An 18 S rDNA based molecular phylogeny of the Mysidacea (Crustacea)

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Phylogeography of the <i>Rhabditis (Pellioditis) marina</i> species complex: evidence for cosmopolitanism, restricted gene flow, recent range expansions and accelerated evolution

The nematode Rhabditis (Pellioditis) marina has a worldwide distribution despite presumably low dispersal abilities. Recent studies on a local scale have illustrated that R. (P.) marina actually consists of several cryptic species which questions its true cosmopolitan distribution. We performed a phylogeographic study to identify micro- and macro-evolutionary processes shaping population structuring and speciation in the R. (P.) marina species complex. The mitochondrial COI gene was screened with the Single Strand Conformation Polymorphism method (SSCP) in 1292 specimens collected from decomposing macroalgae along the coasts of Western Europe, NE America, Mexico, South Africa and Australia. We found evidence for eleven cryptic species within R. (P.) marina that were sympatrically distributed. A strong genetic structuring was observed in all species and a genetic break was observed around the British Isles. A historical signature was present in species PmII showing evidence for two postglacial, northwards orientated expansions and for restricted gene flow with occasional long-distance dispersal. Our data also pointed to a contact zone in the Southern Bight of the North Sea. We found evidence for a true cosmopolitan distribution of nematode species due to occasional long-distance dispersal. In addition, an accelerated COI mutation rate was suggested for R. (P.) marina, which was about ten times higher than the generally applied molecular clock of 2 %. We further hypothesize that the cryptic radiation in R. (P.) marina is largely the result of allopatric speciation, and that the contemporary sympatric distribution results from occasional long-distance dispersal

Disentangling taxonomy within the <i>Rhabditis (Pellioditis) marina</i> (Nematoda, Rhadbitidae) species complex using molecular and morphological tools

Correct taxonomy is a prerequisite for biological research, but currently it is undergoing a serious crisis, resulting in the neglect of many highly diverse groups of organisms. In nematodes, species delimitation remains problematic due to their high morphological variability. Evolutionary approaches using DNA sequences can potentially overcome the problems caused by morphology, but they are also affected by flaws. A holistic approach with a combination of morphological and molecular methods can therefore produce a straightforward delimitation of species. The present study investigates the taxonomic status of some highly divergent mitochondrial haplotypes in the Rhabditis (Pellioditis) marina species complex by using a combination of molecular and morphological tools. We used concordance among phylogenetic trees of three molecular markers (COI, ITS, D2D3) to infer molecular lineages. Subsequently, morphometric data from nearly all lineages were analysed with multivariate techniques. The results showed that highly divergent genotypic clusters were accompanied by morphological differences, and we created a graphical polytomous key for future identifications. This study indisputably demonstrates that R. (P.) marina and R. (P.) mediterranea belong to a huge species complex and that biodiversity in free-living marine nematodes may seriously be underestimated

Mitochondrial DNA variation and cryptic speciation within the free-living marine nematode <i>Pellioditis marina</i>

An inverse correlation between dispersal ability and genetic differentiation among populations of a species is frequently observed in the marine environment. We investigated the population genetic structure of the free-living marine nematode Pellioditis marina. A total of 426 bp of the mitochondrial cytochrome oxidase subunit 1 (COI) gene were surveyed on a geographical scale of approximately 100 km during spring 2003. Nematodes were collected from 2 coastal locations in Belgium, and from 2 estuaries and a saltwater lake (Lake Grevelingen) in The Netherlands. Molecular variation was assessed with the single-strand conformation polymorphism (SSCP) method. In total, 32 different haplotypes were observed, and sequence divergence among 452 individuals ranged from 0.2 to 10.6%. We discovered 4 distinct mitochondrial lineages, with low divergences within the lineages (0.2 to 1.6%) and high divergences between the lineages (5.1 to 10.6%). The nuclear ribosomal ITS (internal transcribed spacer) region showed concordant phylogenetic patterns, suggesting that nematode species diversity may be considerably underestimated. Analysis of molecular variance (AMOVA) indicated a strong genetic differentiation among populations. The Lake Grevelingen population was clearly differentiated from all other populations, but genetic structuring was also significant within the Westerschelde and was correlated with gradients in salinity and pollution. The observed population genetic structure is in accordance with the limited active dispersal capacity of P. marina, but is at variance with its significant potential for passive dispersal. We therefore suggest that autecological characteristics, including short generation time, high colonization potential and local adaptation, may be at the basis of this nematode’s population genetic structure

