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Meta-transcriptomics reveals potential virus transfer between Aedes communis mosquitoes and their parasitic water mites. Virus Evol 2022; 8:veac090. [PMID: 36320615 PMCID: PMC9604308 DOI: 10.1093/ve/veac090] [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: 06/01/2022] [Revised: 08/29/2022] [Accepted: 09/23/2022] [Indexed: 11/14/2022] Open
Abstract
Arthropods harbor a largely undocumented diversity of RNA viruses. Some arthropods, like mosquitoes, can transmit viruses to vertebrates but are themselves parasitized by other arthropod species, such as mites. Very little is known about the viruses of these ectoparasites and how they move through the host–parasite relationship. To address this, we determined the virome of both mosquitoes and the mites that feed on them. The mosquito Aedes communis is an abundant and widely distributed species in Sweden, in northern Europe. These dipterans are commonly parasitized by water mite larvae (Trombidiformes: Mideopsidae) that are hypothesized to impose negative selection pressures on the mosquito by reducing fitness. In turn, viruses are dual-host agents in the mosquito–mite interaction. We determined the RNA virus diversity of mite-free and mite-detached mosquitoes, as well as their parasitic mites, using meta-transcriptomic sequencing. Our results revealed an extensive RNA virus diversity in both mites and mosquitoes, including thirty-seven putative novel RNA viruses that cover a wide taxonomic range. Notably, a high proportion of viruses (20/37) were shared between mites and mosquitoes, while a limited number of viruses were present in a single host. Comparisons of virus composition and abundance suggest potential virus transfer between mosquitoes and mites during their symbiotic interaction. These findings shed light on virome diversity and ecology in the context of arthropod host–parasite–virus relationships.
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RdRp-Scan: A Bioinformatic Resource to Identify and Annotate Divergent RNA Viruses in Metagenomic Sequence Data. Virus Evol 2022; 8:veac082. [PMID: 36533143 PMCID: PMC9752661 DOI: 10.1093/ve/veac082] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Despite a rapid expansion in the number of documented viruses following the advent of metagenomic sequencing, the identification and annotation of highly divergent RNA viruses remains challenging, particularly from poorly characterized hosts and environmental samples. Protein structures are more conserved than primary sequence data, such that structure-based comparisons provide an opportunity to reveal the viral “dusk matter”: viral sequences with low, but detectable, levels of sequence identity to known viruses with available protein structures. Here, we present a new open computational and resource – RdRp-scan – that contains a standardized bioinformatic toolkit to identify and annotate divergent RNA viruses in metagenomic sequence data based on the detection of RNA dependent RNA polymerase (RdRp) sequences. By combining RdRp-specific Hidden Markov models (HMM) and structural comparisons we show that RdRp-scan can efficiently detect RdRp sequences with identity levels as low as 10% to those from known viruses and not identifiable using standard sequence-to-sequence comparisons. In addition, to facilitate the annotation and placement of newly detected and divergent virus-like sequences into the diversity of RNA viruses, RdRp-scan provides new custom and curated databases of viral RdRp sequences and core motifs, as well as pre-built RdRp multiple sequence alignments. In parallel, our analysis of the sequence diversity detected by RdRp-scan revealed that while most of the taxonomically unassigned RdRps fell into pre-established clusters, with some falling into potentially new orders of RNA viruses related to the Wolframvirales and Tolivirales. Finally, a survey of the conserved A, B and C RdRp motifs within the RdRp-scan sequence database revealed additional variations of both sequence and position that might provide new insights into the structure, function and evolution of viral polymerases.
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Human Land-Use Impacts Viral Diversity and Abundance in a New Zealand River. Virus Evol 2022; 8:veac032. [PMID: 35494173 PMCID: PMC9049113 DOI: 10.1093/ve/veac032] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/11/2022] [Accepted: 04/01/2022] [Indexed: 11/29/2022] Open
Abstract
Although water-borne viruses have important implications for the health of humans and other animals, little is known about the impact of human land use on viral diversity and evolution in water systems such as rivers. We used metatranscriptomic sequencing to compare the diversity and abundance of viruses at sampling sites along a single river in New Zealand that differed in human land-use impacts, ranging from pristine to urban. From this, we identified 504 putative virus species, of which 97 per cent were novel. Many of the novel viruses were highly divergent and likely included a new subfamily within the Parvoviridae. We identified at least sixty-three virus species that may infect vertebrates—most likely fish and water birds—from the Astroviridae, Birnaviridae, Parvoviridae, and Picornaviridae. No putative human viruses were detected. Importantly, we observed differences in the composition of viral communities at sites impacted by human land use (farming and urban) compared to native forest sites (pristine). At the viral species level, the urban sites had higher diversity (327 virus species) than the farming (n = 150) and pristine sites (n = 119), and more viruses were shared between the urban and farming sites (n = 76) than between the pristine and farming or urban sites (n = 24). The two farming sites had a lower viral abundance across all host types, while the pristine sites had a higher abundance of viruses associated with animals, plants, and fungi. We also identified viruses linked to agriculture and human impact at the river sampling sites in farming and urban areas that were not present at the native forest sites. Although based on a small sample size, our study suggests that human land use can impact viral communities in rivers, such that further work is needed to reduce the impact of intensive farming and urbanisation on water systems.
