Comparing antiviral strategies against COVID-19 via multiscale within-host modelling.

Within-host models of COVID-19 infection dynamics enable the merits of different forms of antiviral therapy to be assessed in individual patients. A stochastic agent-based model of COVID-19 intracellular dynamics is introduced here, that incorporates essential steps of the viral life cycle targeted by treatment options. Integration of model predictions with an intercellular ODE model of within-host infection dynamics, fitted to patient data, generates a generic profile of disease progression in patients that have recovered in the absence of treatment. This is contrasted with the profiles obtained after variation of model parameters pertinent to the immune response, such as effector cell and antibody proliferation rates, mimicking disease progression in immunocompromised patients. These profiles are then compared with disease progression in the presence of antiviral and convalescent plasma therapy against COVID-19 infections. The model reveals that using both therapies in combination can be very effective in reducing the length of infection, but these synergistic effects decline with a delayed treatment start. Conversely, early treatment with either therapy alone can actually increase the duration of infection, with infectious virions still present after the decline of other markers of infection. This suggests that usage of these treatments should remain carefully controlled in a clinical environment.

Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging.

The specific packaging of the hepatitis C virus (HCV) genome is hypothesised to be driven by Core-RNA interactions. To identify the regions of the viral genome involved in this process, we used SELEX (systematic evolution of ligands by exponential enrichment) to identify RNA aptamers which bind specifically to Core in vitro. Comparison of these aptamers to multiple HCV genomes revealed the presence of a conserved terminal loop motif within short RNA stem-loop structures. We postulated that interactions of these motifs, as well as sub-motifs which were present in HCV genomes at statistically significant levels, with the Core protein may drive virion assembly. We mutated 8 of these predicted motifs within the HCV infectious molecular clone JFH-1, thereby producing a range of mutant viruses predicted to possess altered RNA secondary structures. RNA replication and viral titre were unaltered in viruses possessing only one mutated structure. However, infectivity titres were decreased in viruses possessing a higher number of mutated regions. This work thus identified multiple novel RNA motifs which appear to contribute to genome packaging. We suggest that these structures act as cooperative packaging signals to drive specific RNA encapsidation during HCV assembly.

Selection of 2'F-modified RNA aptamers against prostate-specific antigen and their evaluation for diagnostic and therapeutic applications.

Currently, prostate-specific antigen (PSA) is considered to be the most sensitive marker available for prostate cancer detection and for monitoring of disease progression. In addition to its importance as a tumor marker, PSA has a role in the biological activity of cancer growth and proliferation. Therefore, the inhibition or activation of its biological activity may be used in prostate cancer therapy. Here, we describe the isolation and characterization of new 2'F-modified RNA aptamers directed against PSA. Binding studies demonstrate the ability of these new aptamers to specifically recognize their target with dissociation constants in the nanomolar range. In order to demonstrate the functionality of the selected aptamers, an apta-PCR approach was used for the quantitative detection of PSA, achieving a limit of detection of 11 nM. Furthermore, the potential use of the selected aptamers in therapeutics was demonstrated with the 2'F-modified aptamers being highly stable in human serum and having the ability to moderate the activity of PSA, which will be explored for the treatment of prostate cancer.

Fabrication and characterization of gold nano-wires templated on virus-like arrays of tobacco mosaic virus coat proteins.

The rod-shaped plant virus tobacco mosaic virus (TMV) is widely used as a nano-fabrication template, and chimeric peptide expression on its major coat protein has extended its potential applications. Here we describe a simple bacterial expression system for production and rapid purification of recombinant chimeric TMV coat protein carrying C-terminal peptide tags. These proteins do not bind TMV RNA or form disks at pH 7. However, they retain the ability to self-assemble into virus-like arrays at acidic pH. C-terminal peptide tags in such arrays are exposed on the protein surface, allowing interaction with target species. We have utilized a C-terminal His-tag to create virus coat protein-templated nano-rods able to bind gold nanoparticles uniformly. These can be transformed into gold nano-wires by deposition of additional gold atoms from solution, followed by thermal annealing. The resistivity of a typical annealed wire created by this approach is significantly less than values reported for other nano-wires made using different bio-templates. This expression construct is therefore a useful additional tool for the creation of chimeric TMV-like nano-rods for bio-templating.

