-dependent manner, suggesting that anticancer activity of curaxin, previously attributed to p53-activation and NF-kappaB-inhibition, may also involve induction of interferon response to epigenetic derepression of the cellular 'repeatome'. Moreover, we observed that another type of drugs decondensing chromatin, HDAC inhibitor, also induces TRAIN. Thus, we proposed that TRAIN may be one of the mechanisms ensuring epigenetic integrity of mammalian cells via elimination of cells with desilenced chromatin.
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Affiliation(s)
- Katerina Leonova
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | - Alfiya Safina
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | - Elimelech Nesher
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
- Department of Molecular BiologyAriel UniversityArielIsrael
| | - Poorva Sandlesh
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | - Rachel Pratt
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | | | - Brittany Lipchick
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | - Ilya Gitlin
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | - Costakis Frangou
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | - Igor Koman
- Department of Molecular BiologyAriel UniversityArielIsrael
| | - Jianmin Wang
- Department of BioinformaticsRoswell Park Cancer InstituteBuffaloUnited States
| | - Kirill Kirsanov
- Department of Chemical CarcinogenesisInstitute of Carcinogenesis, Blokhin Cancer Research Center RAMSMoscowRussia
| | - Marianna G Yakubovskaya
- Department of Chemical CarcinogenesisInstitute of Carcinogenesis, Blokhin Cancer Research Center RAMSMoscowRussia
| | - Andrei V Gudkov
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | - Katerina Gurova
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
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Bateta R, Wang J, Wu Y, Weiss BL, Warren WC, Murilla GA, Aksoy S, Mireji PO. Tsetse fly (Glossina pallidipes) midgut responses to Trypanosoma brucei challenge. Parasit Vectors 2017; 10:614. [PMID: 29258576 PMCID: PMC5738168 DOI: 10.1186/s13071-017-2569-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 12/04/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Tsetse flies (Glossina spp.) are the prominent vector of African trypanosome parasites (Trypanosoma spp.) in sub-Saharan Africa, and Glossina pallidipes is the most widely distributed species in Kenya. This species displays strong resistance to infection by parasites, which are typically eliminated in the midgut shortly after acquisition from the mammalian host. Although extensive molecular information on immunity for the related species Glossina morsitans morsitans exists, similar information is scarce for G. pallidipes. METHODS To determine temporal transcriptional responses of G. pallidipes to Trypanosoma brucei brucei challenge, we conducted Illumina based RNA-seq on midgut organ and carcass from teneral females G. pallidipes at 24 and 48 h post-challenge (hpc) with T. b. brucei relative to their respective controls that received normal blood meals (without the parasite). We used a suite of bioinformatics tools to determine differentially expressed and enriched transcripts between and among tissues, and to identify expanded transcripts in G. pallidipes relative to their orthologs G. m. morsitans. RESULTS Midgut transcripts induced at 24 hpc encoded proteins were associated with lipid remodelling, proteolysis, collagen metabolism, apoptosis, and cell growth. Midgut transcripts induced at 48 hpc encoded proteins linked to embryonic growth and development, serine endopeptidases and proteosomal degradation of the target protein, mRNA translation and neuronal development. Temporal expression of immune responsive transcripts at 48 relative to 24 hpc was pronounced, indicative of a gradual induction of host immune responses the following challenge. We also searched for G. m. morsitans orthologous groups that may have experienced expansions in the G. pallidipes genome. We identified ten expanded groups in G. pallidipes with putative immunity-related functions, which may play a role in the higher refractoriness exhibited by this species. CONCLUSIONS There appears to be a lack of strong immune responses elicited by gut epithelia of teneral adults. This in combination with a compromised peritrophic matrix at this stage during the initial phase of T. b. brucei challenge may facilitate the increased parasite infection establishment noted in teneral flies relative to older adults. Although teneral flies are more susceptible than older adults, the majority of tenerals are still able to eliminate parasite infections. Hence, robust responses elicited at a later time point, such as 72 hpc, may clear parasite infections from the majority of flies. The expanded G. m. morsitans orthologous groups in G. pallidipes may also be functionally associated with the enhanced refractoriness to trypanosome infections reported in G. pallidipes relative to G. m. morsitans.