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Revealing RNA virus diversity and evolution in unicellular algae transcriptomes. Virus Evol 2021; 7:veab070. [PMID: 36819971 PMCID: PMC9927876 DOI: 10.1093/ve/veab070] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/04/2021] [Accepted: 08/07/2021] [Indexed: 12/15/2022] Open
Abstract
Remarkably little is known about the diversity and evolution of RNA viruses in unicellular eukaryotes. We screened a total of 570 transcriptomes from the Marine Microbial Eukaryote Transcriptome Sequencing Project that encompasses a wide diversity of microbial eukaryotes, including most major photosynthetic lineages (i.e. the microalgae). From this, we identified thirty new and divergent RNA virus species, occupying a range of phylogenetic positions within the overall diversity of RNA viruses. Approximately one-third of the newly described viruses comprised single-stranded positive-sense RNA viruses from the order Lenarviricota associated with fungi, plants, and protists, while another third were related to the order Ghabrivirales, including members of the protist and fungi-associated Totiviridae. Other viral species showed sequence similarity to positive-sense RNA viruses from the algae-associated Marnaviridae, the double-stranded RNA (ds-RNA) Partitiviridae, as well as tentative evidence for one negative-sense RNA virus related to the Qinviridae. Importantly, we were able to identify divergent RNA viruses from distant host taxa, revealing the ancestry of these viral families and greatly extending our knowledge of the RNA viromes of microalgal cultures. Both the limited number of viruses detected per sample and the low sequence identity to known RNA viruses imply that additional microalgal viruses exist that could not be detected at the current sequencing depth or were too divergent to be identified using sequence similarity. Together, these results highlight the need for further investigation of algal-associated RNA viruses as well as the development of new tools to identify RNA viruses that exhibit very high levels of sequence divergence.
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Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures. Viruses 2020; 12:v12101180. [PMID: 33086653 PMCID: PMC7594059 DOI: 10.3390/v12101180] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Our knowledge of the diversity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae within which few RNA viruses have been documented. By combining total RNA sequencing with sequence and structural-based homology detection, we identified 18 novel RNA viruses in cultured samples from two major groups of microbial algae: the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to the Tombusviridae and Amalgaviridae viral families commonly associated with land plants. This suggests that the evolutionary history of these viruses extends to divergence events between algae and land plants. Seven Ostreobium sp-associated viruses exhibited sequence similarity to the mitoviruses most commonly found in fungi, compatible with horizontal virus transfer between algae and fungi. We also document, for the first time, RNA viruses associated with chlorarachniophytes, including the first negative-sense (bunya-like) RNA virus in microalgae, as well as a distant homolog of the plant virus Virgaviridae, potentially signifying viral inheritance from the secondary chloroplast endosymbiosis that marked the origin of the chlorarachniophytes. More broadly, these data suggest that the scarcity of RNA viruses in algae results from limited investigation rather than their absence.
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Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures. Viruses 2020; 12:v12101180. [PMID: 33086653 DOI: 10.1101/2020.06.08.141184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 05/26/2023] Open
Abstract
Our knowledge of the diversity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae within which few RNA viruses have been documented. By combining total RNA sequencing with sequence and structural-based homology detection, we identified 18 novel RNA viruses in cultured samples from two major groups of microbial algae: the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to the Tombusviridae and Amalgaviridae viral families commonly associated with land plants. This suggests that the evolutionary history of these viruses extends to divergence events between algae and land plants. Seven Ostreobium sp-associated viruses exhibited sequence similarity to the mitoviruses most commonly found in fungi, compatible with horizontal virus transfer between algae and fungi. We also document, for the first time, RNA viruses associated with chlorarachniophytes, including the first negative-sense (bunya-like) RNA virus in microalgae, as well as a distant homolog of the plant virus Virgaviridae, potentially signifying viral inheritance from the secondary chloroplast endosymbiosis that marked the origin of the chlorarachniophytes. More broadly, these data suggest that the scarcity of RNA viruses in algae results from limited investigation rather than their absence.
