scholarly journals An Ancient Lineage of Highly Divergent Parvoviruses Infects both Vertebrate and Invertebrate Hosts

Viruses ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 525 ◽  
Author(s):  
Judit J. Pénzes ◽  
William Marciel de Souza ◽  
Mavis Agbandje-McKenna ◽  
Robert J. Gifford
Keyword(s):  
Host Species ◽  
Laboratory Mice ◽  
The Past ◽  
Protein Encoding ◽  
Luminal Side ◽  
Ancient Lineage ◽  
Characteristic Features ◽  
Host Affiliation ◽  
Encoding Genes ◽  
In Silico Analyses

Chapparvoviruses (ChPVs) comprise a divergent, recently identified group of parvoviruses (family Parvoviridae), associated with nephropathy in immunocompromised laboratory mice and with prevalence in deep sequencing results of livestock showing diarrhea. Here, we investigate the biological and evolutionary characteristics of ChPVs via comparative in silico analyses, incorporating sequences derived from endogenous parvoviral elements (EPVs) as well as exogenous parvoviruses. We show that ChPVs are an ancient lineage within the Parvoviridae, clustering separately from members of both currently established subfamilies. Consistent with this, they exhibit a number of characteristic features, including several putative auxiliary protein-encoding genes, and capsid proteins with no sequence-level homology to those of other parvoviruses. Homology modeling indicates the absence of a β-A strand, normally part of the luminal side of the parvoviral capsid protein core. Our findings demonstrate that the ChPV lineage infects an exceptionally broad range of host species, including both vertebrates and invertebrates. Furthermore, we observe that ChPVs found in fish are more closely related to those from invertebrates than they are to those of amniote vertebrates. This suggests that transmission between distantly related host species may have occurred in the past and that the Parvoviridae family can no longer be divided based on host affiliation.

scholarly journals An ancient lineage of highly divergent parvoviruses infects both vertebrate and invertebrate hosts

2019 ◽  
Author(s):  
Judit J Pénzes ◽  
William Marciel de Souza ◽  
Mavis Agbandje-McKenna ◽  
Robert J. Gifford
Keyword(s):  
Host Species ◽  
Sequence Data ◽  
Structural Features ◽  
Laboratory Mice ◽  
Protein Encoding ◽  
Luminal Side ◽  
Ancient Lineage ◽  
Characteristic Features ◽  
Endogenous Viral Elements ◽  
Encoding Genes

ABSTRACTChapparvoviruses are a highly divergent group of parvoviruses (familyParvoviridae) first identified in 2013. Interest in these poorly characterized viruses has been raised by recent studies indicating that they are the cause of chronic kidney disease that arises spontaneously in laboratory mice. In this study, we investigate the biological and evolutionary characteristics of chapparvoviruses via comparative analysis of genome sequence data. Our analysis, which incorporates sequences derived from endogenous viral elements (EVEs) as well as exogenous viruses, reveals that chapparvoviruses are an ancient lineage within the familyParvoviridae, clustering separately from members of both currently established parvoviral subfamilies. Consistent with this, they exhibit a number of characteristic genomic and structural features, i.e. a large number of putative auxiliary protein-encoding genes, capsid protein genes non-homologous to any hitherto parvoviralcap, as well as a putative capsid structure lacking the canonical fifth strand of the ABIDG sheet comprising the luminal side of the jelly roll. Our findings demonstrate that the chapparvovirus lineage infects an exceptionally broad range of host species, including both vertebrates and invertebrates. Furthermore, we observe that chapparvoviruses found in fish are more closely related to those from invertebrates than they are to those that infect amniote vertebrates. This suggests that transmission between distantly related host species may have occurred in the past. Our study provides the first integrated overview of the chapparvovirus group, and revises current views of parvovirus evolutionAUTHOR SUMMARYChapparvoviruses are a recently identified group of viruses about which relatively little is known. However, recent studies have shown that these viruses cause disease in laboratory mice and are prevalent in the fecal virome of pigs and poultry, raising interest in their potential impact as pathogens, and utility as experimental tools. We examined the genomes of chapparvoviruses and endogenous viral elements (‘fossilized’ virus sequences derived from ancestral viruses) using a variety of bioinformatics-based approaches. We show that the chapparvoviruses have an ancient origin and are evolutionarily distinct from all other related viruses. Accordingly, their genomes and virions exhibit a range of distinct characteristic features. We examine the distribution of these features in the light of chapparvovirus evolutionary history (which we can also infer from genomic data), revealing new insights into chapparvovirus biology.

