Remarkable Evolutionary Rate Variations Among Lineages and Among Genome Compartments in Malaria Parasites of Mammals.

Genes encoded within organelle genomes often evolve at rates different from those in the nuclear genome. Here, we analyzed the relative rates of nucleotide substitution in the mitochondrial, apicoplast, and nuclear genomes in four different lineages of Plasmodium species (malaria parasites) infecting mammals. The rates of substitution in the three genomes exhibit substantial variation among lineages, with the relative rates of nuclear and mitochondrial DNA being particularly divergent between the Laverania (including Plasmodium falciparum) and Vivax lineages (including Plasmodium vivax).

Real-Time Imaging of On-Surface Ullmann Polymerization Reveals an Inhibiting Effect of Adatoms.

Ullmann coupling is a widely used reaction for the on-surface growth of low-dimensional carbon nanomaterials. The irreversible nature of this reaction prevents the "self-healing" of defects, and a detailed knowledge of its mechanism is therefore essential to enable the growth of extended ordered structures. However, the dynamics of the Ullmann polymerization remain largely unexplored, as coupling events occur on a timescale faster than conventional scanning probe microscopy imaging frequencies.

Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent.

Objectives: To determine how the intrinsic severity of successively dominant SARS-CoV-2 variants changed over the course of the pandemic.

Methods: A retrospective cohort analysis in the NHS Greater Glasgow and Clyde (NHS GGC) Health Board. All sequenced non-nosocomial adult COVID-19 cases in NHS GGC with relevant SARS-CoV-2 lineages (B.

The Timing and Magnitude of the Type I Interferon Response Are Correlated with Disease Tolerance in Arbovirus Infection.

Infected hosts possess two alternative strategies to protect themselves against the negative impact of virus infections: resistance, used to abrogate virus replication, and disease tolerance, used to avoid tissue damage without controlling viral burden. The principles governing pathogen resistance are well understood, while less is known about those involved in disease tolerance. Here, we studied bluetongue virus (BTV), the cause of bluetongue disease of ruminants, as a model system to investigate the mechanisms of virus-host interactions correlating with disease tolerance.

The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis.

Objectives: The SARS-CoV-2 Alpha variant was associated with increased transmission relative to other variants present at the time of its emergence and several studies have shown an association between Alpha variant infection and increased hospitalisation and 28-day mortality. However, none have addressed the impact on maximum severity of illness in the general population classified by the level of respiratory support required, or death. We aimed to do this.

Selective Self-Assembly and Modification of Herringbone Reconstructions at a Solid-Liquid Interface of Au(111).

The precise control of molecular self-assembly on surfaces presents many opportunities for the creation of complex nanostructures. Within this endeavor, selective patterning by exploiting molecular interactions at the solid-liquid interface would be a beneficial capability. Using scanning tunneling microscopy at the 1,2,4-trichlorobenzene/Au(111) interface, we observed selective self-assembly of 1,3,5-tris(4-methoxyphenyl)benzene (TMPB) molecules in the face-centered cubic (FCC) regions of Au(111).

Conserved recombination patterns across coronavirus subgenera.

Recombination contributes to the genetic diversity found in coronaviruses and is known to be a prominent mechanism whereby they evolve. It is apparent, both from controlled experiments and in genome sequences sampled from nature, that patterns of recombination in coronaviruses are non-random and that this is likely attributable to a combination of sequence features that favour the occurrence of recombination break points at specific genomic sites, and selection disfavouring the survival of recombinants within which favourable intra-genome interactions have been disrupted. Here we leverage available whole-genome sequence data for six coronavirus subgenera to identify specific patterns of recombination that are conserved between multiple subgenera and then identify the likely factors that underlie these conserved patterns.

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway.

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.

On-Surface Synthesis of Unsaturated Hydrocarbon Chains through C-S Activation.

We use an on-surface synthesis approach to drive the homocoupling reaction of a simple dithiophenyl-functionalized precursor on Cu(111). The C-S activation reaction is initiated at low annealing temperature and yields unsaturated hydrocarbon chains interconnected in a fully conjugated reticulated network. High-resolution atomic force microscopy imaging reveals the opening of the thiophenyl rings and the presence of trans- and cis-oligoacetylene chains as well as pentalene units.

