Differential enrichment of yeast DNA in SARS-CoV-2 and related genomes supports synthetic origin hypothesis

Background: Knowledge about the origin of SARS-CoV-2 is necessary for both a biological and epidemiological understanding of the COVID-19 pandemic. Evidence suggests that a proximal evolutionary ancestor of SARS-CoV-2 belongs to the bat coronavirus family. However, as further evidence for a direct zoonosis remains limited, alternative modes of SARS-CoV-2 biogenesis should be also considered. Results: Here we show that the genomes from SARS-CoV-2 and from SARS-CoV-1 are differentially enriched with short chromosomal sequences from the yeast S. cerevisiae at focal positions that are known to be critical for virus replication, host cell invasion, and host immune response. Specifically, for SARS-CoV-2, we identify two sites: one at the start of the viral replicase domain, and the other at the end of the spike gene past its critical domain junction; for SARS-CoV-1, one at the start of the RNA dependent RNA polymerase gene, and the other at the start of the spike protein’s receptor binding domain. As yeast is not a natural host for this virus family, we propose a directed passage model for viral constructs, including virus replicase, in yeast cells based on co-transformation of virus DNA plasmids carrying yeast selectable genetic markers followed by intra-chromosomal homologous recombination through gene conversion. Highly differential sequence homology data across yeast chromosomes congruent with chromosomes harboring specific auxotrophic markers further support this passage model. Model and data together allow us to infer a hypothetical tripartite genome assembly scheme for the synthetic biogenesis of SARS-CoV-2 and SARS-CoV-1. Conclusions: These results provide evidence that the genome sequences of SARS-CoV-1, SARS-CoV-2, but not that of RaTG13, BANAL-20-52 and all other closest SARS coronavirus family members identified, are carriers of distinct homology signals that might point to large-scale genomic editing during a passage of directed replication and chromosomal integration inside genetically modified yeast cells.

Differential enrichment of yeast DNA in SARS-CoV-2 and related genomes supports synthetic origin hypothesis

Background: Knowledge about the origin of SARS-CoV-2 is necessary for both a biological and epidemiological understanding of the COVID-19 pandemic. Evidence suggests that a proximal evolutionary ancestor of SARS-CoV-2 belongs to the bat coronavirus family. However, as further evidence for a direct zoonosis remains limited, alternative modes of SARS-CoV-2 biogenesis should be also considered. Results: Here we show that genomes from SARS-CoV-2 and from closely related coronaviruses are differentially enriched with short chromosomal sequences from the yeast S. cerevisiae at focal positions that are known to be critical for virus replication, host cell invasion, and host immune response. Specifically, for SARS-CoV-2, we identify two sites: one at the start of the viral replicase domain, and the other at the end of the spike gene past its critical domain junction; for SARS-CoV-1, one at the start of the RNA dependent RNA polymerase gene, and the other at the start of the spike protein’s receptor binding domain. As yeast is not a natural host for this virus family, we propose a directed passage model for viral constructs, including virus replicase, in yeast cells based on co-transformation of virus DNA plasmids carrying yeast selectable genetic markers followed by intra-chromosomal homologous recombination through gene conversion. Highly differential sequence homology data across yeast chromosomes congruent with chromosomes harboring specific auxotrophic markers further support this passage model. Model and data together allow us to infer a hypothetical tripartite genome assembly scheme for the synthetic biogenesis of SARS-CoV-2 and SARS-CoV-1. Conclusions: These results provide evidence that the genome sequences of SARS-CoV-1, SARS-CoV-2, but not that of RaTG13 and all other closest SARS coronavirus family members identified, are carriers of distinct homology signals that might point to large-scale genomic editing during a passage of directed replication and chromosomal integration inside genetically modified yeast cells.

Iron-Rich Spherules of Taihu Lake: Origin Hypothesis of Taihu Lake Basin in China

In this paper, a detailed mineralogical study on iron-rich spherules in Taihu Lake was carried out, and we present a proposed impact-related origin for these iron-rich spherules. The iron-rich spherical concretions in Taihu Lake occur in a specific silty layer formed around ~7 ka B.P., sandwiched between an upper lacustrine deposit layer and a lower hard loess layer, and they are widely distributed and are the most abundant iron-rich concretions in that specific layer in the vicinity of Taihu Lake. The spherules are typically ~0.5 to 3 mm in diameter with a shape very similar to a spherical shape but not exactly rounded and have various apparent aerodynamic shapes, such as spherical, cone, spindle, ellipsoidal, elongated and pear-shaped morphologies. SEM imaging shows that there is no central core and no concentric layers in the spherules. Iron-rich spherical concretions are similar to accretionary lapilli and have a typical colloidal structure with abundant angular quartz grains and trace fragments of clays wrapped in fine cements that are mainly goethite with minor clays and carbon particles. The typical nodule-forming mechanism in aqueous sediments does not sufficiently explain the morphology and internal features of the iron-rich spherules of Taihu Lake, whereas the aerosol formation mechanism under the airburst impact origin hypothesis of the Taihu Lake basin may be a better explanation of the unique mineralogy of the spherules. Specifically, airburst impact plumes could be the reaction chambers of the aerosol to form the accretionary lapilli with a colloidal texture for the interior, while a dense shell and semi-plastic morphological features can form in the falling processes from higher altitudes in the plume.

