Functional characterisation of putative Plasmodium falciparum invasion ligands and their homologues

The apicomplexan parasite Plasmodium falciparum is a major threat to global health, accounting for the majority of malaria-related morbidities and mortalities, totalling to cause ~400,000 deaths per year of which the lives of children under the age of 5 are the most impacted (WHO 2020). This is exacerbated by the onset of resistance against our frontline antimalarials and the lack of an effective licensed vaccine against malaria. Studies which investigate novel interventions against P. falciparum host infection are critical in order produce clinically relevant outcomes. In this thesis, I focussed my studies on the blood stage lifecycle of P. falciparum which is responsible for all clinical symptoms of malaria. More specifically, I examined the molecular mechanisms by which the invasive form of the parasite, the merozoite, uses to invade host red blood cells. The point in time in which merozoites invade red blood cells is defined as a vital crux for the blood stage lifecycle to proceed, whereby blocking invasion prevents further downstream parasite growth and the resulting pathologies. Uncovering the proteins which govern merozoite invasion will aid in informing effective vaccine and antimalarial design in the field. As such, we have identified several conserved genes in P. falciparum which encode proteins with a potential function in merozoites for functional characterisation. We first undertook a study on cytosolically-exposed rhoptry leaflet interacting protein 2 (PfCERLI2), expressed from a duplicated gene of its paralogue PfCERLI1 which is essential for merozoite invasion. Using super-resolution microscopy platforms and Western blot-based membrane assays, we discerned that PfCERLI2 localises to the cytosolic face of the rhoptry, a key invasion organelle, and is more specifically attached to the rhoptry bulb membrane. Our attempts to knock out Pfcerli2 have failed, suggesting it as essential for blood stage growth. To investigate its function, we generated glucosamine-inducible knockdown parasite lines for PfCERLI2 which revealed it as essential for merozoite invasion. Moreover PfCERLI2 appears to be important for establishing proper rhoptry organellar development. Lastly, to determine which proteins may be working in tandem with both PfCERLI1 and PfCERLI2, we utilised dimerization induced quantitative proximity-dependent biotin identification (DiQ-BioID) and quantitative mass spectrometry. The results of this study have revealed the new unexplored biology linked to PfCERLI1 and PfCERLI2’s function in merozoites. Concurrently, we performed a functional characteirsation of P. falciparum C3H1 zinc finger proteins 1 and 2 (PfCZIF1 (Pf3D7_1468400), PfCZIF2 (Pf3D7_0818100)). Our studies have shown PfCZIF1 and PfCZIF2 to be peripherally-attached to a membrane facing the cytosol, with peak expression in schizonts at the point of merozoite development. Functional data in protein truncation and knockout parasite lines have revealed that neither protein in isolation is essential for blood-stage growth, however both cannot be knocked out in tandem suggesting that they fulfil compensatory roles. PfCZIF2 has revealed potential links with the protein PfKAHRP, which is involved in host cell modification. This study has provided the first insights into the functional interplay between PfCZIF1 and PfCZIF2.Thesis (Ph.D.) -- University of Adelaide, School of Biological Sciences, 202

Constructing a word similarity graph from vector based word representation for named entity recognition

In this paper, we discuss a method for identifying a seed word that would best represent a class of named entities in a graphical representation of words and their similarities. Word networks, or word graphs, are representations of vectorized text where nodes are the words encountered in a corpus, and the weighted edges incident on the nodes represent how similar the words are to each other. Word networks are then divided into communities using the Louvain Method for community detection, then betweenness centrality of each node in each community is computed. The most central node in each community represents the most ideal candidate for a seed word of a named entity group which represents the community. Our results from our bilingual data set show that words with similar lexical content, from either language, belong to the same community. Copyright © 2018 by SCITEPRESS - Science and Technology Publications, Lda. All rights reserve

Cell biological analysis reveals an essential role for Pfcerli2 in erythrocyte invasion by malaria parasites

Merozoite invasion of host red blood cells (RBCs) is essential for survival of the human malaria parasite Plasmodium falciparum. Proteins involved with RBC binding and invasion are secreted from dual-club shaped organelles at the apical tip of the merozoite called the rhoptries. Here we characterise P. falciparum Cytosolically Exposed Rhoptry Leaflet Interacting protein 2 (PfCERLI2), as a rhoptry bulb protein that is essential for merozoite invasion. Phylogenetic analyses show that cerli2 arose through an ancestral gene duplication of cerli1. We show that PfCERLI2 is essential for blood-stage growth and localises to the cytosolic face of the rhoptry bulb. Inducible knockdown of PfCERLI2 led to a proportion of merozoites failing to invade and was associated with elongation of the rhoptry organelle during merozoite development and inhibition of rhoptry antigen processing. These findings identify PfCERLI2 as a protein that has key roles in rhoptry biology during merozoite invasion

Challenges for Sustained Observing and Forecasting Systems in the Mediterranean Sea

The Mediterranean community represented in this paper is the result of more than 30 years of EU and nationally funded coordination, which has led to key contributions in science concepts and operational initiatives. Together with the establishment of operational services, the community has coordinated with universities, research centers, research infrastructures and private companies to implement advanced multi-platform and integrated observing and forecasting systems that facilitate the advancement of operational services, scientific achievements and mission-oriented innovation. Thus, the community can respond to societal challenges and stakeholders needs, developing a variety of fit-for-purpose services such as the Copernicus Marine Service. The combination of state-of-the-art observations and forecasting provides new opportunities for downstream services in response to the needs of the heavily populated Mediterranean coastal areas and to climate change. The challenge over the next decade is to sustain ocean observations within the research community, to monitor the variability at small scales, e.g., the mesoscale/submesoscale, to resolve the sub-basin/seasonal and inter-annual variability in the circulation, and thus establish the decadal variability, understand and correct the model-associated biases and to enhance model-data integration and ensemble forecasting for uncertainty estimation. Better knowledge and understanding of the level of Mediterranean variability will enable a subsequent evaluation of the impacts and mitigation of the effect of human activities and climate change on the biodiversity and the ecosystem, which will support environmental assessments and decisions. Further challenges include extending the science-based added-value products into societal relevant downstream services and engaging with communities to build initiatives that will contribute to the 2030 Agenda and more specifically to SDG14 and the UN's Decade of Ocean Science for sustainable development, by this contributing to bridge the science-policy gap. The Mediterranean observing and forecasting capacity was built on the basis of community best practices in monitoring and modeling, and can serve as a basis for the development of an integrated global ocean observing system