Combining extension matrix and integer programming for optimal concept learning

This paper proposes two integer programming models and their GA-based solutions for optimal concept learning. The models are built to obtain the optimal concept description in the form of propositional logic formulas from examples based on completeness, consistency and simplicity. The simplicity of the propositional rules is selected as the objective function of the integer programming models, and the completeness and consistency of the concept are used as the constraints. Considering the real-world problems that certain level of noise is contained in data set, the constraints in model 11 are slacked by adding slack-variables. To solve the integer programming models, genetic algorithm is employed to search the global solution space. We call our approach IP-AE. Its effectiveness is verified by comparing the experimental results with other well- known concept learning algorithms: AQ15 and C4.5.

Polyhedral studies for minimum-span graph labelling with integer distance constraints

This paper studies the polytope of the minimum-span graph labelling problems with integer distance constraints (DC-MSGL). We first introduce a few classes of new valid inequalities for the DC-MSGL defined on general graphs and briefly discuss the separation problems of some of these inequalities. These are the initial steps of a branch-and-cut algorithm for solving the DC-MSGL. Following that, we present our polyhedral results on the dimension of the DC-MSGL polytope, and that some of the inequalities are facet defining, under reasonable conditions, for the polytope of the DC-MSGL on triangular graphs.

Parasites affect song complexity and neural development in a songbird

There is now considerable evidence that female choice drives the evolution of song complexity in many songbird species. However, the underlying basis for such choice remains controversial. The developmental stress hypothesis suggests that early developmental conditions can mediate adult song complexity by perturbing investment in the underlying brain nuclei during their initial growth. Here, we show that adult male canaries (Serinus canaria), infected with malaria (Plasmodium relictum) as juveniles, develop simpler songs as adults compared to uninfected individuals, and exhibit reduced development of the high vocal centre (HVC) song nucleus in the brain. Our results show how developmental stress not only affects the expression of a sexually selected male trait, but also the structure of the underlying song control pathway in the brain, providing a direct link between brain and behaviour. This novel experimental evidence tests both proximate and ultimate reasons for the evolution of complex songs and supports the Hamilton–Zuk hypothesis of parasite-mediated sexual selection. Together, these results propose how developmental costs may help to explain the evolution of honest advertising in the complex songs of birds.

Molecular genetics and comparative genomics reveal RNAi is not functional in malaria parasites

Techniques for targeted genetic disruption in Plasmodium, the causative agent of malaria, are currently intractable for those genes that are essential for blood stage development. The ability to use RNA interference (RNAi) to silence gene expression
would provide a powerful means to gain valuable insight into the pathogenic blood stages but its functionality in Plasmodium remains controversial. Here we have used various RNA-based gene silencing approaches to test the utility of RNAi in malaria
parasites and have undertaken an extensive comparative genomics search using profile hidden Markov models to clarify whether RNAi machinery
exists in malaria. These investigative approaches revealed that Plasmodium lacks the enzymology required for RNAi-based ablation of gene expression
and indeed no experimental evidence for RNAi was observed. In its absence, the most likely explanations for previously reported RNAi-mediated knockdown are either the general toxicity of introduced RNA (with global down-regulation of gene expression) or a specific antisense effect mechanistically distinct from RNAi, which will need systematic
analysis if it is to be of use as a molecular genetic tool for malaria parasites.

New insights into protein export in malaria parasites

In order to survive and promote its virulence the malaria parasite must export hundreds of its proteins beyond an encasing vacuole and membrane into the host red blood cell. In the last few years, several major advances have been made that have significantly contributed to our understanding of this export process. These include: (i) the identification of sequences that direct protein export (a signal sequence and a motif termed PEXEL), which have allowed predictions of the exportomes of Plasmodium species that are the cause of malaria, (ii) the recognition that the fate of proteins destined for export is already decided within the parasite's endoplasmic reticulum and involves the PEXEL motif being recognized and cleaved by the aspartic protease plasmepsin V and (iii) the discovery of the Plasmodium translocon of exported proteins (PTEX) that is responsible for the passage of proteins across the vacuolar membrane. We review protein export in Plasmodium and these latest developments in the field that have now provided a new platform from which trafficking of malaria proteins can be dissected.

