Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum

Background

The identification of genetic changes that confer drug resistance or other phenotypic changes in pathogens can help optimize treatment strategies, support the development of new therapeutic agents, and provide information about the likely function of genes. Elucidating mechanisms of phenotypic drug resistance can also assist in identifying the mode of action of uncharacterized but potent antimalarial compounds identified in high-throughput chemical screening campaigns against Plasmodium falciparum.

Results

Here we show that tiling microarrays can detect de novo a large proportion of the genetic changes that differentiate one genome from another. We show that we detect most single nucleotide polymorphisms or small insertion deletion events and all known copy number variations that distinguish three laboratory isolates using readily accessible methods. We used the approach to discover mutations that occur during the selection process after transfection. We also elucidated a mechanism by which parasites acquire resistance to the antimalarial fosmidomycin, which targets the parasite isoprenoid synthesis pathway. Our microarray-based approach allowed us to attribute in vitro derived fosmidomycin resistance to a copy number variation event in the pfdxr gene, which enables the parasite to overcome fosmidomycin-mediated inhibition of isoprenoid biosynthesis.

Conclusions

We show that newly emerged single nucleotide polymorphisms can readily be detected and that malaria parasites can rapidly acquire gene amplifications in response to in vitro drug pressure. The ability to define comprehensively genetic variability in P. falciparum with a single overnight hybridization creates new opportunities to study parasite evolution and improve the treatment and control of malaria.     

Effects of light on cyanide‐resistant respiration and alternative oxidase function in Arabidopsis seedlings

Mitochondrial alternative oxidase (AOX), the unique respiratory terminal oxidase in plants, catalyzes the energy wasteful cyanide (CN)‐resistant respiration and plays a role in optimizing photosynthesis. Although it has been demonstrated that leaf AOX is upregulated after illumination, the in vivo mechanism of AOX upregulation by light and its physiological significance are still unknown. In this report, red light and blue light‐induced AOX (especially AOX1a) expressions were characterized. Phytochromes, phototropins and cryptochromes, all these photoreceptors mediate the light‐response of AOX1a gene. When aox1a mutant seedlings were grown under a high‐light (HL) condition, photobleaching was more evident in the mutant than the wild‐type plants. More reactive oxygen species (ROS) accumulation and inefficient dissipation of chloroplast reducing‐equivalents in aox1a mutant may account for its worse adaptation to HL stress. When etiolated seedlings were exposed to illumination for 4 h, chlorophyll accumulation was largely delayed in aox1a plants. We first suggest that more reduction of the photosynthetic electron transport chain and more accumulation of reducing‐equivalents in the mutant during de‐etiolation might be the main reasons.     

Vaccination against Eimeria tenella infection using a fraction of E. tenella sporozoites selected by the capacity to activate T cells

At 8 days after a primary Eimeria tenella infection, a subset of T cells, of which the protective role is as yet unclear, circulates in the peripheral blood. In order to investigate this, the in vitro cellular responsiveness of these peripheral blood lymphocytes has been used as selection criterion to identify potentially protective E. tenella sporozoite antigens. The hydrophilic protein phase of purified E. tenella sporozoite homogenates obtained by Triton X-114 extraction was fractionated using preparative gel electrophoresis. Nine fractions, separated according to different molecular weight, were tested for their ability to stimulate T-cell responses. Both the proliferation of peripheral blood lymphocytes and the macrophage activating activity released in the culture supernatants were measured. On the basis of this responsiveness, four fractions were selected and used to vaccinate chickens. All vaccine preparations induced strong T-cell responses. One fraction immunised chickens against subsequent challenge infection, in that the caecal lesion scores were significantly lower as compared with that of the unvaccinated controls. This fraction contained hydrophilic polypeptides with a molecular mass that ranged from 26 to 30 kDa.     

Intra-individual variation in sperm tail length in murine rodents

In eutherian mammals, there are marked interspecific differences in sperm head shape and tail length. In a few species, sperm head variability occurs but intra-individual variation in sperm tail length has rarely been investigated or commented upon. Here, we ask the question: Do murine rodent species that have variable sperm head shapes exhibit greater intra-individual variation in sperm midpiece and total tail lengths than closely related species where little, or no, sperm head variability occurs? From three separate lineages, we selected three pairs of murine rodents, one of which has monomorphic, and the other variable, sperm head shape. These were from southern Asia the bandicoot rats Bandicota bengalensis and Bandicota indica , from southern Africa the veld rats, Aethomys chrysophilus and Aethomys ineptus and from Australia the fawn hopping mouse Notomys cervinus and the spinifex hopping mouse Notomys alexis . Cauda epididymal sperm smears were prepared and sperm midpiece and total tail lengths were determined. A linear mixed-effects model was used to estimate intra-individual variance. The results showed that in all three species where there are variable sperm head shapes ( B. indica , A. ineptus and N. alexis ), statistically significantly greater intra-individual variability of sperm midpiece and total tail lengths occurs ( P <0.0001 in all cases). These species all have relatively smaller testes mass compared with the closely related species with monomorphic sperm populations. This suggests that depressed levels of intermale sperm competition may result in the occurrence of variability in not only the divergent sperm head shape but also in the length of the midpiece as well as that of the total length of the sperm tail.     

Imidazo[1,2-a]pyridines: a potent and selective class of cyclin-dependent kinase inhibitors identified through structure-based hybridisation

High-throughput screening identified the imidazo[1,2-a]pyridine and bisanilinopyrimidine series as inhibitors of the cyclin-dependent kinase CDK4. Comparison of their experimentally-determined binding modes and emerging structure-activity trends led to the development of potent and selective imidazo[1,2-a]pyridine inhibitors for CDK4 and in particular CDK2.     

