Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.     

Assessing the complex sponge microbiota: core,variable and species-specific bacterial communities in marine sponges

Marine sponges are well known for their associations with highly diverse, yet very specific and often highly similar microbiota. The aim of this study was to identify potential bacterial sub-populations in relation to sponge phylogeny and sampling sites and to define the core bacterial community. 16S ribosomal RNA gene amplicon pyrosequencing was applied to 32 sponge species from eight locations around the world''s oceans, thereby generating 2567 operational taxonomic units (OTUs at the 97% sequence similarity level) in total and up to 364 different OTUs per sponge species. The taxonomic richness detected in this study comprised 25 bacterial phyla with Proteobacteria, Chloroflexi and Poribacteria being most diverse in sponges. Among these phyla were nine candidate phyla, six of them found for the first time in sponges. Similarity comparison of bacterial communities revealed no correlation with host phylogeny but a tropical sub-population in that tropical sponges have more similar bacterial communities to each other than to subtropical sponges. A minimal core bacterial community consisting of very few OTUs (97%, 95% and 90%) was found. These microbes have a global distribution and are probably acquired via environmental transmission. In contrast, a large species-specific bacterial community was detected, which is represented by OTUs present in only a single sponge species. The species-specific bacterial community is probably mainly vertically transmitted. It is proposed that different sponges contain different bacterial species, however, these bacteria are still closely related to each other explaining the observed similarity of bacterial communities in sponges in this and previous studies. This global analysis represents the most comprehensive study of bacterial symbionts in sponges to date and provides novel insights into the complex structure of these unique associations.     

Hsp104, Hsp70 and Hsp40 interplay regulates formation, growth and elimination of Sup35 prions

Self-templating amyloid forms of Sup35 constitute the yeast prion [PSI(+)]. How the protein-remodelling factor, Hsp104, collaborates with other chaperones to regulate [PSI(+)] inheritance remains poorly delineated. Here, we report how the Ssa and Ssb components of the Hsp70 chaperone system directly affect Sup35 prionogenesis and cooperate with Hsp104. We identify the ribosome-associated Ssb1:Zuo1:Ssz1 complex as a potent antagonist of Sup35 prionogenesis. The Hsp40 chaperones, Sis1 and Ydj1, preferentially interact with Sup35 oligomers and fibres compared with monomers, and facilitate Ssa1 and Ssb1 binding. Various Hsp70:Hsp40 pairs block prion nucleation by disassembling molten oligomers and binding mature oligomers. By binding fibres, Hsp70:Hsp40 pairs occlude prion recognition elements and inhibit seeded assembly. These inhibitory activities are partially relieved by the nucleotide exchange factor, Fes1. Low levels of Hsp104 stimulate prionogenesis and alleviate inhibition by some Hsp70:Hsp40 pairs. At high concentrations, Hsp104 eliminates Sup35 prions. This activity is reduced when Ssa1, or enhanced when Ssb1, is incorporated into nascent prions. These findings illuminate several facets of the chaperone interplay that underpins [PSI(+)] inheritance.     

Anti-tuberculosis therapy-induced hepatotoxicity among Ethiopian HIV-positive and negative patients

Background

To assess and compare the prevalence, severity and prognosis of anti-TB drug induced hepatotoxicity (DIH) in HIV positive and HIV negative tuberculosis (TB) patients in Ethiopia.

Methodology/Principal Findings

In this study, 103 HIV positive and 94 HIV negative TB patients were enrolled. All patients were evaluated for different risk factors and monitored biochemically and clinically for development of DIH. Sub-clinical hepatotoxicity was observed in 17.3% of the patients and 8 out of the 197 (4.1%) developed clinical hepatotoxicity. Seven of the 8 were HIV positive and 2 were positive for HBsAg.

Conclusions/Significance

Sub-clinical hepatotoxicity was significantly associated with HIV co-infection (p = 0.002), concomitant drug intake (p = 0.008), and decrease in CD4 count (p = 0.001). Stepwise restarting of anti TB treatment was also successful in almost all the patients who developed clinical DIH. We therefore conclude that anti-TB DIH is a major problem in HIV-associated TB with a decline in immune status and that there is a need for a regular biochemical and clinical follow up for those patients who are at risk.     

A fluorometric assay for dihydrofolate reductase

A recording fluorometric assay for dihydrofolate reductase is described. The technique measures the appearance of product, tetrahydrofolate, as the reaction proceeds. The assay can be accomplished with as little as 2 pmol of enzyme and is sufficiently sensitive to allow accurate kinetic studies using very low concentrations of substrate. Kinetic studies of both purified and crude preparations of enzyme are reported.     

