Plasmodium relictum infection and MHC diversity in the house sparrow (Passer domesticus)

Antagonistic coevolution between hosts and parasites has been proposed as a mechanism maintaining genetic diversity in both host and parasite populations. In particular, the high level of genetic diversity usually observed at the major histocompatibility complex (MHC) is generally thought to be maintained by parasite-driven selection. Among the possible ways through which parasites can maintain MHC diversity, diversifying selection has received relatively less attention. This hypothesis is based on the idea that parasites exert spatially variable selection pressures because of heterogeneity in parasite genetic structure, abundance or virulence. Variable selection pressures should select for different host allelic lineages resulting in population-specific associations between MHC alleles and risk of infection. In this study, we took advantage of a large survey of avian malaria in 13 populations of the house sparrow (Passer domesticus) to test this hypothesis. We found that (i) several MHC alleles were either associated with increased or decreased risk to be infected with Plasmodium relictum, (ii) the effects were population specific, and (iii) some alleles had antagonistic effects across populations. Overall, these results support the hypothesis that diversifying selection in space can maintain MHC variation and suggest a pattern of local adaptation where MHC alleles are selected at the local host population level.     

Global phylogeography of the avian malaria pathogen Plasmodium relictum based on MSP1 allelic diversity

Knowing the genetic variation that occurs in pathogen populations and how it is distributed across geographical areas is essential to understand parasite epidemiology, local patterns of virulence, and evolution of host‐resistance. In addition, it is important to identify populations of pathogens that are evolutionarily independent and thus ‘free’ to adapt to hosts and environments. Here, we investigated genetic variation in the globally distributed, highly invasive avian malaria parasite Plasmodium relictum, which has several distinctive mitochondrial haplotyps (cyt b lineages, SGS1, GRW11 and GRW4). The phylogeography of P. relictum was accessed using the highly variable nuclear gene merozoite surface protein 1 (MSP1), a gene linked to the invasion biology of the parasite. We show that the lineage GRW4 is evolutionarily independent of GRW11 and SGS1 whereas GRW11 and SGS1 share MSP1 alleles and thus suggesting the presence of two distinct species (GRW4 versus SGS1 and GRW11). Further, there were significant differences in the global distribution of MSP1 alleles with differences between GRW4 alleles in the New and the Old World. For SGS1, a lineage formerly believed to have both tropical and temperate transmission, there were clear differences in MSP1 alleles transmitted in tropical Africa compared to the temperate regions of Europe and Asia. Further, we highlight the occurrence of multiple MSP1 alleles in GRW4 isolates from the Hawaiian Islands, where the parasite has contributed to declines and extinctions of endemic forest birds since it was introduced. This study stresses the importance of multiple independent loci for understanding patterns of transmission and evolutionary independence across avian malaria parasites.     

Atp11c基因诱捕小鼠遗传背景分析

目的利用PCR(polymerase chain reaction,PCR)和荧光竞争性PCR技术对构建的Atp11c基因诱捕小鼠的遗传背景进行分析。方法通过PCR技术鉴定基因诱捕载体的插入位点和宿主染色体的缺失状态;利用荧光竞争性PCR技术检测宿主染色体内的诱捕载体拷贝数。结果 54对引物的PCR结果确定了诱捕载体在Atp11c第一个内含子中的插入位点,测序结果显示伴随着基因诱捕载体两端大于200 bp的碱基缺失,宿主染色体片段出现了418 bp的碱基删除;荧光竞争性PCR证实诱捕载体为单拷贝整合。结论成功解析了Atp11c基因诱捕小鼠的遗传背景,建立了快速、准确检测诱捕小鼠遗传背景的方案。     

Plasmodium ovale in Bangladesh: genetic diversity and the first known evidence of the sympatric distribution of Plasmodium ovale curtisi and Plasmodium ovale wallikeri in southern Asia

