The Experts below are selected from a list of 237 Experts worldwide ranked by ideXlab platform
Bong-kyun Park - One of the best experts on this subject based on the ideXlab platform.
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Identification of a novel single-stranded, Circular DNA virus from bovine stool.
Journal of General Virology, 2012Co-Authors: Hye Kwon Kim, Seongjun Park, Van Giap Nguyen, Daesub Song, Hyoung Joon Moon, Bo Kyu Kang, Bong-kyun ParkAbstract:We report the identification of a novel single-stranded, Circular DNA virus isolated from bovine stool. The virus, named bovine stool-associated Circular DNA virus (BoSCV), has a genome comprising 2600 bases of Circular ssDNA, with two putative ORFs encoding replicase and capsid proteins, arranged inversely. The stem–loop structure was located between the 3′ ends of the two putative ORFs, as in chimpanzee stool-associated Circular virus (ChimpSCV) and unlike other Circular DNA viruses, including members of the families Circoviridae, Nanoviridae and Geminiviridae. BoSCV was also genetically similar to ChimpSCV, with approximately 30 % identity in the replicase and capsid proteins. A phylogenetic analysis based on the replicase protein showed that BoSCV and ChimpSCV are in the same clade. A field survey using BoSCV-specific PCRs targeting ORF1 detected BoSCV and BoSCV-like sequences in bovine and porcine stool samples. BoSCV appears to belong to a new genus of Circular DNA viruses.
Michael L Wilson - One of the best experts on this subject based on the ideXlab platform.
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novel Circular DNA viruses in stool samples of wild living chimpanzees
Journal of General Virology, 2010Co-Authors: Olga Blinkova, Joseph Victoria, Brandon F Keele, Crickette M Sanz, Jeanbosco N Ndjango, Martine Peeters, Dominic A Travis, Elizabeth V Lonsdorf, Michael L Wilson, Anne E PuseyAbstract:Viral particles in stool samples from wild-living chimpanzees were analysed using random PCR amplification and sequencing. Sequences encoding proteins distantly related to the replicase protein of single-stranded Circular DNA viruses were identified. Inverse PCR was used to amplify and sequence multiple small Circular DNA viral genomes. The viral genomes were related in size and genome organization to vertebrate circoviruses and plant geminiviruses but with a different location for the stem–loop structure involved in rolling circle DNA replication. The replicase genes of these viruses were most closely related to those of the much smaller (∼1 kb) plant nanovirus Circular DNA chromosomes. Because the viruses have characteristics of both animal and plant viruses, we named them chimpanzee stool-associated Circular viruses (ChiSCV). Further metagenomic studies of animal samples will greatly increase our knowledge of viral diversity and evolution.
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Novel Circular DNA viruses in stool samples of wild-living chimpanzees.
The Journal of general virology, 2009Co-Authors: Olga Blinkova, Joseph Victoria, Brandon F Keele, Jeanbosco N Ndjango, Martine Peeters, Elizabeth V Lonsdorf, Crickette Sanz, Dominic Travis, Michael L WilsonAbstract:Viral particles in stool samples from wild-living chimpanzees were analysed using random PCR amplification and sequencing. Sequences encoding proteins distantly related to the replicase protein of single-stranded Circular DNA viruses were identified. Inverse PCR was used to amplify and sequence multiple small Circular DNA viral genomes. The viral genomes were related in size and genome organization to vertebrate circoviruses and plant geminiviruses but with a different location for the stem-loop structure involved in rolling circle DNA replication. The replicase genes of these viruses were most closely related to those of the much smaller (approximately 1 kb) plant nanovirus Circular DNA chromosomes. Because the viruses have characteristics of both animal and plant viruses, we named them chimpanzee stool-associated Circular viruses (ChiSCV). Further metagenomic studies of animal samples will greatly increase our knowledge of viral diversity and evolution.
Birgitte Regenberg - One of the best experts on this subject based on the ideXlab platform.
