The airway fungal microbiome in asthma.

BACKGROUND: Fungal involvement in asthma is associated with severe disease. The full spectrum of fungal species in asthma is not well described and is derived largely from insensitive culture techniques. OBJECTIVES: To use high-throughput sequencing to describe the airway mycobiota in asthmatics with and without fungal sensitization and healthy controls; to compare samples representing different airway compartments; to determine whether the mycobiota was influenced by the fungal composition of outdoor air; and to compare findings with clinically relevant outcomes. METHODS: We amplified the internal transcribed spacer region 2 of the nuclear ribosomal operon to identify the fungal species present. Ninety-seven subjects were recruited and provided sputum (83 asthmatics; 14 healthy subjects), with 29 also undergoing a bronchoscopy. A subset of airway samples were compared with matched outdoor air and mouthwash samples. RESULTS: Two hundred and six taxa at the species level were identified in sputum, most at low relative abundance. Aspergillus fumigatus, Candida albicans and Mycosphaerella tassiana had the highest relative abundances and were the most prevalent species across all subjects. The airway mycobiota consisted of a complex community with high diversity between individuals. Notable shifts in the balance of fungi detected in the lung were associated with asthma status, asthma duration and biomarkers of inflammation. Aspergillus tubingensis, a member of the Aspergillus niger species complex, was most prevalent from bronchoscopic protected brush samples and significantly associated with a low sputum neutrophilia. Cryptococcus pseudolongus, from the Cryptococcus humicola species complex, was more abundant from bronchoscopy samples than sputum, and differentially more abundant in asthma than health. CONCLUSIONS AND CLINICAL RELEVANCE: The airway mycobiota was dominated by a relatively small number of species, but was distinct from the oropharyngeal mycobiota and air samples. Members of the A. niger and C. humicola species complexes may play unexpected roles in the pathogenesis of asthma.

A novel allele of ASY3 is associated with greater meiotic stability in autotetraploid Arabidopsis lyrata.

In this study we performed a genotype-phenotype association analysis of meiotic stability in 10 autotetraploid Arabidopsis lyrata and A. lyrata/A. arenosa hybrid populations collected from the Wachau region and East Austrian Forealps. The aim was to determine the effect of eight meiosis genes under extreme selection upon adaptation to whole genome duplication. Individual plants were genotyped by high-throughput sequencing of the eight meiosis genes (ASY1, ASY3, PDS5b, PRD3, REC8, SMC3, ZYP1a/b) implicated in synaptonemal complex formation and phenotyped by assessing meiotic metaphase I chromosome configurations. Our results reveal that meiotic stability varied greatly (20-100%) between individual tetraploid plants and associated with segregation of a novel ASYNAPSIS3 (ASY3) allele derived from A. lyrata. The ASY3 allele that associates with meiotic stability possesses a putative in-frame tandem duplication (TD) of a serine-rich region upstream of the coiled-coil domain that appears to have arisen at sites of DNA microhomology. The frequency of multivalents observed in plants homozygous for the ASY3 TD haplotype was significantly lower than in plants heterozygous for ASY3 TD/ND (non-duplicated) haplotypes. The chiasma distribution was significantly altered in the stable plants compared to the unstable plants with a shift from proximal and interstitial to predominantly distal locations. The number of HEI10 foci at pachytene that mark class I crossovers was significantly reduced in a plant homozygous for ASY3 TD compared to a plant heterozygous for ASY3 ND/TD. Fifty-eight alleles of the 8 meiosis genes were identified from the 10 populations analysed, demonstrating dynamic population variability at these loci. Widespread chimerism between alleles originating from A. lyrata/A. arenosa and diploid/tetraploids indicates that this group of rapidly evolving genes may provide precise adaptive control over meiotic recombination in the tetraploids, the very process that gave rise to them.

Effects of exposing shrimp larvae (Pandalus borealis) to aquaculture pesticides at field relevant concentrations, with and without food limitation.