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Spectroscopic Investigation of the Kinetic Mechanism Involved in the Association of Potyviral VPg with the Host Plant Translation Initiation Factor eIF4E. Int J Mol Sci 2020; 21:ijms21165618. [PMID: 32764527 PMCID: PMC7460627 DOI: 10.3390/ijms21165618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022] Open
Abstract
The infectious cycle of potyviruses requires the formation of a complex between the viral genome-linked protein VPg and the host eukaryotic translation initiation factor 4E, eIF4E. Mutations associated with plant resistance to potyviruses were previously mapped at the eIF4E surface, while on the virus side, mutations leading to plant resistance breaking were identified within the VPg. In the present study, fluorescence spectroscopy was used to probe the contribution of the VPg intrinsically disordered region bearing amino acids determinant of the resistance breaking, to the VPg–eIF4E binding mechanism. Synthetic peptides encompassing the VPg88–120 central region were found to tightly bind to eIF4E. Fluorescence energy transfer experiments show that, upon binding to eIF4E, the N and C termini of the VPg88–111 fragment move closer to one another, at a distance compatible with a α-helix folding. When the VPg112–120 region, which contains amino acids associated with resistance breakdown, is appended to VPg88–111, the complex formation with eIF4E switches from a single-step to a two-step kinetic model. This study revisits a recent investigation of the VPg–eIF4E complex by specifying the contribution of the VPg central helix and its appended disordered region to VPg association with eIF4E.
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Novel RNA viruses associated with Plasmodium vivax in human malaria and Leucocytozoon parasites in avian disease. PLoS Pathog 2019; 15:e1008216. [PMID: 31887217 PMCID: PMC6953888 DOI: 10.1371/journal.ppat.1008216] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 01/10/2020] [Accepted: 11/13/2019] [Indexed: 12/15/2022] Open
Abstract
Eukaryotes of the genus Plasmodium cause malaria, a parasitic disease responsible for substantial morbidity and mortality in humans. Yet, the nature and abundance of any viruses carried by these divergent eukaryotic parasites is unknown. We investigated the Plasmodium virome by performing a meta-transcriptomic analysis of blood samples taken from patients suffering from malaria and infected with P. vivax, P. falciparum or P. knowlesi. This resulted in the identification of a narnavirus-like sequence, encoding an RNA polymerase and restricted to P. vivax samples, as well as an associated viral segment of unknown function. These data, confirmed by PCR, are indicative of a novel RNA virus that we term Matryoshka RNA virus 1 (MaRNAV-1) to reflect its analogy to a "Russian doll": a virus, infecting a parasite, infecting an animal. Additional screening revealed that MaRNAV-1 was abundant in geographically diverse P. vivax derived from humans and mosquitoes, strongly supporting its association with this parasite, and not in any of the other Plasmodium samples analyzed here nor Anopheles mosquitoes in the absence of Plasmodium. Notably, related bi-segmented narnavirus-like sequences (MaRNAV-2) were retrieved from Australian birds infected with a Leucocytozoon—a genus of eukaryotic parasites that group with Plasmodium in the Apicomplexa subclass hematozoa. Together, these data support the establishment of two new phylogenetically divergent and genomically distinct viral species associated with protists, including the first virus likely infecting Plasmodium parasites. As well as broadening our understanding of the diversity and evolutionary history of the eukaryotic virosphere, the restriction to P. vivax may be of importance in understanding P. vivax-specific biology in humans and mosquitoes, and how viral co-infection might alter host responses at each stage of the P. vivax life-cycle. While parasites are a major cause of human disease, they can themselves be infected by viruses. We asked whether three of the major malaria-causing parasites in humans—Plasmodium vivax, P. falciparum and P. knowlesi—were also infected by viruses. To this end we performed total RNA-Sequencing (“meta-transcriptomics”) on human blood samples infected with these Plasmodium species. This resulted in the discovery of an abundant bi-segmented virus—Matryoshka RNA virus 1 (MaRNAV-1)—in all P. vivax samples tested (but no other Plasmodium species) that contains a replicase segment related to those of narnaviruses, arguably the simplest type of RNA viruses discovered to date. By screening for MaRNAV-1 in a larger set of Plasmodium species we revealed a strong specificity between this virus and P. vivax, as well as the presence of a related virus—MaRNAV-2—in avian Leucocytozoon hematozoa parasites. This is the first discovery of a Plasmodium-associated virus and will assist in revealing the deep evolutionary history of RNA viruses and our understanding of Plasmodium biology and disease processes.
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Hydrodynamic Behavior of the Intrinsically Disordered Potyvirus Protein VPg, of the Translation Initiation Factor eIF4E and of their Binary Complex. Int J Mol Sci 2019; 20:E1794. [PMID: 30978975 PMCID: PMC6479716 DOI: 10.3390/ijms20071794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 01/12/2023] Open
Abstract
Protein intrinsic disorder is involved in many biological processes and good experimental models are valuable to investigate its functions. The potyvirus genome-linked protein, VPg, displays many features of an intrinsically disordered protein. The virus cycle requires the formation of a complex between VPg and eIF4E, one of the host translation initiation factors. An in-depth characterization of the hydrodynamic properties of VPg, eIF4E, and of their binary complex VPg-eIF4E was carried out. Two complementary experimental approaches, size-exclusion chromatography and fluorescence anisotropy, which is more resolving and revealed especially suitable when protein concentration is the limiting factor, allowed to estimate monomers compaction upon complex formation. VPg possesses a high degree of hydration which is in agreement with its classification as a partially folded protein in between a molten and pre-molten globule. The natively disordered first 46 amino acids of eIF4E contribute to modulate the protein hydrodynamic properties. The addition of an N-ter His tag decreased the conformational entropy of this intrinsically disordered region. A comparative study between the two tagged and untagged proteins revealed the His tag contribution to proteins hydrodynamic behavior.
