Parallelism and divergence in immune responses: a comparison of expression levels in two lakes

Question: How do immune phenotypes differ between infected and uninfected wild individuals, and is the effect the same in different populations? Organisms: Threespine stickleback (Gasterosteus aculeatus) from two lake populations on the island of North Uist, Scotland, sampled in May 2015. Methods: For each fish, we recorded length, sex, reproductive status, condition, and parasitic infection. We measured the expression levels of eight genes that act as key markers of immune system function using qPCR, and then examined the relationship between measured factors and immune gene expression profiles within each population. Conclusions: Populations differed significantly in their immune gene expression profiles. Within each population, multiple factors, including condition, reproductive status, and Schistocephalus solidus infection levels, were found to correlate with expression levels of different arms of the immune system

Adaptive HIV-1 evolutionary trajectories are constrained by protein stability

Despite the use of combination antiretroviral drugs for the treatment of HIV-1 infection, the emergence of drug resistance remains a problem. Resistance may be conferred either by a single mutation or a concerted set of mutations. The involvement of multiple mutations can arise due to interactions between sites in the amino acid sequence as a consequence of the need to maintain protein structure. To better understand the nature of such epistatic interactions, we reconstructed the ancestral sequences of HIV-1's Pol protein, and traced the evolutionary trajectories leading to mutations associated with drug resistance. Using contemporary and ancestral sequences we modelled the effects of mutations (i.e. amino acid replacements) on protein structure to understand the functional effects of residue changes. Although the majority of resistance-associated sequences tend to destabilise the protein structure, we find there is a general tendency for protein stability to decrease across HIV-1's evolutionary history. That a similar pattern is observed in the non-drug resistance lineages indicates that non-resistant mutations, for example, associated with escape from the immune response, also impacts on protein stability. Maintenance of optimal protein structure therefore represents a major constraining factor to the evolution of HIV-1

Measuring the immune system of the three-spined stickleback: investigating natural variation by quantifying immune expression in the laboratory and the wild

Current understanding of the immune system comes primarily from lab-based studies. There has been substantial interest in examining how it functions in the wild, but studies have been limited by a lack of appropriate assays and study species. The three-spined stickleback (Gasterosteus aculeatus L.) provides an ideal system in which to advance the study of wild immunology, but requires the development of suitable immune assays. We demonstrate that meaningful variation in the immune response of stickleback can be measured using real-time PCR to quantify the expression of eight genes, representing the innate response and Th1, Th2 and Treg type adaptive responses. Assays are validated by comparing the immune expression profiles of wild and laboratory raised stickleback, and by examining variation across populations on North Uist, Scotland. We also compare the immune response potential of laboratory raised individuals from two Icelandic populations by stimulating cells in culture. Immune profiles of wild fish differed from laboratory-raised fish from the same parental population, with immune expression patterns in the wild converging relative to those in the laboratory. Innate measures differed between wild populations, whilst the adaptive response was associated with variation in age, relative size of fish, reproductive status and S. solidus infection levels. Laboratory-raised individuals from different populations showed markedly different innate immune response potential. The ability to combine studies in the laboratory and in the wild underline the potential of this toolkit to advance our understanding of the ecological and evolutionary relevance of immune system variation in a natural setting

No evidence of local adaptation of immune responses to Gyrodactylus in three-spined stickleback (Gasterosteus aculeatus)

Parasitism represents one of the most widespread lifestyles in the animal kingdom, with the potential to drive coevolutionary dynamics with their host population. Where hosts and parasites evolve together, we may find local adaptation. As one of the main host defences against infection, there is the potential for the immune response to be adapted to local parasites. In this study, we used the three-spined stickleback and its Gyrodactylus parasites to examine the extent of local adaptation of parasite infection dynamics and the immune response to infection. We took two geographically isolated host populations infected with two distinct Gyrodactylus species and performed a reciprocal cross-infection experiment in controlled laboratory conditions. Parasite burdens were monitored over the course of the infection, and individuals were sampled at multiple time points for immune gene expression analysis. We found large differences in virulence between parasite species, irrespective of host, and maladaptation of parasites to their sympatric host. The immune system responded to infection, with a decrease in expression of innate and Th1-type adaptive response genes in fish infected with the less virulent parasite, representing a marker of a possible resistance mechanism. There was no evidence of local adaptation in immune gene expression levels. Our results add to the growing understanding of the extent of host-parasite local adaptation, and demonstrate a systemic immune response during infection with a common ectoparasite. Further immunological studies using the stickleback-Gyrodactylus system can continue to contribute to our understanding of the function of the immune response in natural populations