Modeling continuous bioleach reactors

The results of recent research have shown that the bioleaching of sulfide minerals occurs via a two‐step mechanism. In this mechanism, the sulfide mineral is chemically oxidized by the ferric‐iron in the bioleaching liquor. The ferrous‐iron produced is subsequently oxidized to ferric‐iron by the microorganism. Further research has shown that the rates of both the ferric leaching and ferrous‐iron oxidation are governed by the ferric/ferrous‐iron ratio (i.e., the redox potential). During the steady‐state operation of a bioleach reactor, the rate of iron turnover between the chemical ferric leaching of the mineral and the bacterial oxidation of the ferrous‐iron will define the rate and the redox potential at which the system will operate. The balance between the two rates will in turn depend on the species used, the microbial concentration, the residence time employed, the nature of the sulfide mineral being leached, and its active surface area. The model described proposes that the residence time and microbial species present determine the microbial growth rate, which in turn determines the redox potential in the bioleach liquor. The redox potential of the solution, in turn, determines the degree of leaching of the mineral; that is, conversion in the bioleach reactor. © 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 64: 671–677, 1999.     

The spermatozoon of Eurasian murine rodents: Its morphological diversity and evolution

The murine rodents are the most speciose subfamily of mammals. Here the morphology of the spermatozoon, as determined by scanning and transmission electron microscopy of representative species from four Eurasian clades, is described. Much interspecific variability in all components of the spermatozoon was found to occur, although most species have a bilaterally flattened sperm head with a single apical hook of variable length and orientation. Ultrastructural observations indicate that this apical hook invariably contains a nuclear projection as well as a large extension of the subacrosomal cytoskeleton, as a perforatorium rostrally, and a complex asymmetrical acrosomal extension. These spermatozoa also have relatively long tails that are attached to the lower concave surface of the sperm head. Uniquely, in species in the Apodemus clade, the apical hook is orientated caudally. In a few species a highly derived sperm head morphotype that does not contain an apical hook is present. These sperm heads vary in morphology from being globular in two species of Bandicota, to bilaterally flattened and paddle-shaped in Tokudaia and Micromys. In spermatozoa of the latter two genera the subacrosomal cytoskeleton, which is less extensive than in species with a hooked sperm head, forms an apical extension, but that is not the case in Bandicota. In all species where the sperm head lacks an apical hook the acrosome is more symmetrical. The sperm tail is much shorter in these species, with attachment to the head occurring on the ventral surface in Tokudaia and basal in Micromys and the two species of Bandicota. As the sperm head morphotype with a complex apical hook is present in all the major clades of murine rodents, it is likely to be a plesiomorphic character within each of these clades, with the nonhooked sperm heads, which vary greatly in structure between species of the different lineages, probably being independently derived. The ultrastructural organization of the sperm head of Bandicota, but not those of Micromys or Tokudaia, suggest divergence in some of the morphological events associated with sperm-egg interaction at the time of fertilization.     

Evolution of the spermatozoon in muroid rodents

In the rodent superfamily Muroidea, a model for the evolution of sperm form has been proposed in which it is suggested that a hook-shaped sperm head and long tail evolved from a more simple, nonhooked head and short tail in several different subfamilies. To test this model the shape of the sperm head, with particular emphasis on its apical region, and length of sperm tail were matched to a recent phylogeny based on the nucleotide sequence of several protein-coding nuclear genes from 3 families and 10 subfamilies of muroid rodents. Data from the two other myomorph superfamilies, the Dipodoidea and kangaroo rats in the Geomyoidea, were used for an outgroup comparison. In most species in all 10 muroid subfamilies, apart from in the Murinae, the sperm head has a long rostral hook largely composed of acrosomal material, although its length and cross-sectional shape vary across the various subfamilies. Nevertheless, in a few species of various lineages a very different sperm morphology occurs in which an apical hook is lacking. In the outgroups the three species of dipodid rodents have a sperm head that lacks a hook, whereas in the heteromyids an acrosome-containing apical hook is present. It is concluded that, as the hook-shaped sperm head and long sperm tail occur across the muroid subfamilies, as well as in the heteromyid rodents, it is likely to be the ancestral condition within each of the subfamilies with the various forms of nonhooked sperm heads, that are sometimes associated with short tails, being highly derived states. These findings thus argue against a repeated evolution in various muroid lineages of a complex, hook-shaped sperm head and long sperm tail from a more simple, nonhooked sperm head and short tail. An alternative proposal for the evolution of sperm form within the Muroidea is presented in the light of these data.     

Causal models for a risk-based assessment of stressor pathways for an operational uranium mine

Protection of the environment and people from the potential impacts of uranium mining and milling is a global issue as the world's demand for power generation derived from uranium increases. We present a framework for deriving multiple stressor-pathway causal models for an operational uranium mine that can be used to identify research and monitoring needs for environmental protection. Additionally the framework enabled us to categorize the importance of pathways in the system. An interdisciplinary approach to causal model development was undertaken in order to ensure the potential impacts of mining on the natural environment and human health were identified and assessed by researchers with the appropriate knowledge. An example of a causal model and supporting narrative is provided for the most important stressor pathway, transport of inorganic toxicants via the surface water to surface water pathway. This risk-based screening approach can be applied to mining operations where environmental protection (including human health) is underpinned by quantitative interdisciplinary research and monitoring.