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replicative aging is associated with loss of genetic heterogeneity from extrachromosomal Circular DNA in saccharomyces cerevisiae
Nucleic Acids Research, 2020Co-Authors: Inigo Pradaluengo, Jonathan Houseley, Henrik Devitt Moller, Rasmus Amund Henriksen, Qian Gao, Camilla Eggert Larsen, Sefa Alizadeh, Lasse Maretty, Birgitte RegenbergAbstract:Circular DNA can arise from all parts of eukaryotic chromosomes. In yeast, Circular ribosomal DNA (rDNA) accumulates dramatically as cells age, however little is known about the accumulation of other chromosome-derived circles or the contribution of such circles to genetic variation in aged cells. We profiled Circular DNA in Saccharomyces cerevisiae populations sampled when young and after extensive aging. Young cells possessed highly diverse Circular DNA populations but 94% of the Circular DNA were lost after ∼15 divisions, whereas rDNA circles underwent massive accumulation to >95% of Circular DNA. Circles present in both young and old cells were characterized by replication origins including circles from unique regions of the genome and repetitive regions: rDNA and telomeric Y' regions. We further observed that circles can have flexible inheritance patterns: [HXT6/7circle] normally segregates to mother cells but in low glucose is present in up to 50% of cells, the majority of which must have inherited this circle from their mother. Interestingly, [HXT6/7circle] cells are eventually replaced by cells carrying stable chromosomal HXT6 HXT6/7 HXT7 amplifications, suggesting Circular DNAs are intermediates in chromosomal amplifications. In conclusion, the heterogeneity of Circular DNA offers flexibility in adaptation, but this heterogeneity is remarkably diminished with age.
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replicative aging is associated with loss of genetic heterogeneity from extrachromosomal Circular DNA in saccharomyces cerevisiae
bioRxiv, 2020Co-Authors: Inigo Pradaluengo, Jonathan Houseley, Henrik Devitt Moller, Rasmus Amund Henriksen, Qian Gao, Camilla Eggert Larsen, Sefa Alizadeh, Lasse Maretty, Birgitte RegenbergAbstract:Circular DNA of chromosomal origin form from all parts of eukaryotic genomes. In yeast, Circular rDNA accumulates as cells divide, contributing to replicative aging. However, little is known about how other chromosome-derived circles segregate and contribute to genetic variation as cells age. We identified Circular DNA across the genome of young S. cerevisiae populations and their aged descendants. Young cells had highly diverse Circular DNA populations, but lost 94% of the different Circular DNA after 20 divisions. Circles present in both young and old cells were characterized by replication origins and included circles from unique regions of the genome, rDNA circles and telomeric Y9 circles. The loss in genetic heterogeneity in aged cells was accompanied by massive accumulation of rDNA circles >95% of all Circular DNA. We discovered circles had flexible inherence patterns. Glucose limited conditions selected for cells with glucose-transporter gene circles, [HXT6/7circle], and up to 50% of cells in a population carried them. [HXT6/7circle] cells were eventually substituted by cells carrying stable chromosomal HXT6 HXT6/7 HXT7 amplifications, suggesting Circular DNA were intermediates in chromosomal amplifications. In conclusion, DNA circles can offer a flexible adaptive solution but cells lose genetic heterogeneity from Circular DNA as they undergo replicative aging.
