Figure 3 - uploaded by Tomislav Domazet-Lošo
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The parental genes that generate retrocopies in human and mouse populations tend to be evolutionary ancient. The phylostratigraphic maps of human and mouse protein coding genes are generated using corresponding consensus phylogenies containing 24 internodes (phylostrata - ps). To simplify presentation of the phylostratigraphic results human and mouse phylogenies are overlapped and shown in the lower panel. The two phylogenies differ only in the last two phylostrata (ps23, ps24); i.e. Rodentia-M. musculus vs. Primates-H. sapiens lineage. Protein sequences of all human (Ensemble GRCh38.86) and mouse genes (Ensembl GRCm38.86) are compared by BLAST against the corresponding custom reference database (e-value 0.001) and mapped on the respective phylogeny using the phylostratigraphic approach (140,142,145,148). The distribution of human (483, blue numbers, (37) and mouse parental genes (1659, red numbers, (40) are shown at the top of upper panel. The log-odds chart in the upper panel shows deviation from the expected frequency of parental genes in humans (blue line) and mice (red line). Significance of these deviations is tested by the two-way hypergeometric test adjusted for multiple comparisons (*P < 0.05; **P < 0.01; ***P < 0.001). The gray shaded phylostrata (ps1 - cellular organisms, ps2 - Archaea/Asgard Archaea/Eukaryota and ps4 - Eukaryota) are enriched for parental genes. Starting with Metazoa (ps9), evolutionary more recent phylostrata show significant depletion in the number of parental genes. This phylostratigraphic pattern is effectively unchanged in the range of e-value cut-offs from 1 to 10-20, therefore it could be considered fairly robust (148).

The parental genes that generate retrocopies in human and mouse populations tend to be evolutionary ancient. The phylostratigraphic maps of human and mouse protein coding genes are generated using corresponding consensus phylogenies containing 24 internodes (phylostrata - ps). To simplify presentation of the phylostratigraphic results human and mouse phylogenies are overlapped and shown in the lower panel. The two phylogenies differ only in the last two phylostrata (ps23, ps24); i.e. Rodentia-M. musculus vs. Primates-H. sapiens lineage. Protein sequences of all human (Ensemble GRCh38.86) and mouse genes (Ensembl GRCm38.86) are compared by BLAST against the corresponding custom reference database (e-value 0.001) and mapped on the respective phylogeny using the phylostratigraphic approach (140,142,145,148). The distribution of human (483, blue numbers, (37) and mouse parental genes (1659, red numbers, (40) are shown at the top of upper panel. The log-odds chart in the upper panel shows deviation from the expected frequency of parental genes in humans (blue line) and mice (red line). Significance of these deviations is tested by the two-way hypergeometric test adjusted for multiple comparisons (*P < 0.05; **P < 0.01; ***P < 0.001). The gray shaded phylostrata (ps1 - cellular organisms, ps2 - Archaea/Asgard Archaea/Eukaryota and ps4 - Eukaryota) are enriched for parental genes. Starting with Metazoa (ps9), evolutionary more recent phylostrata show significant depletion in the number of parental genes. This phylostratigraphic pattern is effectively unchanged in the range of e-value cut-offs from 1 to 10-20, therefore it could be considered fairly robust (148).

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Preprint
The major advantage of mRNA vaccines over more conventional approaches is their potential for rapid development and large-scale deployment in pandemic situations. In the current COVID-19 crisis the two mRNA COVID-19 vaccines have been conditionally approved and broadly applied, while others are still in clinical trials. However, there is no previou...

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... These vaccines are believed to possess higher biosafety than DNA-based vaccines because the mRNA is less likely integrated into the genome than a DNA-based vaccine, as the translation of the antigens in the case of mRNA vaccines takes place in the cytoplasm and not in the nucleus, where the DNA vaccines start to work [77]. However, several studies suggest that the risk of genomic integration, even if diminished compared to DNA vaccines, also remains for those based on mRNA, considering that eukaryotic cells may exert, to some extent, a reverse transcription activity [78][79][80] that could produce DNA theoretically starting from the vaccine-delivered mRNAs [81,82]. An advantage of nucleic acid-based vaccines over protein-based vaccines is that they may lead to antigens better mimicking the viral protein structure, including the post-translational modifications. ...
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The recent development of mRNA vaccines against the SARS-CoV-2 infection has turned the spotlight on the potential of nucleic acids as innovative prophylactic agents and as diagnostic and therapeutic tools. Until now, their use has been severely limited by their reduced half-life in the biological environment and the difficulties related to their transport to target cells. These limiting aspects can now be overcome by resorting to chemical modifications in the drug and using appropriate nanocarriers, respectively. Oligonucleotides can interact with complementary sequences of nucleic acid targets, forming stable complexes and determining their loss of function. An alternative strategy uses nucleic acid aptamers that, like the antibodies, bind to specific proteins to modulate their activity. In this review, the authors will examine the recent literature on nucleic acids-based strategies in the COVID-19 era, focusing the attention on their applications for the prophylaxis of COVID-19, but also on antisense- and aptamer-based strategies directed to the diagnosis and therapy of the coronavirus pandemic.