The Experts below are selected from a list of 58572 Experts worldwide ranked by ideXlab platform
Yael Hazan - One of the best experts on this subject based on the ideXlab platform.
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Initial Virome Characterization of the Common Cnidarian Lab Model Nematostella vectensis
Viruses, 2020Co-Authors: Magda Lewandowska, Yael HazanAbstract:The role of Viruses in forming a stable holobiont has been the subject of extensive research in recent years. However, many emerging model organisms still lack any data on the composition of the associated viral communities. Here, we re-analyzed seven publicly available transcriptome datasets of the starlet sea anemone Nematostella vectensis, the most commonly used anthozoan lab model, and searched for viral sequences. We applied a straightforward, yet powerful approach of de novo assembly followed by homology-based Virus Identification and a multi-step, thorough taxonomic validation. The comparison of different lab populations of N. vectensis revealed the existence of the core virome composed of 21 viral sequences, present in all adult datasets. Unexpectedly, we observed an almost complete lack of Viruses in the samples from the early developmental stages, which together with the Identification of the Viruses shared with the major source of the food in the lab, the brine shrimp Artemia salina, shed new light on the course of viral species acquisition in N. vectensis. Our study provides an initial, yet comprehensive insight into N. vectensis virome and sets the first foundation for the functional studies of Viruses and antiviral systems in this lab model cnidarian.
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Initial virome characterization of the common cnidarian lab model Nematostella vectensis
2020Co-Authors: Magda Lewandowska, Yael HazanAbstract:The role of Viruses in forming a stable holobiont has been a subject of extensive research in the recent years. However, many emerging model organisms still lack any data on the composition of the associated viral communities. Here, we re-analyzed seven publicly available transcriptome datasets of the starlet sea anemone Nematostella vectensis, the most commonly used anthozoan lab model, and searched for viral sequences. We applied a straightforward, yet powerful approach of de novo assembly followed by homology-based Virus Identification and a multi-step, thorough taxonomic validation. The comparison of different lab populations of N. vectensis revealed the existence of the core virome composed of 21 viral sequences, present in all adult datasets. Unexpectedly, we observed almost complete lack of Viruses in the samples from the early developmental stages which together with the Identification of the Viruses shared with the major source of the food in the lab, the brine shrimp Artemia salina, shed new light on the course of viral species acquisition in N. vectensis. Our study provides an initial, yet comprehensive insight into N. vectensis virome and sets the first foundation for functional studies of Viruses and antiviral systems in this lab model cnidarian.
Peter P. C. Mertens - One of the best experts on this subject based on the ideXlab platform.
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Serotype Specific Primers and Gel-Based RT-PCR Assays for ‘Typing ’ African Horse Sickness Virus: Identification of Strains from Africa
2013Co-Authors: Narender S. Maan, Sushila Maan, Kyriaki Nomikou, Manjunatha N. Belaganahalli, Katarzyna Bachanek, Peter P. C. MertensAbstract:African horse sickness is a devastating, transboundary animal disease, that is ‘listed ’ by the Office International des Epizooties (OIE). Although attenuated, inactivated and subunit vaccines have been developed for African horse sickness Virus (AHSV), these are serotype-specific and their effective deployment therefore relies on rapid and reliable Identification of Virus type. AHSV serotype is controlled by the specificity of interactions between neutralising antibodies, and components of the outer-capsid, particularly protein VP2 (encoded by AHSV genome segment 2 (Seg-2)). We report the development and evaluation of novel gel based reverse transcription-PCR (RT–PCR) assays targeting AHSV Seg-2, which can be used to very significantly increase the speed and reliability of detection and Identification (compared to Virus neutralisation tests) of the nine serotypes of AHSV. Primer sets were designed targeting regions of Seg-2 that are conserved between strains within each of the AHSV serotype (types 1 to 9). These assays were evaluated using multiple AHSV strains from the orbiVirus reference collection at IAH (www.reoviridae.org/dsRNA_Virus_proteins/ReoID/AHSV-isolates.htm). In each case the Seg-2 primers showed a high level of specificity and failed to cross-amplify the most closely related heterologous AHSV types, or other related orbiViruses (such as bluetongue Virus (BTV), or equine encephalosis Virus (EEV)). The assays are rapid and sensitive, and can be used to detect and type viral RNA in blood, tissue samples, or cultivated viral suspensions within 24 h. They were used to identify AHSV strains from recent outbreaks in sub-Saharan African countries. Thes
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serotype specific primers and gel based rt pcr assays for typing african horse sickness Virus Identification of strains from africa