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genome wide purification of extrachromosomal Circular DNA from eukaryotic cells
Journal of Visualized Experiments, 2016Co-Authors: Henrik Devitt Moller, Rasmus Bojsen, Chris Tachibana, Lance Parsons, David Botstein, Birgitte RegenbergAbstract:Extrachromosomal Circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are reported in other eukaryotes as well. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to evolution of unicellular eukaryotes. Sensitive methods for detecting eccDNA are needed to clarify how these elements affect genome stability and how environmental and biological factors induce their formation in eukaryotic cells. This video presents a sensitive eccDNA-purification method called Circle-Seq. The method encompasses column purification of Circular DNA, removal of remaining linear chromosomal DNA, rolling-circle amplification of eccDNA, deep sequencing, and mapping. Extensive exonuclease treatment was required for sufficient linear chromosomal DNA degradation. The rolling-circle amplification step by φ29 polymerase enriched for Circular DNA over linear DNA. Validation of the Circle-Seq method on three S. cerevisiae CEN.PK populations of 1010 cells detected hundreds of eccDNA profiles in sizes larger than 1 kilobase. Repeated findings of ASP3-1, COS111, CUP1, RSC30, HXT6, HXT7 genes on Circular DNA in both S288c and CEN.PK suggests that DNA Circularization is conserved between strains at these loci. In sum, the Circle-Seq method has broad applicability for genome-scale screening for eccDNA in eukaryotes as well as for detecting specific eccDNA types.
Jonathan Houseley - One of the best experts on this subject based on the ideXlab platform.
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replicative aging is associated with loss of genetic heterogeneity from extrachromosomal Circular DNA in saccharomyces cerevisiae
Nucleic Acids Research, 2020Co-Authors: Inigo Pradaluengo, Jonathan Houseley, Henrik Devitt Moller, Rasmus Amund Henriksen, Qian Gao, Camilla Eggert Larsen, Sefa Alizadeh, Lasse Maretty, Birgitte RegenbergAbstract:Circular DNA can arise from all parts of eukaryotic chromosomes. In yeast, Circular ribosomal DNA (rDNA) accumulates dramatically as cells age, however little is known about the accumulation of other chromosome-derived circles or the contribution of such circles to genetic variation in aged cells. We profiled Circular DNA in Saccharomyces cerevisiae populations sampled when young and after extensive aging. Young cells possessed highly diverse Circular DNA populations but 94% of the Circular DNA were lost after ∼15 divisions, whereas rDNA circles underwent massive accumulation to >95% of Circular DNA. Circles present in both young and old cells were characterized by replication origins including circles from unique regions of the genome and repetitive regions: rDNA and telomeric Y' regions. We further observed that circles can have flexible inheritance patterns: [HXT6/7circle] normally segregates to mother cells but in low glucose is present in up to 50% of cells, the majority of which must have inherited this circle from their mother. Interestingly, [HXT6/7circle] cells are eventually replaced by cells carrying stable chromosomal HXT6 HXT6/7 HXT7 amplifications, suggesting Circular DNAs are intermediates in chromosomal amplifications. In conclusion, the heterogeneity of Circular DNA offers flexibility in adaptation, but this heterogeneity is remarkably diminished with age.
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The adaptive potential of Circular DNA accumulation in ageing cells
Current Genetics, 2020Co-Authors: Ryan M. Hull, Jonathan HouseleyAbstract:Carefully maintained and precisely inherited chromosomal DNA provides long-term genetic stability, but eukaryotic cells facing environmental challenges can benefit from the accumulation of less stable DNA species. Circular DNA molecules lacking centromeres segregate randomly or asymmetrically during cell division, following non-Mendelian inheritance patterns that result in high copy number instability and massive heterogeneity across populations. Such Circular DNA species, variously known as extrachromosomal Circular DNA (eccDNA), microDNA, double minutes or extrachromosomal DNA (ecDNA), are becoming recognised as a major source of the genetic variation exploited by cancer cells and pathogenic eukaryotes to acquire drug resistance. In budding yeast, Circular DNA molecules derived from the ribosomal DNA (ERCs) have been long known to accumulate with age, but it is now clear that aged yeast also accumulate other high-copy protein-coding Circular DNAs acquired through both random and environmentally-stimulated recombination processes. Here, we argue that accumulation of Circular DNA provides a reservoir of heterogeneous genetic material that can allow rapid adaptation of aged cells to environmental insults, but avoids the negative fitness impacts on normal growth of unsolicited gene amplification in the young population.
