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Infectious pancreatic necrosis virus (IPNV) causes economic losses with a highly variable mortality rate worldwide, especially in rainbow trout. The virus has a double-stranded bi-partite RNA genome designated segment A and B. New complete genome sequences of nine rainbow trout isolates from Turkey were determined and subjected to phylogenetic analysis, identifying all as genotype 5 (serotype Sp). A time-dependent change in the extended pathogenicity motif of VP2 from P217T221A247 (PTA) to PTE P217T221E247 over a period of 10 years was identified. A wider analysis of 99 IPNV sequences from Turkey and Iran revealed the emergence of the motif PTE from 2007 to 2017, inducing significant morbidity in fry by 2013. In fact, displacement of the PTA motif, by the PTE motif in IPNV isolates appeared to be connected to a production peak of rainbow trout in 2013. An additional CAI analysis provided more evidence, indicating that rainbow trout culture in Turkey has an influence on the evolution of IPNV. [ABSTRACT FROM AUTHOR]

Abstract Historically, histopathology evaluation is performed by a pathologist generating a qualitative assessment on thin tissue sections on glass slides. In the past decade, there has been a growing interest for tools able to reduce human subjectivity and improve workload. Whole slide scanning technology combined with object orientated image analysis can offer the capacity of generating fast and reliable results. In the present study, we combined the use of these emerging technologies to characterise a mouse model for chronic asthma. We monitored the inflammatory changes over five weeks by measuring the number of neutrophils and eosinophils present in the tissue, as well as, the bronchiolar associated lymphoid tissue (BALT) area on whole lungs sections. We showed that inflammation assessment could be automated efficiently and reliably. In comparison to human evaluation performed on the same set of sections, computer generated data was more descriptive and fully quantitative. Moreover optimisation of our detection parameters allowed us to be to more sensitive and to generate data in a larger dynamic range to traditional experimental evaluation, such as bronchiolar lavage (BAL) inflammatory cell counts obtained by flow cytometry. We also took advantage of the fact that we could increase the number of samples to be analysed within a day. Such optimisation allowed us to determine the best study design and experimental conditions in order to increase statistical significance between groups. In conclusion, we showed that combination of whole slide digital scanning and image analysis could be fully automated and deliver more descriptive and biologically relevant data over traditional methods evaluating histopathological pulmonary changes observed in this mouse model of chronic asthma.

The tolerance of ash trees against the pathogen Hymenoscyphus fraxineus seems to be associated with the occurrence of specific microbial taxa on leaves. A group of bacterial isolates, primarily identified on tolerant trees, was investigated with regard to their taxonomic classification and their potential to suppress the ash dieback pathogen. Examination of OGRI values revealed a separate species position. A phylogenomic analysis, based on orthologous and marker genes, indicated a separate genus position along with the species Achromobacter aestuarii. Furthermore, analysis of the ratio of average nucleotide identities and genome alignment fractions demonstrated genomic dissimilarities typically observed for inter-genera comparisons within this family. As a result of these investigations, the strains are considered to represent a separate species within a new genus, for which the name Schauerella fraxinea gen. nov., sp. nov. is proposed, with the type strain B3P038T (=LMG 33092 T = DSM 115926 T). Additionally, a reclassification of the species Achromobacter aestuarii as Schauerella aestuarii comb. nov. is proposed. In a co-cultivation assay, the strains were able to inhibit the growth of a H. fraxineus strain. Accordingly, a functional analysis of the genome of S. fraxinea B3P038T revealed genes mediating the production of antifungal substances. This potential, combined with the prevalent presence in the phyllosphere of tolerant ash trees, makes this group interesting for an inoculation experiment with the aim of controlling the pathogen in an integrative approach. For future field trials, a strain-specific qPCR system was developed to establish an efficient method for monitoring the inoculation success. [ABSTRACT FROM AUTHOR]

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The persistence of traits introduced into the indigenous bacterial community of poplar plants was investigated using bioluminescence mediated by the luc gene. Three endophytic bacterial strains provided with the IncP-1 α plasmid RP4-Tn-luc were used to inoculate poplar cuttings at different phenological stages. Screening of isolates by bioluminescence and real-time PCR detection of the luc gene revealed stable persistence for at least 10 weeks. Although the inoculated strains became established with a high population density after inoculation at leaf development (April) and senescence (October), the strains were suppressed by the indigenous bacteria at stem elongation (June). Transconjugants could be detected only at this phenological stage. Indigenous bacteria harbouring RP4-Tn-luc became established with densities ranging from 2 × 105 to 9 × 106 CFU g-1 fresh weight 3 and 10 weeks after inoculation. The increased colonization of the cuttings by indigenous bacteria at stem elongation seemed to strongly compete with the introduced strains. Otherwise, the phenological stage of the plants as well as the density of the indigenous recipients could serve as the driver for a more frequent conjugative plasmid transfer. A phylogenetic assignment of transconjugants indicated the transfer of RP4-Tn-luc into six genera of Proteobacteria, mainly Sphingomonas, Stenotrophomonas and Xanthomonas. [ABSTRACT FROM AUTHOR]

A new group of darkly pigmented root-infecting fungi was isolated from cereal roots obtained from six different locations in northeastern Germany. Similar random amplified polymorphic DNA (RAPD) patterns and restriction profiles of amplified rDNA were used as a basis for classifying the isolates in a separate group. The isolates demonstrating mycelial and infection characteristics typical of Gaeumannomyces graminis could be differentiated from the varieties of G. graminis as well as from Gaeumannomyces cylindrasporus/Phialophora graminicola using RAPD Polymerase chain reaction (PCR) and rDNA Restriction-fragment length polymorphism (RFLP) analysis. Phylogenetic analysis of the Internal transcribed spacer (ITS) regions suggests that the isolates from a distinct group (named group 'E') situated within the Gaeumannomyces-Phialophora complex between the branch of the G. graminis varieties and Gaeumannomyces incrustans/Magnaporthe poae. Isolates of group E. produced lobed hyphopodia and were shown in biotests to be non-pathogenic to wheat, oats, Italian Ryegrass and Chewings Fescue, suggesting it is a being parasite which colonizes cereals or grasses without destroying vascular tissue. Furthermore, curved phialospores could be found. Summarizing the results presented, this new group could be classified as a new species of Phialophora. Although isolated of group E were found at only six of the 32 investigated locations, they composed up to 50% of total isolates of the Gaeumannomyces-Phialophora complex at these sites. Because of the non-pathogenic behaviour, the new group may be of value as biological control agents for pathogenic fungi. [ABSTRACT FROM AUTHOR]

The components of leghaemoglobin (Lb) from twelve different Pisum sativum L. cvs and three near-isogenic foliar mutants were investigated by anion-exchange high-performance liquid chromatography (HPCL). Five different Lb component profiles could be found. The number of components varied from four to six dependent on cultivar used. An Lb pattern composed of four Lb components could be detected in thirteen P. sativum cultivars and lines. Ten of them showed an identical profile. In nodules of each cultivar, the two known major components, LbI and LbV, but also LbIV, could be detected. Additionally, cultivar-specific Lb components could be identified, each representing up to 10% of total Lb. One of these components, LbIII, has been described previously, but three new Lb components (LbII, LbVI, and LbVII) were found. The presence of all Lb components detected by HPCL was confirmed by analytical isoelectric focusing. Further, it was shown that age-dependent changes in the relative concentrations of LbI and LbV are common in P. sativum>/em> and that these variations are independent of breeding lines and cultivars. [ABSTRACT FROM AUTHOR]