Cancer genomes and their implications for understanding and managing cancer

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. s1a-s1a
Author(s):  
Bert Vogelstein
Keyword(s):  
Cell Death ◽  
Human Genome ◽  
Genetic Disease ◽  
Basic Science ◽  
Genetic Information ◽  
Genetic Alterations ◽  
The Past ◽  
Protein Encoding ◽  
Cancer Genomes ◽  
Encoding Genes

s1a Research over the past 25 years has shown that cancer is, in essence, a genetic disease. In the past three years, it has become possible to determine the sequence of nearly all the 21,000 protein-encoding genes in the human genome. The results of such sequencing in 68 tumors of the breast, colon, pancreas, or brain have led to new insights about the nature and diversity of the genetic alterations responsible for initiation and progression of tumors. The pathogenesis of solid tumors can best be understood as the cumulative result of alterations in approximately a dozen pathways that each regulate the balance between cell birth and cell death. The challenge for basic science is to understand these pathways in more detail. The challenge for clinical science is to devise approaches to use this new and extensive genetic information to improve diagnosis and therapy. Examples of how these challenges might be achieved in the future will be presented.

scholarly journals Genetic manipulation of schistosomes – progress with integration competent vectors

Parasitology ◽  
2011 ◽  
Vol 139 (5) ◽  
pp. 641-650 ◽  
Author(s):  
SUTAS SUTTIPRAPA ◽  
GABRIEL RINALDI ◽  
PAUL J. BRINDLEY
Keyword(s):  
Schistosoma Japonicum ◽  
Genetic Manipulation ◽  
Draft Genome ◽  
Molecular Tools ◽  
Genome Sequences ◽  
The Past ◽  
New Genes ◽  
Protein Encoding ◽  
History Of ◽  
Encoding Genes

SUMMARYDraft genome sequences forSchistosoma japonicumandS. mansoniare now available. The schistosome genome encodes ∼13 000 protein-encoding genes for which the functions of few are well understood. Nonetheless, the new genes represent potential intervention targets, and molecular tools are being developed to determine their importance. Over the past 15 years, noteworthy progress has been achieved towards development of tools for gene manipulation and transgenesis of schistosomes. A brief history of genetic manipulation is presented, along with a review of the field with emphasis on reports of integration of transgenes into schistosome chromosomes.

scholarly journals What’s all the phos about? Insights into the phosphorylation state of the RNA polymerase II C-terminal domain via mass spectrometry

2021 ◽  
Author(s):  
Blase Matthew LeBlanc ◽  
Rosamaria Yvette Moreno ◽  
Edwin Escobar ◽  
Mukesh Kumar Venkat Ramani ◽  
Jennifer S Brodbelt ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Phosphorylation State ◽  
Terminal Domain ◽  
Carboxy Terminal Domain ◽  
Protein Encoding ◽  
Small Nuclear Rnas ◽  
Rnap Ii ◽  
Carboxy Terminal ◽  
Encoding Genes

RNA polymerase II (RNAP II) is one of the primary enzymes responsible for expressing protein-encoding genes and some small nuclear RNAs. The enigmatic carboxy-terminal domain (CTD) of RNAP II and...

scholarly journals Autotransporter Protein-Encoding Genes of Diarrheagenic Escherichia coli Are Found in both Typical and Atypical Enteropathogenic E. coli Strains

