Profiling the malaria genome: a gene survey of three species of malaria parasite with comparison to other apicomplexan species.

We have undertaken the first comparative pilot gene discovery analysis of approximately 25,000 random genomic and expressed sequence tags (ESTs) from three species of Plasmodium, the infectious agent that causes malaria. A total of 5482 genome survey sequences (GSSs) and 5582 ESTs were generated from mung bean nuclease (MBN) and cDNA libraries, respectively, of the ANKA line of the rodent malaria parasite Plasmodium berghei, and 10,874 GSSs generated from MBN libraries of the Salvador I and Belem lines of Plasmodium vivax, the most geographically wide-spread human malaria pathogen. These tags, together with 2438 Plasmodium falciparum sequences present in GenBank, were used to perform first-pass assembly and transcript reconstruction, and non-redundant consensus sequence datasets created. The datasets were compared against public protein databases and more than 1000 putative new Plasmodium proteins identified based on sequence similarity. Homologs of previously characterized Plasmodium genes were also identified, increasing the number of P. vivax and P. berghei sequences in public databases at least 10-fold. Comparative studies with other species of Apicomplexa identified interesting homologs of possible therapeutic or diagnostic value. A gene prediction program, Phat, was used to predict probable open reading frames for proteins in all three datasets. Predicted and non-redundant BLAST-matched proteins were submitted to InterPro, an integrated database of protein domains, signatures and families, for functional classification. Thus a partial predicted proteome was created for each species. This first comparative analysis of Plasmodium protein coding sequences represents a valuable resource for further studies on the biology of this important pathogen.

Conservation of a novel vacuolar transporter in Plasmodium species and its central role in chloroquine resistance of P. falciparum.

Chloroquine resistance in Plasmodium falciparum has recently been shown to result from mutations in the novel vacuolar transporter, PfCRT. Field studies have demonstrated the importance of these mutations in clinical resistance. Although a pfcrt ortholog has been identified in Plasmodiumvivax, there is no association between in vivo chloroquine resistance and codon mutations in the P. vivax gene. This is consistent with lines of evidence that suggest alternative mechanisms of chloroquine resistance among various malaria parasite species.

Evidence for different mechanisms of chloroquine resistance in 2 Plasmodium species that cause human malaria.

Chloroquine (CQ)-resistant Plasmodium vivax malaria was first reported 12 years ago, nearly 30 years after the recognition of CQ-resistant P. falciparum. Loss of CQ efficacy now poses a severe problem for the prevention and treatment of both diseases. Mutations in a digestive vacuole protein encoded by a 13-exon gene, pfcrt, were shown recently to have a central role in the CQ resistance (CQR) of P. falciparum. Whether mutations in pfcrt orthologues of other Plasmodium species are involved in CQR remains an open question. This report describes pfcrt homologues from P. vivax, P. knowlesi, P. berghei, and Dictyostelium discoideum. Synteny between the P. falciparum and P. vivax genes is demonstrated. However, a survey of patient isolates and monkey-adapted lines has shown no association between in vivo CQR and codon mutations in the P. vivax gene. This is evidence that the molecular events underlying P. vivax CQR differ from those in P. falciparum.

Mycoplasma alligatoris sp. nov., from American alligators.

Mycoplasmas were isolated from multiple tissues of diseased American alligators (Alligator mississippiensis). This paper presents biochemical, serological and molecular genetic characterizations of a lethal pathogen of alligators for which the name Mycoplasma alligatoris sp. nov. is proposed. The type strain is A21JP2T (ATCC 700619T).

Biomagnetic separation of contaminating host leukocytes from plasmodium-infected erythrocytes.

Carlton, J. M-R., Yowell, C. A., Sturrock, K. A., and Dame, J. B. 2001. Biomagnetic separation of contaminating host leukocytes from Plasmodium-infected erythrocytes. Experimental Parasitology 97, 111-114.

Of mice and malaria mutants: unravelling the genetics of drug resistance using rodent malaria models.

It is well recognized that drug resistance is the most significant obstacle to gaining effective malaria control. Despite the enormous advances in the knowledge of the biochemistry and molecular biology of malaria parasites, only a few genes determining resistance to the commonly used drugs have been identified. The idea that rodent malaria parasites should be exploited more widely for such work, in view of the practical problems of studying this subject experimentally in human malaria, is presented.

Co-ordinated programme of gene expression during asexual intraerythrocytic development of the human malaria parasite Plasmodium falciparum revealed by microarray analysis.

