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Nobre SVA, de Andrade GAK, Metz GF, Lucini F, de Albuquerque MP, Victória FDC. Antarctica's hidden mycoviral treasures in fungi isolated from mosses: A first genomic approach. J Basic Microbiol 2024:e202300671. [PMID: 38736205 DOI: 10.1002/jobm.202300671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/15/2024] [Accepted: 04/27/2024] [Indexed: 05/14/2024]
Abstract
This study investigates the presence of mycoviruses in Antarctic fungi and elucidates their evolutionary relationships. To achieve this, we aligned mycoviral gene sequences with genomes of previously sequenced Antarctic endophytic fungi, made available by our research group and accessible via Joint Genome Institute. Our findings reveal that the most prevalent genetic regions in all endophytic fungi are homologous to Partitiviruses, Baculoviridae, and Phycodnaviridae. These regions display evidence of positive selection pressure, suggesting genetic diversity and the accumulation of nonsynonymous mutations. This phenomenon implies a crucial role for these regions in the adaptation and survival of these fungi in the challenging Antarctic ecosystems. The presence of mycoviruses in Antarctic endophytic fungi may indicate shared survival strategies between the virus and its host, shedding light on their evolutionary dynamics. This study underscores the significance of exploring mycoviruses within endophytic fungi and their contributions to genetic diversity. Future research avenues could delve into the functional implications of these conserved mycoviral genetic regions in Antarctic endophytic fungi, providing a comprehensive understanding of this intriguing association and genomic retention of viral region in fungi.
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Affiliation(s)
- Steffany V A Nobre
- Curso de Biotecnologia, Universidade Federal do Pampa, São Gabriel, Brazil
- Núcleo de Estudos da Vegetação Antártica, São Gabriel, Brazil
| | - Guilherme A K de Andrade
- Núcleo de Estudos da Vegetação Antártica, São Gabriel, Brazil
- PPGCB-UNIPAMPA, Programa de Pós-Graduação em Ciências Biológicas, São Gabriel, Brazil
| | - Geferson F Metz
- Núcleo de Estudos da Vegetação Antártica, São Gabriel, Brazil
- PPGCB-UNIPAMPA, Programa de Pós-Graduação em Ciências Biológicas, São Gabriel, Brazil
| | - Fabíola Lucini
- Programa Antártico Brasileiro, Brasilia-DF, Brazil
- Faculdade de Ciências da Saúde-FCS, Federal University of Grande Dourados (UFGD), Dourados, Brazil
| | - Margéli P de Albuquerque
- Núcleo de Estudos da Vegetação Antártica, São Gabriel, Brazil
- Programa Antártico Brasileiro, Brasilia-DF, Brazil
| | - Filipe de C Victória
- Núcleo de Estudos da Vegetação Antártica, São Gabriel, Brazil
- PPGCB-UNIPAMPA, Programa de Pós-Graduação em Ciências Biológicas, São Gabriel, Brazil
- Faculdade de Ciências da Saúde-FCS, Federal University of Grande Dourados (UFGD), Dourados, Brazil
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Athanasopoulou K, Adamopoulos PG, Scorilas A. Unveiling the Human Gastrointestinal Tract Microbiome: The Past, Present, and Future of Metagenomics. Biomedicines 2023; 11:biomedicines11030827. [PMID: 36979806 PMCID: PMC10045138 DOI: 10.3390/biomedicines11030827] [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: 01/31/2023] [Revised: 02/26/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Over 1014 symbiotic microorganisms are present in a healthy human body and are responsible for the synthesis of vital vitamins and amino acids, mediating cellular pathways and supporting immunity. However, the deregulation of microbial dynamics can provoke diverse human diseases such as diabetes, human cancers, cardiovascular diseases, and neurological disorders. The human gastrointestinal tract constitutes a hospitable environment in which a plethora of microbes, including diverse species of archaea, bacteria, fungi, and microeukaryotes as well as viruses, inhabit. In particular, the gut microbiome is the largest microbiome community in the human body and has drawn for decades the attention of scientists for its significance in medical microbiology. Revolutions in sequencing techniques, including 16S rRNA and ITS amplicon sequencing and whole genome sequencing, facilitate the detection of microbiomes and have opened new vistas in the study of human microbiota. Especially, the flourishing fields of metagenomics and metatranscriptomics aim to detect all genomes and transcriptomes that are retrieved from environmental and human samples. The present review highlights the complexity of the gastrointestinal tract microbiome and deciphers its implication not only in cellular homeostasis but also in human diseases. Finally, a thorough description of the widely used microbiome detection methods is discussed.
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Affiliation(s)
- Konstantina Athanasopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
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3
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Chen C, Yan Q, Yao X, Li S, Lv Q, Wang G, Zhong Q, Tang F, Liu Z, Huang Y, An Y, Zhou J, Zhang Q, Zhang A, Ullah H, Zhang Y, Liu C, Zhu D, Li H, Sun W, Ma W. Alterations of the gut virome in patients with systemic lupus erythematosus. Front Immunol 2023; 13:1050895. [PMID: 36713446 PMCID: PMC9874095 DOI: 10.3389/fimmu.2022.1050895] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
Background Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that has been linked to the dysbiosis of the gut microbiome and virome. However, the potential characterization of the gut virome in SLE patients needs to be explored more extensively. Methods Herein, we analyzed the gut viral community of 16 SLE patients and 31 healthy controls using both bulk and virus-like particle (VLP)-based metagenomic sequencing of their fecal samples. A total of 15,999 non-redundant viral operational taxonomic units (vOTUs) were identified from the metagenomic assembled contigs and used for gut virome profiling. Results SLE patients exhibited a significant decrease in gut viral diversity in the bulk metagenome dataset, but this change was not significant in the VLP metagenome dataset. Also, considerable alterations of the overall gut virome composition and remarkable changes in the viral family compositions were observed in SLE patients compared with healthy controls, as observed in both two technologies. We identified 408 vOTUs (177 SLE-enriched and 231 control-enriched) with significantly different relative abundances between patients and controls in the bulk virome, and 18 vOTUs (17 SLE-enriched in 1 control-enriched) in the VLP virome. The SLE-enriched vOTUs included numerous Siphoviridae, Microviridae, and crAss-like viruses and were frequently predicted to infect Bacteroides, Parabacteroides, and Ruminococcus_E, while the control-enriched contained numerous members of Siphoviridae and Myoviridae and were predicted to infect Prevotella and Lachnospirales_CAG-274. We explored the correlations between gut viruses and bacteria and found that some Lachnospirales_CAG-274 and Hungatella_A phages may play key roles in the virus-bacterium network. Furthermore, we explored the gut viral signatures for disease discrimination and achieved an area under the receiver operator characteristic curve (AUC) of above 0.95, suggesting the potential of the gut virome in the prediction of SLE. Conclusion Our findings demonstrated the alterations in viral diversity and taxonomic composition of the gut virome of SLE patients. Further research into the etiology of SLE and the gut viral community will open up new avenues for treating and preventing SLE and other autoimmune diseases.
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Affiliation(s)
- Changming Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xueming Yao
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | | | - Qingbo Lv
- Puensum Genetech Institute, Wuhan, China,College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Guangyang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Qin Zhong
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Fang Tang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Zhengqi Liu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Ying Huang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Yang An
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jing Zhou
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qiongyu Zhang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | | | - Hayan Ullah
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, China
| | - Can Liu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Dan Zhu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Hufan Li
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Wen Sun
- Key Laboratory of Health Cultivation of the Ministry of Education, Beijing University of Chinese Medicine, Beijing, China,*Correspondence: Wen Sun, ; Wukai Ma,
| | - Wukai Ma
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China,*Correspondence: Wen Sun, ; Wukai Ma,
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The Role of Chloroviruses as Possible Infectious Agents for Human Health: Putative Mechanisms of ATCV-1 Infection and Potential Routes of Transmission. Trop Med Infect Dis 2023; 8:tropicalmed8010040. [PMID: 36668947 PMCID: PMC9863483 DOI: 10.3390/tropicalmed8010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
The Chlorovirus genus of the Phycodnaviridae family includes large viruses with a double-stranded DNA genome. Chloroviruses are widely distributed in freshwater bodies around the world and have been isolated from freshwater sources in Europe, Asia, Australia, and North and South America. One representative of chloroviruses is Acanthocystis turfacea chlorella virus 1 (ATCV-1), which is hosted by Chlorella heliozoae. A few publications in the last ten years about the potential effects of ATCV-1 on the human brain sparked interest among specialists in the field of human infectious pathology. The goal of our viewpoint was to compile the scant research on the effects of ATCV-1 on the human body, to demonstrate the role of chloroviruses as new possible infectious agents for human health, and to indicate potential routes of virus transmission. We believe that ATCV-1 transmission routes remain unexplored. We also question whether chlorella-based nutritional supplements are dangerous for ATCV-1 infections. Further research will help to identify the routes of infection, the cell types in which ATCV-1 can persist, and the pathological mechanisms of the virus's effect on the human body.
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Shin E, Schwarz KB, Jones-Brando LV, Florea LD, Sabunciyan S, Wood LD, Yolken RH. Expression of HLA and Autoimmune Pathway Genes in Liver Biopsies of Young Subjects With Autoimmune Hepatitis Type 1. J Pediatr Gastroenterol Nutr 2022; 75:269-275. [PMID: 35759748 PMCID: PMC9365252 DOI: 10.1097/mpg.0000000000003538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/18/2022] [Indexed: 12/10/2022]
Abstract
OBJECTIVES To test the hypothesis that autoimmune hepatitis (AIH type I) in young subjects is due to genetic differences in proinflammatory genes responding to viral triggers in patients and controls. METHODS Intrahepatic gene expression was compared between AIH type I (n = 24, age 9-30 years) patients (hereafter referred to as the AIH group) and controls (n = 21, age 4-25 years). RNA sequencing was performed on complementary DNA (cDNA) libraries made from total RNA extracted from formalin-fixed paraffin-embedded (FFPE) liver biopsy samples. Gene expression levels were quantified, and differentially expressed genes were functionally analyzed. Pathway analysis was performed using the databases Kyoto Encyclopedia of Genes and Genomes (KEGG) and PANTHER. The remaining sequences were mapped to the RefSeq complete set of viral genomes. RESULTS Differential gene analysis identified 181 genes that were significantly differentially expressed (136 upregulated in the AIH group). Autoimmune pathway genes such as CD19 and CD20 which are important in B cell regulation and maturation as well as, CD8 and LY9 , which are T-cell related, were upregulated in our AIH group. Genes implicated in AIH pathogenesis including CXCL10 , which is thought to be associated with AIH severity and progression, complement genes ( C1QA, C1QB , and C1QC ), and human leucocyte antigen ( HLA ) genes ( HLA-DRB1, HLA-DRA, HLA-B , and HLA-C ) were upregulated in samples from the AIH group. Specific viral etiologies were not found. CONCLUSIONS Unbiased next-generation sequencing and differential gene expression analysis of the AIH group has not only added support for the role of B cells in the pathogenesis and treatment of AIH but also has introduced potential new therapeutic targets: CXCL10 (anti- CXCL10 ) and several complement system-related genes.
