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Natural diversity of the malaria vector Anopheles gambiae

CiteULike malaria tags - 5 January 2017 - 1:56pm
bioRxiv (22 December 2016), 096289, doi:10.1101/096289

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
Alistair Miles, Nicholas Harding, Giordano Botta, Chris Clarkson, Tiago Antao, Krzysztof Kozak, Daniel Schrider, Andrew Kern, Seth Redmond, Igor Sharakhov, Richard Pearson, Christina Bergey, Michael Fontaine, Arlete Troco, Abdoulaye Diabate, Carlo Costantini, Kyanne Rohatgi, Nohal Elissa, Boubacar Coulibaly, Joao Dinis, Janet Midega, Charles Mbogo, Henry Mawejje, Jim Stalker, Kirk Rockett, Eleanor Drury, Dan Mead, Anna Jeffreys, Christina Hubbart, Kate Rowlands, Alison Isaacs, Dushyanth Jyothi, Cinzia Malangone, Paul Vauterin, Ben Jeffrey, Ian Wright, Lee Hart, Krzysztof Kluczynski, Victoria Cornelius, Bronwyn MacInnis, Christa Henrichs, Rachel Giacomantonio, Diego Ayala, Philip Bejon, Nora Besansky, Austin Burt, Beniamino Caputo, Alessandra Torre, Charles Godfray, Matthew Hahn, Daniel Neafsey, Samantha O'Loughlin, Joao Pinto, Michelle Riehle, Kenneth Vernick, David Weetman, Craig Wilding, Bradley White, Mara Lawniczak, Martin Donnelly, Dominic Kwiatkowski
Categories: malaria news feeds

Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification.

CiteULike malaria tags - 24 December 2016 - 4:08pm
Malaria journal, Vol. 15, No. 1. (20 December 2016)

Translating genomic technologies into healthcare applications for the malaria parasite Plasmodium falciparum has been limited by the technical and logistical difficulties of obtaining high quality clinical samples from the field. Sampling by dried blood spot (DBS) finger-pricks can be performed safely and efficiently with minimal resource and storage requirements compared with venous blood (VB). Here, the use of selective whole genome amplification (sWGA) to sequence the P. falciparum genome from clinical DBS samples was evaluated, and the results compared with current methods that use leucodepleted VB. Parasite DNA with high (>95%) human DNA contamination was selectively amplified by Phi29 polymerase using short oligonucleotide probes of 8-12 mers as primers. These primers were selected on the basis of their differential frequency of binding the desired (P. falciparum DNA) and contaminating (human) genomes. Using sWGA method, clinical samples from 156 malaria patients, including 120 paired samples for head-to-head comparison of DBS and leucodepleted VB were sequenced. Greater than 18-fold enrichment of P. falciparum DNA was achieved from DBS extracts. The parasitaemia threshold to achieve >5× coverage for 50% of the genome was 0.03% (40 parasites per 200 white blood cells). Over 99% SNP concordance between VB and DBS samples was achieved after excluding missing calls. The sWGA methods described here provide a reliable and scalable way of generating P. falciparum genome sequence data from DBS samples. The current data indicate that it will be possible to get good quality sequence on most if not all drug resistance loci from the majority of symptomatic malaria patients. This technique overcomes a major limiting factor in P. falciparum genome sequencing from field samples, and paves the way for large-scale epidemiological applications.
Samuel Oyola, Cristina Ariani, William Hamilton, Mihir Kekre, Lucas Amenga-Etego, Anita Ghansah, Gavin Rutledge, Seth Redmond, Magnus Manske, Dushyanth Jyothi, Chris Jacob, Thomas Otto, Kirk Rockett, Chris Newbold, Matthew Berriman, Dominic Kwiatkowski
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Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification

CiteULike malaria tags - 22 December 2016 - 11:14am
Malaria Journal, Vol. 15, No. 1. (20 December 2016), doi:10.1186/s12936-016-1641-7
Samuel Oyola, Cristina Ariani, William Hamilton, Mihir Kekre, Lucas Amenga-Etego, Anita Ghansah, Gavin Rutledge, Seth Redmond, Magnus Manske, Dushyanth Jyothi, Chris Jacob, Thomas Otto, Kirk Rockett, Chris Newbold, Matthew Berriman, Dominic Kwiatkowski
Categories: malaria news feeds

Extreme mutation bias and high AT content in Plasmodium falciparum

CiteULike malaria tags - 22 December 2016 - 10:10am
Nucleic Acids Research (19 December 2016), gkw1259, doi:10.1093/nar/gkw1259

