Genome-based population structure analysis of the strawberry plant pathogen Xanthomonas fragariae reveals two distinct groups that evolved independently before its species description

Xanthomonas fragariae is a quarantine organism in Europe, causing angular leaf spots on strawberry plants. It is spreading worldwide in strawberry-producing regions due to import of plant material through trade and human activities. In order to resolve the population structure at the strain level, we have employed high-resolution molecular typing tools on a comprehensive strain collection representing global and temporal distribution of the pathogen. Clustered regularly interspaced short palindromic repeat regions (CRISPRs) and variable number of tandem repeats (VNTRs) were identified within the reference genome of X. fragariae LMG 25863 as a potential source of variation. Strains from our collection were whole-genome sequenced and used in order to identify variable spacers and repeats for discriminative purpose. CRISPR spacer analysis and multiple-locus VNTR analysis (MLVA) displayed a congruent population structure, in which two major groups and a total of four subgroups were revealed. The two main groups were genetically separated before the first X. fragariae isolate was described and are potentially responsible for the worldwide expansion of the bacterial disease. Three primer sets were designed for discriminating CRISPR-associated markers in order to streamline group determination of novel isolates. Overall, this study describes typing methods to discriminate strains and monitor the pathogen population structure, more especially in the view of a new outbreak of the pathogen

Isolation of Salmonella enterica in seropositive classified finishing pig herds

The aim of this study was to assess the probability of detecting Salmonella from pen faecal samples in seropositive classified finishing pig herds. The study involved 77 herds from Denmark (20), the Netherlands (20), Greece (17) and Germany (20). The serological herd status was determined by the blood- sampling of 50 finishing pigs. Bacteriological sampling was performed by 20 pen faecal samples per herd. Over-all, 47 % of the blood samples had an OD% larger than 10 and 23 % larger than 40. Salmonella was isolated from 135 (9.3 %) pen faecal samples in 32 herds (42 %). Twenty-eight of these herds (87.5 %) had a within-herd seroprevalence larger than 50% at sample cut-off OD%\u3e10. A correlation coefficient of 0.62 was found between the proportion of culture positive- and seropositive samples in a herd at cut-off OD % \u3e 10 and of 0.58 at cut-off OD % \u3e 40. Due to the low sensitivity of culture methods, apparent ‘false positive’ serological results may well represent real infections not detected by bacteriological testing. In this study, there was an increasing probability of recovering Salmonella with increasing within-herd seroprevalence

Removal of bacterial plant pathogens in columns filled with quartz and natural sediments under anoxic and oxygenated conditions

Irrigation with surface water carrying plant pathogens poses a risk for agriculture. Managed aquifer recharge enhances fresh water availability while simultaneously it may reduce the risk of plant diseases by removal of pathogens during aquifer passage. We compared the transport of three plant pathogenic bacteria with Escherichia coli WR1 as reference strain in saturated laboratory column experiments filled with quartz sand, or sandy aquifer sediments. E. coli showed the highest removal, followed by Pectobacterium carotovorum, Dickeya solani and Ralstonia solanacearum. Bacterial and non-reactive tracer breakthrough curves were fitted with Hydrus-1D and compared with colloid filtration theory (CFT). Bacterial attachment to fine and medium aquifer sand under anoxic conditions was highest with attachment rates of max. katt1 = 765 day-1 and 355 day-1, respectively. Attachment was the least to quartz sand under oxic conditions (katt1 = 61 day-1). In CFT, sticking efficiencies were higher in aquifer than in quartz sand but there was no differentiation between fine and medium aquifer sand. Overall removal ranged between < 6.8 log10 m−1 in quartz and up to 40 log10 m−1 in fine aquifer sand. Oxygenation of the anoxic aquifer sediments for two weeks with oxic influent water decreased the removal. The results highlight the potential of natural sand filtration to sufficiently remove plant pathogenic bacteria during aquifer storage

Transcriptome analysis of Xanthomonas fragariae in strawberry leaves

Xanthomonas fragariae is a quarantine bacterial pathogen that causes angular leaf spot on strawberry. The aim of our study was to analyse the mechanism of interaction of this bacterium with its host plant at the transcriptome level. For this purpose, mRNAs of X. fragariae growing in Wilbrink's medium and from infected strawberry cv. Elsanta plants were isolated and sequenced using the Illumina MiSeq platform. The expression profiles of the bacteria in Wilbrink's medium and in planta were very diverse. Of the 3939 CDSs recorded, 1995 had significantly different expression in planta (966 and 1029 genes were down- and upregulated, respectively). Among the genes showing increased expression in planta, those with eggNOG/COG (evolutionary genealogy of genes: Non-supervised Orthologous Groups/Cluster of Orthologous Groups) categories associated with bacterial cell motility, signal transduction, transport and metabolism of inorganic ions and carbohydrates and transcription were overrepresented. Among the genes with the most increased expression in planta, genes primarily associated with flagella synthesis and chemotaxis were found. It is also interesting to note that out of the 31 genes localized on a plasmid, 16 were expressed differently in planta, which may indicate their potential role in plant-pathogen interactions. Many genes with differentiated expression that were localized on chromosome and plasmid encode proteins of unknown function

