The grand assault

Designing malaria vaccines to circumvent antigen variability

Prospects for malaria eradication will be greatly enhanced by an effective vaccine, but parasite genetic diversity poses a major impediment to malaria vaccine efficacy. In recent pre-clinical and field trials, vaccines based on polymorphic Plasmodium falciparum antigens have shown efficacy only against homologous strains, raising the specter of allele-specific immunity such as that which plagues vaccines against influenza and HIV. The most advanced malaria vaccine, RTS,S, targets relatively conserved epitopes on the P. falciparum circumsporozoite protein. After more than 40 years of development and testing, RTS,S, has shown significant but modest efficacy against clinical malaria in phase 2 and 3 trials. Ongoing phase 2 studies of an irradiated sporozoite vaccine will ascertain whether the full protection against homologous experimental malaria challenge conferred by high doses of a whole organism vaccine can provide protection against diverse strains in the field. Here we review and evaluate approaches being taken to design broadly cross-protective malaria vaccines.

Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes

BACKGROUND

Massively parallel sequencing technology is revolutionizing approaches to genomic and genetic research. Since its advent, the scale and efficiency of Next-Generation Sequencing (NGS) has rapidly improved. In spite of this success, sequencing genomes or genomic regions with extremely biased base composition is still a great challenge to the currently available NGS platforms. The genomes of some important pathogenic organisms like Plasmodium falciparum (high AT content) and Mycobacterium tuberculosis (high GC content) display extremes of base composition. The standard library preparation procedures that employ PCR amplification have been shown to cause uneven read coverage particularly across AT and GC rich regions, leading to problems in genome assembly and variation analyses. Alternative library-preparation approaches that omit PCR amplification require large quantities of starting material and hence are not suitable for small amounts of DNA/RNA such as those from clinical isolates. We have developed and optimized library-preparation procedures suitable for low quantity starting material and tolerant to extremely high AT content sequences.

RESULTS

We have used our optimized conditions in parallel with standard methods to prepare Illumina sequencing libraries from a non-clinical and a clinical isolate (containing ~53% host contamination). By analyzing and comparing the quality of sequence data generated, we show that our optimized conditions that involve a PCR additive (TMAC), produces amplified libraries with improved coverage of extremely AT-rich regions and reduced bias toward GC neutral templates.

CONCLUSION

We have developed a robust and optimized Next-Generation Sequencing library amplification method suitable for extremely AT-rich genomes. The new amplification conditions significantly reduce bias and retain the complexity of either extremes of base composition. This development will greatly benefit sequencing clinical samples that often require amplification due to low mass of DNA starting material.

In Vitro Anti-plasmodial activity of Trigonella foenum-graecum L

Developing countries, where malaria is one of the most prevalent diseases, still rely on traditional medicine as a source for the treatment of this disease. For the present study, Trigonella foenum-graecum L. (fenugreek) were collected from Coimbatore, Tamilnadu, India. The test plant has been used in India by traditional healers for the treatment of fever as well as other diseases. The active principle was extracted out in different solvent systems to assess the anti-plasmodial potential, with an aim that they can further be utilized to formulate drugs. In vitro anti-plasmodial assay of the extracted fractions of fenugreek leaves was carried out using laboratory adapted chloroquine sensitive and resistant Plasmodium falciparum isolates. Schizont maturation inhibition assay was adopted to analyze the potential of the extracts. Ethanol extract (50%) seemed to possess profound anti-plasmodial activity with IC(50) value of 8.75 ± 0.35 µg ml(-1) and 10.25 ± 0.35 µg ml(-1) against chloroquine sensitive and resistant P. falciparum isolates, respectively. Among the investigated six fractions of the plant extracts, two were found to have significant anti-plasmodial activity with IC(50) values <10 µg ml(-1), namely ethanol and butanol extracts. Two extracts chloroform and ethyl acetate showed moderate activity with IC(50) values ranging from 10 to 20 µg ml(-1), and the other two extracts, hexane and water appeared to be inactive with IC(50) values >85 µg ml(-1). In addition, preliminary phytochemical screening of the various extracts indicated the presence of alkaloids, saponin, tannin like phenolic compounds, flavonoids and steroids.

Discovery: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria

Background

Up to half a billion human clinical cases of malaria are reported each year, resulting in about 2.7 million deaths, most of which occur in sub-Saharan Africa. Due to the over-and misuse of anti-malarials, widespread resistance to all the known drugs is increasing at an alarming rate. Rational methods to select new drug target proteins and lead compounds are urgently needed. The Discovery system provides data mining functionality on extensive annotations of five malaria species together with the human and mosquito hosts, enabling the selection of new targets based on multiple protein and ligand properties.

Methods

A web-based system was developed where researchers are able to mine information on malaria proteins and predicted ligands, as well as perform comparisons to the human and mosquito host characteristics. Protein features used include: domains, motifs, EC numbers, GO terms, orthologs, protein-protein interactions, protein-ligand interactions and host-pathogen interactions among others. Searching by chemical structure is also available.

Results

An in silico system for the selection of putative drug targets and lead compounds is presented, together with an example study on the bifunctional DHFR-TS from Plasmodium falciparum.

Conclusion

The Discovery system allows for the identification of putative drug targets and lead compounds in Plasmodium species based on the filtering of protein and chemical properties.