For reasons that remain unknown, the Plasmodium falciparum genome has an exceptionally high AT content compared to other Plasmodium species and eukaryotes in general - nearly 80% in coding regions and approaching 90% in non-coding regions. Here, we examine how this phenomenon relates to genome-wide patterns of de novo mutation. Mutation accumulation experiments were performed by sequential cloning of six P. falciparum isolates growing in human erythrocytes in vitro for 4 years, with 279 clones sampled for whole genome sequencing at different time points. Genome sequence analysis of these samples revealed a significant excess of G:C to A:T transitions compared to other types of nucleotide substitution, which would naturally cause AT content to equilibrate close to the level seen across the P. falciparum reference genome (80.6% AT). These data also uncover an extremely high rate of small indel mutation relative to other species, primarily associated with repetitive AT-rich sequences, in addition to larger-scale structural rearrangements focused in antigen-coding var genes. In conclusion, high AT content in P. falciparum is driven by a systematic mutational bias and ultimately leads to an unusual level of microstructural plasticity, raising the question of whether this contributes to adaptive evolution.
William Hamilton, Antoine Claessens, Thomas Otto, Mihir Kekre, Rick Fairhurst, Julian Rayner, Dominic Kwiatkowski
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Comparative antibody responses against three antimalarial vaccine candidate antigens from urban and rural exposed individuals in Gabon

CiteULike malaria tags - 21 December 2016 - 11:50am
European Journal of Microbiology and Immunology, Vol. 6, No. 4. (December 2016), pp. 287-297, doi:10.1556/1886.2016.00027
Roméo-Karl Imboumy-Limoukou, Sandrine Oyegue-Liabagui, Stella Ndidi, Irène Pegha-Moukandja, Charlene Kouna, Francis Galaway, Isabelle Florent, Jean Lekana-Douki
Categories: malaria news feeds

Genomes of an entire Plasmodium subgenus reveal paths to virulent human malaria

CiteULike malaria tags - 21 December 2016 - 10:13am
bioRxiv (20 December 2016), 095679, doi:10.1101/095679

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
Thomas Otto, Aude Gilabert, Thomas Crellen, Ulrike Böhme, Céline Arnathau, Mandy Sanders, Samuel Oyola, Alain Okauga, Larson Boundenga, Eric Wuillaume, Barthélémy Ngoubangoye, Nancy Moukodoum, Christophe Paupy, Patrick Durand, Virginie Rougeron, Benjamin Ollomo, François Renaud, Chris Newbold, Matt Berriman, Franck Prugnolle
Categories: malaria news feeds

Comparative genome-wide analysis and evolutionary history of haemoglobin-processing and haem detoxification enzymes in malarial parasites.

CiteULike malaria tags - 15 December 2016 - 2:41pm
Malaria journal, Vol. 15 (29 January 2016)

Malaria parasites have evolved a series of intricate mechanisms to survive and propagate within host red blood cells. Intra-erythrocytic parasitism requires these organisms to digest haemoglobin and detoxify iron-bound haem. These tasks are executed by haemoglobin-specific proteases and haem biocrystallization factors that are components of a large multi-subunit complex. Since haemoglobin processing machineries are functionally and genetically linked to the modes of action and resistance mechanisms of several anti-malarial drugs, an understanding of their evolutionary history is important for drug development and drug resistance prevention. Maximum likelihood trees of genetic repertoires encoding haemoglobin processing machineries within Plasmodium species, and with the representatives of Apicomplexan species with various host tropisms, were created. Genetic variants were mapped onto existing three-dimensional structures. Genome-wide single nucleotide polymorphism data were used to analyse the selective pressure and the effect of these mutations at the structural level. Recent expansions in the falcipain and plasmepsin repertoires are unique to human malaria parasites especially in the Plasmodium falciparum and P. reichenowi lineage. Expansion of haemoglobin-specific plasmepsins occurred after the separation event of Plasmodium species, but the other members of the plasmepsin family were evolutionarily conserved with one copy for each sub-group in every Apicomplexan species. Haemoglobin-specific falcipains are separated from invasion-related falcipain, and their expansions within one specific locus arose independently in both P. falciparum and P. vivax lineages. Gene conversion between P. falciparum falcipain 2A and 2B was observed in artemisinin-resistant strains. Comparison between the numbers of non-synonymous and synonymous mutations suggests a strong selective pressure at falcipain and plasmepsin genes. The locations of amino acid changes from non-synonymous mutations mapped onto protein structures revealed clusters of amino acid residues in close proximity or near the active sites of proteases. A high degree of polymorphism at the haemoglobin processing genes implicates an imposition of selective pressure. The identification in recent years of functional redundancy of haemoglobin-specific proteases makes them less appealing as potential drug targets, but their expansions, especially in the human malaria parasite lineages, unequivocally point toward their functional significance during the independent and repetitive adaptation events in malaria parasite evolutionary history.
Patrath Ponsuwanna, Theerarat Kochakarn, Duangkamon Bunditvorapoom, Krittikorn Kümpornsin, Thomas Otto, Chase Ridenour, Kesinee Chotivanich, Prapon Wilairat, Nicholas White, Olivo Miotto, Thanat Chookajorn
Categories: malaria news feeds

A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

CiteULike malaria tags - 15 December 2016 - 1:16pm
Wellcome Open Research, Vol. 1 (15 November 2016), 4, doi:10.12688/wellcomeopenres.9876.1
Sarah Auburn, Ulrike Böhme, Sascha Steinbiss, Hidayat Trimarsanto, Jessica Hostetler, Mandy Sanders, Qi Gao, Francois Nosten, Chris Newbold, Matthew Berriman, Ric Price, Thomas Otto
Categories: malaria news feeds

