Biology of Wet Bubble disease of cultivated mushrooms

The study examined the physical and biotic factors which affect the host-parasite relationship between the necrotrophic fungus Mycogone perniciosa (Magnus) and its host Aqaricus bisporus (Lange) Sing, in vivo and in vitro and the relevance of these factors to the conditions under which A.bisporus is commercially cultivated. The effect of environmental variables on growth of M.perniciosa varied depending on its developmental stage. Mycelial growth in vitro on media developed specifically for this work was optimum at 25°C, pH 4.1 and C : N ratio 55 : 1. Growth of the fungus occurred on media containing Na-carboxymethylcellulose. sucrose, chitin or galactomannan. The environmental conditions found to be optimum for M.perniciosa in vitro closely paralleled the conditions under which A.bisporus is cultivated commercially. Germination trials showed that verticillate conidia geminate most readily at 18°C. chlamydospores at 25°C. Relative proportions and overall production of the two types of M.perniciosa spores was also temperature dependant. Conidia were air dispersed. M.perniciosa exhibits biotrophic tendencies in the presence of A.bisporus. Saprophytic ability of M.perniciosa appeared greater in the absence than in the presence of the host, with a high susceptibility to fungistasis in composts and casing. Inoculation tests in vitro and in vivo identified a range of fungi as being potential hosts of M.perniciosa. A structural study was made of infected host tissue. M.perniciosa appeared to cause highly localised host cell wall breakdown. The hypothesis that enzymic degradation of host cell walls is an important part of disease development was confirmed by ultrastructural observations and by the assay of wall hydrolase enzymes. The development of infected tissue appeared to be dependant on toxins and growth promoting substances originating from both the host and the pathogen. Disease development was also dependant on antibiosis resulting from other organisms colonising the compost and casing layers. Attempts were made to control M.perniciosa in cropping beds using such antagonistic bacteria. Isolates showing most potential were Pseudomonas bacteria of species group 3 (P.Fluorescens complex). Disease control was expressed as both (i) a reduction in the development of infected sporophore tissue, and (ii) an increase in the yield of healthy sporophores in the presence of the pathogen. Correlation between antagonism of M.perniciosa in vitro and disease control was greatest in the former case. The level of disease control achieved by inoculating antagonistic bacteria to A.bisporus casing heavily infected with M.perniciosa was significant but was highly variable

Melon Cultivation in Sand and Hardwood Sawdust

The growth and productivity of melons, cultivar 'Polidor', were assessed in 2, 4 and 8 litres of sand and hardwood sawdust irrigated to excess with a complete nutrient solution. The plants were grown in a glasshouse set at day/ night temperatures of lS'C/15'C with venting at 26'C. Mean total stem and leaf dry matter after the lmits were harvested were not significantly different between treatments. Mean limit yield (number and weight) was not affected l7y substrate volume but was significantly (P<O.Ol) higher from plants grown in sand. Similarly, mean harvest date for the first lmit was significantly (P<O.Ol) earlier from plants grown in sand compared with sawdus

An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs

Background: Transcription factors (TFs) control transcription by binding to specific regions of DNA called transcription factor binding sites (TFBSs). The identification of TFBSs is a crucial problem in computational biology and includes the subtask of predicting the location of known TFBS motifs in a given DNA sequence. It has previously been shown that, when scoring matches to known TFBS motifs, interdependencies between positions within a motif should be taken into account. However, this remains a challenging task owing to the fact that sequences similar to those of known TFBSs can occur by chance with a relatively high frequency. Here we present a new method for matching sequences to TFBS motifs based on intuitionistic fuzzy sets (IFS) theory, an approach that has been shown to be particularly appropriate for tackling problems that embody a high degree of uncertainty. Results: We propose SCintuit, a new scoring method for measuring sequence-motif affinity based on IFS theory. Unlike existing methods that consider dependencies between positions, SCintuit is designed to prevent overestimation of less conserved positions of TFBSs. For a given pair of bases, SCintuit is computed not only as a function of their combined probability of occurrence, but also taking into account the individual importance of each single base at its corresponding position. We used SCintuit to identify known TFBSs in DNA sequences. Our method provides excellent results when dealing with both synthetic and real data, outperforming the sensitivity and the specificity of two existing methods in all the experiments we performed. Conclusions: The results show that SCintuit improves the prediction quality for TFs of the existing approaches without compromising sensitivity. In addition, we show how SCintuit can be successfully applied to real research problems. In this study the reliability of the IFS theory for motif discovery tasks is proven

Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets

<p>Abstract</p> <p>Background</p> <p>In plant mitochondria, the post-transcriptional RNA editing process converts C to U at a number of specific sites of the mRNA sequence and usually restores phylogenetically conserved codons and the encoded amino acid residues. Sites undergoing RNA editing evolve at a higher rate than sites not modified by the process. As a result, editing sites strongly affect the evolution of plant mitochondrial genomes, representing an important source of sequence variability and potentially informative characters.</p> <p>To date no clear and convincing evidence has established whether or not editing sites really affect the topology of reconstructed phylogenetic trees. For this reason, we investigated here the effect of RNA editing on the tree building process of twenty different plant mitochondrial gene sequences and by means of computer simulations.</p> <p>Results</p> <p>Based on our simulation study we suggest that the editing ‘noise’ in tree topology inference is mainly manifested at the cDNA level. In particular, editing sites tend to confuse tree topologies when artificial genomic and cDNA sequences are generated shorter than 500 bp and with an editing percentage higher than 5.0%. Similar results have been also obtained with genuine plant mitochondrial genes. In this latter instance, indeed, the topology incongruence increases when the editing percentage goes up from about 3.0 to 14.0%. However, when the average gene length is higher than 1,000 bp (<it>rps3</it>, <it>matR</it> and <it>atp1</it>) no differences in the comparison between inferred genomic and cDNA topologies could be detected.</p> <p>Conclusions</p> <p>Our findings by the here reported <it>in silico</it> and <it>in vivo</it> computer simulation system seem to strongly suggest that editing sites contribute in the generation of misleading phylogenetic trees if the analyzed mitochondrial gene sequence is highly edited (higher than 3.0%) and reduced in length (shorter than 500 bp).</p> <p>In the current lack of direct experimental evidence the results presented here encourage, thus, the use of genomic mitochondrial rather than cDNA sequences for reconstructing phylogenetic events in land plants.</p

Fifth European Dirofilaria and Angiostrongylus Days (FiEDAD) 2016

Peer reviewe