Hydroid defenses against predators: the importance of secondary metabolites versus nematocysts

Marine hydroids are commonly thought to be defended by stinging organelles called nematocysts that penetrate predator tissues and inject proteinaceous venoms, but not all hydroids possess these nematocysts. Although an increasing number of bioactive secondary metabolites have been isolated from marine hydroids, ecological roles of these compounds are poorly known. To test the hypothesis that nematocysts and noxious secondary metabolites represent alternative defenses against predation, we examined hydroids from North Carolina, United States for: (1) the palatability of whole polyps before and after nematocysts had been deactivated; (2) the palatability of their chemical extracts; and (3) their nutritional value in terms of organic content, protein content, and levels of refractory structural material (chitin). All hydroids were avoided by a generalist predator, the pinfish Lagodon rhomboides, compared with palatable control foods. Two of these (Halocordyle disticha and Tubularia crocea) became palatable after being treated with potassium chloride to discharge their nematocysts, suggesting that these species rely on nematocysts for defenses against predators. Chemical extracts from nematocyst-defended species had no effect on fish feeding. The four species that remained unpalatable after nematocysts had been discharged (Corydendrium parasiticum, Eudendrium carneum, Hydractinia symbiolongicarpus, Tridentata marginata) possessed chemical extracts that deterred feeding by pinfish. We have isolated and characterized the structures of the deterrent metabolites in two of these species. We found no differences in nutritional content or levels of chitin between nematocyst-defended and chemically defended species, and no evidence that either of these played a role in the rejection of hydroids as prey. Our results suggest that, among hydroids, chemical defenses may be at least as common as nematocyst-based defenses and that the two may represent largely alternative defensive strategies. The four hydroid species with deterrent extracts represent four families and both sub-orders of hydroids, suggesting that chemical defenses in this group may be widespread and have multiple origins. Received: 25 May 1999 / Accepted: 1 February 2000     

The distributions of parthenogenetic ascid mites (Acari: Parasitiformes) do not support the biotic uncertainty hypothesis

Fifteen out of 50 species of ascid mites (30%) that we collected from four synanthropic and seven natural habitats in North America and Australia existed as all-female populations. In contrast to the predictions of the biotic uncertainty hypothesis (i.e. that parthenogenetic species are rare, restricted in distribution and survive through dispersal ability), we found that parthenogentic ascid mites were present in ten out of 11 habitats sampled, but were not superior colonists. In a glasshouse experiment, pasteurized soil in pots was colonized first by bisexual species and only later by all-female species. Furthermore, a habitat requiring strong dispersal abilities (decaying fungal sporocarps) lacked parthenogenetic species and a review of literature and collections indicated that all-female ascid species rarely form the phoretic associations with insects necessary to exploit patchy and ephemeral resources. The assumptions that parthenogens are reproductively superior to but competitively inferior to sexual relatives were not supported by experiments comparing a bisexual and an all-female species of Lasioseius.     

Sympatric population divergence within a highly pelagic seabird species complex (Hydrobates spp.)

Both physical and non‐physical barriers can restrict gene flow among seabird populations. Understanding the relative importance of non‐physical barriers, such as breeding phenology, is key to understanding seabird biodiversity. We investigated drivers of diversification in the Leach's storm‐petrel species complex (Hydrobates spp.) by examining population genetic structure across its range. Variation in the mitochondrial control region and six microsatellite loci was assayed in birds sampled from breeding colonies throughout the North Atlantic and North Pacific (H. leucorhoa leucorhoa), as well as from San Benito Islands (H. l. chapmani), and two seasonal populations in Guadalupe (summer breeding H. socorroensis and winter breeding H. cheimomnestes), Mexico. Weak but significant differentiation was found between populations of H. l. leucorhoa breeding in the Atlantic versus North Pacific, as well as between H. l. chapmani and H. l. leucorhoa, and between H. socorroensis and H. cheimomnestes within Guadalupe. In contrast, strong differentiation in both mitochondrial DNA and microsatellites was found between H. leucorhoa and both H. socorroensis and H. cheimomnestes. Phylogenetic reconstruction suggested the Guadalupe seasonal breeding populations are sister taxa, at least in their mitochondrial DNA. Non‐physical barriers to gene flow appear to be more important than physical barriers in driving divergence within the Leach's storm‐petrel species complex. In particular, allochronic speciation may have occurred between the seasonal populations within Guadalupe. Further work should include higher resolution sequencing to confirm results, and an increased sampling effort, particularly within the California area, to fully resolve the relationship between H. l. leucorhoa and H. l. chapmani.