Plasmodium falciparum is a protozoan parasite responsible for the most severe forms of human malaria. All the clinical symptoms and pathological changes seen during human infection are caused by the asexual blood stages of Plasmodium. Within host red blood cells, the parasite undergoes enormous developmental changes during its maturation. In order to analyse the expression of genes during intraerythrocytic development, DNA microarrays were constructed and probed with stage-specific cDNA. Developmental upregulation of specific mRNAs was found to cluster into functional groups and revealed a co-ordinated programme of gene expression. Those involved in protein synthesis (ribosomal proteins, translation factors) peaked early in development, followed by those involved in metabolism, most dramatically glycolysis genes. Adhesion/invasion genes were turned on later in the maturation process. At the end of intraerythrocytic development (late schizogony), there was a general shut-off of gene expression, although a small set of genes, including a number of protein kinases, were turned on at this stage. Nearly all genes showed some regulation over the course of development. A handful of genes remained constant and should be useful for normalizing mRNA levels between stages. These data will facilitate functional analysis of the P. falciparum genome and will help to identify genes with a critical role in parasite progression and multiplication in the human host.

The ves multigene family of B. bovis encodes components of rapid antigenic variation at the infected erythrocyte surface.

B. bovis, an intraerythrocytic protozoal parasite, establishes chronic infections in cattle in part through rapid variation of the polymorphic, heterodimeric VESA1 protein on the infected erythrocyte surface and sequestration of mature parasites. We describe the characterization of the ves1 alpha gene encoding the VESA1a subunit, thus providing a description of a gene whose product is involved in rapid antigenic variation in a babesial parasite. This three-exon gene, a member of a multigene family (ves), encodes a polypeptide with no cleavable signal sequence, a single predicted transmembrane segment, and a cysteine/lysine-rich domain. Variation appears to involve creation and modification or loss of a novel, transcribed copy of the gene.

Karyotype and synteny among the chromosomes of all four species of human malaria parasite.

The karyotype and chromosomes of the human malaria parasite Plasmodium falciparum have been well characterized in recent years. Here we present karyotype maps of the three other human malaria species, P. vivax, P. malariae and P. ovale. Chromosomes of these species were found to be of significantly higher molecular weight than those of P. falciparum. Some 14 P. vivax chromosomes were distinguishable, and 12-14 P. malariae and P. ovale chromosomes. The chromosome location of 15 genes, known to be present within five synteny groups between P. falciparum and the rodent malarias, were analyzed, and four of these synteny groups were found to be conserved between all of the human malaria species. In addition, a more detailed genome map of P. vivax was made using ten housekeeping and antigen genes. These data represent the first karyotype maps of all species of malaria which infect man.

Gene synteny in species of Plasmodium.

We have attempted to establish the degree of linkage conservation between different species of the malaria parasite Plasmodium. Initially, the chromosome locations of 42 homologous genes were established in parasites from a rodent malaria species and the human malaria parasite P. falciparum. Of these genes, 26 appeared to be conserved within ten synteny groups between the two genomes. Several synteny groups were analysed further by long-range restriction mapping of digested chromosomes. Finally, a fine restriction map of one of the linkage groups was made from the rodent malaria parasites P. berghei and from P. falciparum and from the simian malaria parasite P. knowlesi. The fine-scale organisation of this linkage group appears to have remained intact among the three species, despite the evolutionary distance between them. This provides the first example of linkage conservation between the rodent, simian and human malaria species, which represent three different branches of the inferred phylogenetic tree of the genus Plasmodium.

Restoring abdominal wall integrity in contaminated tissue-deficient wounds using autologous fascia grafts.