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Affiliation(s)
- Emilia Shin
- From the Pediatrics, Johns Hopkins Medical Institutions, Baltimore, MD
| | | | | | - Liliana D. Florea
- the Genetic Medicine, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Sarven Sabunciyan
- From the Pediatrics, Johns Hopkins Medical Institutions, Baltimore, MD
| | | | - Robert H. Yolken
- From the Pediatrics, Johns Hopkins Medical Institutions, Baltimore, MD
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6
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Bhardwaj K, Garg A, Pandey AD, Sharma H, Kumar M, Vrati S. Insights into the human gut virome by sampling a population from the Indian subcontinent. J Gen Virol 2022; 103. [PMID: 35951476 DOI: 10.1099/jgv.0.001774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gut virome plays an important role in human physiology but remains poorly understood. This study reports an investigation of the human gut DNA-virome of a previously unexplored ethnic population through metagenomics of faecal samples collected from individuals residing in Northern India. Analysis shows that, similar to the populations investigated earlier, majority of the identified virome belongs to bacteriophages and a smaller fraction (<20 %) consists of viruses that infect animals, archaea, protists, multiple domains or plants. However, crAss-like phages, in this population, are dominated by the genera VI, VII and VIII. Interestingly, it also reveals the presence of a virus family, Sphaerolipoviridae, which has not been detected in the human gut earlier. Viral families, Siphoviridae, Myoviridae, Podoviridae, Microviridae, Herelleviridae and Phycodnaviridae are detected in all of the analysed individuals, which supports the existence of a core virome. Lysogeny-associated genes were found in less than 10 % of the assembled genomes and a negative correlation was observed in the richness of bacterial and free-viral species, suggesting that the dominant lifestyle of gut phage is not lysogenic. This is in contrast to some of the earlier studies. Further, several hundred high-quality viral genomes were recovered. Detailed characterization of these genomes would be useful for understanding the biology of these viruses and their significance in human physiology.
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Affiliation(s)
- Kanchan Bhardwaj
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-Gurugram Expressway, Faridabad-121 001, Haryana, India.,Manav Rachna International Institute of Research and Studies, Sector-43, Aravali hills, Faridabad-121 004, Haryana, India
| | - Anjali Garg
- Department of Biophysics, University of Delhi, South Campus, New Delhi-110021, India
| | - Abhay Deep Pandey
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-Gurugram Expressway, Faridabad-121 001, Haryana, India
| | - Himani Sharma
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-Gurugram Expressway, Faridabad-121 001, Haryana, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi, South Campus, New Delhi-110021, India
| | - Sudhanshu Vrati
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-Gurugram Expressway, Faridabad-121 001, Haryana, India
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Miao X, Liu C, Liu M, Han X, Zhu L, Bai X. The role of pipe biofilms on dissemination of viral pathogens and virulence factor genes in a full-scale drinking water supply system. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128694. [PMID: 35316639 DOI: 10.1016/j.jhazmat.2022.128694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/24/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Water is an important medium for virus transmission and viral pathogens are increasingly appreciated as a significant water safety issue. However, the effect of pipe biofilms on viral pathogens remains unclear. This research aimed to investigate the dissemination of viruses in a full-scale drinking water supply system (DWSS) and the effect of pipe biofilms on viral pathogens in bulking water. Viral pathogens, pathogenic viral hosts, and viral virulence factors (VFs) were found to disseminate from source water to tap water. The proportion of virus and viral VFs in the biofilm was far less than that in water. The contribution of biofilms in pipe wall to viruses and viral VFs in bulking water was less than 4%, and viruses in the biofilm had no obvious effect on pathogenic viruses in water. Dominant viruses carrying VFs changed from Cyanobacteria virus to Mycobacterium virus after advanced water treatment. Mycobacterium and organics were identified as the key factors influencing composition and abundance of viral VFs, which could explain 41.1% of the variation in viral virulence in the water supply system. Host bacteria and organics may be used as the key targets to control the risk of viruses in DWSSs.
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Affiliation(s)
- Xiaocao Miao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Chenxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Mingkun Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Xue Han
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Lingling Zhu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Xiaohui Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China.
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Petro TM, Agarkova IV, Esmael A, Dunigan DD, Van Etten JL, Pattee GL. Chlorovirus ATCV-1 Accelerates Motor Deterioration in SOD1-G93A Transgenic Mice and Its SOD1 Augments Induction of Inflammatory Factors From Murine Macrophages. Front Neurol 2022; 13:821166. [PMID: 35280283 PMCID: PMC8908019 DOI: 10.3389/fneur.2022.821166] [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: 11/23/2021] [Accepted: 01/31/2022] [Indexed: 11/25/2022] Open
Abstract
Background Genetically polymorphic Superoxide Dismutase 1 G93A (SOD1-G93A) underlies one form of familial Amyotrophic Lateral Sclerosis (ALS). Exposures from viruses may also contribute to ALS, possibly by stimulating immune factors, such as IL-6, Interferon Stimulated Genes, and Nitric Oxide. Recently, chlorovirus ATCV-1, which encodes a SOD1, was shown to replicate in macrophages and induce inflammatory factors. Objective This study aimed to determine if ATCV-1 influences development of motor degeneration in an ALS mouse model and to assess whether SOD1 of ATCV-1 influences production of inflammatory factors from macrophages. Methods Sera from sporadic ALS patients were screened for antibody to ATCV-1. Active or inactivated ATCV-1, saline, or a viral mimetic, polyinosinic:polycytidylic acid (poly I:C) were injected intracranially into transgenic mice expressing human SOD1-G93A- or C57Bl/6 mice. RAW264.7 mouse macrophage cells were transfected with a plasmid vector expressing ATCV-1 SOD1 or an empty vector prior to stimulation with poly I:C with or without Interferon-gamma (IFN-γ). Results Serum from sporadic ALS patients had significantly more IgG1 antibody directed against ATCV-1 than healthy controls. Infection of SOD1-G93A mice with active ATCV-1 significantly accelerated onset of motor loss, as measured by tail paralysis, hind limb tucking, righting reflex, and latency to fall in a hanging cage-lid test, but did not significantly affect mortality when compared to saline-treated transgenics. By contrast, poly I:C treatment significantly lengthened survival time but only minimally slowed onset of motor loss, while heat-inactivated ATCV-1 did not affect motor loss or survival. ATCV-1 SOD1 significantly increased expression of IL-6, IL-10, ISG promoter activity, and production of Nitric Oxide from RAW264.7 cells. Conclusion ATCV-1 chlorovirus encoding an endogenous SOD1 accelerates pathogenesis but not mortality, while poly I:C that stimulates antiviral immune responses delays mortality in an ALS mouse model. ATCV-1 SOD1 enhances induction of inflammatory factors from macrophages.
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Affiliation(s)
- Thomas M. Petro
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE, United States
- Nebraska Center for Virology, University of Nebraska Lincoln, Lincoln, NE, United States
- *Correspondence: Thomas M. Petro
| | - Irina V. Agarkova
- Nebraska Center for Virology, University of Nebraska Lincoln, Lincoln, NE, United States
- Department Plant Pathology, University of Nebraska Lincoln, Lincoln, NE, United States
| | - Ahmed Esmael
- Nebraska Center for Virology, University of Nebraska Lincoln, Lincoln, NE, United States
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha, Egypt
| | - David D. Dunigan
- Nebraska Center for Virology, University of Nebraska Lincoln, Lincoln, NE, United States
- Department Plant Pathology, University of Nebraska Lincoln, Lincoln, NE, United States
| | - James L. Van Etten
- Nebraska Center for Virology, University of Nebraska Lincoln, Lincoln, NE, United States
- Department Plant Pathology, University of Nebraska Lincoln, Lincoln, NE, United States
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Lee CZ, Zoqratt MZHM, Phipps ME, Barr JJ, Lal SK, Ayub Q, Rahman S. The gut virome in two indigenous populations from Malaysia. Sci Rep 2022; 12:1824. [PMID: 35115615 PMCID: PMC8813915 DOI: 10.1038/s41598-022-05656-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/04/2022] [Indexed: 12/30/2022] Open
Abstract
The human gut contains a complex microbiota dominated by bacteriophages but also containing other viruses and bacteria and fungi. There are a growing number of techniques for the extraction, sequencing, and analysis of the virome but currently no standardized protocols. This study established an effective workflow for virome analysis to investigate the virome of stool samples from two understudied ethnic groups from Malaysia: the Jakun and Jehai Orang Asli. By using the virome extraction and analysis workflow with the Oxford Nanopore Technology, long-read sequencing successfully captured close to full-length viral genomes. The virome composition of the two indigenous Malaysian communities were remarkably different from those found in other parts of the world. Additionally, plant viruses found in the viromes of these individuals were attributed to traditional food-seeking methods. This study establishes a human gut virome workflow and extends insights into the healthy human gut virome, laying the groundwork for comparative studies.
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Affiliation(s)
- Chuen Zhang Lee
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | | | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya, Malaysia
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Sunil K Lal
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Qasim Ayub
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Genomics Facility, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Subang Jaya, Malaysia.
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Molina-Grima E, García-Camacho F, Acién-Fernández FG, Sánchez-Mirón A, Plouviez M, Shene C, Chisti Y. Pathogens and predators impacting commercial production of microalgae and cyanobacteria. Biotechnol Adv 2021; 55:107884. [PMID: 34896169 DOI: 10.1016/j.biotechadv.2021.107884] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/25/2021] [Accepted: 12/02/2021] [Indexed: 02/09/2023]
Abstract
Production of phytoplankton (microalgae and cyanobacteria) in commercial raceway ponds and other systems is adversely impacted by phytoplankton pathogens, including bacteria, fungi and viruses. In addition, cultures are susceptible to productivity loss, or crash, through grazing by contaminating zooplankton such as protozoa, rotifers and copepods. Productivity loss and product contamination are also caused by otherwise innocuous invading phytoplankton that consume resources in competition with the species being cultured. This review is focused on phytoplankton competitors, pathogens and grazers of significance in commercial culture of microalgae and cyanobacteria. Detection and identification of these biological contaminants are discussed. Operational protocols for minimizing contamination, and methods of managing it, are discussed.