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replicative aging is associated with loss of genetic heterogeneity from extrachromosomal Circular DNA in saccharomyces cerevisiae
bioRxiv, 2020Co-Authors: Inigo Pradaluengo, Jonathan Houseley, Henrik Devitt Moller, Rasmus Amund Henriksen, Qian Gao, Camilla Eggert Larsen, Sefa Alizadeh, Lasse Maretty, Birgitte RegenbergAbstract:Circular DNA of chromosomal origin form from all parts of eukaryotic genomes. In yeast, Circular rDNA accumulates as cells divide, contributing to replicative aging. However, little is known about how other chromosome-derived circles segregate and contribute to genetic variation as cells age. We identified Circular DNA across the genome of young S. cerevisiae populations and their aged descendants. Young cells had highly diverse Circular DNA populations, but lost 94% of the different Circular DNA after 20 divisions. Circles present in both young and old cells were characterized by replication origins and included circles from unique regions of the genome, rDNA circles and telomeric Y9 circles. The loss in genetic heterogeneity in aged cells was accompanied by massive accumulation of rDNA circles >95% of all Circular DNA. We discovered circles had flexible inherence patterns. Glucose limited conditions selected for cells with glucose-transporter gene circles, [HXT6/7circle], and up to 50% of cells in a population carried them. [HXT6/7circle] cells were eventually substituted by cells carrying stable chromosomal HXT6 HXT6/7 HXT7 amplifications, suggesting Circular DNA were intermediates in chromosomal amplifications. In conclusion, DNA circles can offer a flexible adaptive solution but cells lose genetic heterogeneity from Circular DNA as they undergo replicative aging.
Olga Blinkova - One of the best experts on this subject based on the ideXlab platform.
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novel Circular DNA viruses in stool samples of wild living chimpanzees
Journal of General Virology, 2010Co-Authors: Olga Blinkova, Joseph Victoria, Brandon F Keele, Crickette M Sanz, Jeanbosco N Ndjango, Martine Peeters, Dominic A Travis, Elizabeth V Lonsdorf, Michael L Wilson, Anne E PuseyAbstract:Viral particles in stool samples from wild-living chimpanzees were analysed using random PCR amplification and sequencing. Sequences encoding proteins distantly related to the replicase protein of single-stranded Circular DNA viruses were identified. Inverse PCR was used to amplify and sequence multiple small Circular DNA viral genomes. The viral genomes were related in size and genome organization to vertebrate circoviruses and plant geminiviruses but with a different location for the stem–loop structure involved in rolling circle DNA replication. The replicase genes of these viruses were most closely related to those of the much smaller (∼1 kb) plant nanovirus Circular DNA chromosomes. Because the viruses have characteristics of both animal and plant viruses, we named them chimpanzee stool-associated Circular viruses (ChiSCV). Further metagenomic studies of animal samples will greatly increase our knowledge of viral diversity and evolution.
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Novel Circular DNA viruses in stool samples of wild-living chimpanzees.
The Journal of general virology, 2009Co-Authors: Olga Blinkova, Joseph Victoria, Brandon F Keele, Jeanbosco N Ndjango, Martine Peeters, Elizabeth V Lonsdorf, Crickette Sanz, Dominic Travis, Michael L WilsonAbstract:Viral particles in stool samples from wild-living chimpanzees were analysed using random PCR amplification and sequencing. Sequences encoding proteins distantly related to the replicase protein of single-stranded Circular DNA viruses were identified. Inverse PCR was used to amplify and sequence multiple small Circular DNA viral genomes. The viral genomes were related in size and genome organization to vertebrate circoviruses and plant geminiviruses but with a different location for the stem-loop structure involved in rolling circle DNA replication. The replicase genes of these viruses were most closely related to those of the much smaller (approximately 1 kb) plant nanovirus Circular DNA chromosomes. Because the viruses have characteristics of both animal and plant viruses, we named them chimpanzee stool-associated Circular viruses (ChiSCV). Further metagenomic studies of animal samples will greatly increase our knowledge of viral diversity and evolution.