2012 ◽  
Vol 79 (1) ◽  
pp. 411-414 ◽  
Author(s):  
Afonso G. Abreu ◽  
Vanessa Bueris ◽  
Tatiane M. Porangaba ◽  
Marcelo P. Sircili ◽  
Fernando Navarro-Garcia ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Content Type ◽  
E Coli ◽  
Diarrheagenic Escherichia Coli ◽  
Virulence Markers ◽  
Protein Encoding ◽  
Encoding Genes ◽  
Specific Virulence

ABSTRACTAutotransporter (AT) protein-encoding genes of diarrheagenicEscherichia coli(DEC) pathotypes (cah,eatA,ehaABCDJ,espC,espI,espP,pet,pic,sat, andtibA) were detected in typical and atypical enteropathogenicE. coli(EPEC) in frequencies between 0.8% and 39.3%. Although these ATs have been described in particular DEC pathotypes, their presence in EPEC indicates that they should not be considered specific virulence markers.

scholarly journals Draft Genome Sequence of the Axenic Strain Phormidesmispriestleyi ULC007, a Cyanobacterium Isolated from Lake Bruehwiler (Larsemann Hills, Antarctica)

2017 ◽  
Vol 5 (7) ◽  
Author(s):  
Yannick Lara ◽  
Benoit Durieu ◽  
Luc Cornet ◽  
Olivier Verlaine ◽  
Rosmarie Rippka ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Axenic Strain ◽  
Larsemann Hills ◽  
Freshwater Cyanobacterium ◽  
Protein Encoding ◽  
Encoding Genes

ABSTRACT Phormidesmis priestleyi ULC007 is an Antarctic freshwater cyanobacterium. Its draft genome is 5,684,389 bp long. It contains a total of 5,604 protein-encoding genes, of which 22.2% have no clear homologues in known genomes. To date, this draft genome is the first one ever determined for an axenic cyanobacterium from Antarctica.

Prion Protein-Encoding Genes

Prion Biology ◽  
2013 ◽  
Author(s):  
Sead Chadi ◽  
Rachel Young ◽  
Sandrine Guillou ◽  
Gaelle Tilly ◽  
Frédérique Bitton ◽  
...  
Keyword(s):  
Prion Protein ◽  
Protein Encoding ◽  
Encoding Genes

scholarly journals The microRNA, miR-133b, functions to slow Duchenne muscular dystrophy pathogenesis

2020 ◽  
Author(s):  
Thomas Taetzsch ◽  
Dillon Shapiro ◽  
Randa Eldosougi ◽  
Tracey Myers ◽  
Robert Settlage ◽  
...  
Keyword(s):  
Duchenne Muscular Dystrophy ◽  
Muscular Dystrophy ◽  
Skeletal Muscles ◽  
Tibialis Anterior Muscle ◽  
Muscle Fibers ◽  
Progressive Degeneration ◽  
Protein Encoding ◽  
Small Muscle ◽  
Encoding Genes

AbstractDuchenne muscular dystrophy (DMD) is characterized by progressive degeneration of skeletal muscles. To date, there are no treatments available to slow or prevent the disease. Hence, it remains essential to identify molecular factors that promote muscle biogenesis since they could serve as therapeutic targets for treating DMD. While the muscle enriched microRNA, miR-133b, has been implicated in the biogenesis of muscle fibers, its role in DMD remains unknown. To assess the role of miR-133b in DMD-affected skeletal muscles, we genetically ablated miR-133b in the mdx mouse model of DMD. In the absence of miR-133b, the tibialis anterior muscle of juvenile and adult mdx mice is populated by small muscle fibers with centralized nuclei, exhibits increased fibrosis, and thickened interstitial space. Additional analysis revealed that loss of miR-133b exacerbates DMD-pathogenesis partly by altering the number of satellite cells and levels of protein-encoding genes, including previously identified miR-133b targets as well as genes involved in cell proliferation and fibrosis. Altogether, our data demonstrate that skeletal muscles utilize miR-133b to mitigate the deleterious effects of DMD.

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