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Affiliation(s)
- Emilio Molina-Grima
- Department of Chemical Engineering, University of Almería, 04120 Almería, Spain
| | | | | | | | - Maxence Plouviez
- School of Food and Advanced Technology, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | - Carolina Shene
- Center for Biotechnology and Bioengineering (CeBiB), Center of Food Biotechnology and Bioseparations, BIOREN and Department of Chemical Engineering, Universidad de La Frontera, Francisco Salazar 01145, Temuco 4780000, Chile
| | - Yusuf Chisti
- School of Engineering, Massey University, Private Bag 11 222, Palmerston North, New Zealand.
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Jurasz H, Pawłowski T, Perlejewski K. Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives. Front Microbiol 2021; 12:745076. [PMID: 34745046 PMCID: PMC8564396 DOI: 10.3389/fmicb.2021.745076] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
We describe the most common internal and external sources and types of contamination encountered in viral metagenomic studies and discuss their negative impact on sequencing results, particularly for low-biomass samples and clinical applications. We also propose some basic recommendations for reducing the background noise in viral shotgun metagenomic (SM) studies, which would limit the bias introduced by various classes of contaminants. Regardless of the specific viral SM protocol, contamination cannot be totally avoided; in particular, the issue of reagent contamination should always be addressed with high priority. There is an urgent need for the development and validation of standards for viral metagenomic studies especially if viral SM protocols will be more widely applied in diagnostics.
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Affiliation(s)
- Henryk Jurasz
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Pawłowski
- Division of Psychotherapy and Psychosomatic Medicine, Department of Psychiatry, Wrocław Medical University, Wrocław, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
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12
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Nelson DR, Hazzouri KM, Lauersen KJ, Jaiswal A, Chaiboonchoe A, Mystikou A, Fu W, Daakour S, Dohai B, Alzahmi A, Nobles D, Hurd M, Sexton J, Preston MJ, Blanchette J, Lomas MW, Amiri KMA, Salehi-Ashtiani K. Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution. Cell Host Microbe 2021; 29:250-266.e8. [PMID: 33434515 DOI: 10.1016/j.chom.2020.12.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/08/2020] [Accepted: 11/18/2020] [Indexed: 01/08/2023]
Abstract
Being integral primary producers in diverse ecosystems, microalgal genomes could be mined for ecological insights, but representative genome sequences are lacking for many phyla. We cultured and sequenced 107 microalgae species from 11 different phyla indigenous to varied geographies and climates. This collection was used to resolve genomic differences between saltwater and freshwater microalgae. Freshwater species showed domain-centric ontology enrichment for nuclear and nuclear membrane functions, while saltwater species were enriched in organellar and cellular membrane functions. Further, marine species contained significantly more viral families in their genomes (p = 8e-4). Sequences from Chlorovirus, Coccolithovirus, Pandoravirus, Marseillevirus, Tupanvirus, and other viruses were found integrated into the genomes of algal from marine environments. These viral-origin sequences were found to be expressed and code for a wide variety of functions. Together, this study comprehensively defines the expanse of protein-coding and viral elements in microalgal genomes and posits a unified adaptive strategy for algal halotolerance.
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Affiliation(s)
- David R Nelson
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.
| | - Khaled M Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), UAE University, Al Ain, Abu Dhabi, UAE; Biology Department, College of Science, UAE University, Al Ain, Abu Dhabi, UAE
| | - Kyle J Lauersen
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Ashish Jaiswal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | | | - Alexandra Mystikou
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Weiqi Fu
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sarah Daakour
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Bushra Dohai
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Amnah Alzahmi
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - David Nobles
- UTEX Culture Collection of Algae at the University of Texas at Austin, Austin, TX, USA
| | - Mark Hurd
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Julie Sexton
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Michael J Preston
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Joan Blanchette
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Michael W Lomas
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Khaled M A Amiri
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), UAE University, Al Ain, Abu Dhabi, UAE; Biology Department, College of Science, UAE University, Al Ain, Abu Dhabi, UAE
| | - Kourosh Salehi-Ashtiani
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE; Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.
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13
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Mishra B, Manmode S, Walke G, Chakraborty S, Neralkar M, Hotha S. Synthesis of the hyper-branched core tetrasaccharide motif of chloroviruses. Org Biomol Chem 2021; 19:1315-1328. [PMID: 33459320 DOI: 10.1039/d0ob02176h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chemical synthesis of complex oligosaccharides, especially those possessing hyper-branched structures with one or multiple 1,2-cis glycosidic bonds, is a challenging task. Complementary reactivity of glycosyl donors and acceptors and proper tuning of the solvent/temperature/activator coupled with compromised glycosylation yields for sterically congested glycosyl acceptors are among several factors that make such syntheses daunting. Herein, we report the synthesis of a semi-conserved hyper-branched core tetrasaccharide motif from chloroviruses which are associated with reduced cognitive function in humans as well as in mouse models. The target tetrasaccharide contains four different sugar residues in which l-fucose is connected to d-xylose and l-rhamnose via a 1,2-trans glycosidic bond, whereas with the d-galactose residue is connected through a 1,2-cis glycosidic bond. A thorough and comprehensive study of various accountable factors enabled us to install a 1,2-cis galactopyranosidic linkage in a stereoselective fashion under [Au]/[Ag]-catalyzed glycosidation conditions en route to the target tetrasaccharide motif in 14 steps.
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Affiliation(s)
- Bijoyananda Mishra
- Department of Chemistry, Indian Institute of Science Education and Research, Pune - 411 008, MH, India.
| | - Sujit Manmode
- Department of Chemistry, Indian Institute of Science Education and Research, Pune - 411 008, MH, India.
| | - Gulab Walke
- Department of Chemistry, Indian Institute of Science Education and Research, Pune - 411 008, MH, India.
| | - Saptashwa Chakraborty
- Department of Chemistry, Indian Institute of Science Education and Research, Pune - 411 008, MH, India.
| | - Mahesh Neralkar
- Department of Chemistry, Indian Institute of Science Education and Research, Pune - 411 008, MH, India.
| | - Srinivas Hotha
- Department of Chemistry, Indian Institute of Science Education and Research, Pune - 411 008, MH, India.
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14
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Hadi J, Brightwell G. Safety of Alternative Proteins: Technological, Environmental and Regulatory Aspects of Cultured Meat, Plant-Based Meat, Insect Protein and Single-Cell Protein. Foods 2021; 10:1226. [PMID: 34071292 PMCID: PMC8230205 DOI: 10.3390/foods10061226] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 01/10/2023] Open
Abstract
Food security and environmental issues have become global crises that need transformative solutions. As livestock production is becoming less sustainable, alternative sources of proteins are urgently required. These include cultured meat, plant-based meat, insect protein and single-cell protein. Here, we describe the food safety aspects of these novel protein sources, in terms of their technological backgrounds, environmental impacts and the necessary regulatory framework for future mass-scale production. Briefly, cultured meat grown in fetal bovine serum-based media can be exposed to viruses or infectious prion, in addition to other safety risks associated with the use of genetic engineering. Plant-based meat may contain allergens, anti-nutrients and thermally induced carcinogens. Microbiological risks and allergens are the primary concerns associated with insect protein. Single-cell protein sources are divided into microalgae, fungi and bacteria, all of which have specific food safety risks that include toxins, allergens and high ribonucleic acid (RNA) contents. The environmental impacts of these alternative proteins can mainly be attributed to the production of growth substrates or during cultivation. Legislations related to novel food or genetic modification are the relevant regulatory framework to ensure the safety of alternative proteins. Lastly, additional studies on the food safety aspects of alternative proteins are urgently needed for providing relevant food governing authorities with sufficient data to oversee that the technological progress in this area is balanced with robust safety standards.
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Affiliation(s)
- Joshua Hadi
- AgResearch Ltd., Hopkirk Research Institute, Cnr University Ave and Library Road, Massey University, Palmerston North 4442, New Zealand;
| | - Gale Brightwell
- AgResearch Ltd., Hopkirk Research Institute, Cnr University Ave and Library Road, Massey University, Palmerston North 4442, New Zealand;
- New Zealand Food Safety Science and Research Centre, Massey University Manawatu (Turitea), Tennent Drive, Palmerston North 4474, New Zealand
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15
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Sholar SA, Stepanova OA. The Role of Viruses and Viral Lysis in Changing the Optical Properties of the Water Environment of their Habitat. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921020226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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Perez Garcia G, De Gasperi R, Gama Sosa MA, Perez GM, Otero-Pagan A, Pryor D, Abutarboush R, Kawoos U, Hof PR, Dickstein DL, Cook DG, Gandy S, Ahlers ST, Elder GA. Laterality and region-specific tau phosphorylation correlate with PTSD-related behavioral traits in rats exposed to repetitive low-level blast. Acta Neuropathol Commun 2021; 9:33. [PMID: 33648608 PMCID: PMC7923605 DOI: 10.1186/s40478-021-01128-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/07/2021] [Indexed: 12/14/2022] Open
Abstract
Military veterans who experience blast-related traumatic brain injuries often suffer from chronic cognitive and neurobehavioral syndromes. Reports of abnormal tau processing following blast injury have raised concerns that some cases may have a neurodegenerative basis. Rats exposed to repetitive low-level blast exhibit chronic neurobehavioral traits and accumulate tau phosphorylated at threonine 181 (Thr181). Using data previously reported in separate studies we tested the hypothesis that region-specific patterns of Thr181 phosphorylation correlate with behavioral measures also previously determined and reported in the same animals. Elevated p-tau Thr181 in anterior neocortical regions and right hippocampus correlated with anxiety as well as fear learning and novel object localization. There were no correlations with levels in amygdala or posterior neocortical regions. Particularly striking were asymmetrical effects on the right and left hippocampus. No systematic variation in head orientation toward the blast wave seems to explain the laterality. Levels did not correlate with behavioral measures of hyperarousal. Results were specific to Thr181 in that no correlations were observed for three other phospho-acceptor sites (threonine 231, serine 396, and serine 404). No consistent correlations were linked with total tau. These correlations are significant in suggesting that p-tau accumulation in anterior neocortical regions and the hippocampus may lead to disinhibited amygdala function without p-tau elevation in the amygdala itself. They also suggest an association linking blast injury with tauopathy, which has implications for understanding the relationship of chronic blast-related neurobehavioral syndromes in humans to neurodegenerative diseases.