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Affiliation(s)
- Rosemary Bateta
- Department of Biochemistry, Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, P.O. Box 362, Kikuyu, Kenya
- Department of Biochemistry and Molecular Biology, Egerton University, P.O. Box 536, Njoro, Kenya
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT USA
| | - Jingwen Wang
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT USA
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Yineng Wu
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT USA
| | - Brian L. Weiss
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT USA
| | - Wesley C. Warren
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave., Campus Box 8501, St Louis, MO 63108 USA
| | - Grace A. Murilla
- Department of Biochemistry, Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, P.O. Box 362, Kikuyu, Kenya
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT USA
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT USA
| | - Paul O. Mireji
- Department of Biochemistry, Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, P.O. Box 362, Kikuyu, Kenya
- Department of Biochemistry and Molecular Biology, Egerton University, P.O. Box 536, Njoro, Kenya
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT USA
- Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, P. O. Box 428-80108, Kilifi, Kenya
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Veeravalli K, Schindler T, Dong E, Yamada M, Hamilton R, Laird MW. Strain engineering to reduce acetate accumulation during microaerobic growth conditions inEscherichia coli. Biotechnol Prog 2017; 34:303-314. [DOI: 10.1002/btpr.2592] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/16/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Karthik Veeravalli
- Late Stage Cell Culture, Genentech, Inc., 1 DNA Way; South San Francisco California 94080
| | - Tony Schindler
- Late Stage Cell Culture, Genentech, Inc., 1 DNA Way; South San Francisco California 94080
| | - Emily Dong
- Early Stage Cell Culture, Genentech, Inc., 1 DNA Way; South San Francisco California 94080
| | - Masaki Yamada
- Late Stage Cell Culture, Genentech, Inc., 1 DNA Way; South San Francisco California 94080
| | - Ryan Hamilton
- Late Stage Cell Culture, Genentech, Inc., 1 DNA Way; South San Francisco California 94080
| | - Michael W. Laird
- Early Stage Cell Culture, Genentech, Inc., 1 DNA Way; South San Francisco California 94080
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Kotoka E, Orr M. Modifying SAMseq to account for asymmetry in the distribution of effect sizes when identifying differentially expressed genes. Stat Appl Genet Mol Biol 2017; 16:291-312. [PMID: 29077555 DOI: 10.1515/sagmb-2016-0037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
RNA-Seq is a developing technology for generating gene expression data by directly sequencing mRNA molecules in a sample. RNA-Seq data consist of counts of reads recorded to a particular gene that are often used to identify differentially expressed (DE) genes. A common statistical method used to analyze RNA-Seq data is Significance Analysis of Microarray with emphasis on RNA-Seq data (SAMseq). SAMseq is a nonparametric method that uses a resampling technique to account for differences in sequencing depths when identifying DE genes. We propose a modification of this method that takes into account asymmetry in the distribution of the effect sizes by taking into account the sign of the test statistics. Through simulation studies, we showthat the proposed method, comparedwith the traditional SAMseqmethod and other existing methods provides better power for identifying truly DE genes or more sufficiently controls FDR in most settings where asymmetry is present. We illustrate the use of the proposed method by analyzing an RNA-Seq data set containing C57BL/6J (B6) and DBA/2J (D2) mouse strains samples.
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Pentimone I, Lebrón R, Hackenberg M, Rosso LC, Colagiero M, Nigro F, Ciancio A. Identification of tomato miRNAs responsive to root colonization by endophytic Pochonia chlamydosporia. Appl Microbiol Biotechnol 2017; 102:907-919. [PMID: 29105020 DOI: 10.1007/s00253-017-8608-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 10/18/2022]
Abstract
The molecular mechanisms active during the endophytic phase of the fungus Pochonia chlamydosporia are still poorly understood. In particular, few data are available on the links between the endophyte and the root response, as modulated by noncoding small RNAs. In this study, we describe the microRNAs (miRNAs) that are differentially expressed (DE) in the roots of tomato, colonized by P. chlamydosporia. A genome-wide NGS expression profiling of small RNAs in roots, either colonized or not by the fungus, showed 26 miRNAs upregulated in inoculated roots. Their predicted target genes are involved in the plant information processing system, which recognizes, percepts, and transmits signals, with higher representations in processes such as apoptosis and plant defense regulation. RNAseq data showed that predicted miRNA target genes were downregulated in tomato roots after 4, 7, 10, and 21 days post P. chlamydosporia inoculation. The differential expression of four miRNAs was further validated using qPCR analysis. The P. chlamydosporia endophytic lifestyle in tomato roots included an intricate network of miRNAs and targets. Data provide a first platform of DE tomato miRNAs after P. chlamydosporia colonization. They indicated that several miRNAs are involved in the host response to the fungus, playing important roles for its recognition as a symbiotic microorganism, allowing endophytism by modulating the host defense reaction. Data also indicated that endophytism affects tRNA fragmentation. This is the first study on miRNAs induced by P. chlamydosporia endophytism and related development regulation effects in Solanum lycopersicum.
