Analysis of pir gene expression across the Plasmodium life cycle.

BACKGROUND: Plasmodium interspersed repeat (pir) is the largest multigene family in the genomes of most Plasmodium species. A variety of functions for the PIR proteins which they encode have been proposed, including antigenic variation, immune evasion, sequestration and rosetting. However, direct evidence for these is lacking. The repetitive nature of the family has made it difficult to determine function experimentally. However, there has been some success in using gene expression studies to suggest roles for some members in virulence and chronic infection. METHODS: Here pir gene expression was examined across the life cycle of Plasmodium berghei using publicly available RNAseq data-sets, and at high resolution in the intraerythrocytic development cycle using new data from Plasmodium chabaudi. RESULTS: Expression of pir genes is greatest in stages of the parasite which invade and reside in red blood cells. The marked exception is that liver merozoites and male gametocytes produce a very large number of pir gene transcripts, notably compared to female gametocytes, which produce relatively few. Within the asexual blood stages different subfamilies peak at different times, suggesting further functional distinctions. Representing a subfamily of its own, the highly conserved ancestral pir gene warrants further investigation due to its potential tractability for functional investigation. It is highly transcribed in multiple life cycle stages and across most studied Plasmodium species and thus is likely to play an important role in parasite biology. CONCLUSIONS: The identification of distinct expression patterns for different pir genes and subfamilies is likely to provide a basis for the design of future experiments to uncover their function.

Investigating the effects of inter-annual weather variation (1968-2016) on the functional response of cereal grain yield to applied nitrogen, using data from the Rothamsted Long-Term Experiments.

The effect of weather on inter-annual variation in the crop yield response to nitrogen (N) fertilizer for winter wheat (Triticum aestivvum L.) and spring barley (Hordeum vulgare L.) was investigated using yield data from the Broadbalk Wheat and Hoosfield Spring Barley long-term experiments at Rothamsted Research. Grain yields of crops from 1968 to 2016 were modelled as a function of N rates using a linear-plus-exponential (LEXP) function. The extent to which inter-annual variation in the parameters of these responses was explained by variations in weather (monthly summarized temperatures and rainfall), and by changes in the cultivar grown, was assessed. The inter-annual variability in rainfall and underlying temperature influenced the crop N response and hence grain yields in both crops. Asymptotic yields in wheat were particularly sensitive to mean temperature in November, April and May, and to total rainfall in October, February and June. In spring barley asymptotic yields were sensitive to mean temperature in February and June, and to total rainfall in April to July inclusive and September. The method presented here explores the separation of agronomic and environmental (weather) influences on crop yield over time. Fitting N response curves across multiple treatments can support an informative analysis of the influence of weather variation on the yield variability. Whilst there are issues of the confounding and collinearity of explanatory variables within such models, and that other factors also influence yields over time, our study confirms the considerable impact of weather variables at certain times of the year. This emphasizes the importance of including weather temporal variation when evaluating the impacts of climate change on crops.

Repeated clinical malaria episodes are associated with modification of the immune system in children.

BACKGROUND: There are over 200 million reported cases of malaria each year, and most children living in endemic areas will experience multiple episodes of clinical disease before puberty. We set out to understand how frequent clinical malaria, which elicits a strong inflammatory response, affects the immune system and whether these modifications are observable in the absence of detectable parasitaemia. METHODS: We used a multi-dimensional approach comprising whole blood transcriptomic, cellular and plasma cytokine analyses on a cohort of children living with endemic malaria, but uninfected at sampling, who had been under active surveillance for malaria for 8 years. Children were categorised into two groups depending on the cumulative number of episodes experienced: high (≥ 8) or low (< 5). RESULTS: We observe that multiple episodes of malaria are associated with modification of the immune system. Children who had experienced a large number of episodes demonstrated upregulation of interferon-inducible genes, a clear increase in circulating levels of the immunoregulatory cytokine IL-10 and enhanced activation of neutrophils, B cells and CD8+ T cells. CONCLUSION: Transcriptomic analysis together with cytokine and immune cell profiling of peripheral blood can robustly detect immune differences between children with different numbers of prior malaria episodes. Multiple episodes of malaria are associated with modification of the immune system in children. Such immune modifications may have implications for the initiation of subsequent immune responses and the induction of vaccine-mediated protection.

