Diverse high-affinity DNA aptamers for wild-type and B.1.1.7 SARS-CoV-2 spike proteins from a pre-structured DNA library

We performed in vitro selection experiments to identify DNA aptamers for the S1 subunit of the SARS-CoV-2 spike protein (S1 protein). Using a pool of pre-structured random DNA sequences, we obtained over 100 candidate aptamers after 13 cycles of enrichment under progressively more stringent selection pressure. The top 10 sequences all exhibited strong binding to the S1 protein. Two aptamers, named MSA1 (K_d = 1.8 nM) and MSA5 (K_d = 2.7 nM), were assessed for binding to the heat-treated S1 protein, untreated S1 protein spiked into 50% human saliva and the trimeric spike protein of both the wildtype and the B.1.1.7 variant, demonstrating comparable affinities in all cases. MSA1 and MSA5 also recognized the pseudotyped lentivirus of SARS-CoV-2 with respective K_d values of 22.7 pM and 11.8 pM. Secondary structure prediction and sequence truncation experiments revealed that both MSA1 and MSA5 adopted a hairpin structure, which was the motif pre-designed into the original library. A colorimetric sandwich assay was developed using MSA1 as both the recognition element and detection element, which was capable of detecting the pseudotyped lentivirus in 50% saliva with a limit of detection of 400 fM, confirming the potential of these aptamers as diagnostic tools for COVID-19 detection.     

Anthelmintic efficacy on UK Thoroughbred stud farms

Anthelmintic drugs have been applied indiscriminately to control horse nematodes for over 40 years. We undertook a comprehensive study to investigate efficacy of the four available broad-spectrum anthelmintic drugs on 16 Thoroughbred stud farms using the faecal egg count reduction test. Efficacy against strongyles was determined by calculating the percentage of reduction in faecal egg count between the group mean at Day 0 and Days 14–17 post-treatment and the 95% lower confidence intervals estimated by non-parametric bootstrapping. Individual strongyle faecal egg count reduction tests (n = 429) were performed in which 179, 131, 89 and 30 horses were administered ivermectin, moxidectin, pyrantel and fenbendazole, respectively. Moxidectin was efficacious in all tests (faecal egg count reduction range: 99.8–100%; 95% lower confidence intervals range: 96.8–100%) and reduced efficacy of ivermectin (faecal egg count reduction range: 85.7–100%; 95% lower confidence intervals range: 65–100%) was observed in one group of yearlings. Reduced pyrantel efficacy was observed in five groups of yearlings (faecal egg count reduction range: 0–73%; 95% lower confidence intervals range: 0–59.5%), but pyrantel was found to be efficacious when administered to mares (faecal egg count reduction range: 98–99.4%; 95% lower confidence intervals range: 91.8–99.3%). Low efficacy of fenbendazole was always observed (faecal egg count reduction range: 0.4–41%; 95% lower confidence intervals not calculable). Two further methods for estimating efficacy were applied and outputs obtained using all methodologies were in agreement. Efficacy against Parascaris equorum was assessed on four farms: fenbendazole had acceptable efficacy (faecal egg count reduction range: 97.5–99.9%; 95% lower confidence intervals range: 96.3–99.1%), but reduced efficacy of ivermectin was observed (faecal egg count reduction range: 25.5–91.2%; 95% lower confidence intervals range: 6.7–82.4%). Strongyle faecal egg count were analysed at approximately 2 week intervals for up to 12 weeks after anthelmintic drug administration to determine the egg reappearance period for moxidectin, ivermectin and pyrantel. The egg reappearance period for all three anthelmintic drugs was shorter than previously observed. Overall, our results indicate that ivermectin and moxidectin administration provided acceptable efficacy at 14 days; however, egg reappearance period results suggest that these products are working less effectively than measured previously. As shortened egg reappearance period is believed to be an early indicator of resistance, this highlights the issue of impending multi-drug resistance in strongyles on stud farms.     

Genetic Evidence for the Involvement of the S-Layer Protein Gene sap and the Sporulation Genes spo0A,spo0B,and spo0F in Phage AP50c Infection of Bacillus anthracis

In order to better characterize the Bacillus anthracis typing phage AP50c, we designed a genetic screen to identify its bacterial receptor. Insertions of the transposon mariner or targeted deletions of the structural gene for the S-layer protein Sap and the sporulation genes spo0A, spo0B, and spo0F in B. anthracis Sterne resulted in phage resistance with concomitant defects in phage adsorption and infectivity. Electron microscopy of bacteria incubated with AP50c revealed phage particles associated with the surface of bacilli of the Sterne strain but not with the surfaces of Δsap, Δspo0A, Δspo0B, or Δspo0F mutants. The amount of Sap in the S layer of each of the spo0 mutant strains was substantially reduced compared to that of the parent strain, and incubation of AP50c with purified recombinant Sap led to a substantial reduction in phage activity. Phylogenetic analysis based on whole-genome sequences of B. cereus sensu lato strains revealed several closely related B. cereus and B. thuringiensis strains that carry sap genes with very high similarities to the sap gene of B. anthracis. Complementation of the Δsap mutant in trans with the wild-type B. anthracis sap or the sap gene from either of two different B. cereus strains that are sensitive to AP50c infection restored phage sensitivity, and electron microscopy confirmed attachment of phage particles to the surface of each of the complemented strains. Based on these data, we postulate that Sap is involved in AP50c infectivity, most likely acting as the phage receptor, and that the spo0 genes may regulate synthesis of Sap and/or formation of the S layer.     