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Affiliation(s)
- Isabella Pentimone
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126, Bari, Italy.
| | - Ricardo Lebrón
- Genetics Department & Biotechnology Institute, Biomedical Research Center (CIBM), University of Granada, Granada, Spain
| | - Michael Hackenberg
- Genetics Department & Biotechnology Institute, Biomedical Research Center (CIBM), University of Granada, Granada, Spain
| | - Laura C Rosso
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126, Bari, Italy
| | - Mariantonietta Colagiero
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126, Bari, Italy
| | - Franco Nigro
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari - Aldo Moro, Via G. Amendola 165/A, 70126, Bari, Italy
| | - Aurelio Ciancio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126, Bari, Italy
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RocA Is an Accessory Protein to the Virulence-Regulating CovRS Two-Component System in Group A Streptococcus. Infect Immun 2017; 85:IAI.00274-17. [PMID: 28808155 DOI: 10.1128/iai.00274-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 08/05/2017] [Indexed: 11/20/2022] Open
Abstract
Regulating gene expression during infection is critical to the ability of pathogens to circumvent the immune response and cause disease. This is true for the group A Streptococcus (GAS), a pathogen that causes both invasive (e.g., necrotizing fasciitis) and noninvasive (e.g., pharyngitis) diseases. The control of virulence (CovRS) two-component system has a major role in regulating GAS virulence factor expression. The regulator of cov (RocA) protein, which is a predicted kinase, functions in an undetermined manner through CovRS to alter gene expression and reduce invasive disease virulence. Here, we show that the ectopic expression of a truncated RocA derivative, harboring the membrane-spanning domains but not the dimerization or HATPase domain, is sufficient to complement a rocA mutant strain. Coupled with a previous bioinformatic study, the data are consistent with RocA being a pseudokinase. RocA reduces the ability of serotype M1 GAS isolates to express capsule and to evade killing in human blood, phenotypes that are not observed for M3 or M18 GAS due to isolates of these serotypes naturally harboring mutant rocA alleles. In addition, we found that varying the RocA concentration attenuates the regulatory activity of Mg2+ and the antimicrobial peptide LL-37, which positively and negatively regulate CovS function, respectively. Thus, we propose that RocA is an accessory protein to the CovRS system that influences the ability of GAS to modulate gene expression in response to host factors. A model of how RocA interacts with CovRS, and of the regulatory consequences of such activity, is presented.
