Detecting signatures of balancing selection to identify targets of anti-parasite immunity.

Parasite antigen genes might evolve under frequency-dependent immune selection. The distinctive patterns of polymorphism that result can be detected using population genetic methods that test for signatures of balancing selection, allowing genes encoding important targets of immunity to be identified. Analyses can be complicated by population structures, histories and features of a parasite's genome. However, new sequencing technologies facilitate scans of polymorphism throughout parasite genomes to identify the most exceptional gene specific signatures. We focus on malaria parasites to illustrate challenges and opportunities for detecting targets of frequency-dependent immune selection to discover new potential vaccine candidates

The impact of conservation translocations on vector-borne parasites : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Ecology at Massey University, Palmerston North, New Zealand

Wildlife conservation in New Zealand relies on translocations of endangered species to safe sites. While knowledge of the biology and behaviour of translocated hosts has steadily increased, the role of parasites in wildlife translocations has been largely overlooked. Parasites can affect their host’s survivorship during translocations by causing disease. However, failure to translocate or reintroduce a host specific parasite with its endangered host can contribute to the extinction of the parasite with unforeseen consequences for the future of the host or even the whole ecosystem. The main aims of this study were to establish baseline data on the impact of North Island saddleback translocations on their avian malaria (Plasmodium spp.) parasites as well as gaining further insight into potential vectors in New Zealand. The study was also intended to contribute to the development of recommendations for future parasite screening programmes for native passerine translocations. Saddlebacks and Plasmodium were chosen because of the detailed saddleback translocation history and its known relationship with the parasite. As a result of this study, several Plasmodium lineages previously unrecorded in saddlebacks and New Zealand were identified, for example, the native Kokako01 and one lineage closest related to two lineages from the Americas. Nonetheless, the most frequent lineages found were the cosmopolitan P. elongatum GRW6 and LINN1, and P. vaughani SYAT05, common in birds introduced to New Zealand. This finding suggests that endemic parasites may have already become rare or extinct. In addition, Plasmodium DNA was detected in both native and introduced mosquitoes that may act as vectors. A qPCR assay was developed that was found to be a cost effective and rapid screening tool for the detection of Plasmodium in native birds suffering from acute infection, presenting with clinical symptoms, and in birds that were found dead. . I conclude that future translocations should consider the movement of endemic parasites with their hosts. How this should happen is open for future studies. However, I urge managers to start considering this issue now as New Zealand has already recorded the extinction of one endemic parasite and many more may have already been lost without knowledge

Computing Substrates and Life

Alive matter distinguishes itself from inanimate matter by actively maintaining a high degree of inhomogenous organisation. Information processing is quintessential to this capability. The present paper inquires into the degree to which the information processing aspect of living systems can be abstracted from the physical medium of its implementation. Information processing serving to sustain the complex organisation of a living system faces both the harsh reality of real-time requirements and severe constraints on energy and material that can be expended on the task. This issue is of interest for the potential scope of Artificial Life and its interaction with Synthetic Biology. It is pertinent also for information technology. With regard to the latter aspect, the use of a living cell in a robot control architecture is considered

Whole genome sequencing and microsatellite analysis of the Plasmodium falciparum E5 NF54 strain show that the var, rifin and stevor gene families follow Mendelian inheritance

Background: Plasmodium falciparum exhibits a high degree of inter-isolate genetic diversity in its variant surface antigen (VSA) families: P. falciparum erythrocyte membrane protein 1, repetitive interspersed family (RIFIN) and subtelomeric variable open reading frame (STEVOR). The role of recombination for the generation of this diversity is a subject of ongoing research. Here the genome of E5, a sibling of the 3D7 genome strain is presented. Short and long read whole genome sequencing (WGS) techniques (Ilumina, Pacific Bioscience) and a set of 84 microsatellites (MS) were employed to characterize the 3D7 and non-3D7 parts of the E5 genome. This is the first time that VSA genes in sibling parasites were analysed with long read sequencing technology. Results: Of the 5733 E5 genes only 278 genes, mostly var and rifin/stevor genes, had no orthologues in the 3D7 genome. WGS and MS analysis revealed that chromosomal crossovers occurred at a rate of 0–3 per chromosome. var, stevor and rifin genes were inherited within the respective non-3D7 or 3D7 chromosomal context. 54 of the 84 MS PCR fragments correctly identified the respective MS as 3D7- or non-3D7 and this correlated with var and rifin/stevor gene inheritance in the adjacent chromosomal regions. E5 had 61 var and 189 rifin/stevor genes. One large non-chromosomal recombination event resulted in a new var gene on chromosome 14. The remainder of the E5 3D7-type subtelomeric and central regions were identical to 3D7. Conclusions: The data show that the rifin/stevor and var gene families represent the most diverse compartments of the P. falciparum genome but that the majority of var genes are inherited without alterations within their respective parental chromosomal context. Furthermore, MS genotyping with 54 MS can successfully distinguish between two sibling progeny of a natural P. falciparum cross and thus can be used to investigate identity by descent in field isolates

Shedding of host autophagic proteins from the parasitophorous vacuolar membrane of Plasmodium berghei

The hepatic stage of the malaria parasite Plasmodium is accompanied by an autophagy-mediated host response directly targeting the parasitophorous vacuolar membrane (PVM) harbouring the parasite. Removal of the PVM-associated autophagic proteins such as ubiquitin, p62, and LC3 correlates with parasite survival. Yet, it is unclear how Plasmodium avoids the deleterious effects of selective autophagy. Here we show that parasites trap host autophagic factors in the tubovesicular network (TVN), an expansion of the PVM into the host cytoplasm. In proliferating parasites, PVM-associated LC3 becomes immediately redirected into the TVN, where it accumulates distally from the parasite's replicative centre. Finally, the host factors are shed as vesicles into the host cytoplasm. This strategy may enable the parasite to balance the benefits of the enhanced host catabolic activity with the risk of being eliminated by the cell's cytosolic immune defence

Changes in metabolic phenotypes of Plasmodium falciparum in vitro cultures during gametocyte development.

BACKGROUND: Gametocytes are the Plasmodium life stage that is solely responsible for malaria transmission. Despite their important role in perpetuating malaria, gametocyte differentiation and development is poorly understood. METHODS: To shed light on the biochemical changes that occur during asexual and gametocyte development, metabolic characterization of media from in vitro intra-erythrocytic Plasmodium falciparum cultures was performed throughout gametocyte development by applying 1H nuclear magnetic spectroscopy, and using sham erythrocyte cultures as controls. Spectral differences between parasite and sham cultures were assessed via principal component analyses and partial-least squares analyses, and univariate statistical methods. RESULTS: Clear parasite-associated changes in metabolism were observed throughout the culture period, revealing differences between asexual parasites and gametocyte stages. With culture progression and development of gametocytes, parasitic release of the glycolytic end products lactate, pyruvate, alanine, and glycerol, were found to be dramatically reduced whilst acetate release was greatly increased. Also, uptake of lipid moieties CH(2), CH(3), and CH = CH-CH(2)-CH(2) increased throughout gametocyte development, peaking with maturity. CONCLUSIONS: This study uniquely presents an initial characterization of the metabolic exchange between parasite and culture medium during in vitro P. falciparum gametocyte culture. Results suggest that energy metabolism and lipid utilization between the asexual stages and gametocytes is different. This study provides new insights for gametocyte-specific nutritional requirements to aid future optimization and standardization of in vitro gametocyte cultivation, and highlights areas of novel gametocyte cell biology that deserve to be studied in greater detail and may yield new targets for transmission-blocking drugs