The zebrafish as an emerging model to study DNA damage in aging, cancer and other diseases

Cancer is a disease of the elderly, and old age is its largest risk factor. With age, DNA damage accumulates continuously, increasing the chance of malignant transformation. The zebrafish has emerged as an important vertebrate model to study these processes. Key mechanisms such as DNA damage responses and cellular senescence can be studied in zebrafish throughout its life course. In addition, the zebrafish is becoming an important resource to study telomere biology in aging, regeneration and cancer. Here we review some of the tools and resources that zebrafish researchers have developed and discuss their potential use in the study of DNA damage, cancer and aging related diseases

Adult Drosophila melanogaster evolved for antibacterial defense invest in infection-induced expression of both humoral and cellular immunity genes

<p>Abstract</p> <p>Background</p> <p>While the transcription of innate immunity genes in response to bacterial infection has been well-characterised in the Drosophila model, we recently demonstrated the capacity for such transcription to evolve in flies selected for improved antibacterial defense. Here we use this experimental system to examine how insects invest in constitutive versus infection-induced transcription of immunity genes. These two strategies carry with them different consequences with respect to energetic and pleiotropic costs and may be more or less effective in improving defense depending on whether the genes contribute to humoral or cellular aspects of immunity.</p> <p>Findings</p> <p>Contrary to expectation we show that selection preferentially increased the infection-induced expression of both cellular and humoral immunity genes. Given their functional roles, infection induced increases in expression were expected for the humoral genes, while increases in constitutive expression were expected for the cellular genes. We also report a restricted ability to improve transcription of immunity genes that is on the order of 2-3 fold regardless of total transcription level of the gene.</p> <p>Conclusions</p> <p>The evolved increases in infection-induced expression of the cellular genes may result from specific cross talk with humoral pathways or from generalised strategies for enhancing immunity gene transcription. A failure to see improvements in constitutive expression of the cellular genes suggests either that increases might come at too great a cost or that patterns of expression in adults are decoupled from the larval phase where increases would be most effective. The similarity in fold change increase across all immunity genes may suggest a shared mechanism for the evolution of increased transcription in small, discrete units such as duplication of <it>cis</it>-regulatory elements.</p

Conserved Mosquito/Parasite Interactions Affect Development of Plasmodium falciparum in Africa

In much of sub-Saharan Africa, the mosquito Anopheles gambiae is the main vector of the major human malaria parasite, Plasmodium falciparum. Convenient laboratory studies have identified mosquito genes that affect positively or negatively the developmental cycle of the model rodent parasite, P. berghei. Here, we use transcription profiling and reverse genetics to explore whether five disparate mosquito gene regulators of P. berghei development are also pertinent to A. gambiae/P. falciparum interactions in semi-natural conditions, using field isolates of this parasite and geographically related mosquitoes. We detected broadly similar albeit not identical transcriptional responses of these genes to the two parasite species. Gene silencing established that two genes affect similarly both parasites: infections are hindered by the intracellular local activator of actin cytoskeleton dynamics, WASP, but promoted by the hemolymph lipid transporter, ApoII/I. Since P. berghei is not a natural parasite of A. gambiae, these data suggest that the effects of these genes have not been drastically altered by constant interaction and co-evolution of A. gambiae and P. falciparum; this conclusion allowed us to investigate further the mode of action of these two genes in the laboratory model system using a suite of genetic tools and infection assays. We showed that both genes act at the level of midgut invasion during the parasite's developmental transition from ookinete to oocyst. ApoII/I also affects the early stages of oocyst development. These are the first mosquito genes whose significant effects on P. falciparum field isolates have been established by direct experimentation. Importantly, they validate for semi-field human malaria transmission the concept of parasite antagonists and agonists