Tandem Desulfurization/C-C Coupling Reaction of Tetrathienylbenzenes on Cu(111): Synthesis of Pentacene and an Exotic Ladder Polymer.

Surface-confined reactions represent a powerful approach for the precise synthesis of low-dimensional organic materials. A complete understanding of the pathways of surface reactions would enable the rational synthesis of a wide range of molecules and polymers. Here, we report different reaction pathways of tetrathienylbenzene (T1TB) and its extended congener tetrakis(dithienyl)benzene (T2TB) on Cu(111), investigated using scanning tunneling microscopy, X-ray photoelectron spectroscopy, and density functional theory calculations.

Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function.

Among the 30 nonsynonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (1) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (2) interactions of Spike with ACE2 receptors, and (3) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any virus within which they occurred.

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function.

Among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (i) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (ii) interactions of Spike with ACE2 receptors, and (iii) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any genomes within which they occurred.

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages.

The independent emergence late in 2020 of the B.1.1.

In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2.

Remdesivir (RDV), a broadly acting nucleoside analogue, is the only FDA approved small molecule antiviral for the treatment of COVID-19 patients. To date, there are no reports identifying SARS-CoV-2 RDV resistance in patients, animal models or in vitro. Here, we selected drug-resistant viral populations by serially passaging SARS-CoV-2 in vitro in the presence of RDV.

Identification of Topotactic Surface-Confined Ullmann-Polymerization.

On-surface Ullmann coupling is an established method for the synthesis of 1D and 2D organic structures. A key limitation to obtaining ordered polymers is the uncertainty in the final structure for coupling via random diffusion of reactants over the substrate, which leads to polymorphism and defects. Here, a topotactic polymerization on Cu(110) in a series of differently-halogenated para-phenylenes is identified, where the self-assembled organometallic (OM) reactants of diiodobenzene couple directly into a single, deterministic product, whereas the other precursors follow a diffusion driven reaction.

Long-range migration of H-atoms from electron-induced dissociation of HS on Si(111).

The electron-induced dissociation of chemisorbed HS to give recoiling H-atoms was investigated on a Si(111)-7 × 7 surface at 270 K by scanning tunnelling microscopy and modelled by density functional theory. Two different H-atom migratory pathways were identified: 'short-range' (S-R; 37%) and 'long-range' (L-R; 42%). In S-R reaction the H-atom recoiled by only 4 Å whereas in L-R the average H-recoil distance was 17 Å extending up to 72 Å.

The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape.

The emergence and rapid rise in prevalence of three independent SARS-CoV-2 "501Y lineages", B.1.1.

No evidence for distinct types in the evolution of SARS-CoV-2.

A recent study by Tang et al. claimed that two major types of severe acute respiratory syndrome-coronavirus-2 (CoV-2) had evolved in the ongoing CoV disease-2019 pandemic and that one of these types was more 'aggressive' than the other. Given the repercussions of these claims and the intense media coverage of these types of articles, we have examined in detail the data presented by Tang et al.

Oxygen-Induced 1D to 2D Transformation of On-Surface Organometallic Structures.

While surface-confined Ullmann-type coupling has been widely investigated for its potential to produce π-conjugated polymers with unique properties, the pathway of this reaction in the presence of adsorbed oxygen has yet to be explored. Here, the effect of oxygen adsorption between different steps of the polymerization reaction is studied, revealing an unexpected transformation of the 1D organometallic (OM) chains to 2D OM networks by annealing, rather than the 1D polymer obtained on pristine surfaces. Characterization by scanning tunneling microscopy and X-ray photoelectron spectroscopy indicates that the networks consist of OM segments stabilized by chemisorbed oxygen at the vertices of the segments, as supported by density functional theory calculations.

Synthesis of mesoscale ordered two-dimensional π-conjugated polymers with semiconducting properties.

Two-dimensional materials with high charge carrier mobility and tunable band gaps have attracted intense research effort for their potential use in nanoelectronics. Two-dimensional π-conjugated polymers constitute a promising subclass because the band structure can be manipulated by varying the molecular building blocks while preserving key features such as Dirac cones and high charge mobility. The major barriers to the application of two-dimensional π-conjugated polymers have been the small domain size and high defect density attained in the syntheses explored so far.