Sperm competition roles and ejaculate investment in a promiscuous mammal.

Theoretical models of sperm competition predict how males should allocate sperm and seminal fluid components to ejaculates according to their mating role (dominant vs. subordinate). Here, we present a detailed analysis of ejaculate expenditure according to male roles in the bank vole (Myodes glareolus). Sperm competition occurs regularly in this species, and dominant males typically achieve higher fertilization success than subordinates. Contrary to theoretical predictions, we found that dominant male bank voles invest more sperm per ejaculate than subordinates, both absolutely and relative to body and testes mass. The testes of dominant males were also absolutely (although not relatively) larger than those of subordinates. However, we found no evidence that subordinate males compensate for lower sperm numbers per ejaculate by increasing ejaculation frequency or sperm velocity. Similarly, we found no evidence for differential investment in copulatory plug size according to male roles in sperm competition, although dominant males had significantly larger seminal vesicles (both absolutely and relative to body mass) compared with subordinates. We conclude that sperm competition roles can have significant but unexpected influences on ejaculate investment in mammals with clearly defined differences in male social status.

The scent of senescence: sexual signalling and female preference in house mice.

Sexual signals are expected to be costly to produce and maintain, thus ensuring that only males in good condition can sustain their expression at high levels. When males reach senescence they lose physiological function and condition, which could constrain their ability to invest in costly sexual signals, decreasing their attractiveness to mates. Furthermore, females may have evolved mating preferences that cause avoidance of senesced males to enhance fertilization success and viability of offspring. Among mammals, the size of antlers and other weapons can decrease with senescence, but changes in olfactory sexual signals have been largely unexplored. We examined changes in olfactory signals with senescence in house mice (Mus musculus domesticus), where males excrete volatile and involatile molecules in scent marks that elicit behavioural and priming responses in females. Compared to middle-aged males, the urine of senesced males contained a lower concentration of involatile signalling proteins (major urinary proteins or MUPs), and associated volatiles that bind to these proteins. The reduced intensity of male scent will affect the longevity of scent signals deposited in the environment and, accordingly, females were less attracted to urine from senesced males deposited 12 h previously. Females also discriminated against senesced males encountered behind a mesh barrier. These results reveal that investment in olfactory signalling is reduced during senescence and suggest that senesced males and their scent may be less attractive to females.

Generation of neutralizing aptamers against herpes simplex virus type 2: potential components of multivalent microbicides.

The prophylactic use of topical antiviral agents has recently been validated by the reduction in human immunodeficiency virus (HIV) type 1 infection incidence seen using tonofovir-containing microbicides. In order to develop a wide-spectrum microbicide to prevent infection with a wide range of sexually transmitted viruses, we have previously reported the development of HIV-neutralizing aptamers and here report the isolation and characterization of aptamers that neutralize herpes simplex virus type 2 (HSV-2). These aptamers bind the envelope glycoprotein (gD), are potent (IC(50) of 20-50 nM) and are able to block infection pathways dependent on both major entry receptors, Nectin1 and HVEM. Structural analysis and mutagenesis of these aptamers reveal a core specificity element that could provide the basis for pharmaceutical development. As HSV-2 is a major risk factor for the acquisition of HIV-1, a microbicide capable of preventing HSV-2 infection would not only reduce the morbidity associated with HSV-2, but also that derived from HIV-1.

Simple rules for efficient assembly predict the layout of a packaged viral RNA.

Single-stranded RNA (ssRNA) viruses, which include major human pathogens, package their genomes as they assemble their capsids. We show here that the organization of the viral genomes within the capsids provides intriguing insights into the highly cooperative nature of the assembly process. A recent cryo-electron microscopy structure of bacteriophage MS2, determined with only 5-fold symmetry averaging, has revealed the asymmetric distribution of its encapsidated genome. Here we show that this RNA distribution is consistent with an assembly mechanism that follows two simple rules derived from experiment: (1) the binding of the MS2 maturation protein to the RNA constrains its conformation into a loop, and (2) the capsid must be built in an energetically favorable way. These results provide a new level of insight into the factors that drive efficient assembly of ssRNA viruses in vivo.

