scholarly journals Updated Phylogeny of Chikungunya Virus Reveals Lineage-Specific RNA Architecture

2019 ◽  
Author(s):  
Adriano de Bernardi Schneider ◽  
Roman Ochsenreiter ◽  
Reilly Hostager ◽  
Ivo L. Hofacker ◽  
Daniel Janies ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Chikungunya Virus ◽  
Genetic Data ◽  
Untranslated Regions ◽  
Current Status ◽  
The Public ◽  
Coding Regions ◽  
Evolutionarily Conserved ◽  
The Family ◽  
Duplication Events

Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents, Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the current status of the CHIKV spread, updated analyses of the viral genetic data and metadata are needed. Here, we performed phylogenetic and comparative genomics screens of CHIKV genomes, taking advantage of the public availability of many recently sequenced isolates. Based on these new data and analyses, we derive a revised phylogeny from nucleotide sequences in coding regions. Using this phylogeny, we uncover the presence of several distinct lineages in Africa that were previously considered a single one. In parallel, we performed thermodynamic modeling of CHIKV untranslated regions (UTRs), which revealed evolutionarily conserved structured and unstructured RNA elements in the 3'UTR. We provide evidence for duplication events in recently emerged American isolates of the Asian CHIKV lineage and propose the existence of a flexible 3'UTR architecture among different CHIKV lineages.

scholarly journals Updated phylogeny of Chikungunya virus suggests lineage-specific RNA architecture

2019 ◽  
Author(s):  
Adriano de Bernardi Schneider ◽  
Roman Ochsenreiter ◽  
Reilly Hostager ◽  
Ivo L. Hofacker ◽  
Daniel Janies ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Chikungunya Virus ◽  
Genetic Data ◽  
Untranslated Regions ◽  
Current Status ◽  
The Public ◽  
Coding Regions ◽  
Evolutionarily Conserved ◽  
The Family ◽  
Duplication Events

AbstractChikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents, Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the current status of the CHIKV spread, updated analyses of the viral genetic data and metadata are needed. Here, we performed phylogenetic and comparative genomics screens of CHIKV genomes, taking advantage of the public availability of many recently sequenced isolates. Based on these new data and analyses, we derive a revised phylogeny from nucleotide sequences in coding regions. Using this phylogeny, we uncover the presence of several distinct lineages in Africa that were previously considered a single one. In parallel, we performed thermodynamic modeling of CHIKV untranslated regions (UTRs), which revealed evolutionarily conserved structured and unstructured RNA elements in the 3’UTR. We provide evidence for duplication events in recently emerged American isolates of the Asian CHIKV lineage and propose the existence of a flexible 3’UTR architecture among different CHIKV lineages.

scholarly journals Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture

Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 798 ◽  
Author(s):  
Adriano de Bernardi Schneider ◽  
Roman Ochsenreiter ◽  
Reilly Hostager ◽  
Ivo L. Hofacker ◽  
Daniel Janies ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Chikungunya Virus ◽  
Genetic Data ◽  
Untranslated Regions ◽  
Current Status ◽  
The Public ◽  
Coding Regions ◽  
Evolutionarily Conserved ◽  
The Family ◽  
Duplication Events

Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents: Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the current status of the CHIKV spread, updated analyses of the viral genetic data and metadata are needed. Here, we performed phylogenetic and comparative genomics screens of CHIKV genomes, taking advantage of the public availability of many recently sequenced isolates. Based on these new data and analyses, we derive a revised phylogeny from nucleotide sequences in coding regions. Using this phylogeny, we uncover the presence of several distinct lineages in Africa that were previously considered a single one. In parallel, we performed thermodynamic modeling of CHIKV untranslated regions (UTRs), which revealed evolutionarily conserved structured and unstructured RNA elements in the 3’UTR. We provide evidence for duplication events in recently emerged American isolates of the Asian CHIKV lineage and propose the existence of a flexible 3’UTR architecture among different CHIKV lineages.