Anti-parasitic drugs used in the aquaculture industry are discharged to the sea after treatment of salmon. In this study, the effects of azamethiphos (AZA) in the Salmosan® formulation and deltamethrin (DEL) in the Alpha Max® formulation, have been assessed in Northern shrimp larvae (Pandalus borealis) when administered both separately and in combination. The exposure concentrations were 100 ng/L for AZA and 2 ng/L for DEL, each representing a 1000-fold dilution of the prescribed concentrations for salmon. These two chemicals were combined at these concentrations to give a third treatment (AZA + DEL). When larvae were exposed for two hours on the first, second and third days post hatch (dph), significantly increased mortality and reduced swimming activity were observed for larvae from the DEL and combined AZA + DEL treatments 4 dph, though not in larvae from the AZA treatment. A single pulse exposure, delivered on the first day post hatch, caused similar effects on mortality and swimming activity 4 dph as the three-pulse exposure. Mortality was driven by the presence of DEL in both experiments, with no amplification or reduction of effects observed when DEL and AZA were combined. Larvae were observed for 13 days following the single pulse exposure, with food limitation introduced as an additional stressor on day 4. In the DEL and AZA + DEL treatments mortality continued to increase regardless of food level, with no larvae completing development to stage II. The overriding toxicity of DEL masked any potential effects the reduced food ration may have exerted. Swimming activity was lower for AZA treated larvae than Control larvae 13 dph, when both groups were fed daily, though no other significant changes to mortality, development to stage II, feeding rate or gene expression were observed. Food limited Control and AZA larvae had lower swimming activity and feeding rate than daily fed Control larvae, with expression of pyruvate kinase and myosin genes also downregulated. However, there was no negative effect on survival or successful development to stage II in these treatments. In addition, mesencephalic astrocyte-derived neurotropic factor was downregulated in food limited Control larvae when compared with the daily fed Controls. Results from this study together with reported estimates of dispersion plume concentrations of discharged pesticides indicate that toxic concentrations of deltamethrin could reach shrimp larvae several kilometers from a treated salmon farm.

Interspecific introgression mediates adaptation to whole genome duplication.

Adaptive gene flow is a consequential phenomenon across all kingdoms. Although recognition is increasing, there is no study showing that bidirectional gene flow mediates adaptation at loci that manage core processes. We previously discovered concerted molecular changes among interacting members of the meiotic machinery controlling crossover number upon adaptation to whole-genome duplication (WGD) in Arabidopsis arenosa. Here we conduct a population genomic study to test the hypothesis that adaptation to WGD has been mediated by adaptive gene flow between A. arenosa and A. lyrata. We find that A. lyrata underwent WGD more recently than A. arenosa, suggesting that pre-adapted alleles have rescued nascent A. lyrata, but we also detect gene flow in the opposite direction at functionally interacting loci under the most extreme levels of selection. These data indicate that bidirectional gene flow allowed for survival after WGD, and that the merger of these species is greater than the sum of their parts.

Early life stages of Northern shrimp (Pandalus borealis) are sensitive to fish feed containing the anti-parasitic drug diflubenzuron.

Increasing use of fish feed containing the chitin synthesis inhibiting anti-parasitic drug diflubenzuron (DFB) in salmon aquaculture has raised concerns over its impact on coastal ecosystems. Larvae of Northern shrimp (Pandalus borealis) were exposed to DFB medicated feed under Control conditions (7.0 °C, pH 8.0) and under Ocean Acidification and Warming conditions (OAW, 9.5 °C and pH 7.6). Two weeks' exposure to DFB medicated feed caused significantly increased mortality. The effect of OAW and DFB on mortality of shrimp larvae was additive; 10% mortality in Control, 35% in OAW, 66% in DFB and 92% in OAW + DFB. In OAW + DFB feeding and swimming activity were reduced for stage II larvae and none of the surviving larvae developed to stage IV. Two genes involved in feeding (GAPDH and PRLP) and one gene involved in moulting (DD9B) were significantly downregulated in larvae exposed to OAW + DFB relative to the Control. Due to a shorter intermoult period under OAW conditions, the OAW + DFB larvae were exposed throughout two instead of one critical pre-moult period. This may explain the more serious sub-lethal effects for OAW + DFB than DFB larvae. A single day exposure at 4 days after hatching did not affect DFB larvae, but high mortality was observed for OAW + DFB larvae, possibly because they were exposed closer to moulting. High mortality of shrimp larvae exposed to DFB medicated feed, indicates that the use of DFB in salmon aquaculture is a threat to crustacean zooplankton.

Flow-mediated plasticity in the expression of stickleback nesting glue genes.

Nest construction is an essential component of the reproductive behavior of many species, and attributes of nests - including their location and structure - have implications for both their functional capacity as incubators for developing offspring, and their attractiveness to potential mates. To maximize reproductive success, nests must therefore be suited to local environmental conditions. Male three-spined sticklebacks (Gasterosteus aculeatus) build nests from collected materials and use an endogenous, glue-like multimeric protein - "spiggin" - as an adhesive. Spiggin is encoded by a multigene family, and differential expression of spiggin genes potentially allows plasticity in nest construction in response to variable environments. Here, we show that the expression of spiggin genes is affected significantly by both the flow regime experienced by a fish and its nesting status. Further, we show the effects of flow on expression patterns are gene-specific. Nest-building fish exhibited consistently higher expression levels of the three genes under investigation (Spg-a,Spg-1, and Spg-2) than non-nesting controls, irrespective of rearing flow treatment. Fish reared under flowing-water conditions showed significantly increased levels of spiggin gene expression compared to those reared in still water, but this effect was far stronger for Spg-a than for Spg-1 or Spg-2. The strong effect of flowing water on Spg-a expression, even among non-nesters, suggests that the increased production of spiggin - or of spiggin rich in the component contributed by Spg-a - may allow more rapid and/or effective nest construction under challenging high flow conditions.