Genome bias influences amino acid choices: analysis of amino acid substitution and re-compilation of substitution matrices exclusive to an AT-biased genome

The genomic era has seen a remarkable increase in the number of genomes being sequenced and annotated. Nonetheless, annotation remains a serious challenge for compositionally biased genomes. For the preliminary annotation, popular nucleotide and protein comparison methods such as BLAST are widely employed. These methods make use of matrices to score alignments such as the amino acid substitution matrices. Since a nucleotide bias leads to an overall bias in the amino acid composition of proteins, it is possible that a genome with nucleotide bias may have introduced atypical amino acid substitutions in its proteome. Consequently, standard matrices fail to perform well in sequence analysis of these genomes. To address this issue, we examined the amino acid substitution in the AT-rich genome of Plasmodium falciparum, chosen as a reference and reconstituted a substitution matrix in the genome's context. The matrix was used to generate protein sequence alignments for the parasite proteins that improved across the functional regions. We attribute this to the consistency that may have been achieved amid the target and background frequencies calculated exclusively in our study. This study has important implications on annotation of proteins that are of experimental interest but give poor sequence alignments with standard conventional matrices.

Development of pilot scale production process and characterization of a recombinant multiepitope malarial vaccine candidate FALVAC-1A expressed in Escherichia coli

Among the four human malarial species, Plasmodium falciparum causes most of the mortality associated with malaria. Several approaches are being pursued to develop a suitable malaria vaccine since it may be the most effective weapon to fight against malaria. A highly immunogenic, synthetic protein consisting of 21 epitopes from pre-erythrocytic and blood stages of P. falciparum (FALVAC-1A) was constructed and expressed in Escherichia coli. This vaccine candidate was highly immunogenic and induced protective antibodies in rabbits when produced through lab-scale processes in milligram quantities. In order to take this vaccine candidate for further clinical trial, we optimized the process for industrial scale production and purification. Here we describe various methods used in pilot scale production and characterization of FALVAC-1A. A fed-batch cultivation process in a bioreactor at 10-L scale was optimized to express the protein in high yields as inclusion bodies in E. coli cells with the recombinant plasmids. Methods to solubilize, capture and purify the target protein from the inclusion bodies were optimized and the resultant protein was >95% pure based on SDS-PAGE and RP-HPLC. This protein was then refolded and nativity was confirmed by Far-UV CD spectroscopy. Final purified protein was characterized to estimate yield, purity, mass and confirmed to be free of host cell proteins, nucleic acids and bacterial endotoxins. This study confirms that industrial scale clinical grade FALVAC-1A can be produced in a cost-effective manner for clinical trials.

Comparative ORESTES-sampling of transcriptomes of immune-challenged Biomphalaria glabrata snails

The snail Biomphalaria glabrata (Gastropoda, Mollusca) is an important intermediate host for the human parasite Schistosoma mansoni (Digenea, Trematoda). Anti-pathogen responses of B. glabrata were studied towards a better understanding of snail immunity and host-parasite compatibility. Open reading frame ESTs (ORESTES) were sampled from different transcriptomes of M line strain B. glabrata, 12h post-challenge with Escherichia coli (Gram-negative), Micrococcus luteus (Gram-positive) bacteria or compatible S. mansoni, and controls. The resulting 3123 ORESTES represented 2129 unique sequences (373 clusters, 1756 singletons). Of these, 175 (8.1%) were putative defense factors, including lectins, antimicrobial peptides and components of various immune-effector systems. Comparison of biological processes (GO-terms) within different transcriptomes indicated that B. glabrata increased oxygen transport and metal binding in reaction to all challenges. Comprehensive comparisons of transcriptomes revealed that responses of B. glabrata against bacteria were similar to each other and differed from the ineffective response to S. mansoni. Furthermore, the response to S. mansoni infection was less comprehensive than that to bacteria. Many novel (unknown) sequences were recovered in association with particular challenges. B. glabrata possesses multi-faceted, potent immune defenses. This agrees with the notion that S. mansoni is capable of immune-evasion and prevents effective host defense responses in order to survive in B. glabrata. Future analysis of the numerous unknown sequences recovered from challenged snails may reveal novel immune factors and provide increased understanding of immunity of B. glabrata in relation to parasite-host compatibility.

Parasite genomes

The availability of genome sequences and the associated transcriptome and proteome mapping projects has revolutionised research in the field of parasitology. As more parasite species are sequenced, comparative and phylogenetic comparisons are improving the quality of gene prediction and annotation. Genome sequences of parasites are also providing important data sets for understanding parasite biology and identifying new vaccine candidates and drug targets. We review some of the preliminary conclusions from examination of parasite genome sequences and discuss some of the bioinformatics approaches taken in this analysis.

Correlation of structural development and differential expression of invasion-related molecules in schizonts ofPlasmodium falciparum

During asexual developmentPlasmodiumschizonts undergo a series of complex biochemical and structural changes. Using tightly synchronized cultures of 2P. falciparumlines (clone C10 and strain ITO4) for light microscopy and fluorescence imaging we monitored the timing and sequence of expression of proteins associated with invasion-related organelles. Antibodies to rhoptry, micronemal and dense granule proteins (Rhoptry Associated Protein 1, Apical Membrane Antigen 1, Erythrocyte Binding Antigen 175, Ring-infected Erythrocyte Surface Antigen) and to pellicle-associated proteins (Merozoite Surface Protein 1, PfMyosin-A) were used. Clone C10 developed faster than ITO4; this difference was also found in the timing of protein expression seen by immunofluorescence. Light microscopic data were combined with transmission electron microscopic analysis using serial sectioning of ITO4 schizonts to determine nuclear number and organellar development. Thus a timetable of schizont structural maturation was established. Generally, the timing of organelle-specific antigen expression correlates well with the ultrastructural data. Rhoptries are formed mainly between second and fourth nuclear divisions, micronemes between the end of the fourth nuclear division and merozoite separation from the residual body, while dense granules are generated mainly after the micronemes. PfAMA-1 appears in micronemes before EBA-175, suggesting micronemal heterogeneity.