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17
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Rasmussen TS, Jakobsen RR, Castro-Mejía JL, Kot W, Thomsen AR, Vogensen FK, Nielsen DS, Hansen AK. Inter-vendor variance of enteric eukaryotic DNA viruses in specific pathogen free C57BL/6N mice. Res Vet Sci 2021; 136:1-5. [PMID: 33548686 DOI: 10.1016/j.rvsc.2021.01.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/16/2021] [Accepted: 01/26/2021] [Indexed: 02/06/2023]
Abstract
The laboratory mouse strain C57BL/6 is widely used as an animal model for various applications. It is becoming increasingly clear that the bacterial enteric community highly influences the phenotype. Eukaryotic viruses represent a sparsely investigated member of the enteric microbiome that might also affect the phenotype. We here investigated the presence of enteric eukaryotic DNA viruses (EDVs) in specific pathogen-free (SPF) C57BL/6N mice purchased from three vendors upon arrival and after being fed a low-fat diet (LFD) or high-fat diet (HFD). We detected genetic fragments of EDVs belonging to the viral families of Herpes-, Mimi-, Baculo- and Phycodnaviridae represented by two genera; Chlorovirus and Prasinovirus. The EDVs were detected in the mice upon arrival and persisted for 13 weeks. However, these signals of EDVs were only detected at notable levels in mice fed LFD from 2 out of 3 vendors, which suggested that the enteric composition of these EDVs were affected by both vendor (p < 0.003) and different dietary regimes (p < 0.013). This highlights the need of additional studies assessing the potential function of these EDVs that may influence the mouse phenotype and the reproducibility of animal studies using this C57BL/6N substrain.
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Affiliation(s)
| | | | | | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Allan Randrup Thomsen
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Finn Kvist Vogensen
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | | | - Axel Kornerup Hansen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.
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18
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Larroya A, Pantoja J, Codoñer-Franch P, Cenit MC. Towards Tailored Gut Microbiome-Based and Dietary Interventions for Promoting the Development and Maintenance of a Healthy Brain. Front Pediatr 2021; 9:705859. [PMID: 34277527 PMCID: PMC8280474 DOI: 10.3389/fped.2021.705859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/31/2021] [Indexed: 01/07/2023] Open
Abstract
Mental health is determined by a complex interplay between the Neurological Exposome and the Human Genome. Multiple genetic and non-genetic (exposome) factors interact early in life, modulating the risk of developing the most common complex neurodevelopmental disorders (NDDs), with potential long-term consequences on health. To date, the understating of the precise etiology underpinning these neurological alterations, and their clinical management pose a challenge. The crucial role played by diet and gut microbiota in brain development and functioning would indicate that modulating the gut-brain axis may help protect against the onset and progression of mental-health disorders. Some nutritional deficiencies and gut microbiota alterations have been linked to NDDs, suggesting their potential pathogenic implications. In addition, certain dietary interventions have emerged as promising alternatives or adjuvant strategies for improving the management of particular NDDs, at least in particular subsets of subjects. The gut microbiota can be a key to mediating the effects of other exposome factors such as diet on mental health, and ongoing research in Psychiatry and Neuropediatrics is developing Precision Nutrition Models to classify subjects according to a diet response prediction based on specific individual features, including microbiome signatures. Here, we review current scientific evidence for the impact of early life environmental factors, including diet, on gut microbiota and neuro-development, emphasizing the potential long-term consequences on health; and also summarize the state of the art regarding the mechanisms underlying diet and gut microbiota influence on the brain-gut axis. Furthermore, we describe the evidence supporting the key role played by gut microbiota, diet and nutrition in neurodevelopment, as well as the effectiveness of certain dietary and microbiome-based interventions aimed at preventing or treating NDDs. Finally, we emphasize the need for further research to gain greater insight into the complex interplay between diet, gut microbiome and brain development. Such knowledge would help towards achieving tailored integrative treatments, including personalized nutrition.
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Affiliation(s)
- Ana Larroya
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Valencia, Spain
| | - Jorge Pantoja
- Department of Pediatrics, University Hospital De la Plana, Vila-Real, Castellón, Spain.,Foundation for the Promotion of Health and Biomedical Research in the Valencian Region (FISABIO), Valencia, Spain
| | - Pilar Codoñer-Franch
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Region (FISABIO), Valencia, Spain.,Department of Pediatrics, Dr. Peset University Hospital, Valencia, Spain.,Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, Valencia, Spain
| | - María Carmen Cenit
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Valencia, Spain.,Department of Pediatrics, University Hospital De la Plana, Vila-Real, Castellón, Spain.,Foundation for the Promotion of Health and Biomedical Research in the Valencian Region (FISABIO), Valencia, Spain
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19
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Zhao Z. Comparison of microbial communities and the antibiotic resistome between prawn mono- and poly-culture systems. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 207:111310. [PMID: 32937228 DOI: 10.1016/j.ecoenv.2020.111310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/01/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance genes (ARGs) in mariculture sediments pose a potential risk to public health due to their ability to transfer from environmental bacteria to human pathogens. Long term, this may reduce pathogen susceptibility to antibiotics in medical settings. In recent years, the poly-culture of multiple species has become a popular mariculture approach in China, thanks to its environmental and economic benefits. However, differences in microbial communities and antibiotic resistome between mono- and poly-culture systems are still unclear. In this study, microbial community composition and profiles of entire (microbial DNA) and mobile (plasmid and phage) ARGs in prawn mono- and poly-culture systems were investigated using metagenomics. The abundance of several viruses and human pathogens were enhanced in prawn poly-culture ponds, when compared to monoculture systems. In contrast, sediments from poly-culture systems had a lower diversity and ARG abundance when compared to mono-culture approaches. These ARG variations were predominantly related to mobile genetic elements. Prawn mariculture activities exerted a unique selectivity for ARGs in plasmids, and this selectivity was not influenced by culture methods. The findings of this study have important implications for the selection of mariculture systems in preventing pollution with ARGs.
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Affiliation(s)
- Zelong Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, PR China.
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20
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Schulfer A, Santiago-Rodriguez TM, Ly M, Borin JM, Chopyk J, Blaser MJ, Pride DT. Fecal Viral Community Responses to High-Fat Diet in Mice. mSphere 2020; 5:e00833-19. [PMID: 32102942 PMCID: PMC7045389 DOI: 10.1128/msphere.00833-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
Alterations in diet can have significant impact on the host, with high-fat diet (HFD) leading to obesity, diabetes, and inflammation of the gut. Although membership and abundances in gut bacterial communities are strongly influenced by diet, substantially less is known about how viral communities respond to dietary changes. Examining fecal contents of mice as the mice were transitioned from normal chow to HFD, we found significant changes in the relative abundances and the diversity in the gut of bacteria and their viruses. Alpha diversity of the bacterial community was significantly diminished in response to the diet change but did not change significantly in the viral community. However, the diet shift significantly impacted the beta diversity in both the bacterial and viral communities. There was a significant shift away from the relatively abundant Siphoviridae accompanied by increases in bacteriophages from the Microviridae family. The proportion of identified bacteriophage structural genes significantly decreased after the transition to HFD, with a conserved loss of integrase genes in all four experimental groups. In total, this study provides evidence for substantial changes in the intestinal virome disproportionate to bacterial changes, and with alterations in putative viral lifestyles related to chromosomal integration as a result of shift to HFD.IMPORTANCE Prior studies have shown that high-fat diet (HFD) can have profound effects on the gastrointestinal (GI) tract microbiome and also demonstrate that bacteria in the GI tract can affect metabolism and lean/obese phenotypes. We investigated whether the composition of viral communities that also inhabit the GI tract are affected by shifts from normal to HFD. We found significant and reproducible shifts in the content of GI tract viromes after the transition to HFD. The differences observed in virome community membership and their associated gene content suggest that these altered viral communities are populated by viruses that are more virulent toward their host bacteria. Because HFD also are associated with significant shifts in GI tract bacterial communities, we believe that the shifts in the viral community may serve to drive the changes that occur in associated bacterial communities.
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Affiliation(s)
| | | | - Melissa Ly
- Department of Pathology, University of California, San Diego, California, USA
| | - Joshua M Borin
- Division of Biological Sciences, University of California, San Diego, California, USA
| | - Jessica Chopyk
- Department of Pathology, University of California, San Diego, California, USA
| | - Martin J Blaser
- New York University, New York, New York, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - David T Pride
- Department of Pathology, University of California, San Diego, California, USA
- Department of Medicine, University of California, San Diego, California, USA
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21
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Van Etten JL, Agarkova IV, Dunigan DD. Chloroviruses. Viruses 2019; 12:E20. [PMID: 31878033 PMCID: PMC7019647 DOI: 10.3390/v12010020] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 12/20/2022] Open
Abstract
Chloroviruses are large dsDNA, plaque-forming viruses that infect certain chlorella-like green algae; the algae are normally mutualistic endosymbionts of protists and metazoans and are often referred to as zoochlorellae. The viruses are ubiquitous in inland aqueous environments throughout the world and occasionally single types reach titers of thousands of plaque-forming units per ml of native water. The viruses are icosahedral in shape with a spike structure located at one of the vertices. They contain an internal membrane that is required for infectivity. The viral genomes are 290 to 370 kb in size, which encode up to 16 tRNAs and 330 to ~415 proteins, including many not previously seen in viruses. Examples include genes encoding DNA restriction and modification enzymes, hyaluronan and chitin biosynthetic enzymes, polyamine biosynthetic enzymes, ion channel and transport proteins, and enzymes involved in the glycan synthesis of the virus major capsid glycoproteins. The proteins encoded by many of these viruses are often the smallest or among the smallest proteins of their class. Consequently, some of the viral proteins are the subject of intensive biochemical and structural investigation.
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Affiliation(s)
- James L. Van Etten
- Department of Plant Pathology, Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA; (I.V.A.); (D.D.D.)
