High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes

Abstract Background Pectobacterium parmentieri is a newly established species within the plant pathogenic family Pectobacteriaceae. Bacteria belonging to this species are causative agents of diseases in economically important crops (e.g. potato) in a wide range of different environmental conditions, encountered in Europe, North America, Africa, and New Zealand. Severe disease symptoms result from the activity of P. parmentieri virulence factors, such as plant cell wall degrading enzymes. Interestingly, we observe significant phenotypic differences among P. parmentieri isolates regarding virulence factors production and the abilities to macerate plants. To establish the possible genomic basis of these differences, we sequenced 12 genomes of P. parmentieri strains (10 isolated in Poland, 2 in Belgium) with the combined use of Illumina and PacBio approaches. De novo genome assembly was performed with the use of SPAdes software, while annotation was conducted by NCBI Prokaryotic Genome Annotation Pipeline. Results The pan-genome study was performed on 15 genomes (12 de novo assembled and three reference strains: P. parmentieri CFBP 8475T, P. parmentieri SCC3193, P. parmentieri WPP163). The pan-genome includes 3706 core genes, a high number of accessory (1468) genes, and numerous unique (1847) genes. We identified the presence of well-known genes encoding virulence factors in the core genome fraction, but some of them were located in the dispensable genome. A significant fraction of horizontally transferred genes, virulence-related gene duplications, as well as different CRISPR arrays were found, which can explain the observed phenotypic differences. Finally, we found also, for the first time, the presence of a plasmid in one of the tested P. parmentieri strains isolated in Poland. Conclusions We can hypothesize that a large number of the genes in the dispensable genome and significant genomic variation among P. parmentieri strains could be the basis of the potential wide host range and widespread diffusion of P. parmentieri. The obtained data on the structure and gene content of P. parmentieri strains enabled us to speculate on the importance of high genomic plasticity for P. parmentieri adaptation to different environments

Asymbiotic germination, seedling development and plantlet propagation of Encyclia aff. oncidioides - an endangered orchid

In order to estimate the best germination conditions of Encyclia aff. oncidioides seeds, five different media (Fast, Knudson C modified by Vajrabhaya, Murashige and Skoog, PB2 and modified Vacin and Went) with different concentrations of plant growth regulators such as benzyladenine (BA), naphthaleneacetic acid (NAA) and gibberellic acid (GA3) were tested. No beneficial effect was observed when BA and NAA were applied to the germination medium and GA3 inhibited germination. The effect of light, activated charcoal, coconut water and casein hydrolysate on seed germination was also studied. The growth rate of seedlings on three different media supplemented with activated charcoal and plant growth regulators was checked. The applied plant growth regulators had no beneficial effect on the further growth of seedlings. Fast and PB2 media with 0.2% activated charcoal proved to be the best for E. aff. oncidioides seed germination, seedling development and plantlet propagation

A systematic review of dementia focused assistive technology

This paper presents a systematic review which explores the nature of assistive technologies currently being designed, developed and evaluated for dementia sufferers and their carers. A search through four large databases, followed by filtering by relevance, led to the identification and subsequent review of papers. Our review revealed that the majority of research in this area focuses on the support of day-to-day living activities, safety monitoring, memory aids and preventing social isolation. We conclude that the majority of AT currently available support day-to-day living activities, safety monitoring and assisting healthcare. However these devices merely address the ‘ease of living’ rather than focusing on ‘quality of life’. Although there are some devices which address social symptoms of Dementia, few address behavioural issues such as aggression and virtually none are available to support recreational activities. After discussing the implications of these findings, we finally reflect on general design issues for assistive technologies in this domain that became apparent during the review

Detection, identification and differentiation of Pectobacterium and Dickeya species causing potato blackleg and tuber soft rot: a review

The soft rot Enterobacteriaceae (SRE) Pectobacterium and Dickeya species (formerly classified as pectinolytic Erwinia spp.) cause important diseases on potato and other arable and horticultural crops. They may affect the growing potato plant causing blackleg and are responsible for tuber soft rot in storage thereby reducing yield and quality. Efficient and cost-effective detection and identification methods are essential to investigate the ecology and pathogenesis of the SRE as well as in seed certification programmes. The aim of this review was to collect all existing information on methods available for SRE detection. The review reports on the sampling and preparation of plant material for testing and on over thirty methods to detect, identify and differentiate the soft rot and blackleg causing bacteria to species and subspecies level. These include methods based on biochemical characters, serology, molecular techniques which rely on DNA sequence amplification as well as several less-investigated ones

Cytotoxic activity of Paris quadrifolia extract and isolated saponin fractions against human tumor cell lines

Steroidal saponins isolated from many plant species belonging to Monocotyledones display potent cytotoxic activity towards many human tumor cells. We examined the cytotoxic effects of crude Paris quadrifolia extract for the first time, testing isolated saponin-rich fractions against four different human cell lines using the [(3-(4,5- dimethylthiazol-2-yl)]-2,5-diphenyltetrazolium bromide (MTT) assay. Cytotoxic activity was tested against human promyelocytic leukemia (HL-60) cells, human cervical adenocarcinoma (HeLa) cells and human breast cancer (MDA-MB-468) cells. Human skin fibroblasts were used as non-neoplastic control cells. Our results show significant activity of the weakly water-soluble solid residue and butanolic fraction against HL-60 and HeLa cells. The solid residue exerted cytotoxicity against all tested cell lines