Dynamic allostery controls coat protein conformer switching during MS2 phage assembly.

Previously, an RNA stem-loop (TR) encompassing 19 nt of the genome of bacteriophage MS2 was shown to act as an allosteric effector of conformational switching in the coat protein during in vitro capsid assembly. TR RNA binding to symmetric coat protein dimers results in conformational changes, principally at the FG-loop connecting the F and G beta-strands in each subunit, yielding an asymmetric structure. The FG-loops define the quasi-equivalent conformers of the coat protein subunit (A, B, and C) in the T=3 capsid. Efficient assembly of this capsid in vitro requires that both symmetrical and asymmetrical forms of the coat protein dimer be present in solution, implying that they closely resemble the quasi-equivalent dimers (A/B and C/C) seen in the final capsid. Experiments show that assembly can be triggered by a number of RNA stem-loops unrelated to TR in sequence and detailed secondary structure, suggesting that there is little sequence specificity to the allosteric effect. Since the stem-loop binding site on the coat protein dimer is distal to the FG-loops the mechanism of this switching effect needs to be investigated. We have analyzed the vibrational modes of both TR-bound and RNA-free coat protein dimers using an all-atom normal-mode analysis. The results suggest that asymmetric contacts between the A-duplex RNA phosphodiester backbone and the EF-loop in one coat protein subunit result in the FG-loop of that subunit becoming more dynamic, whilst the equivalent loop on the other monomer decreases its mobility. The increased dynamic behaviour occurs in the FG-loop of the subunit required to undergo the largest conformational change when adopting the quasi-equivalent B conformation. The free energy barrier on the pathway to form this new structure would consequently be reduced compared to the unbound subunit. Our results also imply that the allosteric effect should be independent of the base sequence of the bound stem-loop, as observed experimentally. As a test of this model, we also examined the vibrational modes of a known assembly mutant, W82R, which cannot assemble beyond dimer. This mutation leads to an increased mobility of the DE-loop rather than the FG-loop after TR binding, consistent with the non-assembling phenotype of this mutant protein.

Sperm competition and brain size evolution in mammals.

The 'expensive tissue hypothesis' predicts a size trade-off between the brain and other energetically costly organs. A specific version of this hypothesis, the 'expensive sexual tissue hypothesis', argues that selection for larger testes under sperm competition constrains brain size evolution. We show here that there is no general evolutionary trade-off between brain and testis mass in mammals. The predicted negative relationship between these traits is not found for rodents, ungulates, primates, carnivores, or across combined mammalian orders, and neither does total brain mass vary according to the level of sperm competition as determined by mating system classifications. Although we are able to confirm previous reports of a negative relationship between brain and testis mass in echolocating bats, our results suggest that mating system may be a better predictor of brain size in this group. We conclude that the expensive sexual tissue hypothesis accounts for little or none of the variance in brain size in mammals, and suggest that a broader framework is required to understand the costs of brain size evolution and how these are met.

Monogamy and the battle of the sexes.

Sexual conflict has been suggested to be important in the evolution of reproductive traits, with much recent theoretical and empirical evidence emphasizing its role in generating sexually antagonistic coevolution in the context of promiscuous mating. Here we shift attention to the role of sexual conflict in a monogamous mating context. Conflicts can arise, for example, when males are successful in imposing monandry at a cost to female fitness, or when females impose monogyny on males. Conflict over remating can also generate monogamy. For example, when males invest heavily in attempting to impose female monandry, the cost of their investment may prevent them from securing additional mates. We emphasize that sexual conflicts need not always generate sexually antagonistic coevolution, and that it is important to consider whether mating decisions are controlled primarily by males or females. Finally, we briefly discuss approaches to distinguish between conflict and classical modes of sexual selection, as this highlights difficulties associated with deciding whether monogamy is enforced by one sex or the other. We suggest that documenting the current fitness consequences of mate choice and mating patterns provides insight into the relative importance of classic and conflict modes of selection.