Protein export in Plasmodium parasites : from the endoplasmic reticulum to the vacuolar export machine

It is somewhat paradoxical that the malaria parasite’s survival strategy involves spending almost all of its blood-stage existence residing behind a two-membrane barrier in a host red blood cell, yet giving considerable attention to exporting parasite-encoded proteins back across these membranes. These exported proteins are thought to play diverse roles and are crucial in pathogenic processes, such as re-modelling of the erythrocyte cytoskeleton and mediating the export of a major virulence protein known as Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), and in metabolic processes such as nutrient uptake and solute exchange. Despite these varied roles most exported proteins have at least one common link; they share a trafficking pathway that begins with entry into the endoplasmic reticulum and concludes with passage across the vacuole membrane via a proteinaceous translocon known as the Plasmodium translocon of exported proteins (PTEX). In this commentary we review recent advances in our understanding of this export pathway and suggest several models by which different aspects of the process may be interconnected.

Toward forward genetic screens in malaria-causing parasites using the piggyBac transposon

The ability to analyze gene function in malaria-causing Plasmodium parasites has received a boost with a recent paper in BMC Genomics that describes a genome-wide mutagenesis system in the rodent malaria species Plasmodium berghei using the transposon piggyBac. This advance holds promise for identifying and validating new targets for intervention against malaria. But further improvements are still needed for the full power of genome-wide molecular genetic screens to be utilized in this organism.

A tale of two parasites : the comparative epidemiology of cryptosporidiosis and giardiasis

New Zealand has a higher reported incidence of cryptosporidiosis and giardiasis than most other developed countries. This study aimed to describe and compare the epidemiology of these infections in New Zealand, to better understand their impact on public health and to gain insight into their probable modes of transmission. We analysed cryptosporidiosis and giardiasis notification data for a 10-year period (1997–2006). Highest rates for both diseases were in Europeans, children aged 0–5 years, and those living in low-deprivation areas. Cryptosporidiosis distribution was consistent with mainly farm animal (zoonotic) reservoirs. There was a dose–response relationship with increasing grades of rurality, marked spring seasonality, and positive correlation with farm animal density. Giardiasis distribution was consistent with predominantly human (anthroponotic) reservoirs, with an important contribution from overseas travel. Further research should focus on methods to reduce transmission of Cryptosporidium in rural areas and on reducing anthroponotic transmission of Giardia.

PTEX is an essential nexus for protein export in malaria parasites

During the blood stages of malaria, several hundred parasite-encoded proteins are exported beyond the double-membrane barrier that separates the parasite from the host cell cytosol. These proteins have a variety of roles that are essential to virulence or parasite growth. There is keen interest in understanding how proteins are exported and whether common machineries are involved in trafficking the different classes of exported proteins. One potential trafficking machine is a protein complex known as the Plasmodium translocon of exported proteins (PTEX). Although PTEX has been linked to the export of one class of exported proteins, there has been no direct evidence for its role and scope in protein translocation. Here we show, through the generation of two parasite lines defective for essential PTEX components (HSP101 or PTEX150), and analysis of a line lacking the non-essential component TRX2 (ref. 12), greatly reduced trafficking of all classes of exported proteins beyond the double membrane barrier enveloping the parasite. This includes proteins containing the PEXEL motif (RxLxE/Q/D) and PEXEL-negative exported proteins (PNEPs). Moreover, the export of proteins destined for expression on the infected erythrocyte surface, including the major virulence factor PfEMP1 in Plasmodium falciparum, was significantly reduced in PTEX knockdown parasites. PTEX function was also essential for blood-stage growth, because even a modest knockdown of PTEX components had a strong effect on the parasite's capacity to complete the erythrocytic cycle both in vitro and in vivo. Hence, as the only known nexus for protein export in Plasmodium parasites, and an essential enzymic machine, PTEX is a prime drug target.