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1. A novel genotype of avian hepatitis E virus identified in chickens and common pheasants (Phasianus colchicus), extending its host range

Author

Miguel Matos, Ivana Bilic, Jana Tvarogová, Nicola Palmieri, Danuta Furmanek, Malwina Gotowiecka, Dieter Liebhart, and Michael Hess

Subjects
Medicine, Science
Abstract

Abstract In 2019, outbreaks of hepatitis-splenomegaly syndrome (HSS) were observed in six commercial layer chicken flocks, belonging to three different Polish farms, and characterized by increased mortality, hemorrhagic hepatitis with attached blood clots on the liver surface, and splenomegaly. Diseased flocks were initially investigated for the presence of avian hepatitis E virus (aHEV) – the etiological agent of HSS – by conventional reverse transcriptase polymerase chain reaction, which revealed aHEV sequences clustering separately from all known aHEV genotypes. Additionally, an aHEV genome was identified for the first time in common pheasants, from a flock in France, using Next Generation Sequencing. This genome clustered together with the Polish aHEVs here investigated. Complete genome aHEV sequences from the HSS outbreaks confirmed the divergent cluster, with a shared nucleotide sequence identity of 79.6–83.2% with other aHEVs, which we propose to comprise a novel aHEV genotype – genotype 7. Histology and immunohistochemistry investigations in the liver and spleen established an association between aHEV and the observed lesions in the affected birds, consolidating the knowledge on the pathogenesis of aHEV, which is still largely unknown. Thus, the present investigation extends the natural host range and genotypes of aHEV and strengthens knowledge on the pathogenesis of HSS.

Published
2022
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2. The genetic network underlying the evolution of pathogenicity in avian Escherichia coli

Author

Nicola Palmieri, Ilias Apostolakos, Surya Paudel, and Michael Hess

Subjects
GWAS, APEC, pathogenicity (infectivity), Escherichia coli (E. coli), protein–protein interaction (PPI) network, Veterinary medicine, SF600-1100
Abstract

IntroductionColibacillosis is a worldwide prevalent disease in poultry production linked to Escherichia coli strains that belong to the avian pathogenic E. coli (APEC) pathotype. While many virulence factors have been linked to APEC isolates, no single gene or set of genes has been found to be exclusively associated with the pathotype. Moreover, a comprehensive description of the biological processes linked to APEC pathogenicity is currently lacking.MethodsIn this study, we compiled a dataset of 2015 high-quality avian E. coli genomes from pathogenic and commensal isolates, based on publications from 2000 to 2021. We then conducted a genome-wide association study (GWAS) and integrated candidate gene identification with available protein-protein interaction data to decipher the genetic network underlying the biological processes connected to APEC pathogenicity.ResultsOur GWAS identified variations in gene content for 13 genes and SNPs in 3 different genes associated with APEC isolates, suggesting both gene-level and SNP-level variations contribute to APEC pathogenicity. Integrating protein-protein interaction data, we found that 15 of these genes clustered in the same genetic network, suggesting the pathogenicity of APEC might be due to the interplay of different regulated pathways. We also found novel candidate genes including an uncharacterized multi-pass membrane protein (yciC) and the outer membrane porin (ompD) as linked to APEC isolates.DiscussionOur findings suggest that convergent pathways related to nutrient uptake from host cells and defense from host immune system play a major role in APEC pathogenicity. In addition, the dataset curated in this study represents a comprehensive historical genomic collection of avian E. coli isolates and constitutes a valuable resource for their comparative genomics investigations.

Published
2023
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3. Gene expression of peripheral blood mononuclear cells and CD8+ T cells from gilts after PRRSV infection

Author

Emil Lagumdzic, Clara P. S. Pernold, Reinhard Ertl, Nicola Palmieri, Maria Stadler, Spencer Sawyer, Melissa R. Stas, Heinrich Kreutzmann, Till Rümenapf, Andrea Ladinig, and Armin Saalmüller

Subjects
PRRSV, CD8+ T cells, PBMCs, RNA-Seq, transcriptome, swine, Immunologic diseases. Allergy, RC581-607
Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) is a positive-stranded RNA virus, which emerged in Europe and U.S.A. in the late 1980s and has since caused huge economic losses. Infection with PRRSV causes mild to severe respiratory and reproductive clinical symptoms in pigs. Alteration of the host immune response by PRRSV is associated with the increased susceptibility to secondary viral and bacterial infections resulting in more serious and chronic disease. However, the expression profiles underlying innate and adaptive immune responses to PRRSV infection are yet to be further elucidated. In this study, we investigated gene expression profiles of PBMCs and CD8+ T cells after PRRSV AUT15-33 infection. We identified the highest number of differentially expressed genes in PBMCs and CD8+ T cells at 7 dpi and 21 dpi, respectively. The gene expression profile of PBMCs from infected animals was dominated by a strong innate immune response at 7 dpi which persisted through 14 dpi and 21 dpi and was accompanied by involvement of adaptive immunity. The gene expression pattern of CD8+ T cells showed a strong adaptive immune response to PRRSV, leading to the formation of highly differentiated CD8+ T cells starting from 14 dpi. The hallmark of the CD8+ T-cell response was the increased expression of effector and cytolytic genes (PRF1, GZMA, GZMB, GZMK, KLRK1, KLRD1, FASL, NKG7), with the highest levels observed at 21 dpi. Temporal clustering analysis of DEGs of PBMCs and CD8+ T cells from PRRSV-infected animals revealed three and four clusters, respectively, suggesting tight transcriptional regulation of both the innate and the adaptive immune response to PRRSV. The main cluster of PBMCs was related to the innate immune response to PRRSV, while the main clusters of CD8+ T cells represented the initial transformation and differentiation of these cells in response to the PRRSV infection. Together, we provided extensive transcriptomics data explaining gene signatures of the immune response of PBMCs and CD8+ T cells after PRRSV infection. Additionally, our study provides potential biomarker targets useful for vaccine and therapeutics development.