Local environment and density-dependent feedbacks determine population growth in a forest herb

Linking spatial variation in environmental factors to variation in demographic rates is essential for a mechanistic understanding of the dynamics of populations. However, we still know relatively little about such links, partly because feedbacks via intraspecific density make them difficult to observe in natural populations. We conducted a detailed field study and investigated simultaneous effects of environmental factors and the intraspecific density of individuals on the demography of the herb Lathyrus vernus. In regression models of vital rates we identified effects associated with spring shade on survival and growth, while density was negatively correlated with these vital rates. Density was also negatively correlated with average individual size in the study plots, which is consistent with self-thinning. In addition, average plant sizes were larger than predicted by density in plots that were less shaded by the tree canopy, indicating an environmentally determined carrying capacity. A size-structured integral projection model based on the vital rate regressions revealed that the identified effects of shade and density were strong enough to produce differences in stable population sizes similar to those observed in the field. The results illustrate how the local environment can determine dynamics of populations and that intraspecific density may have to be more carefully considered in studies of plant demography and population viability analyses of threatened species. We conclude that demographic approaches incorporating information about both density and key environmental factors are powerful tools for understanding the processes that interact to determine population dynamics and abundances.     

Seagrass feeding choices and digestive strategies of the herbivorous fish Sarpa salpa

This is the first study investigating the plant–herbivore interaction between Sarpa salpa, which has overgrazed seagrass transplants in Portugal, and the seagrasses Cymodocea nodosa, Zostera marina and Zostera noltii, which have been considered for restoration. When offered the choice between the three seagrasses in outdoor tanks, adult S. salpa clearly preferred Z. noltii. Testing the seagrasses separately, mean ± s.d. feeding rates ranged from 21 ± 11 g seagrass fresh mass kg^?1 fish mass day^?1 for Z. marina to 32 ± 9 g seagrass fresh mass kg^?1 fish mass day^?1 for C. nodosa and 40 ± 11 g seagrass fresh mass kg^?1 fish mass day^?1 for Z. noltii (temperature = 16° C). Food‐processing rate in S. salpa did not differ between seagrasses, and there was no evidence of a regulation of processing rate according to food intake. Seagrasses differed substantially in nitrogen content and C:N, with C. nodosa containing the highest nitrogen content and lowest C:N (2·5 ± 0·1% and 14·0 ± 1·0), followed by Z. noltii (2·1 ± 0·1% and 17·0 ± 1·0) and Z. marina (1·4 ± 0·1% and 26·0 ± 2·0). Food‐processing rate in S. salpa and the nutritional value of the seagrasses were not correlated with the observed feeding preference and rate. The study suggests that C. nodosa and Z. marina are less at risk of overgrazing by S. salpa and might thus be preferable to Z. noltii for seagrass restoration in areas with noticeable abundances of this fish.     

Single-nucleotide polymorphism associations in common with immune responses to measles and rubella vaccines

Single-nucleotide polymorphisms (SNPs) in candidate immune response genes were evaluated for associations with measles- and rubella-specific neutralizing antibodies, interferon (IFN)-γ, and interleukin (IL)-6 secretion in two separate association analyses in a cohort of healthy immunized subjects. We identified six SNP associations shared between the measles-specific and rubella-specific immune responses, specifically neutralizing antibody titers (DDX58), secreted IL-6 (IL10RB, IL12B), and secreted IFN-γ (IFNAR2, TLR4). An intronic SNP (rs669260) in the antiviral innate immune receptor gene, DDX58, was significantly associated with increased neutralizing antibody titers for both measles and rubella viral antigens post-MMR vaccination (p values 0.02 and 0.0002, respectively). Significant associations were also found between IL10RB (rs2284552; measles study p value 0.006, rubella study p value 0.00008) and IL12B (rs2546893; measles study p value 0.005, rubella study p value 0.03) gene polymorphisms and variations in both measles- and rubella virus-specific IL-6 responses. We also identified associations between individual SNPs in the IFNAR2 and TLR4 genes that were associated with IFN-γ secretion for both measles and rubella vaccine-specific immune responses. These results are the first to indicate that there are SNP associations in common across measles and rubella vaccine immune responses and that SNPs from multiple genes involved in innate and adaptive immune response regulation may contribute to the overall human antiviral response.     

‘The best borough in the country for cohesion!’: managing place and multiculture in local government

Abstract

In the interface between national and local levels of UK government, narratives of place are made to fit particular tropes of ‘success’ or ‘failure’ at multiculturalism. Thinking through ‘community cohesion’ policy in England between 2001 and 2010, this article shows how (reputations of) relative success at ‘living together with difference’ become a medium through which local government practitioners negotiate the space between national and local priorities, needs and ambitions, by examining how practitioners in English local authorities negotiate narratives of ‘failed multiculturalism’ associated with the places they work and, in doing so, how they re-inscribe or subvert local reputations and their ‘elsewheres’.