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22
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Petrzik K, Koloniuk I, Sehadová H, Sarkisova T. Chrysoviruses Inhabited Symbiotic Fungi of Lichens. Viruses 2019; 11:v11121120. [PMID: 31817044 PMCID: PMC6949994 DOI: 10.3390/v11121120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/26/2019] [Accepted: 11/30/2019] [Indexed: 12/28/2022] Open
Abstract
A lichen body is formed most often from green alga cells trapped in a net of ascomycetous fungi and accompanied by endolichenic or parasitic fungi, other algae, and symbiotic or free-living bacteria. The lichen’s microcosmos is inhabited by mites, insects, and other animals for which the lichen is a source of food or a place to live. Novel, four-segmented dsRNA viruses were detected in saxicolous Chrysothrixchlorina and Lepraria incana lichens. Comparison of encoded genome proteins revealed classification of the viruses to the genus Alphachrysovirus and a relationship to chrysoviruses from filamentous ascomycetous fungi. We propose the names Chrysothrix chrysovirus 1 (CcCV1) and Lepraria chrysovirus 1 (LiCV1) as acronyms for these viruses. Surprisingly, observation of Chrysothrix chlorina hybridization with fluorescent-labelled virus probe by confocal microscope revealed that the CcCV1 virus is not present in the lichen body-forming fungus but in accompanying endolichenic Penicilliumcitreosulfuratum fungus. These are the first descriptions of mycoviruses from a lichen environment.
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Affiliation(s)
- Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic; (I.K.); (T.S.)
- Correspondence: ; Tel.: +420-387-775-549
| | - Igor Koloniuk
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic; (I.K.); (T.S.)
| | - Hana Sehadová
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic;
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Tatiana Sarkisova
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic; (I.K.); (T.S.)
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23
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Withers JB, Mondol V, Pawlica P, Rosa-Mercado NA, Tycowski KT, Ghasempur S, Torabi SF, Steitz JA. Idiosyncrasies of Viral Noncoding RNAs Provide Insights into Host Cell Biology. Annu Rev Virol 2019; 6:297-317. [PMID: 31039329 PMCID: PMC6768742 DOI: 10.1146/annurev-virology-092818-015811] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Like their host cells, many viruses express noncoding RNAs (ncRNAs). Despite the technical challenge of ascribing function to ncRNAs, diverse biological roles for virally expressed ncRNAs have been described, including regulation of viral replication, modulation of host gene expression, host immune evasion, cellular survival, and cellular transformation. Insights into conserved interactions between viral ncRNAs and host cell machinery frequently lead to novel findings concerning host cell biology. In this review, we discuss the functions and biogenesis of ncRNAs produced by animal viruses. Specifically, we describe noncanonical pathways of microRNA (miRNA) biogenesis and novel mechanisms used by viruses to manipulate miRNA and messenger RNA stability. We also highlight recent advances in understanding the function of viral long ncRNAs and circular RNAs.
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Affiliation(s)
- Johanna B Withers
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
- Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Vanessa Mondol
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Paulina Pawlica
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Nicolle A Rosa-Mercado
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Kazimierz T Tycowski
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
- Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Salehe Ghasempur
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Seyed F Torabi
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
- Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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24
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Asplund M, Kjartansdóttir KR, Mollerup S, Vinner L, Fridholm H, Herrera JAR, Friis-Nielsen J, Hansen TA, Jensen RH, Nielsen IB, Richter SR, Rey-Iglesia A, Matey-Hernandez ML, Alquezar-Planas DE, Olsen PVS, Sicheritz-Pontén T, Willerslev E, Lund O, Brunak S, Mourier T, Nielsen LP, Izarzugaza JMG, Hansen AJ. Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries. Clin Microbiol Infect 2019; 25:1277-1285. [PMID: 31059795 DOI: 10.1016/j.cmi.2019.04.028] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/12/2019] [Accepted: 04/18/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Sample preparation for high-throughput sequencing (HTS) includes treatment with various laboratory components, potentially carrying viral nucleic acids, the extent of which has not been thoroughly investigated. Our aim was to systematically examine a diverse repertoire of laboratory components used to prepare samples for HTS in order to identify contaminating viral sequences. METHODS A total of 322 samples of mainly human origin were analysed using eight protocols, applying a wide variety of laboratory components. Several samples (60% of human specimens) were processed using different protocols. In total, 712 sequencing libraries were investigated for viral sequence contamination. RESULTS Among sequences showing similarity to viruses, 493 were significantly associated with the use of laboratory components. Each of these viral sequences had sporadic appearance, only being identified in a subset of the samples treated with the linked laboratory component, and some were not identified in the non-template control samples. Remarkably, more than 65% of all viral sequences identified were within viral clusters linked to the use of laboratory components. CONCLUSIONS We show that high prevalence of contaminating viral sequences can be expected in HTS-based virome data and provide an extensive list of novel contaminating viral sequences that can be used for evaluation of viral findings in future virome and metagenome studies. Moreover, we show that detection can be problematic due to stochastic appearance and limited non-template controls. Although the exact origin of these viral sequences requires further research, our results support laboratory-component-linked viral sequence contamination of both biological and synthetic origin.
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Affiliation(s)
- M Asplund
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - K R Kjartansdóttir
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - S Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - L Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - H Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark
| | - J A R Herrera
- Disease Systems Biology Programme, Panum Instituttet, Copenhagen, Denmark; Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - J Friis-Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - T A Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - R H Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - I B Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - S R Richter
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - A Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M L Matey-Hernandez
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - D E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - P V S Olsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - T Sicheritz-Pontén
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
| | - E Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - O Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - S Brunak
- Disease Systems Biology Programme, Panum Instituttet, Copenhagen, Denmark; Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - T Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - L P Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark
| | - J M G Izarzugaza
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - A J Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
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25
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Pinzón N, Bertrand S, Subirana L, Busseau I, Escrivá H, Seitz H. Functional lability of RNA-dependent RNA polymerases in animals. PLoS Genet 2019; 15:e1007915. [PMID: 30779744 PMCID: PMC6396948 DOI: 10.1371/journal.pgen.1007915] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 03/01/2019] [Accepted: 12/24/2018] [Indexed: 11/18/2022] Open
Abstract
RNA interference (RNAi) requires RNA-dependent RNA polymerases (RdRPs) in many eukaryotes, and RNAi amplification constitutes the only known function for eukaryotic RdRPs. Yet in animals, classical model organisms can elicit RNAi without possessing RdRPs, and only nematode RNAi was shown to require RdRPs. Here we show that RdRP genes are much more common in animals than previously thought, even in insects, where they had been assumed not to exist. RdRP genes were present in the ancestors of numerous clades, and they were subsequently lost at a high frequency. In order to probe the function of RdRPs in a deuterostome (the cephalochordate Branchiostoma lanceolatum), we performed high-throughput analyses of small RNAs from various Branchiostoma developmental stages. Our results show that Branchiostoma RdRPs do not appear to participate in RNAi: we did not detect any candidate small RNA population exhibiting classical siRNA length or sequence features. Our results show that RdRPs have been independently lost in dozens of animal clades, and even in a clade where they have been conserved (cephalochordates) their function in RNAi amplification is not preserved. Such a dramatic functional variability reveals an unexpected plasticity in RNA silencing pathways. RNA interference (RNAi) is a conserved gene regulation system in eukaryotes. In non-animal eukaryotes, it necessitates RNA-dependent RNA polymerases (“RdRPs”). Among animals, only nematodes appear to require RdRPs for RNAi. Yet additional animal clades have RdRPs and it is assumed that they participate in RNAi. Here, we find that RdRPs are much more common in animals than previously thought, but their genes were independently lost in many lineages. Focusing on a species with RdRP genes (a cephalochordate), we found that it does not use them for RNAi. While RNAi is the only known function for eukaryotic RdRPs, our results suggest additional roles. Eukaryotic RdRPs thus have a complex evolutionary history in animals, with frequent independent losses and apparent functional diversification.
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Affiliation(s)
- Natalia Pinzón
- Institut de Génétique Humaine, UMR 9002 CNRS and université de Montpellier, 141, rue de la Cardonille, 34396 Montpellier CEDEX 5, France
| | - Stéphanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Lucie Subirana
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Isabelle Busseau
- Institut de Génétique Humaine, UMR 9002 CNRS and université de Montpellier, 141, rue de la Cardonille, 34396 Montpellier CEDEX 5, France
| | - Hector Escrivá
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Hervé Seitz
- Institut de Génétique Humaine, UMR 9002 CNRS and université de Montpellier, 141, rue de la Cardonille, 34396 Montpellier CEDEX 5, France
- * E-mail:
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26
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Wang Y, Wu Y, Xiong D, Ye X. Total Synthesis of a Hyperbranched
N
‐Linked Hexasaccharide Attached to ATCV‐1 Major Capsid Protein without Precedent. CHINESE J CHEM 2018. [DOI: 10.1002/cjoc.201800533] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yong‐Shi Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical SciencesPeking University Xue Yuan Road No. 38, Beijing 100191 China
| | - Yong Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical SciencesPeking University Xue Yuan Road No. 38, Beijing 100191 China
| | - De‐Cai Xiong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical SciencesPeking University Xue Yuan Road No. 38, Beijing 100191 China
- State Key Laboratory of Drug ResearchShanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 200031 China
| | - Xin‐Shan Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical SciencesPeking University Xue Yuan Road No. 38, Beijing 100191 China
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27
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Filée J. Giant viruses and their mobile genetic elements: the molecular symbiosis hypothesis. Curr Opin Virol 2018; 33:81-88. [DOI: 10.1016/j.coviro.2018.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 01/28/2023]
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28
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Zhang QY, Gui JF. Diversity, evolutionary contribution and ecological roles of aquatic viruses. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1486-1502. [DOI: 10.1007/s11427-018-9414-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/26/2018] [Indexed: 01/21/2023]
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29
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Lin S, Lowary TL. Synthesis of the Highly Branched Hexasaccharide Core of Chlorella Virus N-Linked Glycans. Chemistry 2018; 24:16992-16996. [PMID: 30280442 DOI: 10.1002/chem.201804795] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Indexed: 01/09/2023]
Abstract
Chlorella viruses produce N-linked glycoproteins with carbohydrate moieties that differ in structure from all other N-linked glycans. In addition, unlike most viruses, these organisms do not hijack the biosynthetic machinery of the host to make glycocoproteins; instead, they produce their own carbohydrate-processing enzymes. A better understanding of the function and assembly of these fascinating and structurally-unprecedented glycans requires access to probe molecules. This work describes the first synthesis of a chlorella virus N-linked glycan, a highly branched hexasaccharide that contains the pentasaccharide present in all of the >15 structures reported to date. The target molecule includes a glucosyl-asparagine linkage and a "hyperbranched" fucose residue in which all of the hydroxyl groups are glycosylated. Both convergent and linear approaches were investigated with the latter being successful in providing the target in 16 steps and 13 % overall yield.