A heteroskedastic model of Park Grass spring hay yields in response to weather suggests continuing yield decline with climate change in future decades.

UK grasslands perform important environmental and economic functions, but their future productivity under climate change is uncertain. Spring hay yields from 1902 to 2016 at one site (the Park Grass Long Term Experiment) in southern England under four different fertilizer regimes were modelled in response to weather (seasonal temperature and rainfall). The modelling approach applied comprised: (1) a Bayesian model comparison to model parametrically the heteroskedasticity in a gamma likelihood function; (2) a Bayesian varying intercept multiple regression model with an autoregressive lag one process (to incorporate the effect of productivity in the previous year) of the response of hay yield to weather from 1902 to 2016. The model confirmed that warmer and drier years, specifically, autumn, winter and spring, in the twentieth and twenty-first centuries reduced yield. The model was applied to forecast future spring hay yields at Park Grass under different climate change scenarios (HadGEM2 and GISS RCP 4.5 and 8.5). This application indicated that yields are forecast to decline further between 2020 and 2080, by as much as 48-50%. These projections are specific to Park Grass, but implied a severe reduction in grassland productivity in southern England with climate change during the twenty-first century.

The impact of weather and increased atmospheric CO2 from 1892 to 2016 on simulated yields of UK wheat.

Climate change effects on UK winter wheat grain yield are complex: warmer temperature, negative; greater carbon dioxide (CO2) concentration, positive; but other environmental variables and their timing also affect yield. In the absence of long-term experiments where temperature and CO2 concentration were manipulated separately, we applied the crop simulation model Sirius with long-term daily meteorological data (1892-2016) for Rothamsted, Hertfordshire, UK (2007-2016 mean growing season temperature 1.03°C warmer than 1892-1991), and CO2 concentration over this period, to investigate the separate effects of historic CO2 and weather on simulated grain yield in three wheat cultivars of the modern era. We show a slight decline in simulated yield over the period 1892-2016 from the effect of weather (daily temperature, rainfall and sunshine hours) at fixed CO2 (294.50 ppm, 1892 reference value), but a maximum 9.4% increase when accounting for increasing atmospheric CO2 (from 294.50 to 404.21 ppm), differing slightly among cultivars. Notwithstanding considerable inter-annual variation, the slight yield decline at 294.50 ppm CO2 over this 125-year period from the historic weather simulations for Rothamsted agrees with the expected decline from temperature increase alone, but the positive yield trend with actual CO2 values does not match the recent stagnation in UK wheat yield.

Tissue macrophages and interferon-gamma signalling control blood-stage Plasmodium chabaudi infections derived from mosquito-transmitted parasites.

Natural infection with Plasmodium parasites, the causative agents of malaria, occurs via mosquito vectors. However, most of our knowledge of the immune response to the blood stages of Plasmodium is from infections initiated by injection of serially blood-passaged infected red blood cells, resulting in an incomplete life cycle in the mammalian host. Vector transmission of the rodent malaria parasite, Plasmodium chabaudi chabaudi AS has been shown to give rise to a more attenuated blood-stage infection in C57Bl/6J mice, when compared to infections initiated with serially blood-passaged P. chabaudi-infected red blood cells. In mouse models, the host immune response induced by parasites derived from natural mosquito transmission is likely to more closely resemble the immune responses to Plasmodium infections in humans. It is therefore important to determine how the host response differs between the two types of infections. As the spleen is considered to be a major contributor to the protective host response to P. chabaudi, we carried out a comparative transcriptomic analysis of the splenic response to recently mosquito-transmitted and serially blood-passaged parasites in C57Bl/6J mice. The attenuated infection arising from recently mosquito-transmitted parasites is characterised by an earlier and stronger myeloid- and IFNγ-related response. Analyses of spleen lysates from the two infections similarly showed stronger or earlier inflammatory cytokine and chemokine production in the recently mosquito-transmitted blood-stage infections. Furthermore, tissue macrophages, including red pulp macrophages, and IFNγ-signalling in myeloid cells, are required for the early control of P. chabaudi recently mosquito-transmitted parasites, thus contributing to the attenuation of mosquito-transmitted infections. The molecules responsible for this early activation response to recently-transmitted blood-stage parasites in mice would be important to identify, as they may help to elucidate the nature of the initial interactions between blood-stage parasites and the host immune system in naturally transmitted malaria.