Measuring the immune system of the three-spined stickleback: investigating natural variation by quantifying immune expression in the laboratory and the wild

Current understanding of the immune system comes primarily from lab-based studies. There has been substantial interest in examining how it functions in the wild, but studies have been limited by a lack of appropriate assays and study species. The three-spined stickleback (Gasterosteus aculeatus L.) provides an ideal system in which to advance the study of wild immunology, but requires the development of suitable immune assays. We demonstrate that meaningful variation in the immune response of stickleback can be measured using real-time PCR to quantify the expression of eight genes, representing the innate response and Th1, Th2 and Treg type adaptive responses. Assays are validated by comparing the immune expression profiles of wild and laboratory raised stickleback, and by examining variation across populations on North Uist, Scotland. We also compare the immune response potential of laboratory raised individuals from two Icelandic populations by stimulating cells in culture. Immune profiles of wild fish differed from laboratory-raised fish from the same parental population, with immune expression patterns in the wild converging relative to those in the laboratory. Innate measures differed between wild populations, whilst the adaptive response was associated with variation in age, relative size of fish, reproductive status and S. solidus infection levels. Laboratory-raised individuals from different populations showed markedly different innate immune response potential. The ability to combine studies in the laboratory and in the wild underline the potential of this toolkit to advance our understanding of the ecological and evolutionary relevance of immune system variation in a natural setting

The ecological and evolutionary importance of immune system variation in the three-spined stickleback

Placing our understanding of the function of the immune system into a more natural setting remains a fundamental challenge in biology, particularly how natural variation shapes the immune response and what the evolutionary consequences of such variation are. In this thesis, I use the three-spined stickleback as a model system for wild immunological studies. First, I developed a set of markers to measure the expression levels of key immune system genes using quantitative real-time PCR, representing the innate and adaptive immune response, and then used them to address a number of questions. I demonstrated that there are underlying differences in innate and adaptive gene expression levels between populations, as well as in innate immune response potential, which may reflect the contrasting challenges faced in these populations. By sampling individuals from multiple wild populations, I was able to demonstrate how a range of factors contribute to shaping immune system function, including sex, reproductive status, and infection with the common parasites Schistocephalus solidus and Gyrodactylus arcuatus. Next, I exposed laboratory raised fish to natural conditions and examined their response. Again, a range of factors where identified which appear to shape immune expression levels, particularly reproductive investment and infection with G. arcuatus. I also used this approach to demonstrate that immune system variation can be linked to Eda genotype, the gene which controls lateral plate phenotypic divergence during adaptive radiations. Finally, I performed a controlled infection experiment in the laboratory to show that both the innate and adaptive systems respond to Gyrodactylus infection. This thesis provides the basis for further immunological studies in stickleback, and adds to our growing understanding of the relevance of natural variation in shaping the immune response

Carbonated water injection (CWI) - a productive way of using CO2 for oil recovery and CO2 storage

AbstractThe main advantage of CO2 is that at most reservoir conditions it is a supercritical fluid which is likely to develop miscibility with the oil. In reservoirs that miscibility cannot be achieved, CO2 injection can lead to additional oil recovery by mixing with the oil and favourably modifying the flow properties of the oil. Displacement and recovery of oil by CO2 injection has been studied and applied in the field extensively in the past three decades. Concerns over the environmental impact of CO2 have led to a resurgence of interest in CO2 injection in oil reservoirs. The injection of CO2 can enhance oil recovery from these reservoirs and at the same time help mitigating the problem of increased CO2 concentrations in the atmosphere by storing large quantities of CO2 for a long period of time.CO2 injection projects so far have been mainly limited geographically to oil fields located in areas where large quantities of CO2 have been available mainly from natural resources. Various CO2 injection strategies e.g. cyclic injection, continuous CO2 flood, alternating (WAG) or simultaneous injection of CO2 and water have been applied in these fields. With the new global interest in CO2 injection, many other reservoir settings and scenarios are being considered for CO2 injection in oil reservoirs. This may require injection strategies other than those conventionally used for CO2 injection especially for offshore reservoirs or in cases where the supply of CO2 can be variable or limited.An alternative CO2 injection strategy is carbonated (CO2-enriched) water injection. In carbonated water, CO2 exists as a dissolved phase as opposed to a free phase eliminating the problems of gravity segregation and poor sweep efficiency, which are characteristics of a typical CO2 injection project. In fact, both viscosity and density of water increase as a result of the dissolution of CO2 in water. In terms of CO2 storage, through carbonated water injection, large volumes of CO2 can be injected into the reservoir without the risk of leakage of CO2 through caprock.Using the results of a series of high-pressure flow visualisation experiments, we reveal the underlying physical processes taking place during CWI. The results show that CWI, compared to conventional water injection, improves oil recovery in both secondary (pre-waterflood) and tertiary (post-waterflood) injection modes. Several key mechanisms taking place at the pore level during CWI leading to additional recovery are presented and discussed. Both conventional (light) oil and viscous oil was used in the experiments