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First Experimental Assessment of Protein Intrinsic Disorder Involvement in an RNA Virus Natural Adaptive Process. Mol Biol Evol 2019; 35:38-49. [PMID: 29029259 PMCID: PMC5850501 DOI: 10.1093/molbev/msx249] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Intrinsic disorder (ID) in proteins is defined as a lack of stable structure in physiological conditions. Intrinsically disordered regions (IDRs) are highly abundant in some RNA virus proteomes. Low topological constraints exerted on IDRs are expected to buffer the effect of numerous deleterious mutations and could be related to the remarkable adaptive potential of RNA viruses to overcome resistance of their host. To experimentally test this hypothesis in a natural pathosystem, a set of four variants of Potato virus Y (PVY; Potyvirus genus) containing various ID degrees in the Viral genome-linked (VPg) protein, a key determinant of potyvirus adaptation, was designed. To estimate the ID contribution to the VPg-based PVY adaptation, the adaptive ability of the four PVY variants was monitored in the pepper host (Capsicum annuum) carrying a recessive resistance gene. Intriguingly, the two mutants with the highest ID content displayed a significantly higher ability to restore infection in the resistant host, whereas the less intrinsically disordered mutant was unable to restore infection. The role of ID on virus adaptation may be due either to a larger exploration of evolutionary pathways or the minimization of fitness penalty caused by resistance-breaking mutations. This pioneering study strongly suggests the positive impact of ID in an RNA virus adaptive capacity.
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Comparative analysis of mutational robustness of the intrinsically disordered viral protein VPg and of its interactor eIF4E. PLoS One 2019; 14:e0211725. [PMID: 30763345 PMCID: PMC6375565 DOI: 10.1371/journal.pone.0211725] [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: 11/21/2018] [Accepted: 01/20/2019] [Indexed: 01/02/2023] Open
Abstract
Conformational intrinsic disorder is a feature present in many virus proteins. Intrinsically disordered regions (IDRs) have weaker structural requirement than ordered regions and mutations in IDRs could have a lower impact on the virus fitness. This could favor its exploration of adaptive solutions. The potyviral protein VPg contains IDRs with determinants for adaptation to its host plant. To experimentally assess whether IDRs are more resistant to mutations than ordered regions, the biologically relevant interaction between mutant libraries of both VPg and the eukaryotic translation initiation factor 4E (eIF4E) and their respective wild type partner was examined using yeast two hybrid assay. Our data shows that VPg is significantly more robust to mutations than eIF4E and as such belongs to a particular class of intrinsically disordered proteins. This result is discussed from the standpoint of IDRs involvement in the virus adaptive processes.
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Abstract
The threat of bacteria resistant to multiple antibiotics poses a major public health problem requiring immediate and coordinated action worldwide. While infectious pathogens have become increasingly resistant to commercially available drugs, antibiotic discovery programs in major pharmaceutical companies have produced no new antibiotic scaffolds in 40 years. As a result, new strategies must be sought to obtain a steady supply of novel scaffolds capable of countering the spread of resistance. The bacterial ribosome is a major target for antimicrobials and is inhibited by more than half of the antibiotics used today. Recent studies showing that the ribosome is a target for several classes of ribosomally synthesized antimicrobial peptides point to ribosome-targeting peptides as a promising source of antibiotic scaffolds. In this Perspective, we revisit the current paradigm of antibiotic discovery by proposing that the bacterial ribosome can be used both as a target and as a tool for the production and selection of peptide-based antimicrobials. Turning the ribosome into a high-throughput platform for the directed evolution of peptide-based antibiotics could be achieved in different ways. One possibility would be to use a combination of state-of-the-art microfluidics and genetic reprogramming techniques, which we will review briefly. If it is successful, this strategy has the potential to produce new classes of antibiotics for treating multi-drug-resistant pathogens.