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Affiliation(s)
- Sicheng Lin
- Alberta Glycomics Centre and Department of Chemistry, The University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Todd L Lowary
- Alberta Glycomics Centre and Department of Chemistry, The University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
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30
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Is the Virus Important? And Some Other Questions. Viruses 2018; 10:v10080442. [PMID: 30126254 PMCID: PMC6116253 DOI: 10.3390/v10080442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/14/2018] [Accepted: 08/15/2018] [Indexed: 11/22/2022] Open
Abstract
The motivation for focusing on a specific virus is often its importance in terms of impact on human interests. The chlorella viruses are a notable exception and 40 years of research has made them the undisputed model system for large icosahedral dsDNA viruses infecting eukaryotes. Their status has changed from inconspicuous and rather odd with no ecological relevance to being the Phycodnaviridae type strain possibly affecting humans and human cognitive functioning in ways that remain to be understood. The Van Etten legacy is the backbone for research on Phycodnaviridae. After highlighting some of the peculiarities of chlorella viruses, we point to some issues and questions related to the viruses we choose for our research, our prejudices, what we are still missing, and what we should be looking for.
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31
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Flaviani F, Schroeder DC, Lebret K, Balestreri C, Highfield AC, Schroeder JL, Thorpe SE, Moore K, Pasckiewicz K, Pfaff MC, Rybicki EP. Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current. Front Microbiol 2018; 9:1474. [PMID: 30065704 PMCID: PMC6056678 DOI: 10.3389/fmicb.2018.01474] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 06/13/2018] [Indexed: 12/13/2022] Open
Abstract
Microbes occupy diverse ecological niches and only through recent advances in next generation sequencing technologies have the true microbial diversity been revealed. Furthermore, lack of perceivable marine barriers to genetic dispersal (i.e., mountains or islands) has allowed the speculation that organisms that can be easily transported by currents and therefore proliferate everywhere. That said, ocean currents are now commonly being recognized as barriers for microbial dispersal. Here we analyzed samples collected from a total of six stations, four located in the Indian Ocean, and two in the Southern Ocean. Amplicon sequencing was used to characterize both prokaryotic and eukaryotic plankton communities, while shotgun sequencing was used for the combined environmental DNA (eDNA), microbial eDNA (meDNA), and viral fractions. We found that Cyanobacteria dominated the prokaryotic component in the South-West Indian Ocean, while γ-Proteobacteria dominated the South-East Indian Ocean. A combination of γ- and α-Proteobacteria dominated the Southern Ocean. Alveolates dominated almost exclusively the eukaryotic component, with variation in the ratio of Protoalveolata and Dinoflagellata depending on station. However, an increase in haptophyte relative abundance was observed in the Southern Ocean. Similarly, the viral fraction was dominated by members of the order Caudovirales across all stations; however, a higher presence of nucleocytoplasmic large DNA viruses (mainly chloroviruses and mimiviruses) was observed in the Southern Ocean. To our knowledge, this is the first that a statistical difference in the microbiome (from viruses to protists) between the subtropical Indian and Southern Oceans. We also show that not all phylotypes can be found everywhere, and that meDNA is not a suitable resource for monitoring aquatic microbial diversity.
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Affiliation(s)
- Flavia Flaviani
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa.,Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom
| | - Declan C Schroeder
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom.,School of Biological Sciences, University of Reading, Reading, United Kingdom.,College of Veterinary Medicine, University of Minnesota Twin Cities, Minneapolis, MN, United States
| | - Karen Lebret
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom.,Limnology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Cecilia Balestreri
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom
| | - Andrea C Highfield
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom
| | - Joanna L Schroeder
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, United Kingdom
| | - Sally E Thorpe
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Karen Moore
- Exeter Sequencing Service, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Konrad Pasckiewicz
- Exeter Sequencing Service, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Maya C Pfaff
- Department of Environmental Affairs, Oceans and Coasts, Cape Town, South Africa
| | - Edward P Rybicki
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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32
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Sarkar A, Harty S, Lehto SM, Moeller AH, Dinan TG, Dunbar RIM, Cryan JF, Burnet PWJ. The Microbiome in Psychology and Cognitive Neuroscience. Trends Cogn Sci 2018; 22:611-636. [PMID: 29907531 DOI: 10.1016/j.tics.2018.04.006] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 02/07/2023]
Abstract
Psychology and microbiology make unlikely friends, but the past decade has witnessed striking bidirectional associations between intrinsic gut microbes and the brain, relationships with largely untested psychological implications. Although microbe-brain relationships are receiving a great deal of attention in biomedicine and neuroscience, psychologists have yet to join this journey. Here, we illustrate microbial associations with emotion, cognition, and social behavior. However, despite considerable enthusiasm and potential, technical and conceptual limitations including low statistical power and lack of mechanistic descriptions prevent a nuanced understanding of microbiome-brain-behavior relationships. Our goal is to describe microbial effects in domains of cognitive significance and the associated challenges to stimulate interdisciplinary research on the contribution of this hidden kingdom to psychological processes.
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Affiliation(s)
- Amar Sarkar
- Department of Experimental Psychology, University of Oxford, Oxford, UK; Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, UK; Trinity College, University of Cambridge, Cambridge, UK.
| | - Siobhán Harty
- Department of Experimental Psychology, University of Oxford, Oxford, UK; Trinity College Institute of Neuroscience and School of Psychology, Trinity College Dublin, Dublin 2, Ireland
| | - Soili M Lehto
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland; Institute of Clinical Medicine / Psychiatry, University of Eastern Finland, Kuopio, Finland; Department of Psychiatry, Kuopio University Hospital, Kuopio, Finland
| | - Andrew H Moeller
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA, USA
| | - Timothy G Dinan
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Sciences, University College Cork, Cork, Ireland
| | - Robin I M Dunbar
- Department of Experimental Psychology, University of Oxford, Oxford, UK
| | - John F Cryan
- Department of Psychiatry and Neurobehavioural Sciences, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience University College Cork, Cork, Ireland
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33
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Pannaraj PS, Ly M, Cerini C, Saavedra M, Aldrovandi GM, Saboory AA, Johnson KM, Pride DT. Shared and Distinct Features of Human Milk and Infant Stool Viromes. Front Microbiol 2018; 9:1162. [PMID: 29910789 PMCID: PMC5992295 DOI: 10.3389/fmicb.2018.01162] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/14/2018] [Indexed: 01/01/2023] Open
Abstract
Infants acquire many of their microbes from their mothers during the birth process. The acquisition of these microbes is believed to be critical in the development of the infant immune system. Bacteria also are transmitted to the infant through breastfeeding, and help to form the microbiome of the infant gastrointestinal (GI) tract; it is unknown whether viruses in human milk serve to establish an infant GI virome. We examined the virome contents of milk and infant stool in a cohort of mother-infant pairs to discern whether milk viruses colonize the infant GI tract. We observed greater viral alpha diversity in milk than in infant stool, similar to the trend we found for bacterial communities from both sites. When comparing beta diversity, viral communities were mostly distinguishable between milk and infant stool, but each was quite distinct from adult stool, urine, and salivary viromes. There were significant differences in viral families in the infant stool (abundant bacteriophages from the family Siphoviridae) compared to milk (abundant bacteriophages from the family Myoviridae), which may reflect significant differences in the bacterial families identified from both sites. Despite the differences in viral taxonomy, we identified a significant number of shared viruses in the milk and stool from all mother-infant pairs. Because of the significant proportion of bacteriophages transmitted in these mother-infant pairs, we believe the transmission of milk phages to the infant GI tract may help to shape the infant GI microbiome.
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Affiliation(s)
- Pia S Pannaraj
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States.,Department of Pediatrics, Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Melissa Ly
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Chiara Cerini
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Monica Saavedra
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Grace M Aldrovandi
- Department of Pediatrics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Abdul A Saboory
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Kevin M Johnson
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - David T Pride
- Department of Pathology, University of California, San Diego, San Diego, CA, United States.,Department of Medicine, University of California, San Diego, San Diego, CA, United States
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34
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The Geographic Structure of Viruses in the Cuatro Ciénegas Basin, a Unique Oasis in Northern Mexico, Reveals a Highly Diverse Population on a Small Geographic Scale. Appl Environ Microbiol 2018; 84:AEM.00465-18. [PMID: 29625974 DOI: 10.1128/aem.00465-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/21/2018] [Indexed: 12/28/2022] Open
Abstract
The Cuatro Ciénegas Basin (CCB) is located in the Chihuahuan desert in the Mexican state of Coahuila; it has been characterized as a site with high biological diversity despite its extreme oligotrophic conditions. It has the greatest number of endemic species in North America, containing abundant living microbialites (including stromatolites and microbial mats) and diverse microbial communities. With the hypothesis that this high biodiversity and the geographic structure should be reflected in the virome, the viral communities in 11 different locations of three drainage systems, Churince, La Becerra, and Pozas Rojas, and in the intestinal contents of 3 different fish species, were analyzed for both eukaryotic and prokaryotic RNA and DNA viruses using next-generation sequencing methods. Double-stranded DNA (dsDNA) virus families were the most abundant (72.5% of reads), followed by single-stranded DNA (ssDNA) viruses (2.9%) and ssRNA and dsRNA virus families (0.5%). Thirteen families had dsDNA genomes, five had ssDNA, three had dsRNA, and 16 had ssRNA. A highly diverse viral community was found, with an ample range of hosts and a strong geographical structure, with very even distributions and signals of endemicity in the phylogenetic trees from several different virus families. The majority of viruses found were bacteriophages but eukaryotic viruses were also frequent, and the large diversity of viruses related to algae were a surprise, since algae are not evident in the previously analyzed aquatic systems of this ecosystem. Animal viruses were also frequently found, showing the large diversity of aquatic animals in this oasis, where plants, protozoa, and archaea are rare.IMPORTANCE In this study, we tested whether the high biodiversity and geographic structure of CCB is reflected in its virome. CCB is an extraordinarily biodiverse oasis in the Chihuahuan desert, where a previous virome study suggested that viruses had followed the marine ancestry of the marine bacteria and, as a result of their long isolation, became endemic to the site. In this study, which includes a larger sequencing coverage and water samples from other sites within the valley, we confirmed the high virus biodiversity and uniqueness as well as the strong biogeographical diversification of the CCB. In addition, we also analyzed fish intestinal contents, finding that each fish species eats different prey and, as a result, presents different viral compositions even if they coexist in the same pond. These facts highlight the high and novel virus diversity of CCB and its "lost world" status.