Daño moral colectivo en el derecho del consumo chileno: Situación actual y proyecciones

The work presented aims to analyze the current state of moral damages in collective or diffuse procedures resulting from the implementation of Law No. 21,081 that reforms the Consumer Protection Law No. 19,496. We start with a general overview of moral damage, differentiating between individual and collective interests. Later, we assess the modification introduced by article 51 No. 2 of the Consumer Protection Law, which conceptually restructured the origin hypothesis: physical and psychological integrity and the dignity of consumers. The assessment becomes critical due to the legislator’s understanding of legal assets that generate compensation and collective interests, thus concluding that the suitable path, in order to talk of collective non-pecuniary damages - in a more refined sense - can be constructed by an adequate notion of dignity within the context of consumer relations.

Health Disturbances of Negative Nutritional Shocks

The Fetal Origin Hypothesis show that the prenatal development period is a critical period for birth outcomes. Applying a panel data fixed effect model and using the universe of birth records in the US, I find that exposure to the holy month Ramadan, during which Muslim mothers fast for the whole day, during prenatal development has negative birth outcomes. Exposure to a full month of fasting is associated with 96 grams lower birth-weight. These results are robust across specifications and do not appear to be driven by mothers’ selective fertility.

Crick Wobble and Superwobble in Standard Genetic Code Evolution

Wobble coding is inevitable during evolution of the Standard Genetic Code (SGC). It ultimately splits half of NN U/C/A/G coding boxes with different assignments. Further, it contributes to pervasive SGC order by reinforcing close spacing for identical SGC assignments. But wobble cannot appear too soon, or it will inhibit encoding and more decisively, obstruct evolution of full coding tables. However, these prior results assumed Crick wobble, NN U/C and NN A/G, read by a single adaptor RNA. Superwobble translates NN U/C/A/G codons, using one adaptor RNA with an unmodified 5′ anticodon U (appropriate to earliest coding) in modern mitochondria, plastids, and mycoplasma. Assuming the SGC was selected when evolving codes most resembled it, characteristics of the critical selection events can be calculated. For example, continuous superwobble infrequently evolves SGC-like coding tables. So, continuous superwobble is a very improbable origin hypothesis. In contrast, late-arising superwobble shares late Crick wobble’s frequent resemblance to SGC order. Thus late superwobble is possible, but yields SGC-like assignments less frequently than late Crick wobble. Ancient coding ambiguity, most simply, arose from Crick wobble alone. This is consistent with SGC assignments to NAN codons.

Efficiency of eclogite removal from continental lithosphere and its implications for cratonic diamonds

Continental lithospheric mantle (CLM) may have been built from subducted slabs, but the apparent lack of concurrent oceanic crust in CLM, known as the mass imbalance problem, remains unresolved. Here, we present a simple dynamic model to evaluate the likelihood of losing dense eclogitized oceanic crust from CLM by gravitational instability. Our model allowed us to assess the long-term evolution of such crust removal, based on how thermal and viscosity profiles change over time across the continental lithosphere. We found that the oceanic crust incorporated early into CLM can quickly escape to the asthenosphere, whereas that incorporated after a certain age would be preserved in CLM. This study provides a plausible explanation for the mass imbalance problem posed by the oceanic ridge origin hypothesis of CLM and points to the significance of preservation bias inherent to the studies of cratonic diamonds.

Evolution of Photorespiratory Glycolate Oxidase among Archaeplastida

Photorespiration has been shown to be essential for all oxygenic phototrophs in the present-day oxygen-containing atmosphere. The strong similarity of the photorespiratory cycle in cyanobacteria and plants led to the hypothesis that oxygenic photosynthesis and photorespiration co-evolved in cyanobacteria, and then entered the eukaryotic algal lineages up to land plants via endosymbiosis. However, the evolutionary origin of the photorespiratory enzyme glycolate oxidase (GOX) is controversial, which challenges the common origin hypothesis. Here, we tested this hypothesis using phylogenetic and biochemical approaches with broad taxon sampling. Phylogenetic analysis supported the view that a cyanobacterial GOX-like protein of the 2-hydroxy-acid oxidase family most likely served as an ancestor for GOX in all eukaryotes. Furthermore, our results strongly indicate that GOX was recruited to the photorespiratory metabolism at the origin of Archaeplastida, because we verified that Glaucophyta, Rhodophyta, and Streptophyta all express GOX enzymes with preference for the substrate glycolate. Moreover, an “ancestral” protein synthetically derived from the node separating all prokaryotic from eukaryotic GOX-like proteins also preferred glycolate over l-lactate. These results support the notion that a cyanobacterial ancestral protein laid the foundation for the evolution of photorespiratory GOX enzymes in modern eukaryotic phototrophs.

Interspecific gene flow and an intermediate molecular profile of Dyckia julianae (Bromeliaceae), an endemic species from southern Brazil

When related species are distributed in sympatric populations, hybridization may occur. Likewise, one or more of these species may have arisen through historical hybridization between taxa. Here, we aim to elucidate the occurrence of hybridization among three Dyckia spp. (Bromeliaceae) from southern Brazil. We used seven nuclear and six plastid microsatellite loci to assess patterns of genetic diversity, population structure and hybridization in the three species. Furthermore, we performed manual crosses between species to test compatibility and fertility. The results showed that Dyckia julianae has an intermediate molecular profile, low gene flow occurs between Dyckia hebdingii and Dyckia choristaminea and higher gene flow occurs between D. julianae and the other two species. Plastid microsatellites identified 12 haplotypes that are shared among the species. The manual crosses between D. julianae and the other two species produced viable seeds, but no crosses between D. hebdingii and D. choristaminea generated fruits. Our data suggest that the reproductive barrier between D. julianae and the other two species is permeable. Further investigation into the hybrid origin hypothesis of D. julianae should be undertaken, as well as the mechanisms involved in reproductive isolation between D. hebdingii and D. choristaminea.