PLOS ONE, 2011Co-Authors: Narender S. Maan, Sushila Maan, Kyriaki Nomikou, Manjunatha N. Belaganahalli, Katarzyna Bachanekbankowska, Peter P. C. MertensAbstract:: African horse sickness is a devastating, transboundary animal disease, that is 'listed' by the Office International des Epizooties (OIE). Although attenuated, inactivated and subunit vaccines have been developed for African horse sickness Virus (AHSV), these are serotype-specific and their effective deployment therefore relies on rapid and reliable Identification of Virus type. AHSV serotype is controlled by the specificity of interactions between neutralising antibodies, and components of the outer-capsid, particularly protein VP2 (encoded by AHSV genome segment 2 (Seg-2)). We report the development and evaluation of novel gel based reverse transcription-PCR (RT-PCR) assays targeting AHSV Seg-2, which can be used to very significantly increase the speed and reliability of detection and Identification (compared to Virus neutralisation tests) of the nine serotypes of AHSV. Primer sets were designed targeting regions of Seg-2 that are conserved between strains within each of the AHSV serotype (types 1 to 9). These assays were evaluated using multiple AHSV strains from the orbiVirus reference collection at IAH (www.reoviridae.org/dsRNA_Virus_proteins/ReoID/AHSV-isolates.htm). In each case the Seg-2 primers showed a high level of specificity and failed to cross-amplify the most closely related heterologous AHSV types, or other related orbiViruses (such as bluetongue Virus (BTV), or equine encephalosis Virus (EEV)). The assays are rapid and sensitive, and can be used to detect and type viral RNA in blood, tissue samples, or cultivated viral suspensions within 24 h. They were used to identify AHSV strains from recent outbreaks in sub-Saharan African countries. These methods also generate cDNAs suitable for sequencing and phylogenetic analyses of Seg-2, identifying distinct Virus lineages within each Virus-type and helping to identify strain movements/origins. The RT-PCR methods described here provide a robust and versatile tool for rapid and specific detection and Identification of AHSV serotypes 1 to 9.
Magda Lewandowska - One of the best experts on this subject based on the ideXlab platform.
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Initial Virome Characterization of the Common Cnidarian Lab Model Nematostella vectensis
Viruses, 2020Co-Authors: Magda Lewandowska, Yael HazanAbstract:The role of Viruses in forming a stable holobiont has been the subject of extensive research in recent years. However, many emerging model organisms still lack any data on the composition of the associated viral communities. Here, we re-analyzed seven publicly available transcriptome datasets of the starlet sea anemone Nematostella vectensis, the most commonly used anthozoan lab model, and searched for viral sequences. We applied a straightforward, yet powerful approach of de novo assembly followed by homology-based Virus Identification and a multi-step, thorough taxonomic validation. The comparison of different lab populations of N. vectensis revealed the existence of the core virome composed of 21 viral sequences, present in all adult datasets. Unexpectedly, we observed an almost complete lack of Viruses in the samples from the early developmental stages, which together with the Identification of the Viruses shared with the major source of the food in the lab, the brine shrimp Artemia salina, shed new light on the course of viral species acquisition in N. vectensis. Our study provides an initial, yet comprehensive insight into N. vectensis virome and sets the first foundation for the functional studies of Viruses and antiviral systems in this lab model cnidarian.
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Initial virome characterization of the common cnidarian lab model Nematostella vectensis
2020Co-Authors: Magda Lewandowska, Yael HazanAbstract:The role of Viruses in forming a stable holobiont has been a subject of extensive research in the recent years. However, many emerging model organisms still lack any data on the composition of the associated viral communities. Here, we re-analyzed seven publicly available transcriptome datasets of the starlet sea anemone Nematostella vectensis, the most commonly used anthozoan lab model, and searched for viral sequences. We applied a straightforward, yet powerful approach of de novo assembly followed by homology-based Virus Identification and a multi-step, thorough taxonomic validation. The comparison of different lab populations of N. vectensis revealed the existence of the core virome composed of 21 viral sequences, present in all adult datasets. Unexpectedly, we observed almost complete lack of Viruses in the samples from the early developmental stages which together with the Identification of the Viruses shared with the major source of the food in the lab, the brine shrimp Artemia salina, shed new light on the course of viral species acquisition in N. vectensis. Our study provides an initial, yet comprehensive insight into N. vectensis virome and sets the first foundation for functional studies of Viruses and antiviral systems in this lab model cnidarian.
Joseph L Derisi - One of the best experts on this subject based on the ideXlab platform.