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Dissecting the Biochemical and Transcriptomic Effects of a Locally Applied Heat Treatment on Developing Cabernet Sauvignon Grape Berries. FRONTIERS IN PLANT SCIENCE 2017; 8:53. [PMID: 28197155 PMCID: PMC5281624 DOI: 10.3389/fpls.2017.00053] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/10/2017] [Indexed: 05/20/2023]
Abstract
Reproductive development of grapevine and berry composition are both strongly influenced by temperature. To date, the molecular mechanisms involved in grapevine berries response to high temperatures are poorly understood. Unlike recent data that addressed the effects on berry development of elevated temperatures applied at the whole plant level, the present work particularly focuses on the fruit responses triggered by direct exposure to heat treatment (HT). In the context of climate change, this work focusing on temperature effect at the microclimate level is of particular interest as it can help to better understand the consequences of leaf removal (a common viticultural practice) on berry development. HT (+ 8°C) was locally applied to clusters from Cabernet Sauvignon fruiting cuttings at three different developmental stages (middle green, veraison and middle ripening). Samples were collected 1, 7, and 14 days after treatment and used for metabolic and transcriptomic analyses. The results showed dramatic and specific biochemical and transcriptomic changes in heat exposed berries, depending on the developmental stage and the stress duration. When applied at the herbaceous stage, HT delayed the onset of veraison. Heating also strongly altered the berry concentration of amino acids and organic acids (e.g., phenylalanine, γ-aminobutyric acid and malate) and decreased the anthocyanin content at maturity. These physiological alterations could be partly explained by the deep remodeling of transcriptome in heated berries. More than 7000 genes were deregulated in at least one of the nine experimental conditions. The most affected processes belong to the categories "stress responses," "protein metabolism" and "secondary metabolism," highlighting the intrinsic capacity of grape berries to perceive HT and to build adaptive responses. Additionally, important changes in processes related to "transport," "hormone" and "cell wall" might contribute to the postponing of veraison. Finally, opposite effects depending on heating duration were observed for genes encoding enzymes of the general phenylpropanoid pathway, suggesting that the HT-induced decrease in anthocyanin content may result from a combination of transcript abundance and product degradation.
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Protein intrinsic disorder within the Potyvirus genus: from proteome-wide analysis to functional annotation. MOLECULAR BIOSYSTEMS 2016; 12:634-52. [PMID: 26699268 DOI: 10.1039/c5mb00677e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Within proteins, intrinsically disordered regions (IDRs) are devoid of stable secondary and tertiary structures under physiological conditions and rather exist as dynamic ensembles of inter-converting conformers. Although ubiquitous in all domains of life, the intrinsic disorder content is highly variable in viral genomes. Over the years, functional annotations of disordered regions at the scale of the whole proteome have been conducted for several animal viruses. But to date, similar studies applied to plant viruses are still missing. Based on disorder prediction tools combined with annotation programs and evolutionary studies, we analyzed the intrinsic disorder content in Potyvirus, using a 10-species dataset representative of this genus diversity. In this paper, we revealed that: (i) the Potyvirus proteome displays high disorder content, (ii) disorder is conserved during Potyvirus evolution, suggesting a functional advantage of IDRs, (iii) IDRs evolve faster than ordered regions, and (iv) IDRs may be associated with major biological functions required for the Potyvirus cycle. Notably, the proteins P1, Coat protein (CP) and Viral genome-linked protein (VPg) display a high content of conserved disorder, enriched in specific motifs mimicking eukaryotic functional modules and suggesting strategies of host machinery hijacking. In these three proteins, IDRs are particularly conserved despite their high amino acid polymorphism, indicating a link to adaptive processes. Through this comprehensive study, we further investigate the biological relevance of intrinsic disorder in Potyvirus biology and we propose a functional annotation of potyviral proteome IDRs.
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VvGOLS1 and VvHsfA2 are involved in the heat stress responses in grapevine berries. PLANT & CELL PHYSIOLOGY 2012; 53:1776-92. [PMID: 22952249 DOI: 10.1093/pcp/pcs121] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Among various environmental factors, temperature is a major regulator affecting plant growth, development and fruit composition. Grapevine is the most cultivated fruit plant throughout the world, and grapes are used for wine production and human consumption. The molecular mechanisms involved in grapevine tolerance to high temperature, especially at the fruit level, are poorly understood. To better characterize the sensitivity of berries to the microenvironment, high temperature conditions were locally applied to Vitis vinifera Cabernet Sauvignon clusters. Two genes, VvGOLS1 and VvHsfA2, up-regulated by this treatment, were identified and further characterized. The expression profile of VvGOLS1 correlated positively with galactinol accumulation in heat-stressed berries. However, no galactinol derivatives, such as raffinose and stachyose, accumulated upon heat stress. Heterologous expression of VvGOLS1 in Escherichia coli showed that it encodes a functional galactinol synthase. Transient expression assays showed that the heat stress factor VvHsfA2 transactivates the promoter of VvGOLS1 in a heat stress-dependent manner. Taken together, our results highlight the intrinsic capacity of grape berries to perceive heat stress and to initiate adaptive responses, suggesting that galactinol may play a signaling role in these responses.
