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Article ; Online: Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts.

Matyášek, Roman / Kovařík, Aleš

2020 Volume 11, Issue 7

Abstract: The pandemic caused by the spread of SARS-CoV-2 has led to considerable interest in its evolutionary origin and genome structure. Here, we analyzed mutation patterns in 34 human SARS-CoV-2 isolates and a closely related RaTG13 isolated ... ...

Abstract	The pandemic caused by the spread of SARS-CoV-2 has led to considerable interest in its evolutionary origin and genome structure. Here, we analyzed mutation patterns in 34 human SARS-CoV-2 isolates and a closely related RaTG13 isolated from
MeSH term(s)	Animals ; Base Sequence ; Betacoronavirus/classification ; Betacoronavirus/genetics ; Betacoronavirus/isolation & purification ; Chiroptera/virology ; CpG Islands ; Cytosine/metabolism ; Evolution, Molecular ; Humans ; Phylogeny ; Polymorphism, Single Nucleotide ; Severe acute respiratory syndrome-related coronavirus/classification ; Severe acute respiratory syndrome-related coronavirus/genetics ; Severe acute respiratory syndrome-related coronavirus/isolation & purification ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics ; Uracil/metabolism
Chemical Substances	Spike Glycoprotein, Coronavirus ; Uracil (56HH86ZVCT) ; Cytosine (8J337D1HZY)
Keywords	covid19
Language	English
Publishing date	2020-07-07
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes11070761
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts

Roman Matyášek / Aleš Kovařík

Genes, Vol 11, Iss 761, p

2020 Volume 761

Abstract	The pandemic caused by the spread of SARS-CoV-2 has led to considerable interest in its evolutionary origin and genome structure. Here, we analyzed mutation patterns in 34 human SARS-CoV-2 isolates and a closely related RaTG13 isolated from Rhinolophus affinis (a horseshoe bat). We also evaluated the CpG dinucleotide contents in SARS-CoV-2 and other human and animal coronavirus genomes. Out of 1136 single nucleotide variations (~4% divergence) between human SARS-CoV-2 and bat RaTG13, 682 (60%) can be attributed to C>U and U>C substitutions, far exceeding other types of substitutions. An accumulation of C>U mutations was also observed in SARS-CoV2 variants that arose within the human population. Globally, the C>U substitutions increased the frequency of codons for hydrophobic amino acids in SARS-CoV-2 peptides, while U>C substitutions decreased it. In contrast to most other coronaviruses, both SARS-CoV-2 and RaTG13 exhibited CpG depletion in their genomes. The data suggest that C-to-U conversion mediated by C deamination played a significant role in the evolution of the SARS-CoV-2 coronavirus. We hypothesize that the high frequency C>U transitions reflect virus adaptation processes in their hosts, and that SARS-CoV-2 could have been evolving for a relatively long period in humans following the transfer from animals before spreading worldwide.
Keywords	evolution ; cytosine deamination ; CpG depletion ; coronavirus ; SARS-CoV-2 ; mutation bias ; Genetics ; QH426-470 ; covid19
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Analyses of the Updated "Animal rDNA Loci Database" with an Emphasis on Its New Features.

Sochorová, Jana / Gálvez, Francisco / Matyášek, Roman / Garcia, Sònia / Kovařík, Aleš

International journal of molecular sciences

2021 Volume 22, Issue 21

Abstract: We report on a major update to the animal rDNA loci database, which now contains cytogenetic information for 45S and 5S rDNA loci in more than 2600 and 1000 species, respectively.The data analyses show the following: (i) A high variability in 5S and 45S ... ...

Abstract	We report on a major update to the animal rDNA loci database, which now contains cytogenetic information for 45S and 5S rDNA loci in more than 2600 and 1000 species, respectively.The data analyses show the following: (i) A high variability in 5S and 45S loci numbers, with both showing 50-fold or higher variability. However, karyotypes with an extremely high number of loci were rare, and medians generally converged to two 5S sites and two 45S rDNA sites per diploid genome. No relationship was observed between the number of 5S and 45S loci. (ii) The position of 45S rDNA on sex chromosomes was relatively frequent in some groups, particularly in arthropods (14% of karyotypes). Furthermore, 45S rDNA was almost exclusively located in microchromosomes when these were present (in birds and reptiles). (iii) The proportion of active NORs (positively stained with silver staining methods) progressively decreased with an increasing number of 45S rDNA loci, and karyotypes with more than 12 loci showed, on average, less than 40% of active loci. In conclusion, the updated version of the database provides some new insights into the organization of rRNA genes in chromosomes. We expect that its updated content will be useful for taxonomists, comparative cytogeneticists, and evolutionary biologists. .
MeSH term(s)	Animals ; DNA, Ribosomal/genetics ; Databases, Genetic ; Evolution, Molecular ; Karyotype ; Karyotyping ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 5S/genetics ; Species Specificity
Chemical Substances	DNA, Ribosomal ; RNA, Ribosomal ; RNA, Ribosomal, 5S ; RNA, ribosomal, 45S
Language	English
Publishing date	2021-10-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms222111403
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Article ; Online: Mutational Asymmetries in the SARS-CoV-2 Genome May Lead to Increased Hydrophobicity of Virus Proteins.