Last parasite standing

CiteULike malaria tags - 15 December 2016 - 12:53pm
Nature Reviews Microbiology, Vol. 15, No. 1. (09 December 2016), pp. 4-4, doi:10.1038/nrmicro.2016.181

This month's Genome Watch describes how whole-genome sequencing used for surveillance purposes has enabled the identification of new drug resistance markers in the malaria parasite.
Gavin Rutledge, Thomas Otto
Categories: malaria news feeds

Frequent ectopic recombination of virulence factor genes in telomeric chromosome clusters of P. falciparum

CiteULike malaria tags - 14 December 2016 - 5:16pm
Nature, Vol. 407, No. 6807. (26 October 2000), pp. 1018-1022, doi:10.1038/35039531

Persistent and recurrent infections by Plasmodium falciparum malaria parasites result from the ability of the parasite to undergo antigenic variation and evade host immune attack1, 2. P. falciparum parasites generate high levels of variability in gene families that comprise virulence determinants of cytoadherence and antigenic variation3, 4, 5, 6, 7, such as the var genes. These genes encode the major variable parasite protein (PfEMP-1), and are expressed in a mutually exclusive manner at the surface of the erythrocyte infected by P. falciparum8, 9, 10, 11, 12. Here we identify a mechanism by which var gene sequences undergo recombination at frequencies much higher than those expected from homologous crossover events alone13. These recombination events occur between subtelomeric regions of heterologous chromosomes, which associate in clusters near the nuclear periphery in asexual blood-stage parasites or in bouquet-like configurations near one pole of the elongated nuclei in sexual parasite forms. We propose that the alignment of var genes in heterologous chromosomes facilitates gene conversion and promotes the diversity of antigenic and adhesive phenotypes. The association of virulence factors with a specific nuclear subcompartment may also have implications for variation during mitotic recombination in asexual blood stages.
Lucio Freitas-Junior, Emmanuel Bottius, Lindsay Pirrit, Kirk Deitsch, Christine Scheidig, Francoise Guinet, Ulf Nehrbass, Thomas Wellems, Artur Scherf
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Plasmodium vivax vaccine research – we’ve only just begun

CiteULike malaria tags - 9 December 2016 - 11:36am
International Journal for Parasitology (November 2016), doi:10.1016/j.ijpara.2016.09.006

Blood-stage vaccine development is particularly critical for Plasmodium vivax. Large-scale protein arrays are powering an expansion in vaccine antigen screening. Structural studies allow antigen design to focus on critical pan-reactive epitopes. Further information on immune mechanisms and antigen diversity is needed. Plasmodium vivax parasites cause the majority of malaria cases outside Africa, and are increasingly being acknowledged as a cause of severe disease. The unique attributes of P. vivax biology, particularly the capacity of the dormant liver stage, the hypnozoite, to maintain blood-stage infections even in the absence of active transmission, make blood-stage vaccines particularly attractive for this species. However, P. vivax vaccine development remains resolutely in first gear, with only a single blood-stage candidate having been evaluated in any depth. Experience with Plasmodium falciparum suggests that a much broader search for new candidates and a deeper understanding of high priority targets will be required to make significant advances. This review discusses some of the particular challenges of P. vivax blood-stage vaccine development, highlighting both recent advances and key remaining barriers to overcome in order to move development forward.
Wai-Hong Tham, James Beeson, Julian Rayner
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Characterizing the impact of sustained sulfadoxine/pyrimethamine use upon the Plasmodium falciparum population in Malawi

CiteULike malaria tags - 9 December 2016 - 11:15am
Malaria Journal, Vol. 15, No. 1. (29 November 2016), doi:10.1186/s12936-016-1634-6
Matt Ravenhall, Ernest Benavente, Mwapatsa Mipando, Anja Jensen, Colin Sutherland, Cally Roper, Nuno Sepúlveda, Dominic Kwiatkowski, Jacqui Montgomery, Kamija Phiri, Anja Terlouw, Alister Craig, Susana Campino, Harold Ocholla, Taane Clark
Categories: malaria news feeds

Decreased Rate of Plasma Arginine Appearance in Murine Malaria May Explain Hypoargininemia in Children With Cerebral Malaria

CiteULike malaria tags - 8 December 2016 - 12:34pm
Journal of Infectious Diseases, Vol. 214, No. 12. (15 December 2016), pp. 1840-1849, doi:10.1093/infdis/jiw452

Background. Plasmodium infection depletes arginine, the substrate for nitric oxide synthesis, and impairs endothelium-dependent vasodilation. Increased conversion of arginine to ornithine by parasites or host arginase is a proposed mechanism of arginine depletion.
Matthew Alkaitis, Honghui Wang, Allison Ikeda, Carol Rowley, Ian MacCormick, Jessica Chertow, Oliver Billker, Anthony Suffredini, David Roberts, Terrie Taylor, Karl Seydel, Hans Ackerman
Categories: malaria news feeds