scholarly journals Functional RNA Structures in the 3'UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses

2019 ◽  
Author(s):  
Roman Ochsenreiter ◽  
Ivo L. Hofacker ◽  
Michael T. Wolfinger
Keyword(s):  
Life Cycle ◽  
Comparative Genomics ◽  
In Silico ◽  
Wide Distribution ◽  
Viral Life Cycle ◽  
Untranslated Regions ◽  
Structural Elements ◽  
Rna Structures ◽  
Evolutionarily Conserved ◽  
To Come

Untranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3'UTR of tick-borne, insect-specific and no-known-vector flaviviruses in silico. Our data support the wide distribution of previously experimentally characterized exoribonuclease resistant RNAs xrRNAs within tick-borne and no-known-vector flaviviruses and provide evidence for the existence of a cascade of duplicated RNA structures within insect-specific flaviviruses. On a broader scale, our findings indicate that viral 3'UTRs represent a flexible scaffold for evolution to come up with novel xrRNAs

scholarly journals Functional RNA Structures in the 3’UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses

2019 ◽  
Author(s):  
Roman Ochsenreiter ◽  
Ivo L. Hofacker ◽  
Michael T. Wolfinger
Keyword(s):  
Life Cycle ◽  
Comparative Genomics ◽  
In Silico ◽  
Wide Distribution ◽  
Viral Life Cycle ◽  
Untranslated Regions ◽  
Structural Elements ◽  
Rna Structures ◽  
Evolutionarily Conserved ◽  
To Come

AbstractUntranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3’UTR of tick-borne, insect-specific and no-known-vector flavivirusesin silico. Our data support the wide distribution of previously experimentally characterized exoribonuclease resistant RNAs (xrRNAs) within tick-borne and no-known-vector flaviviruses and provide evidence for the existence of a cascade of duplicated RNA structures within insect-specific flaviviruses. On a broader scale, our findings indicate that viral 3’UTRs represent a flexible scaffold for evolution to come up with novel xrRNAs.

scholarly journals Two novel bornaviruses identified in colubrid and viperid snakes

2021 ◽  
Author(s):  
Florian Pfaff ◽  
Dennis Rubbenstroth
Keyword(s):  
Novel Species ◽  
Viral Proteins ◽  
Untranslated Regions ◽  
The Novel ◽  
Coding Regions ◽  
The Family ◽  
Novel Virus ◽  
Chamaeleo Calyptratus ◽  
Bothrops Atrox ◽  
Virus Genomes

AbstractWe present the complete genome sequences of Caribbean watersnake bornavirus (CWBV) and Mexican black-tailed rattlesnake bornavirus (MRBV), which we identified in archived raw transcriptomic read data of a Caribbean watersnake (Tretanorhinus variabilis) and a Mexican black-tailed rattlesnake (Crotalus molossus nigrescens), respectively. The genomes of CWBV and MRBV have a length of about 8,900 nucleotides and comprise the complete coding regions and the untranslated regions. The overall genomic makeup and predicted gene content is typical for members of the genus Orthobornavirus within the family Bornaviridae. Alternative splicing was detected for the L and M genes. Based on a phylogenetic analysis of all viral proteins, we consider both viruses to be members of a single novel species within the genus Orthobornavirus. Both viruses form a distinct outgroup to all currently known orthobornaviruses. Based on the novel virus genomes, we furthermore identified closely related endogenous bornavirus-like nucleoprotein sequences in transcriptomic data of veiled chameleons (Chamaeleo calyptratus) and a common lancehead (Bothrops atrox).

scholarly journals Functional RNA Structures in the 3′UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses

Viruses ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 298 ◽  
Author(s):  
Roman Ochsenreiter ◽  
Ivo Hofacker ◽  
Michael Wolfinger
Keyword(s):  
Life Cycle ◽  
Comparative Genomics ◽  
In Silico ◽  
Wide Distribution ◽  
Viral Life Cycle ◽  
Untranslated Regions ◽  
Structural Elements ◽  
Rna Structures ◽  
Evolutionarily Conserved ◽  
To Come

Untranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3 ′ UTR of tick-borne, insect-specific and no-known-vector flaviviruses in silico. Our data support the wide distribution of previously experimentally characterized exoribonuclease resistant RNAs (xrRNAs) within tick-borne and no-known-vector flaviviruses and provide evidence for the existence of a cascade of duplicated RNA structures within insect-specific flaviviruses. On a broader scale, our findings indicate that viral 3 ′ UTRs represent a flexible scaffold for evolution to come up with novel xrRNAs.