Methodological concepts for integrated assessment of agricultural and environmental policies in SEAMLESS-IF

Agricultural and Food Policy, Environmental Economics and Policy, Farm Management, Land Economics/Use,

Late onset of development of natural anti-nonGal antibodies in infant humans and baboons:implications for xenotransplantation in infants

If an ABO-incompatible heart is transplanted into an infant before natural antibodies have developed to the specific donor carbohydrate A/B antigen(s), then B-cell tolerance to the donor A/B antigen is achieved, and these antibodies never develop. Anti-carbohydrate antibodies play a role in the rejection of wild type (WT) and alpha1,3-galactosyltransferase gene-knockout (GT-KO) pig xenografts. We investigated development of these antibodies in infant baboons and humans. Serum samples from infant baboons (n = 42) and humans (n = 42) were tested by flow cytometry for immunoglobulin M and immunoglobulin G binding to peripheral blood mononuclear cells from WT and GT-KO pigs, and for complement-dependent cytotoxicity. The presence of anti-blood group antibodies was tested in baboon serum. In infant baboons and humans, cytotoxic anti-Galalpha1,3Gal antibodies develop during the first 3 months, and steadily increase with age, whereas cytotoxic anti-nonGal antibodies are either absent or minimal in the majority of cases throughout the first year of life. Anti-blood group antibodies were not detected before 16 weeks of age. Our data suggest GT-KO pig organ/cell transplants could be carried out in early infancy in the absence of preformed cytotoxic anti-nonGalalpha1,3Gal antibodies.</p

Galaxy Zoo: the dependence of morphology and colour on environment

We analyse the relationships between galaxy morphology, colour, environment and stellar mass using data for over 100,000 objects from Galaxy Zoo, the largest sample of visually classified morphologies yet compiled. We conclusively show that colour and morphology fractions are very different functions of environment. Both are sensitive to stellar mass; however, at fixed stellar mass, while colour is also highly sensitive to environment, morphology displays much weaker environmental trends. Only a small part of both relations can be attributed to variation in the stellar mass function with environment. Galaxies with high stellar masses are mostly red, in all environments and irrespective of their morphology. Low stellar-mass galaxies are mostly blue in low-density environments, but mostly red in high-density environments, again irrespective of their morphology. The colour-density relation is primarily driven by variations in colour fractions at fixed morphology, in particular the fraction of spiral galaxies that have red colours, and especially at low stellar masses. We demonstrate that our red spirals primarily include galaxies with true spiral morphology. We clearly show there is an environmental dependence for colour beyond that for morphology. Before using the Galaxy Zoo morphologies to produce the above results, we first quantify a luminosity-, size- and redshift-dependent classification bias that affects this dataset, and probably most other studies of galaxy population morphology. A correction for this bias is derived and applied to produce a sample of galaxies with reliable morphological type likelihoods, on which we base our analysis.Comment: 25 pages, 20 figures (+ 6 pages, 11 figures in appendices); moderately revised following referee's comments; accepted by MNRA

A European longitudinal study in Salmonella seronegative-and seropositive classified finishing pig herds

A study was performed to assess the stability of an assigned Salmonella status of finishing pig herds over time, seasonal variation in the incidence of herd infections, the herd incidence of Salmonella infections from the grower to the finisher production stage and the correlation between serological and bacteriological herd classification

Human extrahepatic and intrahepatic cholangiocyte organoids show region-specific differentiation potential and model cystic fibrosis-related bile duct disease

The development, homeostasis, and repair of intrahepatic and extrahepatic bile ducts are thought to involve distinct mechanisms including proliferation and maturation of cholangiocyte and progenitor cells. This study aimed to characterize human extrahepatic cholangiocyte organoids (ECO) using canonical Wnt-stimulated culture medium previously developed for intrahepatic cholangiocyte organoids (ICO). Paired ECO and ICO were derived from common bile duct and liver tissue, respectively. Characterization showed both organoid types were highly similar, though some differences in size and gene expression were observed. Both ECO and ICO have cholangiocyte fate differentiation capacity. However, unlike ICO, ECO lack the potential for differentiation towards a hepatocyte-like fate. Importantly, ECO derived from a cystic fibrosis patient showed no CFTR channel activity but normal chloride channel and MDR1 transporter activity. In conclusion, this study shows that ECO and ICO have distinct lineage fate and that ECO provide a competent model to study extrahepatic bile duct diseases like cystic fibrosis