Matyášek, Roman / Řehůřková, Kateřina / Berta Marošiová, Kristýna / Kovařík, Aleš

Genes

2021 Volume 12, Issue 6

Abstract: The genomic diversity of SARS-CoV-2 has been a focus during the ongoing COVID-19 pandemic. Here, we analyzed the distribution and character of emerging mutations in a data set comprising more than 95,000 virus genomes covering eight major SARS-CoV-2 ... ...

Abstract	The genomic diversity of SARS-CoV-2 has been a focus during the ongoing COVID-19 pandemic. Here, we analyzed the distribution and character of emerging mutations in a data set comprising more than 95,000 virus genomes covering eight major SARS-CoV-2 lineages in the GISAID database, including genotypes arising during COVID-19 therapy. Globally, the C>U transitions and G>U transversions were the most represented mutations, accounting for the majority of single-nucleotide variations. Mutational spectra were not influenced by the time the virus had been circulating in its host or medical treatment. At the amino acid level, we observed about a 2-fold excess of substitutions in favor of hydrophobic amino acids over the reverse. However, most mutations constituting variants of interests of the S-protein (spike) lead to hydrophilic amino acids, counteracting the global trend. The C>U and G>U substitutions altered codons towards increased amino acid hydrophobicity values in more than 80% of cases. The bias is explained by the existing differences in the codon composition for amino acids bearing contrasting biochemical properties. Mutation asymmetries apparently influence the biochemical features of SARS CoV-2 proteins, which may impact protein-protein interactions, fusion of viral and cellular membranes, and virion assembly.
MeSH term(s)	APOBEC Deaminases ; Alleles ; Amino Acid Substitution ; Amino Acids/chemistry ; Amino Acids/genetics ; COVID-19/virology ; Evolution, Molecular ; Genetic Variation ; Genome, Viral ; Genotype ; Host-Pathogen Interactions ; Humans ; Hydrophobic and Hydrophilic Interactions ; Mutation ; Phylogeny ; Polymorphism, Single Nucleotide ; Protein Binding ; Protein Interaction Domains and Motifs ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Viral Proteins/chemistry ; Viral Proteins/genetics
Chemical Substances	Amino Acids ; Spike Glycoprotein, Coronavirus ; Viral Proteins ; APOBEC Deaminases (EC 3.5.4.5)
Language	English
Publishing date	2021-05-27
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12060826
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Article ; Online: Crystallization as a selection force at the polymerization of nucleotides in a prebiotic context.

Šponer, Judit E / Šponer, Jiří / Výravský, Jakub / Matyášek, Roman / Kovařík, Aleš / Dudziak, Wojciech / Ślepokura, Katarzyna

iScience

2023 Volume 26, Issue 9, Page(s) 107600

Abstract: Accumulation and selection of nucleotides is one of the most challenging problems surrounding the origin of the first RNA molecules on our planet. In the current work we propose that guanosine 3',5' cyclic monophosphate could selectively crystallize upon ...

Abstract	Accumulation and selection of nucleotides is one of the most challenging problems surrounding the origin of the first RNA molecules on our planet. In the current work we propose that guanosine 3',5' cyclic monophosphate could selectively crystallize upon evaporation of an acidic prebiotic pool containing various other nucleotides. The conditions of the evaporative crystallization are fully compatible with the subsequent acid catalyzed polymerization of this cyclic nucleotide reported in earlier studies and may be relevant in a broad range of possible prebiotic environments. Albeit cytidine 3',5' cyclic monophosphate has the ability to selectively accumulate under the same conditions, its crystal structure is not likely to support polymer formation.
Language	English
Publishing date	2023-08-09
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.107600
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts

Matyásek, Roman / Kovarík, Ales

Abstract	The pandemic caused by the spread of SARS-CoV-2 has led to considerable interest in its evolutionary origin and genome structure. Here, we analyzed mutation patterns in 34 human SARS-CoV-2 isolates and a closely related RaTG13 isolated from Rhinolophus affinis (a horseshoe bat). We also evaluated the CpG dinucleotide contents in SARS-CoV-2 and other human and animal coronavirus genomes. Out of 1136 single nucleotide variations (~4% divergence) between human SARS-CoV-2 and bat RaTG13, 682 (60%) can be attributed to C>U and U>C substitutions, far exceeding other types of substitutions. An accumulation of C>U mutations was also observed in SARS-CoV2 variants that arose within the human population. Globally, the C>U substitutions increased the frequency of codons for hydrophobic amino acids in SARS-CoV-2 peptides, while U>C substitutions decreased it. In contrast to most other coronaviruses, both SARS-CoV-2 and RaTG13 exhibited CpG depletion in their genomes. The data suggest that C-to-U conversion mediated by C deamination played a significant role in the evolution of the SARS-CoV-2 coronavirus. We hypothesize that the high frequency C>U transitions reflect virus adaptation processes in their hosts, and that SARS-CoV-2 could have been evolving for a relatively long period in humans following the transfer from animals before spreading worldwide.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #639723
Database	COVID19

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Article: Mutational Asymmetries in the SARS-CoV-2 Genome May Lead to Increased Hydrophobicity of Virus Proteins

Matyášek, Roman / Řehůřková, Kateřina / Berta Marošiová, Kristýna / Kovařík, Aleš

Genes. 2021 May 27, v. 12, no. 6

2021

Abstract	The genomic diversity of SARS-CoV-2 has been a focus during the ongoing COVID-19 pandemic. Here, we analyzed the distribution and character of emerging mutations in a data set comprising more than 95,000 virus genomes covering eight major SARS-CoV-2 lineages in the GISAID database, including genotypes arising during COVID-19 therapy. Globally, the C>U transitions and G>U transversions were the most represented mutations, accounting for the majority of single-nucleotide variations. Mutational spectra were not influenced by the time the virus had been circulating in its host or medical treatment. At the amino acid level, we observed about a 2-fold excess of substitutions in favor of hydrophobic amino acids over the reverse. However, most mutations constituting variants of interests of the S-protein (spike) lead to hydrophilic amino acids, counteracting the global trend. The C>U and G>U substitutions altered codons towards increased amino acid hydrophobicity values in more than 80% of cases. The bias is explained by the existing differences in the codon composition for amino acids bearing contrasting biochemical properties. Mutation asymmetries apparently influence the biochemical features of SARS CoV-2 proteins, which may impact protein–protein interactions, fusion of viral and cellular membranes, and virion assembly.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; amino acids ; codons ; data collection ; databases ; genetic variation ; hydrophilicity ; hydrophobicity ; medical treatment ; mutation ; virion ; viruses
Language	English
Dates of publication	2021-0527
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12060826
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Analyses of the Updated “Animal rDNA Loci Database” with an Emphasis on Its New Features

Jana Sochorová / Francisco Gálvez / Roman Matyášek / Sònia Garcia / Aleš Kovařík

International Journal of Molecular Sciences, Vol 22, Iss 11403, p

2021 Volume 11403

Abstract: We report on a major update to the animal rDNA loci database, which now contains cytogenetic information for 45S and 5S rDNA loci in more than 2600 and 1000 species, respectively. The data analyses show the following: (i) A high variability in 5S and 45S ...

Abstract	We report on a major update to the animal rDNA loci database, which now contains cytogenetic information for 45S and 5S rDNA loci in more than 2600 and 1000 species, respectively. The data analyses show the following: (i) A high variability in 5S and 45S loci numbers, with both showing 50-fold or higher variability. However, karyotypes with an extremely high number of loci were rare, and medians generally converged to two 5S sites and two 45S rDNA sites per diploid genome. No relationship was observed between the number of 5S and 45S loci. (ii) The position of 45S rDNA on sex chromosomes was relatively frequent in some groups, particularly in arthropods (14% of karyotypes). Furthermore, 45S rDNA was almost exclusively located in microchromosomes when these were present (in birds and reptiles). (iii) The proportion of active NORs (positively stained with silver staining methods) progressively decreased with an increasing number of 45S rDNA loci, and karyotypes with more than 12 loci showed, on average, less than 40% of active loci. In conclusion, the updated version of the database provides some new insights into the organization of rRNA genes in chromosomes. We expect that its updated content will be useful for taxonomists, comparative cytogeneticists, and evolutionary biologists.
Keywords	ribosomal DNA ; rDNA ; rRNA genes ; nucleolar organizer regions ; karyotype ; sex chromosome ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	590
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The origin of exon 3 skipping of paternal GLOBOSA pre-mRNA in some Nicotiana tabacum lines correlates with a point mutation of the very last nucleotide of the exon.

Fulneček, Jaroslav / Matyášek, Roman

Molecular genetics and genomics : MGG

2015 Volume 291, Issue 2, Page(s) 801–818

Abstract: In plants, genome duplication followed by genome diversification and selection is recognized as a major evolutionary process. Rapid epigenetic and genetic changes that affect the transcription of parental genes are frequently observed after ... ...