First records of bats (Mammalia: Chiroptera) from Muong Phang cultural and historical site, Dien Bien province, Northwestern Vietnam

2017 ◽  
Vol 39 (3) ◽  
pp. 296-302
Author(s):  
Dao Nhan Loi ◽  
Vu Dinh Thong
Keyword(s):  
Conservation Status ◽  
Forest Area ◽  
Sound Recordings ◽  
The Public ◽  
The Family ◽  
Biological Taxa

The internationally renowned Muong Phang Cultural and Historical Site is located in the Dien Bien Phu region, northwestern Vietnam, and has received special attention from the public because of its great biodiversity. This site has a large forest area and other habitats including lakes, streams, rivers and paddyfield. These habitats would be ideal homes for bats and other biological taxa. However, in general, the wildlife of the Muong Phang Cultural and Historical Site receives little attention from scientists and authorities. Between 2014 and 2016, we conducted  series of surveys for bats in Muong Phang. Bat capture and sound recordings were the main procedure to obtain materials and data necessary for the assessment of diversity and conservation status. The results of the surveys this time revealed that there are 19 species of bats belonging to 7 genera, 5 families in the study area. Of these, a Myotis sp. is different from all the previously recorded Myotis bats from Vietnam, and, a Rhinolophus sp. is different from every described species of the family Rhinolophidae. This paper provides the first records of bats from Muong Phang with remarks on their taxonomy and conservation status.   Citation: Dao Nhan Loi, Vu Dinh Thong, 2017. First records of bats (Mammalia: Chiroptera) from Muong Phang cultural and historical site, Dien Bien province, Northwestern Vietnam. Tap chi Sinh hoc, 39(3): 296-302. DOI: 10.15625/0866-7160/v39n3.10641. *Corresponding author: [email protected]. Received 29 August 2017, accepted 10 September 2017 

Current Status in the Design and Development of Agonists and Antagonists of Adenosine A3 Receptor as Potential Therapeutic Agents

2019 ◽  
Vol 25 (25) ◽  
pp. 2772-2787 ◽  
Author(s):  
Raghu P. Mailavaram ◽  
Omar H.A. Al-Attraqchi ◽  
Supratik Kar ◽  
Shinjita Ghosh
Keyword(s):  
Drug Target ◽  
Therapeutic Agents ◽  
G Protein Coupled Receptors ◽  
Current Status ◽  
Renal Diseases ◽  
Adenosine A3 Receptor ◽  
Drug Candidates ◽  
Novel Drugs ◽  
The Family ◽  
G Protein Coupled

Adenosine receptors (ARs) belongs to the family of G-protein coupled receptors (GPCR) that are responsible for the modulation of a wide variety of physiological functions. The ARs are also implicated in many diseases such as cancer, arthritis, cardiovascular and renal diseases. The adenosine A3 receptor (A3AR) has emerged as a potential drug target for the progress of new and effective therapeutic agents for the treatment of various pathological conditions. This receptor’s involvement in many diseases and its validity as a target has been established by many studies. Both agonists and antagonists of A3AR have been extensively investigated in the last decade with the goal of developing novel drugs for treating diseases related to immune disorders, inflammation, cancer, and others. In this review, we shall focus on the medicinal chemistry of A3AR ligands, exploring the diverse chemical classes that have been projected as future leading drug candidates. Also, the recent advances in the therapeuetic applications of A3AR ligands are highlighted.

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