Data feedback and behavioural change intervention to improve primary care prescribing safety (EFIPPS):multicentre, three arm, cluster randomised controlled trial

Objective: To evaluate the effectiveness of feedback on safety of prescribing compared with moderately enhanced usual care. Design: Three arm, highly pragmatic cluster randomised trial. Setting and participants: 262/278 (94%) primary care practices in three Scottish health boards. Interventions: Practices were randomised to: "usual care," consisting of emailed educational material with support for searching to identify patients (88 practices at baseline, 86 analysed); usual care plus feedback on practice's high risk prescribing sent quarterly on five occasions (87 practices, 86 analysed); or usual care plus the same feedback incorporating a behavioural change component (87 practices, 86 analysed). Main outcome measures: The primary outcome was a patient level composite of six prescribing measures relating to high risk use of antipsychotics, non-steroidal anti-inflammatories, and antiplatelets. Secondary outcomes were the six individual measures. The primary analysis compared high risk prescribing in the two feedback arms against usual care at 15 months. Secondary analyses examined immediate change and change in trend of high risk prescribing associated with implementation of the intervention within each arm. Results: In the primary analysis, high risk prescribing as measured by the primary outcome fell from 6.0% (3332/55 896) to 5.1% (2845/55 872) in the usual care arm, compared with 5.9% (3341/56 194) to 4.6% (2587/56 478) in the feedback only arm (odds ratio 0.88 (95% confidence interval 0.80 to 0.96) compared with usual care; P=0.007) and 6.2% (3634/58 569) to 4.6% (2686/58 582) in the feedback plus behavioural change component arm (0.86 (0.78 to 0.95); P=0.002). In the pre-specified secondary analysis of change in trend within each arm, the usual care educational intervention had no effect on the existing declining trend in high risk prescribing. Both types of feedback were associated with significantly more rapid decline in high risk prescribing after the intervention compared with before. Conclusions: Feedback of prescribing safety data was effective at reducing high risk prescribing. The intervention would be feasible to implement at scale in contexts where electronic health records are in general use

Exploring extensions to the standard cosmological model and the impact of baryons on small scales

It has been claimed that the standard model of cosmology (ΛCDM) cannot easily account for a number of observations on relatively small scales, motivating extensions to the standard model. Here, we introduce a new suite of cosmological simulations that systematically explores three plausible extensions: warm dark matter, self-interacting dark matter, and a running of the scalar spectral index of density fluctuations. Current observational constraints are used to specify the additional parameters that come with these extensions. We examine a large range of observable metrics on small scales, including the halo mass function, density, and circular velocity profiles, the abundance of satellite subhaloes, and halo concentrations. For any given metric, significant degeneracies can be present between the extensions. In detail, however, the different extensions have quantitatively distinct mass and radial dependencies, suggesting that a multiprobe approach over a range of scales can be used to break the degeneracies. We also demonstrate that the relative effects on the radial density profiles in the different extensions (compared to the standard model) are converged down to significantly smaller radii than are the absolute profiles. We compare the derived cosmological trends with the impact of baryonic physics using the EAGLE and ARTEMIS simulations. Significant degeneracies are also present between baryonic physics and cosmological variations (with both having similar magnitude effects on some observables). Given the inherent uncertainties both in the modelling of galaxy formation physics and extensions to ΛCDM, a systematic and simultaneous exploration of both is strongly warranted