IFNL cytokines do not modulate human or murine NK cell functions

The interferon-lambda (IFNL) cytokines have been shown to be important in HCV infection with SNPs in the IFNL3 gene associated with both natural and treatment induced viral clearance. We have recently shown that rs1299860 (an IFNL3 associated SNP) and an NK cell gene, KIR2DS3, synergised to increase the odds of chronic infection in a homogenous cohort of Irish women infected with HCV. To characterise a biological basis for the genetic synergy, we investigated for any evidence that IFNL cytokines regulate NK cell functions. Using a range of functional responses, we did not find any evidence of NK cell activation by IFNL3, IFNL1 or IFNL2 cytokines. Similar results were found using human and murine NK cells. In addition, and in contrast to our preliminary study, we did not find any evidence that IFNL cytokines inhibited NK cell cytokine production; thus, the biological basis for the genetic synergy remains to be discovered.     

Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae

Biological systems remain robust against certain genetic and environmental challenges. Robustness allows the exploration of ecological adaptations. It is unclear what factors contribute to increasing robustness. Gene duplication has been considered to increase genetic robustness through functional redundancy, accelerating the evolution of novel functions. However, recent findings have questioned the link between duplication and robustness. In particular, it remains elusive whether ancient duplicates still bear potential for innovation through preserved redundancy and robustness. Here we have investigated this question by evolving the yeast Saccharomyces cerevisiae for 2200 generations under conditions allowing the accumulation of deleterious mutations, and we put mechanisms of mutational robustness to a test. S. cerevisiae declined in fitness along the evolution experiment, but this decline decelerated in later passages, suggesting functional compensation of mutated genes. We resequenced 28 genomes from experimentally evolved S. cerevisiae lines and found more mutations in duplicates—mainly small-scale duplicates—than in singletons. Genetically interacting duplicates evolved similarly and fixed more amino acid–replacing mutations than expected. Regulatory robustness of the duplicates was supported by a larger enrichment for mutations at the promoters of duplicates than at those of singletons. Analyses of yeast gene expression conditions showed a larger variation in the duplicates’ expression than that of singletons under a range of stress conditions, sparking the idea that regulatory robustness allowed a wider range of phenotypic responses to environmental stresses, hence faster adaptations. Our data support the persistence of genetic and regulatory robustness in ancient duplicates and its role in adaptations to stresses.Biological systems are inherently robust to perturbations, maintaining the same phenotypes in the face of environmental and genetic challenges (Gu et al. 2003; Stelling et al. 2004; Wagner 2005b). Robustness is key to the emergence of biological complexity and diversification as more robust systems can explore a larger set of phenotypes, allowing greater potential for evolving novel adaptations (Draghi et al. 2010; Payne and Wagner 2014). Determining the factors that provide systems with robustness would pave the way for a more complete understanding of the origin of adaptations and biological complexity. However, despite major efforts in understanding robustness (Wagner 2012), the factors that increase robustness of biological systems and their characterization remain to be determined.Gene duplication has been considered to have a major role in genetic robustness (Lynch and Conery 2000), as the presence of two copies performing identical or overlapping functions confers immunity to the deleterious effects of mutations occurring in one of the gene copies. Additionally, gene duplication has been credited with great importance in generating evolutionary novelties (Ohno 1999) because the selection-free exploration of the genotype space, due to genetic redundancy, allows one gene copy to probe a wider range of phenotypes (Payne and Wagner 2014). Arguably, gene duplication provides an invaluable opportunity to explore the link between genetic robustness and evolvability. Indeed, a number of studies have shown that major gene duplication events, such as whole-genome duplication (WGD) in angiosperms (Wendel 2000; Blanc and Wolfe 2004a) and animals (Otto and Whitton 2000; Hoegg et al. 2004), are concomitant with the emergence of morphological, metabolic, and physiological innovations (Otto and Whitton 2000; Holub 2001; Lespinet et al. 2002; Hoegg et al. 2004; Kim et al. 