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HAN G, ZHANG S, DONG Y. Anaerobic metabolism and thermal tolerance: The importance of opine pathways on survival of a gastropod after cardiac dysfunction. Integr Zool 2017; 12:361-370. [DOI: 10.1111/1749-4877.12229] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Guodong HAN
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences; Xiamen University; Xiamen China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Xiamen University; Xiamen China
| | - Shu ZHANG
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences; Xiamen University; Xiamen China
| | - Yunwei DONG
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences; Xiamen University; Xiamen China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Xiamen University; Xiamen China
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Hsu FM, Yen MR, Wang CT, Lin CY, Wang CJR, Chen PY. Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize. Epigenetics Chromatin 2017; 10:42. [PMID: 28854962 PMCID: PMC5577757 DOI: 10.1186/s13072-017-0148-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 08/08/2017] [Indexed: 11/11/2022] Open
Abstract
Background
DNA methylation plays important roles in many regulatory processes in plants. It is economically infeasible to profile genome-wide DNA methylation at a single-base resolution in maize, given its genome size of ~2.5 Gb. As an alternative, we adapted region of interest (ROI)-directed reduced representation bisulfite sequencing (RRBS) to survey genome-wide methylation in maize. Results We developed a pipeline for selecting restriction enzymes in silico and experimentally showed that, in the maize genome, MseI- and CviQI-digested fragments are precisely enriched in promoters and gene bodies, respectively. We proceeded with comparisons of epigenomes and transcriptomes between shoots and tassels and found that the occurrences of highly methylated, tissue-specific, mCHH islands upstream of transcription start sites (TSSs) were positively correlated with differential gene expression. Furthermore, 5′ regulatory regions between TSS and mCHH islands often contain putative binding sites of known transcription factors (TFs) that regulate the flowering process and the timing of the transition from the vegetative to the reproductive phase. By integrating MNase-seq and siRNA-seq data, we found that regions of mCHH islands accumulate 21nt-siRNAs in a tissue-specific manner, marking the transition to open chromatin, thereby ensuring the accessibility of TFs for tissue-specific gene regulation. Conclusions Our ROI-directed RRBS pipeline is eminently applicable to DNA methylation profiling of large genomes. Our results provide novel insights into the tissue-specific epigenomic landscapes in maize, demonstrating that DNA methylation and siRNA and chromatin accessibility constitute a critical, interdependent component that orchestrates the transition from the vegetative to the reproductive phase. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0148-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fei-Man Hsu
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan.,Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chi-Ting Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chien-Yu Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chung-Ju Rachel Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan.
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan.
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Gerdol M, Fujii Y, Hasan I, Koike T, Shimojo S, Spazzali F, Yamamoto K, Ozeki Y, Pallavicini A, Fujita H. The purplish bifurcate mussel Mytilisepta virgata gene expression atlas reveals a remarkable tissue functional specialization. BMC Genomics 2017; 18:590. [PMID: 28789640 PMCID: PMC5549309 DOI: 10.1186/s12864-017-4012-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/02/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Mytilisepta virgata is a marine mussel commonly found along the coasts of Japan. Although this species has been the subject of occasional studies concerning its ecological role, growth and reproduction, it has been so far almost completely neglected from a genetic and molecular point of view. In the present study we present a high quality de novo assembled transcriptome of the Japanese purplish mussel, which represents the first publicly available collection of expressed sequences for this species. RESULTS The assembled transcriptome comprises almost 50,000 contigs, with a N50 statistics of ~1 kilobase and a high estimated completeness based on the rate of BUSCOs identified, standing as one of the most exhaustive sequence resources available for mytiloid bivalves to date. Overall this data, accompanied by gene expression profiles from gills, digestive gland, mantle rim, foot and posterior adductor muscle, presents an accurate snapshot of the great functional specialization of these five tissues in adult mussels. CONCLUSIONS We highlight that one of the most striking features of the M. virgata transcriptome is the high abundance and diversification of lectin-like transcripts, which pertain to different gene families and appear to be expressed in particular in the digestive gland and in the gills. Therefore, these two tissues might be selected as preferential targets for the isolation of molecules with interesting carbohydrate-binding properties. In addition, by molecular phylogenomics, we provide solid evidence in support of the classification of M. virgata within the Brachidontinae subfamily. This result is in agreement with the previously proposed hypothesis that the morphological features traditionally used to group Mytilisepta spp. and Septifer spp. within the same clade are inappropriate due to homoplasy.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34126 Trieste, Italy
| | - Yuki Fujii
- Department of Pharmacy, Faculty of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298 Japan
| | - Imtiaj Hasan
- Department of Life and Environmental System Science, Graduate School of NanoBio Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, 236-0027 Japan