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Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing
2016Co-Authors: Nathan L Yozwiak, Angel Balmaseda, Mark D. Stenglein, Eva Harris, Peter Skewes-cox, Joseph L DerisiAbstract:Dengue Virus is an emerging infectious agent that infects an estimated 50–100 million people annually worldwide, yet current diagnostic practices cannot detect an etiologic pathogen in,40 % of dengue-like illnesses. Metagenomic approaches to pathogen detection, such as viral microarrays and deep sequencing, are promising tools to address emerging and non-diagnosable disease challenges. In this study, we used the Virochip microarray and deep sequencing to characterize the spectrum of Viruses present in human sera from 123 Nicaraguan patients presenting with dengue-like symptoms but testing negative for dengue Virus. We utilized a barcoding strategy to simultaneously deep sequence multiple serum specimens, generating on average over 1 million reads per sample. We then implemented a stepwise bioinformatic filtering pipeline to remove the majority of human and low-quality sequences to improve the speed and accuracy of subsequent unbiased database searches. By deep sequencing, we were able to detect Virus sequence in 37% (45/123) of previously negative cases. These included 13 cases with Human HerpesVirus 6 sequences. Other samples contained sequences with similarity to sequences from Viruses in the Herpesviridae, Flaviviridae, Circoviridae, Anelloviridae, Asfarviridae, and Parvoviridae families. In some cases, the putative viral sequences were virtually identical to known Viruses
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Virus Identification in unknown tropical febrile illness cases using deep sequencing
PLOS Neglected Tropical Diseases, 2012Co-Authors: Nathan L Yozwiak, Peter Skewescox, Angel Balmaseda, Mark D. Stenglein, Eva Harris, Joseph L DerisiAbstract:Dengue Virus is an emerging infectious agent that infects an estimated 50–100 million people annually worldwide, yet current diagnostic practices cannot detect an etiologic pathogen in ∼40% of dengue-like illnesses. Metagenomic approaches to pathogen detection, such as viral microarrays and deep sequencing, are promising tools to address emerging and non-diagnosable disease challenges. In this study, we used the Virochip microarray and deep sequencing to characterize the spectrum of Viruses present in human sera from 123 Nicaraguan patients presenting with dengue-like symptoms but testing negative for dengue Virus. We utilized a barcoding strategy to simultaneously deep sequence multiple serum specimens, generating on average over 1 million reads per sample. We then implemented a stepwise bioinformatic filtering pipeline to remove the majority of human and low-quality sequences to improve the speed and accuracy of subsequent unbiased database searches. By deep sequencing, we were able to detect Virus sequence in 37% (45/123) of previously negative cases. These included 13 cases with Human HerpesVirus 6 sequences. Other samples contained sequences with similarity to sequences from Viruses in the Herpesviridae, Flaviviridae, Circoviridae, Anelloviridae, Asfarviridae, and Parvoviridae families. In some cases, the putative viral sequences were virtually identical to known Viruses, and in others they diverged, suggesting that they may derive from novel Viruses. These results demonstrate the utility of unbiased metagenomic approaches in the detection of known and divergent Viruses in the study of tropical febrile illness.
Mikhail Pooggin - One of the best experts on this subject based on the ideXlab platform.
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Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization
Frontiers in Microbiology, 2018Co-Authors: Mikhail PoogginAbstract:RNA interference (RNAi)-based antiviral defense generates small interfering RNAs that represent the entire genome sequences of both RNA and DNA Viruses as well as viroids and viral satellites. Therefore, deep sequencing and bioinformatics analysis of small RNA population (small RNA-ome) allows not only for universal Virus detection and genome reconstruction but also for complete virome reconstruction in mixed infections. Viral infections (like other stress factors) can also perturb the RNAi and gene silencing pathways regulating endogenous gene expression and repressing transposons and host genome-integrated endogenous viral elements which can potentially be released from the genome and contribute to disease. This review describes the application of small RNA-omics for Virus detection, virome reconstruction and antiviral defense characterization in cultivated and non-cultivated plants. Reviewing available evidence from a large and ever growing number of studies of naturally or experimentally infected hosts revealed that all families of land plant Viruses, their satellites and viroids spawn characteristic small RNAs which can be assembled into contigs of sufficient length for Virus, satellite or viroid Identification and for exhaustive reconstruction of complex viromes. Moreover, the small RNA size, polarity and hotspot profiles reflect virome interactions with the plant RNAi machinery and allow to distinguish between silent endogenous viral elements and their replicating episomal counterparts. Models for the biogenesis and functions of small interfering RNAs derived from all types of RNA and DNA Viruses, satellites and viroids as well as endogenous viral elements are presented and discussed.