2004; Maere et al. 2005).Despite the apparent causal link between gene duplication and evolutionary innovation, the neutral exploration of genotype space by a duplicated gene requires the persistence of both gene copies for long periods. This clashes with the evolutionary instability of genetic redundancy, illustrated by the fact that 92% of duplicates in Saccharomyces cerevisiae, originated through WGD roughly 100 million years ago (Mya) (Wolfe and Shields 1997), have returned to single gene copies in extant S. cerevisiae. The rate of preservation of genes in duplicate varies, however, among organisms, with some exhibiting up to 30% of their genes in duplicate (Blanc and Wolfe 2004b; Cui et al. 2006). Genetic robustness, along with other factors such as selection for increasing gene dosage (Conant and Wolfe 2008) and gene balance (Birchler et al. 2005; Freeling and Thomas 2006), has been proposed to allow the persistence of genes in duplicate for longer periods of time, thereby providing opportunity for innovation through mutation (Gu et al. 2003; Fares et al. 2013). This claim is supported by larger fitness effects associated with the deletion of singletons compared to duplicates in yeast (Gu et al. 2003), functional compensation of deleted gene copies (VanderSluis et al. 2010), higher robustness of duplicates to transient gene knockdowns in Caenorhabditis elegans (Conant and Wagner 2004), and the contribution of gene duplicates to provide functional back-up against deleterious human mutations (Hsiao and Vitkup 2008). Recent studies have challenged, however, the link between gene duplication and genetic robustness, revealing a more complex relationship between duplicate preservation, genetic redundancy, and robustness. For example, using synthetic lethality genetic maps, Ihmels et al. (2007) found that duplicates, although exhibiting functional compensation, account for only 25% of the mutational robustness of a system. Furthermore, Wagner (2000) analyzed a number of duplicated genes and found no evidence of compensatory effects for null mutations between gene copies with high sequence or expression similarities. Moreover, a recent study has shown that in natural populations of yeast, close duplicates are unlikely to provide substantial functional compensation (Plata and Vitkup 2013). Thus, it is unresolved whether gene duplication provides mutational robustness through genetic redundancy. Since genetic redundancy and robustness are directly linked to evolvability, finding whether or not gene duplication provides sufficient genetic robustness to overcome the energetic and metabolic cost of maintaining additional genetic material is crucial to link gene duplication with the evolution of novel traits. Also, finding appreciable genetic redundancy between the copies of ancient duplicates would support their potential for future biological innovations.The studies conducted so far to probe the link between gene duplication, genetic redundancy, and mutational robustness have been obscured by the complex mixture of the genomic signatures of natural selection and genetic drift. These mixed signatures make it difficult to disentangle the role of genetic redundancy and mutational robustness in the emergence of novel functions from that of selection favoring adaptive mutations. Moreover, most studies ignore the role of the mechanism of duplication, WGD versus small-scale duplication (SSD), in providing mutational robustness and thus opportunity for innovation (Carretero-Paulet and Fares 2012; Fares et al. 2013). It is expected that the present genetic robustness and incomplete functional compensation of today’s duplicates are the remainders of an ancient larger genetic robustness that emerged at the time of gene duplication. Owing to the functional diversification of duplicates, quantification of preserved genetic robustness is complex and requires a direct test of the robustness of current, long-term preserved duplicates to deleterious mutations. Therefore, a definitive resolution of the controversy of whether ancient gene duplicates provide genetic robustness must come from testing the impact of deleterious mutations on duplicates in comparison with singletons. In this study, we resolved the controversy by conducting an experiment that allows the accumulation of deleterious mutations in the genome of S. cerevisiae. Using experimental evolution allows disentangling adaptive mutations from deleterious and neutral mutations and testing hypotheses under tightly controlled experimental conditions, which are not possible in comparative genomics studies. We test, for the first time, whether duplicates tolerate more deleterious mutations in their coding and regulatory regions than expected under the assumption of no genetic robustness.     