Individual-level variations in malaria susceptibility and acquisition of clinical protection.

After decades of research, our understanding of when and why individuals infected with Plasmodium falciparum develop clinical malaria is still limited. Correlates of immune protection are often sought through prospective cohort studies, where measured host factors are correlated against the incidence of clinical disease over a set period of time. However, robustly inferring individual-level protection from these population-level findings has proved difficult due to small effect sizes and high levels of variance underlying such data. In order to better understand the nature of these inter-individual variations, we analysed the long-term malaria epidemiology of children ≤12 years old growing up under seasonal exposure to the parasite in the sub-location of Junju, Kenya. Despite the cohort's limited geographic expanse (ca. 3km x 10km), our data reveal a high degree of spatial and temporal variability in malaria prevalence and incidence rates, causing individuals to experience varying levels of exposure to the parasite at different times during their life. Analysing individual-level infection histories further reveal an unexpectedly high variability in the rate at which children experience clinical malaria episodes. Besides exposure to the parasite, measured as disease prevalence in the surrounding area, we find that the birth time of year has an independent effect on the individual's risk of experiencing a clinical episode. Furthermore, our analyses reveal that those children with a history of an above average number of episodes are more likely to experience further episodes during the upcoming transmission season. These findings are indicative of phenotypic differences in the rates by which children acquire clinical protection to malaria and offer important insights into the natural variability underlying malaria epidemiology.

10-year longitudinal study of malaria in children: Insights into acquisition and maintenance of naturally acquired immunity.

Background: Studies of long-term malaria cohorts have provided essential insights into how Plasmodium falciparum interacts with humans, and influences the development of antimalarial immunity. Immunity to malaria is acquired gradually after multiple infections, some of which present with clinical symptoms. However, there is considerable variation in the number of clinical episodes experienced by children of the same age within the same cohort. Understanding this variation in clinical symptoms and how it relates to the development of naturally acquired immunity is crucial in identifying how and when some children stop experiencing further malaria episodes. Where variability in clinical episodes may result from different rates of acquisition of immunity, or from variable exposure to the parasite. Methods: Using data from a longitudinal cohort of children residing in an area of moderate P. falciparum transmission in Kilifi district, Kenya, we fitted cumulative episode curves as monotonic-increasing splines, to 56 children under surveillance for malaria from the age of 5 to 15. Results: There was large variability in the accumulation of numbers of clinical malaria episodes experienced by the children, despite being of similar age and living in the same general location. One group of children from a particular sub-region of the cohort stopped accumulating clinical malaria episodes earlier than other children in the study. Despite lack of further clinical episodes of malaria, these children had higher asymptomatic parasite densities and higher antibody titres to a panel of P. falciparum blood-stage antigens. Conclusions: This suggests development of clinical immunity rather than lack of exposure to the parasite, and supports the view that this immunity to malaria disease is maintained by a greater exposure to P. falciparum, and thus higher parasite burdens. Our study illustrates the complexity of anti-malaria immunity and underscores the need for analyses which can sufficiently reflect the heterogeneity within endemic populations.