Necrotizing abdominal wall infections, enteric fistulae, or exposed prosthetic material after ventral hernia repair often results in a loss of abdominal wall integrity. Further surgical reconstruction with prosthetic material is usually contraindicated in the contaminated wound because of the high infection rate necessitating prosthetic removal and further abdominal wall debridement. Consequently, for the past 9 years, we have been using free grafts of autologous fascia lata to replace deficient abdominal wall fascia and muscle in situations where prosthetic material is contraindicated and local tissue rearrangement (i.e., component separation) would be inadequate. Thirty-two patients (mean age 59 years) underwent abdominal wall reconstruction with autologous fascia lata grafts. Indications included exposed mesh (31 percent), enteric fistulae (28 percent), enteric contamination (22 percent), wound infection (13 percent), and immunosuppression alone (6 percent); 31 percent of all patients were immunosuppressed secondary to either a solid organ transplant or a systemic inflammatory disorder. Fascia grafts (mean size 10 x 17 cm) were sutured to the surrounding abdominal wall and covered by local skin flap advancement and/or myocutaneous flap rotation. All abdominal reconstructions were initially successful. Subsequent local abdominal wall complications included cellulitis (n = 3), seroma (n = 2), and skin dehiscence with exposed fascia grafts (n = 7). Five of seven patients with skin dehiscence healed by secondary intention, whereas two had split-thickness skin grafts successfully applied to the granulating fascia. Thigh donor site complications included hematoma (n = 1), skin dehiscence (n = 1), and seroma (n = 2). There have been no cases of lateral knee instability. The average follow-up period is 27 months (range 3 to 106 months). Recurrent hernia has been seen in three patients (9 percent). Interestingly, laparotomy has been performed through an intact fascia lata patch in three patients for unrelated intra-abdominal conditions. In each case, the graft was intact and revascularized, confirming experimental animal data performed in our laboratory. Recurrent hernia has not been observed through the laparotomy site. Our 9-year experience has demonstrated that in the face of large, contaminated abdominal wounds where prosthetic material is contraindicated and local tissue rearrangement would be inadequate, fascia lata autografts are a reliable adjuvant to abdominal wall reconstruction.

Adaptive changes in Plasmodium transmission strategies following chloroquine chemotherapy.

Both theory and data suggest that malaria parasites divert resources from within-host replication to the production of transmission stages (gametocytes) when conditions deteriorate. Increased investment into transmission stages should therefore follow subcurative treatment with antimalarial drugs, but relevant clinical studies necessarily lack adequate control groups. We therefore carried out controlled experiments to test this hypothesis, using a rodent malaria (Plasmodium chabaudi) model. Infections treated with a subcurative dose of the antimalarial chloroquine showed an earlier peak and a greater rate of gametocyte production relative to untreated controls. These alterations led to correlated changes in infectivity to mosquitoes, with the consequence that chloroquine treatment had no effect on the proportion of mosquitoes infected. Treatment of human malaria commonly does not result in complete parasite clearance. If surviving parasites produce compensatory increases in their rate of gametocyte production similar to those reported here, such treatment may have minimal effect on decreasing, and may actually increase, transmission. Importantly, if increased investment in transmission is a generalized stress response, the effect might be observed following a variety of antimalarial treatments, including other drugs and potential vaccines. Similar parasite life history counter-adaptations to intervention strategies are likely to occur in many disease-causing organisms.

Use of random amplified polymorphic DNA (RAPD) technique in inheritance studies of Plasmodium falciparum.

Effectiveness of random amplified polymorphic DNA (RAPD), a technique using 1 10-base primer to amplify random segments of genomic DNA, and some of its possible uses were tested in the A + T-rich genome of Plasmodium falciparum. The best concentrations of MgCl2, 60% G + C primer, and DNA were determined to be 4.0 mM, 0.4 microM, and 90-180 ng/15 microliters reaction, respectively. Use of 30% G + C primers did not allow amplification to occur. Application of RAPD to DNA of parent and progeny clones from a P. falciparum cross showed that polymorphisms identified in the parentals and tracked in the progeny were inherited in a Mendelian fashion and that RAPD-identified polymorphisms could be used as genetic markers. Some of these polymorphic markers were located on more than 1 chromosome, whereas others were specific for a single chromosome. Two of these markers, each located on chromosome 3 of 1 of the parental parasites, were missing from 2 of the 18 progeny, suggesting that deletions, or crossover events had occurred. RAPD markers also identified a higher number of nonparental-type progeny than expected, thus confirming previous observations for high genetic variability in malaria parasites.

Sexual-stage-specific RNA expression of a new Plasmodium falciparum gene detected by in situ hybridisation.

A gene, Pf77, transcribed in the sexual stages of Plasmodium falciparum was isolated from a genomic expression library with a polyclonal antibody raised to gametocyte proteins. The entire coding region was obtained from a series of overlapping genomic and cDNA clones (from gametocyte RNA). A single open reading frame is present with no introns and no tandem repeat sequences. A Pf77 probe hybridised to a single transcript present in RNA prepared from purified gametocytes and could not be detected in RNA prepared from asexual blood stages. In situ hybridisation studies confirmed that the expression of Pf77 mRNA is sexual-stage-specific and in addition, showed that Pf77 mRNA is present only in female gametocytes during the vertebrate stages of the parasite's development.