The provision of a time-critical elective surgical service during the COVID-19 Crisis: a UK experience

IntroductionWith the emergence of the COVID-19 pandemic, all elective surgery was temporarily suspended in the UK, allowing for diversion of resource to manage the anticipated surge of critically unwell patients. Continuing to deliver time-critical surgical care is important to avoid excess morbidity and mortality from pathologies unrelated to COVID-19. We describe the implementation and short-term surgical outcomes from a system to deliver time-critical elective surgical care to patients during the COVID-19 pandemic.Materials and methodsA protocol for the prioritisation and safe delivery of time-critical surgery at a COVID-19 ‘clean’ site was implemented at the Nuffield Health Exeter Hospital, an independent sector hospital in the southwest of England. Outcomes to 30 days postoperatively were recorded, including unplanned admissions after daycase surgery, readmissions and complications, as well as the incidence of perioperative COVID-19 infection in patients and staff.ResultsA total of 128 surgical procedures were performed during a 31-day period by a range of specialties including breast, plastics, urology, gynaecology, vascular and cardiology. There was one unplanned admission and and two readmissions. Six complications were identified, and all were Clavien-Dindo grade 1 or 2. All 128 patients had preoperative COVID-19 swabs, one of which was positive and the patient had their surgery delayed. Ten patients were tested for COVID-19 postoperatively, with none testing positive.ConclusionThis study has demonstrated the implementation of a safe system for delivery of time-critical elective surgical care at a COVID-19 clean site. Other healthcare providers may benefit from implementation of similar methodology as hospitals plan to restart elective surgery.     

Rapid recalibration of temporal order judgements: Response bias accounts for contradictory results

Recent history influences subsequent perception, decision‐making and motor behaviours. In this article, we address a discrepancy in the effects of recent sensory history on the perceived timing of auditory and visual stimuli. In the synchrony judgement (SJ) task, similar timing relationships in consecutive trials seem more synchronous (i.e. less like the repeated temporal order). This effect is known as rapid recalibration and is consistent with a negative perceptual aftereffect. Interestingly, the opposite is found in the temporal order judgement (TOJ) task (positive rapid recalibration). We aimed to determine whether a simple bias to repeat judgements on consecutive trials (choice‐repetition bias) could account for the discrepant results in these tasks. Preliminary simulations and analyses indicated that a choice‐repetition bias could produce apparently positive rapid recalibration in the TOJ and not the SJ task. Our first experiment revealed no evidence of rapid recalibration of TOJs, but negative rapid recalibration of associated confidence. This suggests that timing perception was rapidly recalibrated, but that the negative recalibration effect was obfuscated by a positive bias effect. In our second experiment, we experimentally mitigated the choice‐repetition bias effect and found negative rapid recalibration of TOJs. We therefore conclude that timing perception is negatively rapidly recalibrated, and this is observed consistently across timing tasks. These results contribute to a growing body of evidence that indicates multisensory perception is constantly undergoing recalibration, such that perceptual synchrony is maintained. This work also demonstrates that participants’ task responses reflect judgements that are contaminated by independent biases of perception and decision‐making.     

Skeletal muscle metastasis from uterine leiomyosarcoma

A case of a 68-year-old woman who presented with a rapidly enlarging painful right thigh mass is presented. She had a known diagnosis of uterine leiomyosarcoma following a hysterectomy for dysfunctional uterine bleeding. She subsequently developed a single hepatic metastatic deposit that responded well to radiofrequency ablation. Whole-body MRI and MRA revealed a vascular mass in the sartorius muscle and a smaller adjacent mass in the gracilis muscle, proven to represent metastatic leiomyosarcoma of uterine origin. To our knowledge, metastatic uterine leiomyosarcoma to the skeletal muscle has not been described previously in the English medical literature.