In spite of the high prevalence of malaria in Bangladesh and other southern Asian countries, there remains a substantial shortage of knowledge about the less common human malaria parasites. Recent studies indicate that Plasmodium ovale is made up of two species, namely Plasmodium ovale wallikeri and Plasmodium ovale curtisi. Genus- and species-specific nested PCR analyses of the ssrRNA gene was used to detect P. ovale infections among 2,246 diagnostic samples. Plasmodium ovale infections were further differentiated by nested PCR of the potra gene and multilocus sequence analysis of the cox1, porbp2 and the ssrRNA genes. Both P. ovale curtisi and P. ovale wallikeri occur sympatrically in the Chittagong Hill Tracts, Bangladesh and all patients presented with a mild or asymptomatic symptom complex at the time of diagnosis. The pathogens can be differentiated by nested PCRs targeting the ssrRNA and potra genes, and display dimorphism in multilocus sequence analyses. We believe that we report the first evidence of sympatric P. ovale curtisi and P. ovale wallikeri in southern Asia within a relatively confined study area of less than 5,000 km(2). High rates of mixed infections, the emergence of "new" human malaria parasite species and the evidence of zoonotic capability call for optimised diagnostic strategies for a new era of eradication.     

Positive relationships between genetic diversity and abundance in fishes

Molecular markers, such as mitochondrial DNA and microsatellite loci, are widely studied to assess population genetics and phylogeography; however, the selective neutrality of these markers is increasingly being questioned. Given the importance of molecular markers in fisheries science and conservation, we evaluated the neutrality of both mtDNA and microsatellite loci through their associations with population size. We surveyed mtDNA and microsatellite data from the primary literature and determined whether genetic diversity increased with abundance across a total of 105 marine and freshwater fishes, with both global fisheries catch data and body size as proxies for abundance (with an additional 57 species for which only body size data were assessed). We found that microsatellite data generally yielded higher associations with abundance than mtDNA data, and within mtDNA analyses, number of haplotypes and haplotype diversity were more strongly associated with abundance than nucleotide diversity, particularly for freshwater fishes. We compared genetic diversity between freshwater and marine fishes and found that marine fishes had higher values of all measures of genetic diversity than freshwater fishes. Results for both mtDNA and microsatellites generally conformed to neutral expectations, although weaker relationships were often found between mtDNA nucleotide diversity and ‘abundance’ compared to any other genetic statistic. We speculate that this is because of historical events unrelated to natural selection, although a role for selection cannot be ruled out.     

Molecular markers and genetic diversity of Plasmodium vivax

Enhanced understanding of the transmission dynamics and population genetics for Plasmodium vivax is crucial in predicting the emergence and spread of novel parasite phenotypes with major public health implications, such as new relapsing patterns, drug resistance and increased virulence. Suitable molecular markers are required for these population genetic studies. Here, we focus on two groups of molecular markers that are commonly used to analyse natural populations of P. vivax. We use markers under selective pressure, for instance, antigen-coding polymorphic genes, and markers that are not under strong natural selection, such as most minisatellite and microsatellite loci. First, we review data obtained using genes encoding for P. vivax antigens: circumsporozoite protein, merozoite surface proteins 1 and 3α, apical membrane antigen 1 and Duffy binding antigen. We next address neutral or nearly neutral molecular markers, especially microsatellite loci, providing a complete list of markers that have already been used in P. vivax populations studies. We also analyse the microsatellite loci identified in the P. vivax genome project. Finally, we discuss some practical uses for P. vivax genotyping, for example, detecting multiple-clone infections and tracking the geographic origin of isolates.     

Analysis of the cps1 gene provides evidence for a septation checkpoint in Schizosaccharomyces pombe

The fission yeast gene cps1, which encodes the catalytic subunit of β-glucan synthase, was isolated in a screen for mutants that show an increase in ploidy at the restrictive temperature. cps1 mutants display defects in both polarity and septation at the permissive temperature, and become swollen and multinucleate at the restrictive temperature. Analysis of the interaction of cps1 with other mutations suggests the existence of a septation checkpoint, which requires the activity of the protein kinase wee1 for function.     

Analysis of genetic diversity at the iron-containing superoxide dismutase locus in Plasmodium falciparum wild isolates

In order to investigate the genetic diversity of iron-containing superoxide dismutase (FeSOD) from Plasmodium falciparum, a potential anti-malarial therapeutic target, we cloned and sequenced Plasmodium FeSOD from 26 blood samples from non-infected patients. Fifteen clones had the same nucleotide sequence as that of the FeSOD gene of the P. falciparum strain HB3 cultivated in vitro. The other 11 clones presented mutations responsible for punctual amino acid changes which did not modify key residues for the function or the structure of the enzyme. The high sequence conservation between FeSOD from the isolates confirms that this enzyme could represent a therapeutic target.     

