Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana

We present MultiGO, a web-enabled tool for the identification of biologically relevant gene sets from hierarchically clustered gene expression trees (http://ekhidna.biocenter.helsinki.fi/poxo/multigo). High-throughput gene expression measuring techniques, such as microarrays, are nowadays often used to monitor the expression of thousands of genes. Since these experiments can produce overwhelming amounts of data, computational methods that assist the data analysis and interpretation are essential. MultiGO is a tool that automatically extracts the biological information for multiple clusters and determines their biological relevance, and hence facilitates the interpretation of the data. Since the entire expression tree is analysed, MultiGO is guaranteed to report all clusters that share a common enriched biological function, as defined by Gene Ontology annotations. The tool also identifies a plausible cluster set, which represents the key biological functions affected by the experiment. The performance is demonstrated by analysing drought-, cold- and abscisic acid-related expression data sets from Arabidopsis thaliana. The analysis not only identified known biological functions, but also brought into focus the less established connections to defense-related gene clusters. Thus, in comparison to analyses of manually selected gene lists, the systematic analysis of every cluster can reveal unexpected biological phenomena and produce much more comprehensive biological insights to the experiment of interest.     

Maternal antibodies postpone hantavirus infection and enhance individual breeding success

The transfer of maternal antibodies from mother to progeny is a well-known phenomenon in avian and mammalian species. Optimally, they protect the newborn against the pathogens in the environment. The effect of maternal antibodies on microparasite transmission dynamics may have important consequences for both the fitness of the host and the epizootic processes of the pathogens. However, there is a scarcity of studies examining these effects in free-living wild species. We studied the influence of maternal antibodies against the zoonotic Puumala hantavirus (PUUV) on the fitness of bank voles (Clethrionomys glareolus) and on PUUV transmission by exposing young maternal antibody-positive (MatAb+) and negative (MatAb-) bank voles (n=160) to PUUV in experimental populations. PUUV-specific maternal antibodies delayed the timing of infection. Females were more susceptible to PUUV infection than males. Interestingly, both the females and the males with maternal antibodies matured earlier than the other individuals in the population. Our results highlight the significance of maternal antibodies in the transmission of a pathogen and in the breeding success of the carriers.     

The effects of diet quality and quantity on plumage colour and growth of great tit Parus major nestlings: a food manipulation experiment along a pollution gradient

The yellow carotenoid-based plumage coloration of great tit Parus major nestlings is found to be paler in polluted and urban environments. Because carotenoid pigmentation is often considered to be a condition dependent trait in birds we wanted to find out whether food-limitation and poor nestling condition could explain the pale plumage colour in a polluted area. P. major nestlings were supplemented with variable diets along a well known heavy metal pollution gradient around a copper smelter: two food treatments with carotenoids, one food treatment with little carotenoid and one unsupplemented control. Our field experiment showed that nestlings in the polluted area grew better with carotenoid rich diets, while such effect was not found in the unpolluted area. Nestlings showed higher plasma carotenoid (lutein) levels and higher plumage carotenoid chroma values in the unpolluted area than in the polluted area. However, plasma lutein levels or plumage colour were not associated with heavy metal levels in nestling faeces (a proxy for dietary exposure). Our results provide only weak evidence for carotenoid-based colouration to be condition-dependent in great tit nestlings as we found a positive relationship between body mass and carotenoid chroma in the non-supplemented control group only. The positive relationship between body mass and plumage colour intensity is more likely to be produced by the fact that good availability of caterpillars, an important food source for P. major, also means a good availability of carotenoids to nestlings. Our results suggest that main reason for pale nestling plumage in the polluted area is lower quality invertebrate food, and not nutrition-related oxidative stress.     

Altering substrate chain length specificity of an acylhomoserine lactone synthase in bacterial communication

Quorum sensing mediated by specific signal compounds (autoinducers) allows bacteria to monitor their cell density and enables a synchronized regulation of target gene sets. The best studied group of autoinducers are the acylhomoserine lactones (AHSLs), which are central to the regulation of virulence in many plant and animal pathogens. Variation of the acyl side chain of the AHSLs underlies the observed species specificity of this communication system. Here we show that even different strains of the plant pathogen Erwinia carotovora employ different dialects of this language and demonstrate the molecular basis for the acyl chain length specificity of distinct AHSL synthases. Under physiological concentrations, only the cognate AHSL with the "right" acyl chain is recognized as a signal that will switch on virulence genes. Mutagenesis of the AHSL synthase gene expI(SCC1) identified the changes M127T and F69L as sufficient to effectively alter ExpI(SCC1) (an N-3-oxohexanoyl-l-homoserine lactone producer) substrate specificity to that of an N-3-oxooctanoyl-l-homoserine lactone producer. Our data identify critical residues that define the size of the substrate-binding pocket of the AHSL synthase and will help in understanding and manipulating this bacterial language.     

Microwave-assisted synthesis of quinoline, isoquinoline, quinoxaline and quinazoline derivatives as CB2 receptor agonists

Quinoline, isoquinoline, quinoxaline, and quinazoline derivatives were synthesized using microwave-assisted synthesis and their CB1/CB2 receptor activities were determined using the [3?S]GTPγS binding assay. Most of the prepared quinoline, isoquinoline, and quinoxalinyl phenyl amines showed low-potency partial CB2 receptor agonists activity. The most potent CB2 ligand was the 4-morpholinylmethanone derivative (compound 40e) (-log EC?? = 7.8; E(max) = 75%). The isoquinolin-1-yl(3-trifluoromethyl-phenyl)amine (compound 26c) was a high efficacy CB2 agonist (-log EC?? = 5.8; E(max) = 128%). No significant CB1 receptor activation or inactivation was shown in these studies, except 40e, which showed weak CB1 agonist activity (CB1 -log EC?? = 5.0). These ligands serve as novel templates for the development of selective CB2 receptor agonist.     

Dispersion of vendace eggs and larvae around potential nursery areas reveals their reproductive strategy

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The PmrA-PmrB two-component system responding to acidic pH and iron controls virulence in the plant pathogen Erwinia carotovora ssp. carotovora

Efficient response to environmental cues is crucial to successful infection by plant-pathogenic bacteria such as Erwinia carotovora ssp. carotovora. The expression of the main virulence genes of this pathogen, encoding extracellular enzymes that degrade the plant-cell wall, is subject to complex regulatory machinery where two-component systems play an important role. In this paper, we describe for the first time the involvement of the PmrA-PmrB two-component system in regulation of virulence in a plant-pathogenic bacterium. Disruption of pmrB resulted in reduced virulence both in potato and in Arabidopsis. This is apparently due to reduced production of the extracellular enzymes. In contrast, a pmrA mutant exhibited increased levels of these enzymes implying negative regulation of the corresponding genes by PmrA. Furthermore, the pmrB but not pmrA mutant exhibited highly increased resistance to the cationic antimicrobial peptide polymyxin B suggesting alterations in cell surface properties of the mutant. A similar increase of polymyxin resistance was detected in the wild type at mildly acidic pH with low Mg2+. Functional pmrA is essential for bacterial survival on excess iron at acidic pH, regardless of the Mg2+ concentration. We propose that PmrA-PmrB TCS is involved in controlling of bacterial response to external pH and iron and is crucial for bacterial virulence and survival in planta.