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[Clinical attitudes toward periodontal risk]. Orthod Fr 1998; 69:123-9. [PMID: 9643041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
After having defined the conditions that will start the loss of attached gingiva, the author develops the characteristic of the patient at periodontal risk. He then explains the value of the interview as well as that of the clinical and microbiological exams, insisting on the therapeutic outcome of those exams, and on the effect of the flora.
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Effects of sanguinarium, chlorhexidine and tetracycline on neutrophil viability and functions in vitro. J Periodontal Res 1997; 32:335-44. [PMID: 9138200 DOI: 10.1111/j.1600-0765.1997.tb00542.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The effectiveness of an ideal antimicrobial agent depends on its ability to kill microbes with minimal toxicity to host cells. Depending on the treatment regimen, antimicrobial agents come into contact with host cells for various intervals of time. Sanguinarium (SANG), chlorhexidine (CHX) and tetracycline (TET) are 3 antimicrobial agents frequently used in the management of periodontal infections. However, their effects on host immune cells during different treatment regimens are not known. Due to their ability to serve as the first line of host defense against microbial infections, we have compared the effects of these antimicrobial agents on human neutrophil functions and viability. The results show that SANG is not lytic to neutrophils from peripheral blood or crevicular fluid, at all concentrations tested. However, exposures of neutrophils to very low concentrations of SANG (0.001%) inhibits neutrophil chemotaxis, oxidative metabolism and degranulation within 5 min. Increasing the exposure time results in a similar inhibition of neutrophil functions, albeit at 50-100 fold lower concentrations of SANG. CHX rapidly disrupts the cell membrane of both crevicular and peripheral blood neutrophils at concentrations above 0.005% within 5 min, and inhibition of all neutrophil functions is due to its lytic properties. While TET is least toxic to neutrophils, a dose dependent inhibition of neutrophil functions is dependent on the calcium concentrations of the cellular environment, and is observed only above 0.04% or higher concentrations in the absence of calcium. The data suggest that a critical cumulative concentration of these drugs is essential for their toxicity and inhibition of neutrophil functions. Therefore, both the length of exposure and the dose of the drug both are critical while considering the effectiveness of SANG, CHX or TET in the treatment of infections. Furthermore, due to differences in their mechanisms of action, the consequences of their effects on neutrophils may have significant bearing on tissue pathology as well as on their therapeutic efficacy.
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[Postoperative inhalation treatment after paranasal sinus interventions. A placebo-controlled, double-blind and randomized study]. HNO 1991; 39:433-8. [PMID: 1769866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A placebo-controlled, double-blind study with Ems brine inhalations as postoperative treatment after endoscopic endonasal sinus surgery was conducted on 30 patients. After informed consent had been obtained, the patients were treated with either Ems brine or saline solution (200 ml) 3 times a day for 10 days. The parameters measured were rhinomanometry, X-ray films of the sinuses, endoscopy, saccharin clearance and a subjective evaluation by the physician and by the patient based on a visual analogue scale. The difficulty of choosing parameters for assessing the treatment was that comparable clinical studies and a single predictive parameter were not available. The bacteriological test and the saccharin clearance test were not significantly different between the two groups. Recovery, swelling, crusting, bleeding and signs of inflammation, opacity on sinus X-ray films, and nasal flow as measured by rhinomanometry were all significantly better in the group inhaling brine solution (P less than 0.05).
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19
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Abstract
Polymorphonuclear neutrophils (PMN) are the predominant cell type in the established lesion of recurrent aphthous stomatitis (RAS). The function of these cells was studied in 15 patients with RAS and 15 age and sex matched controls. Production of oxygen radicals was assessed using cytochrome-c and nitroblue tetrazolium dye (NBT) reduction assays. Oxidative metabolism was found to be similar for experimental and control groups in both stimulated and non-stimulated assays. Adherence to glass surfaces by PMN was also measured. Adherence of PMN, both from patients and controls, was significantly reduced by serum, but to a lesser extent by serum from patients compared to controls. This effect of serum on adherence was reversed by phorbol myristate acetate (PMA) stimulation. These studies suggest that increased adherence of stimulated PMN, due to humoral factors, may be involved in perpetuating ulcerative lesions in RAS.
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20
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In vitro survival of Bacteroides intermedius in five transport media, alone or in the presence of Streptococcus sanguis. ORAL MICROBIOLOGY AND IMMUNOLOGY 1990; 5:320-3. [PMID: 2129136 DOI: 10.1111/j.1399-302x.1990.tb00433.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The survival rate of Bacteroides intermedius was first tested in monoculture, and Streptococcus sanguis was then added in 5 different transport media; 2 nonnutritious media, the viability-preserving medium of the University of Göteborg No. IV (VMG IV), reduced transport fluid (RTF), and 3 nutritious media, thioglycolate medium (TG), peptone yeast extract medium (PY) and PY medium with 1% glucose (PYG). All manipulations were carried out in an anaerobic chamber. After a given transport time (6 or 24 h) aliquots were spread on plates containing solid PY medium by means of an automated spiral system device, thus permitting counts after incubation. The slight variations in the counts of B. intermedius in monoculture, not exceeding 0.5 log10 in the 5 media tested, indicated its good survival capability, i.e. at least 24 h. By contrast, when S. sanguis was added, it was only possible to use nutritious media such as PY or TG for 6 h. In the glocose-containing media (PYG, TG), the multiplication of rapidly glucose-fermenting microorganisms such as streptococci influenced the B. intermedius survival rate. Therefore, the transport time for oral microbiological samples needs to be reduced as much as possible. The use of excessively rich media (particularly media containing a high level of glucose) should be avoided.