Population genetic evidence for rapid changes in intraspecific diversity and allelic cycling of a specialist defense gene in Zea

Two patterns of plant defense gene evolution are emerging from molecular population genetic surveys. One is that specialist defenses experience stronger selection than generalist defenses. The second is that specialist defenses are more likely to be subject to balancing selection, i.e., evolve in a manner consistent with balanced-polymorphism or trench-warfare models of host-parasite coevolution. Because most of the data of specialist defenses come from Arabidopsis thaliana, we examined the genetic diversity and evolutionary history of three defense genes in two outcrossing species, the autotetraploid Zea perennis and its most closely related extant relative the diploid Z. diploperennis. Intraspecific diversity at two generalist defenses, the protease inhibitors wip1 and mpi, were consistent with a neutral model. Like previously studied genes in these taxa, wip1 and mpi harbored similar levels of diversity in Z. diploperennis and Z. perennis. In contrast, the specialist defense hm2 showed strong although distinctly different departures from a neutral model in the two species. Z. diploperennis appears to have experienced a strong and recent selective sweep. Using a rejection-sampling coalescent method, we estimate the strength of selection on Z. diploperennis hm2 to be approximately 3.0%, which is approximately equal to the strength of selection on tb1 during maize domestication. Z. perennis hm2 harbors three highly diverged alleles, two of which are found at high frequency. The distinctly different patterns of diversity may be due to differences in the phase of host-parasite coevolutionary cycles, although higher hm2 diversity in Z. perennis may also reflect reduced efficacy of selection in the autotetraploid relative to its diploid relative.     

A gene trap integration provides an early in situ marker for hepatic specification of the foregut endoderm

We report the characterization of a gene trap integration that provides an in situ marker for one of the earliest events in liver development. Expression of the reporter gene is observed at the nine-somite stage in the hepatic field of the foregut endoderm. At 10.5 days post-coitus expression is observed exclusively and at high levels in the majority of cells in the developing liver bud. As development proceeds the proportion of expressing cells decreases with expression in adult liver being restricted to a few sporadic cells. This therefore provides the earliest, most specific in situ marker of the hepatic lineage reported to date and will be useful in the further characterization of the inductive events involved in hepatic specification. Molecular characterization of the gene trap insertion suggests that the expression pattern is the result of alternative promoter use in the ankyrin repeat-containing gene, gtar.     

A perspective on positive relationships between genetic diversity and abundance in fishes

Given over 90 combined years in academic and professional activities related to genetics and fishery management (FU 57, JS 36—see Waples et al. 2008 ), we are pleased to provide an invited perspective generated by the interesting and useful article of McCusker & Bentzen (2010) . These authors reaffirm the apparent signature of neutrality of mitochondrial and microsatellite markers through an exhaustive analysis of archived genotypic data for 105 marine and freshwater fishes. They note that their conclusions are consistent with earlier and less comprehensive analyses and that they do not exclude the operation of some selective activity (e.g. genetic ‘draft’), which may be overwhelmed by N_e‐related stochastic processes. Here, we provide a complementary focus, recalling relevant issues related to neutrality and selection in applications of molecular variations in fishery management.     

Plant water uptake along a diversity gradient provides evidence for complementarity in hydrological niches

Biodiversity enhances a variety of ecosystem processes, and yet the underlying mechanisms through which these relationships occur remain a critical knowledge gap. Here, we used the natural abundance of stable isotopes to measure depth of water uptake in five common grassland species (Asclepias tuberosa, Lespedeza capitata, Liatris aspera, Schizachyrium scoparium and Sorghastrum nutans) growing across an experimental grassland diversity gradient. Using this approach, we addressed the following questions: 1) does the depth‐specific provenance of water uptake differ among species and/or do interspecific differences in water source manifest with increasing community diversity? 2) Does the isotopic niche space occupied by plants change with increasing diversity? 3) Is plasticity in water uptake depth across a diversity gradient associated with functional plant responses? We found that the depth of soil water used by plants was inherently different among species when grown in monocultures. All species used less shallow soil water and more intermediate‐depth soil water in mixed assemblages than in monocultures, resulting in similar interspecific differences in water source across the diversity gradient. However, plasticity in the locations of water used were positively associated with increases in plant growth in higher diversity treatments. These results indicate that plasticity in water‐use may contribute to positive biodiversity–productivity relationships commonly observed in temperate grasslands.     