Differential gene expression during the moult cycle of Antarctic krill (Euphausia superba).

BACKGROUND: All crustaceans periodically moult to renew their exoskeleton. In krill this involves partial digestion and resorption of the old exoskeleton and synthesis of new cuticle. Molecular events that underlie the moult cycle are poorly understood in calcifying crustaceans and even less so in non-calcifying organisms such as krill. To address this we constructed an Antarctic krill cDNA microarray in order to generate gene expression profiles across the moult cycle and identify possible activation pathways. RESULTS: A total of 26 different cuticle genes were identified that showed differential gene expression across the moult cycle. Almost all cuticle genes were up regulated during premoult and down regulated during late intermoult. There were a number of transcripts with significant sequence homology to genes potentially involved in the synthesis, breakdown and resorption of chitin. During early premoult glutamine synthetase, a gene involved in generating an amino acid used in the synthesis of glucosamine, a constituent of chitin, was up regulated more than twofold. Mannosyltransferase 1, a member of the glycosyltransferase family of enzymes that includes chitin synthase was also up regulated during early premoult. Transcripts homologous to a ß-N-acetylglucosaminidase (ß-NAGase) precursor were expressed at a higher level during late intermoult (prior to apolysis) than during premoult. This observation coincided with the up regulation during late intermoult, of a coatomer subunit epsilon involved in the production of vesicles that maybe used to transport the ß-NAGase precursors into the exuvial cleft. Trypsin, known to activate the ß-NAGase precursor, was up regulated more than fourfold during premoult. The up regulation of a predicted oligopeptide transporter during premoult may allow the transport of chitin breakdown products across the newly synthesised epi- and exocuticle layers. CONCLUSION: We have identified many genes differentially expressed across the moult cycle of krill that correspond with known phenotypic structural changes. This study has provided a better understanding of the processes involved in krill moulting and how they may be controlled at the gene expression level.

Differential gene expression during smoltification of Atlantic salmon (Salmo salar L.): a first large-scale microarray study.

The life cycle of the Atlantic salmon (Salmo salar) involves a period of 1 to 3 years in freshwater followed by migration to the sea where the salmon undergoes rapid growth. In preparation for the marine environment, while still in freshwater, the salmon undergo a transformation from a freshwater dwelling parr to a saltwater adapted smolt, a process known as smoltification. The Atlantic salmon Transcriptome Analysis of Important Traits of Salmon/Salmon Genome Project (TRAITS/SGP) cDNA microarray was used to investigate how gene expression alters during smoltification. Genes differentially expressed during smoltification were identified by comparing gene expression profiles in smolt brain, gill, and kidney tissue samples with those of parr. Of the three tissues investigated, the number of differentially expressed genes was the greatest in gill. Many of the differentially expressed genes could be assigned to one of four main categories: growth, metabolism, oxygen transport, and osmoregulation. Quantitative polymerase chain reaction successfully confirmed the differential expression of seven of the upregulated genes. The TRAITS/SGP cDNA microarray was used to successfully demonstrate for the first time how gene expression mediates smoltification in the Atlantic salmon. Changes in gene expression observed in this study reflected the physiological and biochemical changes recorded by previous studies describing the parr-smolt transformation. This study significantly increases our knowledge of smoltification and will benefit future studies in this area of research.

Variable leucine-rich repeats of tomato disease resistance genes Cf-2 and Cf-5 determine specificity.

SUMMARY The tomato Cf-2 and Cf-5 genes confer race specific resistance to infection by the leaf mould pathogen Cladosporium fulvum. The encoded proteins induce a defence response upon recognition of the fungal Avr2 and Avr5 determinants, respectively. Each resistance protein is comprised largely of leucine-rich repeats (LRRs) and the specificity of recognition is thought to occur through a particular domain. We have investigated this further using domain swaps between Cf-2 and Cf-5. Engineered chimeric genes containing portions of Cf-2 and Cf-5 were expressed and shown to be functional. The results clearly show that the specificity for the particular avirulence determinant is restricted to a region of each gene that encodes a subset of LRRs containing the highest level of intergenic variability. In addition, two non-functional mutants of Cf-5 were characterized and their significance discussed.