Plasmodium falciparum and Plasmodium vivax: so similar, yet very different

Malaria absorption peaks acquired through the skin of patients with infrared light can detect patients with varying parasitemia

To eliminate malaria, scalable tools that are rapid, affordable, and can detect patients with low parasitemia are required. Non-invasive diagnostic tools that are rapid, reagent-free, and affordable would also provide a justifiable platform for testing malaria in asymptomatic patients. However, non-invasive surveillance techniques for malaria remain a diagnostic gap. Here, we show near-infrared Plasmodium absorption peaks acquired non-invasively through the skin using a miniaturized hand-held near-infrared spectrometer. Using spectra from the ear, these absorption peaks and machine learning techniques enabled non-invasive detection of malaria-infected human subjects with varying parasitemia levels in less than 10 s.

Plasmodium Purine Metabolism and Its Inhibition by Nucleoside and Nucleotide Analogues

Malaria still affects around 200 million people and is responsible for more than 400,000 deaths per year, mostly children in subequatorial areas. This disease is caused by parasites of the Plasmodium genus. Only a few WHO-recommended treatments are available to prevent or cure plasmodial infections, but genetic mutations in the causal parasites have led to onset of resistance against all commercial antimalarial drugs. New drugs and targets are being investigated to cope with this emerging problem, including enzymes belonging to the main metabolic pathways, while nucleoside and nucleotide analogues are also a promising class of potential drugs. This review highlights the main metabolic pathways targeted for the development of potential antiplasmodial therapies based on nucleos(t)ide analogues, as well as the different series of purine-containing nucleoside and nucleotide derivatives designed to inhibit Plasmodium falciparum purine metabolism.

Can Mixed Parasite Infections Thwart Targeted Malaria Elimination Program in India?

India is highly endemic to malaria with prevalence of all five species of human malaria parasites of Plasmodium genus. India is set for malaria elimination by 2030. Since cases of mixed Plasmodium species infections remain usually undetected but cause huge disease burden, in order to understand the distributional prevalence of both monospecies infections and mixed species infections in India, we collated published data on the differential infection incidences of the five different malaria parasites based on PCR diagnostic assay. About 11% of total cases were due to mixed species infection. Among several interesting observations on both single and mixed parasitic infections, incidences of Plasmodium falciparum monoinfection were found to be significantly higher than P. vivax monoinfection. Also, P. malariae seems to be emerging as a potential malaria threat in India. Putting all the facts together, it appears that the dream of achieving malaria elimination in India will not be completely successful without dealing with mixed species infection.

The adenosine deaminases of Plasmodium vivax and Plasmodium falciparum exhibit surprising differences in ligand specificity

Plasmodium vivax and Plasmodium falciparum cause malaria, so proteins essential for their survival in vivo are potential anti-malarial drug targets. Adenosine deaminases (ADA) catalyze the irreversible conversion of adenosine into inosine, and play a critical role in the purine salvage pathways of Plasmodia and their mammalian hosts. Currently, the number of selective inhibitors of Plasmodium ADAs is limited. One potent and widely used inhibitor of the human ADA (hADA), erythro-9-(2-hydroxy-3-nonly)adenine (EHNA), is a very weak inhibitor (K(i)=120 μM) of P. falciparum ADA (pfADA). EHNA-like compounds are thus excluded from consideration as potential inhibitors of Plasmodium ADA in general. However, EHNA activity in P. vivax ADA (pvADA) has not been reported. Here we applied computational molecular modeling to identify ligand recognition mechanisms unique to P. vivax and P. falciparum ADA. Our biochemical experiments show that EHNA is at least 60-fold more potent against pvADA (K(i)=1.9 μM) than against pfADA. The D172A pvADA mutant is bound even more tightly (K(i)=0.9 μM). These results improve our understanding of the mechanisms of ADA ligand recognition and species-selectivity, and facilitate the rational design of novel EHNA-based ADA inhibitors as anti-malarial drugs. To demonstrate a practical application of our findings we have computationally predicted a novel potential inhibitor of pvADA that will not interact with the human ADA.