Trans stimulation provides evidence for a drug efflux carrier as the mechanism of chloroquine resistance in Plasmodium falciparum

The mechanism underpinning chloroquine drug resistance in the human malarial parasite Plasmodium falciparum has remained controversial. Currently considered models to explain the resistance phenotype include acquisition of a chloroquine efflux pump, changes in intracellular chloroquine partitioning, diminished binding affinity of chloroquine to its intracellular target, heme, and changes in heme crystallization. To challenge these different models, we have investigated chloroquine accumulation under trans-stimulation conditions and in the presence and absence of glucose. We show that, in chloroquine-sensitive strains, labeled chloroquine accumulation is steadily reduced as the pre-equilibrated chloroquine concentration is raised. In the resistant cells, the extent of accumulation is, strikingly, raised at the lower levels of preloading, in comparison with resistant controls in the absence of chloroquine. The trans-stimulation effect observed in chloroquine-resistant cells is strictly energy-dependent. The data are interpreted in terms of a model in which chloroquine is bound to intracellular binding sites, not different as between sensitive and resistant cells, but where, in resistant cells, there exists an energy-dependent carrier that moves chloroquine out of this intracellular compartment. A mathematical model describing the kinetics of these processes is presented.     

Application of sequence-specific labeled 16S rRNA gene oligonucleotide probes for genetic profiling of cyanobacterial abundance and diversity by array hybridization

DNA sequence information for the small-subunit rRNA gene (16S rDNA) obtained from cyanobacterial cultures was used to investigate the presence of cyanobacteria and their abundance in natural habitats. Eight planktonic communities developing in lakes characterized by relatively low algal biomass (mesotrophic) and in lakes with correspondingly high biomass (eutrophic) were selected for the study. The organismal compositions of the water samples were analyzed genetically, using multiplex sequence-specific labeling of oligonucleotide probes targeted to 16S rDNA and subsequent hybridization of the labeled probes to their respective complements spotted onto a solid support (DNA array). Ten probes were established to determine the relative abundances of the discernible cyanobacteria encountered in the selected lakes. The probes were generally specific for their targets, as determined through analyses of clone cultures. Reproducible abundance profiles were established for the lakes investigated in the subsequent analyses of natural cyanobacterial communities. The results from the genetic analyses were then compared with information obtained from standard hydrobiological and hydrochemical analyses. Qualitatively, there were relatively good correlations among the groups of organisms (Nostoc, Microcystis, and Planktothrix species) found in the different lakes. The levels of correlation were lower for the quantitative data. This may, however, be due to differences in sample processing technique. The conclusions from these comparisons are that the genetic abundance profiles may provide a foundation for separating and quantifying genetically distinct groups of cyanobacteria in their natural habitats.     

Sugar enrichment provides evidence for a role of nitrogen fixation in coral bleaching

The disruption of the coral–algae symbiosis (coral bleaching) due to rising sea surface temperatures has become an unprecedented global threat to coral reefs. Despite decades of research, our ability to manage mass bleaching events remains hampered by an incomplete mechanistic understanding of the processes involved. In this study, we induced a coral bleaching phenotype in the absence of heat and light stress by adding sugars. The sugar addition resulted in coral symbiotic breakdown accompanied by a fourfold increase of coral‐associated microbial nitrogen fixation. Concomitantly, increased N:P ratios by the coral host and algal symbionts suggest excess availability of nitrogen and a disruption of the nitrogen limitation within the coral holobiont. As nitrogen fixation is similarly stimulated in ocean warming scenarios, here we propose a refined coral bleaching model integrating the cascading effects of stimulated microbial nitrogen fixation. This model highlights the putative role of nitrogen‐fixing microbes in coral holobiont functioning and breakdown.