Four-probe electrical characterization of Pt-coated TMV-based nanostructures.

The electrical transport and structural properties of tobacco mosaic virus (TMV)-based nanostructures have been studied. Electroless deposition was used to coat the TMV outer surface with a 13 nm thick homogeneous Pt layer. SEM, TEM and electrical characterization of the obtained nanostructures has been performed. Using four independently controlled scanning tunnelling microscope tips we were able to perform four-point probe resistance measurements on linear virus assemblies and demonstrate the continuous nature of the metallic coating. The measured resistivity values of the virial nanowires exceeded the bulk value by 10-100 times; notwithstanding this the coated structure allowed high current densities, of the order of 10(5)-10(8) A cm(-2). The four-probe technique proved to be useful for analysing the electrical properties of bio-inorganic nanowires.

Haemoparasites of common shrews (Sorex araneus) in Northwest England.

The presence of haemoparasites belonging to the taxa Anaplasma, Bartonella and Trypanosoma was determined among 76 common shrews (Sorex araneus) from Northwest England. Anaplasma phagocytophilum DNA was recovered from the blood of 1 shrew (1.3%), with the amplified 16S rRNA sequence identical to one previously reported from a bank vole (Clethrionomys glareolus). Trypanosoma spp. DNA was detected in 9 shrews (11.8%), the amplified 18S rDNA fragments being indistinguishable from one another, and distinct from previously published data. This represents the first report of trypanosome infection in S. araneus and suggests they are susceptible to an uncharacterized Trypanosoma species. Blood from 11 shrews (14.5%) yielded Bartonella spp., with characterization of isolates using comparative sequence analysis of partial gltA and 16S-23S rRNA intergenic spacer regions revealing 2 different genotypes. Phylogenetic inference from alignment of partial gltA sequences found that both UK S. araneus types formed a well-supported cluster with Bartonella sp. isolated from S. araneus in Sweden. No significant effect of host age, sex, or year of collection was found on prevalence of Bartonella or trypanosome infections. The results of this survey demonstrate that common shrews in the UK are susceptible to haemoparasitic infections, at prevalences similar to those reported from sympatric rodents.

Sperm competition and diversity in rodent copulatory behaviour.

The copulatory behaviour of male mammals is characterized by striking diversity in patterns of copulatory stimulation and ejaculation frequency. We conducted comparative analyses of rodents to investigate the potential influence of sperm competition in the evolution of copulatory behaviour. We found that increasing sperm competition is associated with faster rates of stimulation and earlier ejaculation among species in which males perform multiple intromissions prior to ejaculation, but with no overall change in the number of intromissions per ejaculation. Increasing sperm competition is also associated with a higher frequency of repeated ejaculations with the same female, and with shorter refractory periods between repeated copulations. Increasing sperm competition level thus appears to select for male ability to ejaculate more rapidly and more frequently with each female mated. As prolonged copulations are known to reduce female remating rates, these findings indicate that males may experience opposing selection pressures on copulatory behaviour with respect to offensive and defensive aspects of sperm competition. We conclude that sperm competition is likely to be an important selection pressure explaining diversity in mammalian copulatory behaviour.

Sperm competition in mammals.

Although Darwin identified the evolutionary significance of competition between males in the context of reproduction, it is only in the past few decades that we have begun to appreciate the importance of competition at the gametic level. Sperm competition, defined as competition between the sperm of two or more males for fertilization of the same set of ova, is now recognised as a key selective force shaping male reproductive anatomy, physiology and behaviour across diverse animal groups, including mammals. The aim of this article is to provide a brief review of the selective consequences of sperm competition in mammals, with emphasis on recent theoretical advances and empirical controversies. Evidence of female influences on sperm competition outcomes in mammals is also discussed, and it is concluded that understanding the selective pressures driving coevolution between male and female reproductive traits remains a major challenge for researchers in this field.

Use of simulated clients in training veterinary undergraduates in communication skills.