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21
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[Sanguinarine. Its role in periodontal therapy]. L' INFORMATION DENTAIRE 1990; 72:3473-8. [PMID: 2272691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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22
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[Diagnosis of risk in periodontology]. L' INFORMATION DENTAIRE 1990; 72:2965-80. [PMID: 2228183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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23
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[Immune response during experimental periodontitis in mice]. JOURNAL DE PARODONTOLOGIE 1990; 9:175-8. [PMID: 2213541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Four groups of mice, each of a different genotype, were orally inoculated with Actinomyces viscosus. The resulting periodontal bone loss was monitored and the isotype specific anti-A. viscosus serum humoral immune responses measured by ELISA. Maximum periodontal bone loss occurred in all genotypes with inoculation of 1.6 x 107 colony forming units of A. viscosus. IgG and IgM isotype levels increased with inoculation of 1.6 x 107 colony forming units of A. viscosus in three of the four groups, indicating that IgA may be important in producing periodontal bone loss.
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24
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[Iatrogenic interdental brushing. Apropos of a case]. JOURNAL DE PARODONTOLOGIE 1990; 9:51-5. [PMID: 2384877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A case of severe dentinal abrasion most probably due to erroneous use of interproximal brushes is shown and discussed as well.
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25
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[Importance of alternating theoretical and practical education of the psychiatric nurse]. Soins Psychiatr 1989:36-40. [PMID: 2749331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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26
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[The periodontium and neutrophils in septic granulomatosis (apropos of a case)]. JOURNAL DE PARODONTOLOGIE 1988; 7:29-37. [PMID: 3164072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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27
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[The place of antibiotics in periodontics]. L' INFORMATION DENTAIRE 1987; 69:3429-33. [PMID: 3504426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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28
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[Scaling and polishing. An essential attitude in periodontics]. L' INFORMATION DENTAIRE 1987; 69:3449-53. [PMID: 3332871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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29
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[Diagnosis of periodontal disease in 1987]. L' INFORMATION DENTAIRE 1987; 69:3405-9. [PMID: 3504423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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30
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[Microscopy in daily practice]. L' INFORMATION DENTAIRE 1987; 69:3413-6. [PMID: 3504424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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31
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Suppression of lymphocyte and fibroblast proliferation by Actinomyces viscosus-activated murine macrophages. J Periodontal Res 1987; 22:456-60. [PMID: 2963104 DOI: 10.1111/j.1600-0765.1987.tb02055.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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32
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[Focus on conservative and surgical treatment]. JOURNAL DE PARODONTOLOGIE 1987; 6:173-84. [PMID: 3309259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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33
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Ontogenèse des canaux sécréteurs d'origine primaire dans le bourgeon de Pin maritime. ACTA ACUST UNITED AC 1986. [DOI: 10.1139/b86-390] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In the bud of Pinus pinaster Ait., two resin ducts are formed at the base of each very young scale on each side of the procambial strand. They differentiate in the acropetal and basipetal directions as do the vascular tissues. During the basipetal differentiation, the resin ducts from each scale anastomose in a definite way: the left resin duct of each scale is connected with the right duct of the n – 8 scale rank and the right duct, with the left duct of the n – 5 scale rank. The resin canal system of the shoot is then constituted of only 13 resin ducts. The resin ducts of the maritime pine are formed on a schizolysigenous pattern: a schizogenous process induces the formation of the lumen; then a transitory stage with two secretory layers takes place before a lysigenous process which enhances the enlargement of the duct lumen. Observations were done using light and electron microscopy.