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35
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Houdek P. Economic Holobiont: Influence of Parasites, Microbiota and Chemosignals on Economic Behavior. Front Behav Neurosci 2018; 12:77. [PMID: 29765310 PMCID: PMC5938411 DOI: 10.3389/fnbeh.2018.00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 04/09/2018] [Indexed: 11/29/2022] Open
Abstract
The article is a perspective on utilization of microorganisms and chemosignals in studying human economic behavior. Research in biological roots of economic development has already confirmed that parasitic pressure influenced the creation and development of cultural norms and institutions. However, other effects of microorganisms on human groups and individual decision-making and behavior are heavily understudied. The perspective discusses how parasitic infections, sexually transmitted organisms and microbiota (i.e., “human holobiont”) could causally influence risk-seeking behavior, impulsivity, social dominance, empathy, political views and gender differences. As a case study, the parasite Toxoplasma gondii and its influence on economic preferences, personal characteristics and human appearance are examined. I also briefly review how chemosignals influence decision-making, particularly in the social preferences domain. I mention some predictions that arise from the paradigm of economic holobiont for the economic science. The conclusion summarizes limitations of the discussed findings and the stated speculations.
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Affiliation(s)
- Petr Houdek
- Faculty of Social and Economic Studies, Jan Evangelista Purkyně University in Ústí nad Labem, Ústí nad Labem, Czechia
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36
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Aherfi S, Nappez C, Lepidi H, Bedotto M, Barassi L, Jardot P, Colson P, La Scola B, Raoult D, Bregeon F. Experimental Inoculation in Rats and Mice by the Giant Marseillevirus Leads to Long-Term Detection of Virus. Front Microbiol 2018; 9:463. [PMID: 29619012 PMCID: PMC5871663 DOI: 10.3389/fmicb.2018.00463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/27/2018] [Indexed: 11/13/2022] Open
Abstract
The presence of the giant virus of amoeba Marseillevirus has been identified at many different sites on the human body, including in the bloodstream of asymptomatic subjects, in the lymph nodes of a child with adenitis, in one adult with Hodgkin's disease, and in the pharynx of an adult. A high seroprevalence of the Marseillevirus has been recorded in the general population. Whether Marseillevirus can disseminate and persist within a mammal after entry remains unproven. We aimed to assess the ability of the virus to disseminate and persist into healthy organisms, especially in the lymphoid organs. Parenteral inoculations were performed by intraperitoneal injection (in rats and mice) or intravenous injection (in rats). Airway inoculation was performed by aerosolization (in mice). Dissemination and persistence were assessed by using PCR and amebal co-culture. Serologies were performed by immunofluorescent assay. Pathological examination was conducted after standard and immunohistochemistry staining. After intraperitoneal inoculation in mice and rats, Marseillevirus was detected in the bloodstream during the first 24 h. Persistence was noted until the end of the experiment, i.e., at 14 days in rats. After intravenous inoculation in rats, the virus was first detected in the blood until 48 h and then in deep organs with infectious virus detected until 14 and 21 days in the liver and the spleen, respectively. Its DNA was detected for up to 30 days in the liver and the spleen. After aerosolization in mice, infectious Marseillevirus was present in the lungs and nasal associated lymphoid tissue until 30 days post inoculation but less frequently and at a lower viral load in the lung than in the nasal associated lymphoid tissue. No other site of dissemination was found after aerosol exposure. Despite no evidence of disease being observed, the 30-day long persistence of Marseillevirus in rats and mice, regardless of the route of inoculation, supports the hypothesis of an infective potential of the virus in certain conditions. Its constant and long-term detection in nasal associated lymphoid tissue in mice after an aerosol exposure suggests the involvement of naso-pharyngeal associated lymphoid tissues in protecting the host against environmental Marseillevirus.
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Affiliation(s)
- Sarah Aherfi
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Claude Nappez
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Hubert Lepidi
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France.,Laboratoire d'Anatomopathologie, Centre Hospitalo Universitaire Timone, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Marielle Bedotto
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Lina Barassi
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Priscilla Jardot
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Philippe Colson
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Bernard La Scola
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Didier Raoult
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France
| | - Fabienne Bregeon
- Institut Hospitalo Universitaire Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Centre Hospitalo Universitaire Timone, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Marseille, France.,Service des Explorations Fonctionnelles Respiratoires Centre Hospitalo Universitaire Nord, Pôle Cardio-Vasculaire et thoracique, Assistance Publique des Hôpitaux de Marseille, Marseille, France
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Perez-Garcia G, Gama Sosa MA, De Gasperi R, Lashof-Sullivan M, Maudlin-Jeronimo E, Stone JR, Haghighi F, Ahlers ST, Elder GA. Chronic post-traumatic stress disorder-related traits in a rat model of low-level blast exposure. Behav Brain Res 2018; 340:117-125. [DOI: 10.1016/j.bbr.2016.09.061] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/25/2016] [Accepted: 09/26/2016] [Indexed: 01/01/2023]
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Malan-Muller S, Valles-Colomer M, Raes J, Lowry CA, Seedat S, Hemmings SM. The Gut Microbiome and Mental Health: Implications for Anxiety- and Trauma-Related Disorders. ACTA ACUST UNITED AC 2018; 22:90-107. [DOI: 10.1089/omi.2017.0077] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Stefanie Malan-Muller
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Mireia Valles-Colomer
- Department of Microbiology and Immunology, Rega Institute, KU Leuven–University of Leuven, Leuven, Belgium
- VIB, Center for Microbiology, Leuven, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven–University of Leuven, Leuven, Belgium
- VIB, Center for Microbiology, Leuven, Belgium
| | - Christopher A. Lowry
- Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, Boulder, Colorado
- Military and Veteran Microbiome: Consortium for Research and Education (MVM-Core), Aurora, Colorado
- Department of Psychiatry, Neurology & Physical Medicine and Rehabilitation, Anschutz School of Medicine, University of Colorado, Aurora, Colorado
- VA Rocky Mountain Mental Illness Research, Education, and Clinical Center (MIRECC), Denver, Colorado
- Center for Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Sian M.J. Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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Aherfi S, Colson P, Raoult D. Marseillevirus in the Pharynx of a Patient with Neurologic Disorders. Emerg Infect Dis 2018; 22:2008-2010. [PMID: 27767918 PMCID: PMC5088024 DOI: 10.3201/eid2211.160189] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Colson P, Aherfi S, La Scola B. Evidence of giant viruses of amoebae in the human gut. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.humic.2017.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Leigh BA, Djurhuus A, Breitbart M, Dishaw LJ. The gut virome of the protochordate model organism, Ciona intestinalis subtype A. Virus Res 2017; 244:137-146. [PMID: 29155033 DOI: 10.1016/j.virusres.2017.11.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 11/14/2017] [Accepted: 11/14/2017] [Indexed: 02/06/2023]
Abstract
The identification of host-specific bacterial and viral communities associated with diverse animals has led to the concept of the metaorganism, which defines the animal and all of its associated microbes as a single unit. Here we sequence the viruses found in the gut (i.e., the gut virome) of the marine invertebrate model system, Ciona intestinalis subtype A, in samples collected one year apart. We present evidence for a host-associated virome that is distinct from the surrounding seawater and contains some temporally-stable members. Comparison of gut tissues before and after starvation in virus-free water enabled the differentiation between the Ciona-specific virome and transient viral communities associated with dietary sources. The Ciona gut viromes were dominated by double-stranded DNA tailed phages (Order Caudovirales) and sequence assembly yielded a number of complete circular phage genomes, most of which were highly divergent from known genomes. Unique viral communities were found in distinct gut niches (stomach, midgut and hindgut), paralleling the compartmentalization of bacterial communities. Additionally, integrase and excisionase genes, including many that are similar to prophage sequences within the genomes of bacterial genera belonging to the Ciona core microbiome, were prevalent in the viromes, indicating the active induction of prophages within the gut ecosystem. Knowledge of the gut virome of this model organism lays the foundation for studying the interactions between viruses, bacteria, and host immunity.
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Affiliation(s)
- Brittany A Leigh
- University of South Florida, College of Marine Science, St. Petersburg, FL, USA; University of South Florida, Department of Pediatrics, Children's Research Institute, St. Petersburg, FL, USA
| | - Anni Djurhuus
- University of South Florida, College of Marine Science, St. Petersburg, FL, USA
| | - Mya Breitbart
- University of South Florida, College of Marine Science, St. Petersburg, FL, USA
| | - Larry J Dishaw
- University of South Florida, Department of Pediatrics, Children's Research Institute, St. Petersburg, FL, USA.
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Bienenstock J, Kunze WA, Forsythe P. Disruptive physiology: olfaction and the microbiome-gut-brain axis. Biol Rev Camb Philos Soc 2017; 93:390-403. [DOI: 10.1111/brv.12348] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/30/2017] [Accepted: 06/02/2017] [Indexed: 12/21/2022]
Affiliation(s)
- John Bienenstock
- McMaster Brain-Body Institute at St Joseph's Healthcare Hamilton; 50 Charlton Ave. E. Room T3304 Hamilton L8N 4A6 Canada
- Department of Pathology and Molecular Medicine; McMaster University, 1280 Main St. W.; Hamilton L8S 4L8 Canada
| | - Wolfgang A. Kunze
- McMaster Brain-Body Institute at St Joseph's Healthcare Hamilton; 50 Charlton Ave. E. Room T3304 Hamilton L8N 4A6 Canada
- Department of Psychiatry & Behavioural Sciences; McMaster University, 1280 Main St. W.; Hamilton L8S 4L8 Canada
| | - Paul Forsythe
- McMaster Brain-Body Institute at St Joseph's Healthcare Hamilton; 50 Charlton Ave. E. Room T3304 Hamilton L8N 4A6 Canada
- Firestone Institute for Respiratory Health; Hamilton 50 Charlton Ave. E., Room T3302 L8N 4A6 Canada
- Department of Medicine; McMaster University, 1280 Main St. W.; Hamilton L8S 4L8 Canada
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Ergün C, Urhan M, Ayer A. A review on the relationship between gluten and schizophrenia: Is gluten the cause? Nutr Neurosci 2017; 21:455-466. [PMID: 28393621 DOI: 10.1080/1028415x.2017.1313569] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Schizophrenia is a chronic disease that possesses various clinical manifestations. It presents rather heterogeneous characteristics with respect to onset type, symptoms, and the course of the disease. Although the lifetime prevalence is as low as 1%, it can cause serious disability. Thus, it is very important to develop efficient treatment methods. In some studies, it is hypothesized that removing gluten from the diet leads to a significant improvement in disease symptoms. Epidemiological studies revealed that the prevalence of celiac disease among schizophrenic patients is almost two times higher than that of the general population. OBJECTIVE In this review, we evaluate the effects of gluten and celiac disease on the onset of schizophrenia. Efficacy of gluten-free diet applications, antibody response against gluten, and the interaction of the brain-gut axis and the presence of common genetic points are also investigated. METHODS Without any publication date restriction, Pubmed database searches were made for 'schizophrenia, gluten, gliadin, celiac disease, exorphin, brain-gut axis, psychiatric disorders.' The keywords and the articles about the schizophrenia-celiac disease relationship are included in our review. RESULTS Several studies presented evidence to suggest that symptoms associated with schizophrenia were minimized when gluten was excluded from patients' diets. Immunological searches revealed that most schizophrenic patients with increased anti-gliadin antibodies did not possess celiac disease; yet, the presence of increased antibodies against gliadin can be the share point of the immunological abnormalities found in both of the diseases. DISCUSSION There were no consistent results in the clinical, immunological, microbiological, and epidemiological studies that investigated the relationship between schizophrenia and celiac disease. This presents a need for a larger scale study to confirm the presence of this suggested correlation between schizophrenia and celiac disease. The underlying mechanisms between the two diseases should be explored.