Platform for Plasmodium vivax vaccine discovery and development

Plasmodium vivax is the most prevalent malaria parasite on the American continent. It generates a global burden of 80-100 million cases annually and represents a tremendous public health problem, particularly in the American and Asian continents. A malaria vaccine would be considered the most cost-effective measure against this vector-borne disease and it would contribute to a reduction in malaria cases and to eventual eradication. Although significant progress has been achieved in the search for Plasmodium falciparum antigens that could be used in a vaccine, limited progress has been made in the search for P. vivax components that might be eligible for vaccine development. This is primarily due to the lack of in vitro cultures to serve as an antigen source and to inadequate funding. While the most advanced P. falciparum vaccine candidate is currently being tested in Phase III trials in Africa, the most advanced P. vivax candidates have only advanced to Phase I trials. Herein, we describe the overall strategy and progress in P. vivax vaccine research, from antigen discovery to preclinical and clinical development and we discuss the regional potential of Latin America to develop a comprehensive platform for vaccine development.

Characterization, comparative genomics, and evolutionary inferences of a human drug metabolizing (NAT2) gene

Aim

The present-day genetic architecture of a species bears much significance to its closely related species. In recent availability of whole genome sequence data for closely related species, it is possible to detect genetic similarities/differences in specific lineages and infer the role of evolutionary forces in bringing such similarities/differences. In this respect, NAT2 gene, responsible for drug metabolism, is conserved across a few taxa and, thus, comparative genomic studies could be useful for better pharmacogenetic realization.

Methods

DNA sequences of human NAT2 gene were retrieved from NCBI and characterized. Comparative and evolutionary analyses were performed with sequences from four mammalian taxa and one avian taxon with different statistical algorithms.

Results

The observed genetic architecture of NAT2 gene was different across the taxa. Phylogenetic inferences revealed that human and chimpanzee are diverged recently and fowl was found to be diverged from rest of the taxa significantly. Also, gene length, microsatellites, Ka/Ks, secondary structure, and distribution of CpG islands were observed across taxa.

Conclusions

The detail architecture of NAT2 gene and its evolutionary history in different taxa show relationships with other taxa. Future population-based study in NAT2 would unravel the correlation between nucleotide changes and differential ability of drug metabolization in humans.

Identifying and characterizing a member of the RhopH1/Clag family in Plasmodium vivax

Plasmodium vivax malaria caused is a public health problem that produces very high morbidity worldwide. During invasion of red blood cells the parasite requires the intervention of high molecular weight complex rhoptry proteins that are also essential for cytoadherence. PfClag9, a member of the RhopH multigene family, has been identified as being critical during Plasmodium falciparum infection. This study describes identifying and characterizing the pfclag9 ortholog in P. vivax (hereinafter named pvclag7). The pvclag7 gene is transcribed at the end of the intraerythrocytic cycle and is recognized by sera from humans who have been infected by P. vivax. PvClag7 subcellular localization has been also determined and, similar to what occurs with PfClag9, it co-localize with other proteins from the Rhoptry high molecular weight complex.

A genome alignment algorithm based on compression

BACKGROUND

Traditional genome alignment methods consider sequence alignment as a variation of the string edit distance problem, and perform alignment by matching characters of the two sequences. They are often computationally expensive and unable to deal with low information regions. Furthermore, they lack a well-principled objective function to measure the performance of sets of parameters. Since genomic sequences carry genetic information, this article proposes that the information content of each nucleotide in a position should be considered in sequence alignment. An information-theoretic approach for pairwise genome local alignment, namely XMAligner, is presented. Instead of comparing sequences at the character level, XMAligner considers a pair of nucleotides from two sequences to be related if their mutual information in context is significant. The information content of nucleotides in sequences is measured by a lossless compression technique.

RESULTS

Experiments on both simulated data and real data show that XMAligner is superior to conventional methods especially on distantly related sequences and statistically biased data. XMAligner can align sequences of eukaryote genome size with only a modest hardware requirement. Importantly, the method has an objective function which can obviate the need to choose parameter values for high quality alignment. The alignment results from XMAligner can be integrated into a visualisation tool for viewing purpose.