A Phylogenetic Analysis of the Globins in Fungi

BACKGROUND: ALL GLOBINS BELONG TO ONE OF THREE FAMILIES: the F (flavohemoglobin) and S (sensor) families that exhibit the canonical 3/3 α-helical fold, and the T (truncated 3/3 fold) globins characterized by a shortened 2/2 α-helical fold. All eukaryote 3/3 hemoglobins are related to the bacterial single domain F globins. It is known that Fungi contain flavohemoglobins and single domain S globins. Our aims are to provide a census of fungal globins and to examine their relationships to bacterial globins. RESULTS: Examination of 165 genomes revealed that globins are present in >90% of Ascomycota and ∼60% of Basidiomycota genomes. The S globins occur in Blastocladiomycota and Chytridiomycota in addition to the phyla that have FHbs. Unexpectedly, group 1 T globins were found in one Blastocladiomycota and one Chytridiomycota genome. Phylogenetic analyses were carried out on the fungal globins, alone and aligned with representative bacterial globins. The Saccharomycetes and Sordariomycetes with two FHbs form two widely divergent clusters separated by the remaining fungal sequences. One of the Saccharomycete groups represents a new subfamily of FHbs, comprising a previously unknown N-terminal and a FHb missing the C-terminal moiety of its reductase domain. The two Saccharomycete groups also form two clusters in the presence of bacterial FHbs; the surrounding bacterial sequences are dominated by Proteobacteria and Bacilli (Firmicutes). The remaining fungal FHbs cluster with Proteobacteria and Actinobacteria. The Sgbs cluster separately from their bacterial counterparts, except for the intercalation of two Planctomycetes and a Proteobacterium between the Fungi incertae sedis and the Blastocladiomycota and Chytridiomycota. CONCLUSION: Our results are compatible with a model of globin evolution put forward earlier, which proposed that eukaryote F, S and T globins originated via horizontal gene transfer of their bacterial counterparts to the eukaryote ancestor, resulting from the endosymbiotic events responsible for the origin of mitochondria and chloroplasts

Phenotypic and Genome-Wide Analysis of an Antibiotic-Resistant Small Colony Variant (SCV) of Pseudomonas aeruginosa

Small colony variants (SCVs) are slow-growing bacteria, which often show increased resistance to antibiotics and cause latent or recurrent infections. It is therefore important to understand the mechanisms at the basis of this phenotypic switch.One SCV (termed PAO-SCV) was isolated, showing high resistance to gentamicin and to the cephalosporine cefotaxime. PAO-SCV was prone to reversion as evidenced by emergence of large colonies with a frequency of 10(-5) on media without antibiotics while it was stably maintained in presence of gentamicin. PAO-SCV showed a delayed growth, defective motility, and strongly reduced levels of the quorum sensing Pseudomonas quinolone signal (PQS). Whole genome expression analysis further suggested a multi-layered antibiotic resistance mechanism, including simultaneous over-expression of two drug efflux pumps (MexAB-OprM, MexXY-OprM), the LPS modification operon arnBCADTEF, and the PhoP-PhoQ two-component system. Conversely, the genes for the synthesis of PQS were strongly down-regulated in PAO-SCV. Finally, genomic analysis revealed the presence of mutations in phoP and phoQ genes as well as in the mexZ gene encoding a repressor of the mexXY and mexAB-oprM genes. Only one mutation occurred only in REV, at nucleotide 1020 of the tufA gene, a paralog of tufB, both encoding the elongation factor Tu, causing a change of the rarely used aspartic acid codon GAU to the more common GAC, possibly causing an increase of tufA mRNA translation. High expression of phoP and phoQ was confirmed for the SCV variant while the revertant showed expression levels reduced to wild-type levels.By combining data coming from phenotypic, gene expression and proteome analysis, we could demonstrate that resistance to aminoglycosides in one SCV mutant is multifactorial including overexpression of efflux mechanisms, LPS modification and is accompanied by a drastic down-regulation of the Pseudomonas quinolone signal quorum sensing system

IlsA, A Unique Surface Protein of Bacillus cereus Required for Iron Acquisition from Heme, Hemoglobin and Ferritin

The human opportunistic pathogen Bacillus cereus belongs to the B. cereus group that includes bacteria with a broad host spectrum. The ability of these bacteria to colonize diverse hosts is reliant on the presence of adaptation factors. Previously, an IVET strategy led to the identification of a novel B. cereus protein (IlsA, Iron-regulated leucine rich surface protein), which is specifically expressed in the insect host or under iron restrictive conditions in vitro. Here, we show that IlsA is localized on the surface of B. cereus and hence has the potential to interact with host proteins. We report that B. cereus uses hemoglobin, heme and ferritin, but not transferrin and lactoferrin. In addition, affinity tests revealed that IlsA interacts with both hemoglobin and ferritin. Furthermore, IlsA directly binds heme probably through the NEAT domain. Inactivation of ilsA drastically decreases the ability of B. cereus to grow in the presence of hemoglobin, heme and ferritin, indicating that IlsA is essential for iron acquisition from these iron sources. In addition, the ilsA mutant displays a reduction in growth and virulence in an insect model. Hence, our results indicate that IlsA is a key factor within a new iron acquisition system, playing an important role in the general virulence strategy adapted by B. cereus to colonize susceptible hosts