Abstract	In plants, genome duplication followed by genome diversification and selection is recognized as a major evolutionary process. Rapid epigenetic and genetic changes that affect the transcription of parental genes are frequently observed after polyploidization. The pattern of alternative splicing is also frequently altered, yet the related molecular processes remain largely unresolved. Here, we study the inheritance and expression of parental variants of three floral organ identity genes in allotetraploid tobacco. DEFICIENS and GLOBOSA are B-class genes, and AGAMOUS is a C-class gene. Parental variants of these genes were found to be maintained in the tobacco genome, and the respective mRNAs were present in flower buds in comparable amounts. However, among five tobacco cultivars, we identified two in which the majority of paternal GLOBOSA pre-mRNA transcripts undergo exon 3 skipping, producing an mRNA with a premature termination codon. At the DNA level, we identified a G-A transition at the very last position of exon 3 in both cultivars. Although alternative splicing resulted in a dramatic decrease in full-length paternal GLOBOSA mRNA, no phenotypic effect was observed. Our finding likely serves as an example of the initiation of homoeolog diversification in a relatively young polyploid genome.
MeSH term(s)	Alternative Splicing/genetics ; Exons/genetics ; Gene Expression Regulation, Plant ; Homeodomain Proteins/biosynthesis ; Homeodomain Proteins/genetics ; Nucleotides/genetics ; Plant Proteins/biosynthesis ; Plant Proteins/genetics ; Point Mutation/genetics ; Polyploidy ; RNA Precursors/genetics ; Nicotiana/genetics ; Transcription, Genetic
Chemical Substances	GLOBOSA protein, plant ; Homeodomain Proteins ; Nucleotides ; Plant Proteins ; RNA Precursors
Language	English
Publishing date	2015-11-25
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2044817-X
ISSN	1617-4623 ; 1617-4615
ISSN (online)	1617-4623
ISSN	1617-4615
DOI	10.1007/s00438-015-1149-9
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Article ; Online: Intragenomic heterogeneity of intergenic ribosomal DNA spacers in Cucurbita moschata is determined by DNA minisatellites with variable potential to form non-canonical DNA conformations.

Matyášek, Roman / Kuderová, Alena / Kutílková, Eva / Kučera, Marek / Kovařík, Aleš

DNA research : an international journal for rapid publication of reports on genes and genomes

2019 Volume 26, Issue 3, Page(s) 273–286

Abstract: The intergenic spacer (IGS) of rDNA is frequently built of long blocks of tandem repeats. To estimate the intragenomic variability of such knotty regions, we employed PacBio sequencing of the Cucurbita moschata genome, in which thousands of rDNA copies ... ...

Abstract	The intergenic spacer (IGS) of rDNA is frequently built of long blocks of tandem repeats. To estimate the intragenomic variability of such knotty regions, we employed PacBio sequencing of the Cucurbita moschata genome, in which thousands of rDNA copies are distributed across a number of loci. The rRNA coding regions are highly conserved, indicating intensive interlocus homogenization and/or high selection pressure. However, the IGS exhibits high intragenomic structural diversity. Two repeated blocks, R1 (300-1250 bp) and R2 (290-643 bp), account for most of the IGS variation. They exhibit minisatellite-like features built of multiple periodically spaced short GC-rich sequence motifs with the potential to adopt non-canonical DNA conformations, G-quadruplex-folded and left-handed Z-DNA. The mutual arrangement of these motifs can be used to classify IGS variants into five structural families. Subtle polymorphisms exist within each family due to a variable number of repeats, suggesting the coexistence of an enormous number of IGS variants. The substantial length and structural heterogeneity of IGS minisatellites suggests that the tempo of their divergence exceeds the tempo of the homogenization of rDNA arrays. As frequently occurring among plants, we hypothesize that their instability may influence transcription regulation and/or destabilize rDNA units, possibly spreading them across the genome.
MeSH term(s)	Cucurbita/genetics ; DNA, Ribosomal Spacer/chemistry ; DNA, Ribosomal Spacer/genetics ; DNA, Ribosomal Spacer/metabolism ; Genetic Variation ; Minisatellite Repeats ; Nucleic Acid Conformation ; Sequence Analysis, DNA
Chemical Substances	DNA, Ribosomal Spacer
Language	English
Publishing date	2019-06-23
Publishing country	England
Document type	Journal Article
ZDB-ID	1212508-8
ISSN	1756-1663 ; 1340-2838
ISSN (online)	1756-1663
ISSN	1340-2838
DOI	10.1093/dnares/dsz008
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