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Affiliation(s)
- Can Ergün
- a Faculty of Health Sciences, Department of Nutrition and Dietetics , Bahçeşehir University , Beşiktaş, Istanbul , Turkey
| | - Murat Urhan
- b Manisa Mental Health and Diseases Hospital , Şehitler Street, 45020 Manisa , Turkey
| | - Ahmet Ayer
- b Manisa Mental Health and Diseases Hospital , Şehitler Street, 45020 Manisa , Turkey
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Wilhelm SW, Bird JT, Bonifer KS, Calfee BC, Chen T, Coy SR, Gainer PJ, Gann ER, Heatherly HT, Lee J, Liang X, Liu J, Armes AC, Moniruzzaman M, Rice JH, Stough JMA, Tams RN, Williams EP, LeCleir GR. A Student's Guide to Giant Viruses Infecting Small Eukaryotes: From Acanthamoeba to Zooxanthellae. Viruses 2017; 9:E46. [PMID: 28304329 PMCID: PMC5371801 DOI: 10.3390/v9030046] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/07/2017] [Accepted: 03/09/2017] [Indexed: 12/15/2022] Open
Abstract
The discovery of infectious particles that challenge conventional thoughts concerning "what is a virus" has led to the evolution a new field of study in the past decade. Here, we review knowledge and information concerning "giant viruses", with a focus not only on some of the best studied systems, but also provide an effort to illuminate systems yet to be better resolved. We conclude by demonstrating that there is an abundance of new host-virus systems that fall into this "giant" category, demonstrating that this field of inquiry presents great opportunities for future research.
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Affiliation(s)
- Steven W Wilhelm
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Jordan T Bird
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Kyle S Bonifer
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Benjamin C Calfee
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Tian Chen
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Samantha R Coy
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - P Jackson Gainer
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Eric R Gann
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Huston T Heatherly
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Jasper Lee
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Xiaolong Liang
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Jiang Liu
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - April C Armes
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Mohammad Moniruzzaman
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - J Hunter Rice
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Joshua M A Stough
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Robert N Tams
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Evan P Williams
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Gary R LeCleir
- The Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, USA.
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Janowski AB, Krishnamurthy SR, Lim ES, Zhao G, Brenchley JM, Barouch DH, Thakwalakwa C, Manary MJ, Holtz LR, Wang D. Statoviruses, A novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals. Virology 2017; 504:36-44. [PMID: 28152382 PMCID: PMC5515247 DOI: 10.1016/j.virol.2017.01.010] [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: 10/11/2016] [Revised: 01/13/2017] [Accepted: 01/17/2017] [Indexed: 01/21/2023]
Abstract
Next-generation sequencing has expanded our understanding of the viral populations that constitute the mammalian virome. We describe a novel taxon of viruses named Statoviruses, for Stool associated Tombus-like viruses, present in multiple metagenomic datasets. These viruses define a novel clade that is phylogenetically related to the RNA virus families Tombusviridae and Flaviviridae. Five distinct statovirus types were identified in human, macaque, mouse, and cow gastrointestinal tract samples. The prototype genome, statovirus A, was frequently identified in macaque stool samples from multiple geographically distinct cohorts. Another genome, statovirus C1, was discovered in a stool sample from a human child with fever, cough, and rash. Further experimental data will clarify whether these viruses are infectious to mammals or if they originate from another source present in the mammalian gastrointestinal tract.
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Affiliation(s)
- Andrew B Janowski
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - Siddharth R Krishnamurthy
- Department of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Efrem S Lim
- Department of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Guoyan Zhao
- Department of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Jason M Brenchley
- Lab of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research Beth Israel Deaconess Medical Center, Boston, MA, USA; Ragon Institute of MGH, MIT, and Harvard, Boston, MA, USA
| | - Chrissie Thakwalakwa
- Department of Community Health, College of Medicine, University of Malawi, Blantyre 3, Malawi
| | - Mark J Manary
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - Lori R Holtz
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - David Wang
- Department of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
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Hadidi A, Flores R, Candresse T, Barba M. Next-Generation Sequencing and Genome Editing in Plant Virology. Front Microbiol 2016; 7:1325. [PMID: 27617007 PMCID: PMC4999435 DOI: 10.3389/fmicb.2016.01325] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/11/2016] [Indexed: 01/18/2023] Open
Abstract
Next-generation sequencing (NGS) has been applied to plant virology since 2009. NGS provides highly efficient, rapid, low cost DNA, or RNA high-throughput sequencing of the genomes of plant viruses and viroids and of the specific small RNAs generated during the infection process. These small RNAs, which cover frequently the whole genome of the infectious agent, are 21-24 nt long and are known as vsRNAs for viruses and vd-sRNAs for viroids. NGS has been used in a number of studies in plant virology including, but not limited to, discovery of novel viruses and viroids as well as detection and identification of those pathogens already known, analysis of genome diversity and evolution, and study of pathogen epidemiology. The genome engineering editing method, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been successfully used recently to engineer resistance to DNA geminiviruses (family, Geminiviridae) by targeting different viral genome sequences in infected Nicotiana benthamiana or Arabidopsis plants. The DNA viruses targeted include tomato yellow leaf curl virus and merremia mosaic virus (begomovirus); beet curly top virus and beet severe curly top virus (curtovirus); and bean yellow dwarf virus (mastrevirus). The technique has also been used against the RNA viruses zucchini yellow mosaic virus, papaya ringspot virus and turnip mosaic virus (potyvirus) and cucumber vein yellowing virus (ipomovirus, family, Potyviridae) by targeting the translation initiation genes eIF4E in cucumber or Arabidopsis plants. From these recent advances of major importance, it is expected that NGS and CRISPR-Cas technologies will play a significant role in the very near future in advancing the field of plant virology and connecting it with other related fields of biology.
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Affiliation(s)
- Ahmed Hadidi
- United States Department of Agriculture – Agricultural Research ServiceBeltsville, MD, USA
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia–Consejo Superior de Investigaciones CientíficasValencia, Spain
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de BordeauxBordeaux, France
| | - Marina Barba
- Consiglio per la Ricerca in Agricoltura e l’analisi dell’Economia Agraria, Centro di Ricerca per la Patologia VegetaleRome, Italy
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Aherfi S, Colson P, Audoly G, Nappez C, Xerri L, Valensi A, Million M, Lepidi H, Costello R, Raoult D. Marseillevirus in lymphoma: a giant in the lymph node. THE LANCET. INFECTIOUS DISEASES 2016; 16:e225-e234. [PMID: 27502174 DOI: 10.1016/s1473-3099(16)30051-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 03/18/2016] [Accepted: 04/07/2016] [Indexed: 12/12/2022]
Abstract
The family Marseilleviridae is a new clade of giant viruses whose original member, marseillevirus, was described in 2009. These viruses were isolated using Acanthamoeba spp primarily from the environment. Subsequently, a close relative of marseillevirus was isolated from the faeces of a healthy young man, and others were detected in blood samples of blood donors and recipients and in a child with lymph node adenitis. In this Grand Round we describe the detection of marseillevirus by PCR, fluorescence in-situ hybridisation, direct immunofluorescence, and immunohistochemistry in the lymph node of a 30-year-old woman diagnosed with Hodgkin's lymphoma, together with IgG antibodies to marseillevirus. A link with viruses and bacteria has been reported for many lymphomas. We review the literature describing these associations, the criteria used to consider a causal association, and the underlying mechanisms of lymphomagenesis. Our observations suggest that consideration should be given to marseillevirus infections as an additional viral cause or consequence of Hodgkin's lymphoma, and that this hypothesis should be tested further.
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Affiliation(s)
- Sarah Aherfi
- Research Unit on Emerging Infectious and Tropical Diseases (URMITE), CNRS UMR 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France; Méditerranée Infection Foundation (IHU), Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Colson
- Research Unit on Emerging Infectious and Tropical Diseases (URMITE), CNRS UMR 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France; Méditerranée Infection Foundation (IHU), Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Gilles Audoly
- Research Unit on Emerging Infectious and Tropical Diseases (URMITE), CNRS UMR 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France
| | - Claude Nappez
- Research Unit on Emerging Infectious and Tropical Diseases (URMITE), CNRS UMR 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France
| | - Luc Xerri
- Département de Bio-Pathologie, Oncologie moléculaire, Hématologie et Immunologie des tumeurs, Aix-Marseille Université, Marseille, France; Institut Paoli-Calmettes, Marseille, France
| | - Audrey Valensi
- Research Unit on Emerging Infectious and Tropical Diseases (URMITE), CNRS UMR 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France
| | - Matthieu Million
- Research Unit on Emerging Infectious and Tropical Diseases (URMITE), CNRS UMR 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France; Méditerranée Infection Foundation (IHU), Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Hubert Lepidi
- Research Unit on Emerging Infectious and Tropical Diseases (URMITE), CNRS UMR 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France; Méditerranée Infection Foundation (IHU), Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Regis Costello
- Technological Advances for Genomics and Clinics (TAGC), Inserm UMR 1090, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- Research Unit on Emerging Infectious and Tropical Diseases (URMITE), CNRS UMR 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Marseille, France; Méditerranée Infection Foundation (IHU), Assistance Publique-Hôpitaux de Marseille, Marseille, France.
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Kim GH, Klochkova TA, Lee DJ, Im SH. Chloroplast virus causes green-spot disease in cultivated Pyropia of Korea. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.05.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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