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34
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[Are the criteria for success in periodontal treatment the same for the patient and the dentist?]. REVUE D'ODONTO-STOMATOLOGIE 1986; 15:425-30. [PMID: 3468577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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35
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[Antibiotics in periodontics. Round table held 23 November 1985]. REVUE D'ODONTO-STOMATOLOGIE 1986; 15:303-21. [PMID: 3464061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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36
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[Oxidative metabolism and chlorhexidine]. JOURNAL DE PARODONTOLOGIE 1985; 4:377-82. [PMID: 3869246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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37
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Secretion of a chemotactic factor for neutrophils and eosinophils by alveolar macrophages from asthmatic patients. J Allergy Clin Immunol 1984; 74:827-34. [PMID: 6334110 DOI: 10.1016/0091-6749(84)90186-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The studies presented in this article demonstrate the release of an IgE-dependent chemotactic factor for polymorphonuclear neutrophils (PMN) and eosinophils by alveolar macrophages (AMs) from normal subjects (n = 15) and allergic asthmatic patients (n = 15). A 60-minute incubation of normal AMs previously sensitized by 20% nonheated allergic sera with anti-human IgE antibody or the related allergen induced the release of a chemotactic activity (CA) for PMN and eosinophils in culture supernatants. When AMs were obtained from asthmatic patients, direct incubation with anti-IgE or the related allergen induced the same CA, whereas incubation with an unrelated allergen failed to produce CA (neutrophil CA after addition of anti-IgE, 22.5 +/- 3.5 cells per high power field; with related allergen, 15.8 +/- 3.6; with unrelated allergen, 0.7 +/- 1.8; p less than 0.0001). A partial characterization of the neutrophil chemotactic factor was carried out. Enzymatic treatment by trypsin or carboxypeptidase or by heating (56 degrees C for 3 hr) failed to abolish the neutrophil CA. After gel filtration the greater part of the neutrophil CA (80%) was recovered among low-molecular-weight components (300 to 1300 daltons). A preliminary deactivation of PMN by leukotriene B4 suppressed the CA of AM supernatants. These results indicate that IgE-dependent stimulation of AMs produces a neutrophil and eosinophil CA, present in a low-molecular-weight fraction possibly related to leukotrienes, and emphasizes the role of AMs in inflammatory lung processes during allergic asthma.
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38
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Heterogeneity of human eosinophils. II. Variability of respiratory burst activity related to cell density. Clin Exp Immunol 1984; 57:735-42. [PMID: 6467687 PMCID: PMC1536255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Recent work has suggested that there may be heterogeneity amongst human eosinophils. In order to study this further, blood and tissue eosinophils were separated by density gradient centrifugation in discontinuous gradients of metrizamide. Blood eosinophils were obtained from 16 patients with blood eosinophil counts above 1 X 10(9)/l. Resident eosinophils were isolated from alveolar fluid in three of these patients and from pleural effusion in two others. A large proportion of the eosinophils in these patients were of light buoyant density (hypodense) and a high percentage of these showed morphological evidence of hypogranulation. Hypodense eosinophils had a reduced capacity to reduce nitroblue tetrazolium or develop chemiluminescence after stimulation with phorbol myristate acetate. It was concluded that there is structural and metabolic heterogeneity amongst blood and tissue eosinophils in patients with a variety of eosinophilic disorders.
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39
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[The tolerance of dental alloys in the oral environment]. LE CHIRURGIEN-DENTISTE DE FRANCE 1983; 53:37-52. [PMID: 6574890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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40
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[European dental density]. LE CHIRURGIEN-DENTISTE DE FRANCE 1982; 52:41-2. [PMID: 6963195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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41
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A rapid densitometric microassay for nitroblue tetrazolium reduction and application of the microassay to macrophages. JOURNAL OF THE RETICULOENDOTHELIAL SOCIETY 1981; 30:581-593. [PMID: 6281430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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42
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Abstract
Fifteen patients, eight males and seven females, ranging from 30 to 88 years of age with advanced periodontal disease were selected for this study. Biopsies and blood samples were taken of both normal and inflamed gingival tissues, and processed for detection of nonspecific esterase and acid phosphatase activity in monocytes and macrophages. Activated macrophages, as indicated by their intense reaction to acid phosphatase and nonspecific esterase, were found in the gingival epithelium, lamina propria, perivascular tissues and in the blood vessels in human chronic periodontitis. Blood smears of monocytes showed variability of stain intensity suggesting that their activation occurred in blood vessels where they marginate and emigrate into the perivascular tissues in chronic periodontitis. They then appear as macrophages that migrate through the connective tissue, penetrate the basement membrane and continue through the epithelium. The nonspecific esterase stain identified T-cells, by a singular dot-like granule, and plasma cells by multiple granules in the cytoplasm. Lymphocytes containing multiple cytoplasmic nonspecific esterase positive granules commonly were found only in the perivascular connective tissue and may represent B-cell differentiation to plasma cells. The plasma cell predominance, the presence of T-cells and activated macrophages indicated both humoral and cell-mediated responses are operative in human chronic periodontitis.
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43
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[Professional diseases]. CAHIERS D'ODONTO-STOMATOLOGIE 1979; 11:31-4. [PMID: 293202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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44
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[Finishing: how and by whom?]. LE CHIRURGIEN-DENTISTE DE FRANCE 1975; 45:25-6. [PMID: 1073062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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45
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[Salient points of an interview with Dr. Rolf Braun]. LE CHIRURGIEN-DENTISTE DE FRANCE 1975; 45:29-30. [PMID: 1073056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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