A course in communication skills has been developed specifically for veterinary students, based on those delivered at many medical schools, and making extensive use of professional actors as simulated clients. Its aim is to raise awareness of the importance of communication among veterinary undergraduates at all stages of the curriculum, and it allows them to role-play in acted-out scenarios. Facilitated small groups provide an environment in which students can receive feedback on their own performance and also give feedback to their colleagues. An independent evaluation suggests that the opportunity to role-play increased the students' confidence in communicating with others. They were able to identify their personal strengths as communicators and gain insights into the aspects of communication they could improve. Feedback and subsequent discussions were highly valued, with the actors playing a crucial role in providing feedback from the client's perspective. Students were able to use the knowledge they acquired when consulting with real clients. Most of the students suggested that the course should continue in its current format, but with more time provided for it in the curriculum.

Female multiple mating behaviour, early reproductive failure and litter size variation in mammals.

Female promiscuity is widespread among mammals, although its function is poorly understood. Recently, much interest has been generated by the hypothesis that female promiscuity, combined with post-copulatory paternity-biasing mechanisms, may function to reduce the costs of reproductive failure resulting from genetic incompatibility. Here, a comparative approach is used to determine if average rates of reproductive failure differ for polytocous mammal species with contrasting levels of female multiple-mating behaviour. After control for phylogeny, promiscuous species were found to have significantly lower rates of early reproductive failure than monogamous and polygynous species, in which females are relatively monandrous. Monandrous females appear to compensate for higher early reproductive failure with increased ova production, and thus produce comparable average litter sizes to those of more promiscuous females. However, there is significantly more variation around the average litter sizes produced by relatively monandrous females. These findings are broadly consistent with predictions of the genetic incompatibility avoidance hypothesis, although it is emphasized that alternative explanations cannot be ruled out on the basis of the comparative evidence presented. Further studies are needed to explore ecological correlates of multiple-mating behaviour, to investigate potential post-copulatory paternity-biasing mechanisms, and to identify the causes of reproductive failure in natural mammal populations.

Life history consequences of mammal sibling rivalry.

Mammal life history traits relating to growth and reproduction are extremely diverse. Sibling rivalry may contribute to selection pressures influencing this diversity, because individuals that are relatively large at birth typically have an advantage in competition for milk. However, selection for increased growth rate is likely to be constrained by kin selection and physiological costs. Here, we present and test a model examining the ESS (evolutionarily stable strategy) balance between these constraints and advantages associated with increased prenatal growth in mammal sibling rivalry. Predictions of the model are supported by results of comparative analyses for the Carnivora and Insectivora, which demonstrate an increase in prenatal growth rate with increasing intensity of postnatal scramble competition, and a decrease in postnatal growth rate relative to size at birth. Because increased prenatal growth rates are predicted to select for reduced gestation length under certain conditions, our study also indicates that sibling rivalry may contribute to selection pressures influencing variation in altriciality and precociality among mammals.

Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex.

We have determined the X-ray structures of six MS2 RNA hairpin-coat-protein complexes having five different substitutions at the hairpin loop base -5. This is a uracil in the wild-type hairpin and contacts the coat protein both by stacking on to a tyrosine side chain and by hydrogen bonding to an asparagine side chain. The RNA consensus sequence derived from coat protein binding studies with natural sequence variants suggested that the -5 base needs to be a pyrimidine for strong binding. The five -5 substituents used in this study were 5-bromouracil, pyrimidin-2-one, 2-thiouracil, adenine, and guanine. The structure of the 5-bromouracil complex was determined to 2.2 A resolution, which is the highest to date for any MS2 RNA-protein complex. All the complexes presented here show very similar conformations, despite variation in affinity in solution. The results suggest that the stacking of the -5 base on to the tyrosine side chain is the most important driving force for complex formation. A number of hydrogen bonds that are present in the wild-type complex are not crucial for binding, as they are missing in one or more of the complexes. The results also reveal the flexibility of this RNA-protein interface, with respect to functional group variation, and may be generally applicable to other RNA-protein complexes.