CONCLUSIONS

The information-theoretic approach for sequence alignment is shown to overcome the mentioned problems of conventional character matching alignment methods. The article shows that, as genomic sequences are meant to carry information, considering the information content of nucleotides is helpful for genomic sequence alignment.

AVAILABILITY

Downloadable binaries, documentation and data can be found at ftp://ftp.infotech.monash.edu.au/software/DNAcompress-XM/XMAligner/.

Single nucleotide polymorphisms, putatively neutral DNA markers and population genetic parameters in Indian Plasmodium vivax isolates

With a view to developing putatively neutral markers based on Single Nucleotide Polymorphisms (SNPs) in the human malaria parasite, Plasmodium vivax, we utilized the published whole genome sequence information of P. falciparum and P. vivax to find a ~200 kb conserved syntenic region between these two species. We have selected 27 non-coding DNA fragments (in introns and intergenic regions) of variable length (300–750 bp) in P. vivax in this syntenic region. PCR of P. vivax isolates of a population sample from India could successfully amplify 17 fragments. Subsequently, DNA sequencing and sequence analysis confirmed the polymorphic status of only 11 fragments. Altogether, 18 SNPs were detected and 2 different measures of nucleotide diversity showed variable patterns across different fragments; in general, introns were less variable than the intergenic regions. All 11 polymorphic fragments were found to be evolving according to a neutral equilibrium model and thus could be utilized as putatively neutral markers for population genetic studies in P. vivax. Different molecular population genetics parameters were also estimated, providing initial insight into the population genetics of Indian P. vivax.

Malaria parasite genome scan: insights into antimalarial resistance

Genome scan and genotype-phenotype association study offer excellent opportunities to unearth drug/vaccine targets in human pathogens including malaria parasites. A recently conducted such study in worldwide isolates in the most devastating malaria parasite Plasmodium falciparum has reported important genomic information on genetic basis of antimalarial resistance. Several unknown genes were also found to be under strong influence of natural selection. The findings provide important insights into the malaria parasite genome evolution in general and to use this information to develop more focused malaria control strategies, in particular.

Evolutionary genetic insights into Plasmodium falciparum functional genes

Complex and rapidly evolving behavior of the human malaria parasite Plasmodium falciparum have always been mysterious to the evolutionary biologists, as the parasite is the most virulent and now becoming the most prevalent malaria parasite species across the globe. With the availability of complete genome sequence of P. falciparum, better understanding of the genome design and evolution could be possible. We herein utilized the available information of all known functional genes from whole genome of P. falciparum and investigate the differential mode of gene evolution. The study comparing P. falciparum functional genes with Plasmodium vivax revealed about 82% of genes to be conserved in the later species and the rest, 18% to be totally unique to P. falciparum. Genetic architectural pattern of functional genes shows absence of introns in about a half of the conserved genes, whereas almost all unique genes have introns. Similarly, distribution of intron number and length were also observed to be different for conserved and unique genes of P. falciparum. Statistically significant positive correlations between total intron length and gene lengths were detected in 11 chromosomes for unique genes, whereas only in three chromosomes for conserved genes. Preference of intron presence in some P. falciparum genes were also detected which provide functional relevance of introns. The study provides, for the first time, a detail evolutionary analysis of functional genes of a devastating malaria parasite. The marked differences in organization of introns between the unique and conserved genes in P. falciparum, and the contribution of introns to genome complexity are some of the hallmarks of the study.

Seventy-five years of Resochin in the fight against malaria

The four different forms of human malaria have threatened humanity since time immemorial and to this day, they exact a death toll of one to three million people annually. Synthetic anti-malarial agents have been in development since early 1900. Perhaps the most successful and widely used drug, Resochin (chloroquine), was discovered 75 years ago; for a long time, it was the drug of choice and to this day, it is still used in many regions of the world as a reliable treatment against simpler forms of malaria. In regions where it has not been in use against malaria tropica for quite some time due to the development of resistances, it has regained some of its efficacy. This review traces the discovery and the mechanism of action of this substance, illustrates the significance of malaria today, and underlines the need for controlled and reliable therapeutic measures.