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Toru Koike
- Department of Pharmacy, Faculty of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298 Japan
| | - Shunsuke Shimojo
- Department of Pharmacy, Faculty of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298 Japan
| | - Francesca Spazzali
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34126 Trieste, Italy
| | - Kaname Yamamoto
- Department of Pharmacy, Faculty of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298 Japan
| | - Yasuhiro Ozeki
- Department of Life and Environmental System Science, Graduate School of NanoBio Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, 236-0027 Japan
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34126 Trieste, Italy
| | - Hideaki Fujita
- Department of Pharmacy, Faculty of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298 Japan
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Zhou T, Li N, Liu S, Jin Y, Fu Q, Gao S, Liu Y, Liu Z. The NCK and ABI adaptor genes in catfish and their involvement in ESC disease response. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 73:119-123. [PMID: 28341353 DOI: 10.1016/j.dci.2017.03.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/20/2017] [Accepted: 03/20/2017] [Indexed: 06/06/2023]
Abstract
Adaptor proteins non-catalytic region of tyrosine kinase (NCK) and Abelson interactor (ABI) are crucial for disease response. NCK1 was identified to be a candidate gene for enteric septicemia of catfish (ESC) disease resistance, and was speculated to play similar roles during ESC and enteropathogenic Escherichia coli (EPEC) pathogenicity. ABI1 was reported as a positional candidate gene for bacterial cold water disease (BCWD) resistance in rainbow trout. In this study, three NCK genes and six ABI genes were identified in the channel catfish (Ictalurus punctatus) genome and blue catfish (I. furcatus) transcriptome, and annotated by domain structures, phylogenetic and syntenic analyses. Their expression patterns were examined in the intestine and liver of catfish after challenge with Edwardsiella ictaluri. In the intestine, NCK1, ABI2a, ABI2b, ABI3a were differentially expressed after E. ictaluri infection. In the liver, NCK2a, NCK2b, ABI1b, ABI2a, ABI2b were significantly upregulated in ESC susceptible fish. In general, the NCK and ABI genes, with exception of ABI3a gene and NCK1 gene, were expressed at higher levels in susceptible fish after infection than in control fish, but were expressed at lower levels in resistant fish than in the control fish. Taken together, these results support the notion that NCK and ABI genes are involved in disease processes facilitating pathogenesis of the E. ictaluri bacteria.
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Affiliation(s)
- Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ning Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Yulin Jin
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Qiang Fu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Sen Gao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Yang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
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Chandra S, Kazmi AZ, Ahmed Z, Roychowdhury G, Kumari V, Kumar M, Mukhopadhyay K. Genome-wide identification and characterization of NB-ARC resistant genes in wheat (Triticum aestivum L.) and their expression during leaf rust infection. PLANT CELL REPORTS 2017; 36:1097-1112. [PMID: 28401336 DOI: 10.1007/s00299-017-2141-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/04/2017] [Indexed: 05/06/2023]
Abstract
NB-ARC domain-containing resistance genes from the wheat genome were identified, characterized and localized on chromosome arms that displayed differential yet positive response during incompatible and compatible leaf rust interactions. Wheat (Triticum aestivum L.) is an important cereal crop; however, its production is affected severely by numerous diseases including rusts. An efficient, cost-effective and ecologically viable approach to control pathogens is through host resistance. In wheat, high numbers of resistance loci are present but only few have been identified and cloned. A comprehensive analysis of the NB-ARC-containing genes in complete wheat genome was accomplished in this study. Complete NB-ARC encoding genes were mined from the Ensembl Plants database to predict 604 NB-ARC containing sequences using the HMM approach. Genome-wide analysis of orthologous clusters in the NB-ARC-containing sequences of wheat and other members of the Poaceae family revealed maximum homology with Oryza sativa indica and Brachypodium distachyon. The identification of overlap between orthologous clusters enabled the elucidation of the function and evolution of resistance proteins. The distributions of the NB-ARC domain-containing sequences were found to be balanced among the three wheat sub-genomes. Wheat chromosome arms 4AL and 7BL had the most NB-ARC domain-containing contigs. The spatio-temporal expression profiling studies exemplified the positive role of these genes in resistant and susceptible wheat plants during incompatible and compatible interaction in response to the leaf rust pathogen Puccinia triticina. Two NB-ARC domain-containing sequences were modelled in silico, cloned and sequenced to analyze their fine structures. The data obtained in this study will augment isolation, characterization and application NB-ARC resistance genes in marker-assisted selection based breeding programs for improving rust resistance in wheat.
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Affiliation(s)
- Saket Chandra
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Andaleeb Z Kazmi
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Zainab Ahmed
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Gargi Roychowdhury
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Veena Kumari
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Manish Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Kunal Mukhopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
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