Published
2023
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4. Complete genomes of the eukaryotic poultry parasite Histomonas meleagridis: linking sequence analysis with virulence / attenuation

Author

Nicola Palmieri, Marcelo de Jesus Ramires, Michael Hess, and Ivana Bilic

Subjects
Histomonas meleagridis, Virulent, Attenuated, Histomonosis, Genome, Turkey, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Histomonas meleagridis is a protozoan parasite and the causative agent of histomonosis, an important poultry disease whose significance is underlined by the absence of any treatment and prophylaxis. The recent successful in vitro attenuation of the parasite urges questions about the underlying mechanisms. Results Whole genome sequence data from a virulent and an attenuated strain originating from the same parental lineage of H. meleagridis were recruited using Oxford Nanopore Technology (ONT) and Illumina platforms, which were combined to generate megabase-sized contigs with high base-level accuracy. Inspecting the genomes for differences identified two substantial deletions within a coding sequence of the attenuated strain. Additionally, one single nucleotide polymorphism (SNP) and indel targeting coding sequences caused the formation of premature stop codons, which resulted in the truncation of two genes in the attenuated strain. Furthermore, the genome of H. meleagridis was used for characterizing protein classes of clinical relevance for parasitic protists. The comparative analysis with the genomes of Trichomonas vaginalis, Tritrichomonas foetus and Entamoeba histolytica identified ~ 2700 lineage-specific gene losses and 9 gene family expansions in the H. meleagridis lineage. Conclusions Taken as a whole, the obtained data provide the first hints to understand the molecular basis of attenuation in H. meleagridis and constitute a genomics platform for future research on this important poultry pathogen.

Published
2021
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5. Infection dynamics of Salmonella Infantis strains displaying different genetic backgrounds – with or without pESI-like plasmid – vary considerably

Author

Victoria Drauch, Christian Kornschober, Nicola Palmieri, Michael Hess, and Claudia Hess

Subjects
Salmonella Infantis, broiler chicken, pESI-like plasmid, virulence, infection, experimental study, Infectious and parasitic diseases, RC109-216, Microbiology, QR1-502
Abstract

Food-borne infections with Salmonella are among the most common causes of human diseases worldwide, and infections with the serovar Infantis are becoming increasingly important. So far, diverse phenotypes and genotypes of S. Infantis have been reported. Therefore, the present study aimed to investigate the infection dynamics of two different S. Infantis strains in broilers. For this purpose, 15 birds were infected on day 2 of life with 108 CFU/ml of a pESI+ or a pESI– S. Infantis strain, respectively. Ten uninfected birds served as in-contact birds to monitor transmission. In both groups, an increase of infection was observed from 7 days of age onwards, reaching its peak at 28 days. However, the pESI+ strain proved significantly more virulent being re-isolated from most cloacal swabs and organs by direct plating. In contrast, the pESI– strain could be re-isolated from cloacal swabs and caeca only when enrichment was applied. Although the excretion of this strain was limited, the transmission level to in-contact birds was similar to the pESI+ strain. Differences in infection dynamics were also reflected in the antibody response: whereas the pESI+ strain provoked a significant increase in antibodies, antibody levels following infection with the pESI– strain remained in the range of negative control birds. The actual findings provide for the first time evidence of S. Infantis strain-specific infectivity in broilers and confirm previous observations in the field regarding differences in persistence on farms and resistance against disinfectants.

Published
2021
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6. Sequencing of five poultry strains elucidates phylogenetic relationships and divergence in virulence genes in Morganella morganii

Author

Nicola Palmieri, Claudia Hess, Michael Hess, and Merima Alispahic

Subjects
Morganella morganii, Poultry, NGS data, MALDI-TOF MS, Antimicrobial resistance, Virulence genes, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background M. morganii is a bacterium frequently associated with urinary infections in humans. While many human strains are sequenced, only the genomes of few poultry strains are available. Here, we performed a detailed characterization of five highly resistant Morganella morganii strains isolated in association with Escherichia coli from diseased domestic Austrian poultry flocks, namely geese, turkeys and chicken layers. Additionally, we sequenced the genomes of these strains by NGS and analyzed phylogenetic clustering, resistance and virulence genes in the context of host-specificity. Results Two strains were identified to be Extended Spectrum Beta Lactamase (ESBL) and one as AmpC beta-lactamases (AMP-C) phenotype, while two were ESBL negative. By integrating the genome sequences of these five poultry strains with all the available M. morganii genomes, we constructed a phylogenetic tree that clearly separates the Morganella genus into two clusters (M1 and M2), which approximately reflect the proposed subspecies classification (morganii and sibonii). Additionally, we found no association between phylogenetic structure and host, suggesting interspecies transmission. All five poultry strains contained genes for resistance to aminocoumarins, beta-lactams, colistin, elfamycins, fluoroquinolones, phenicol, rifampin and tetracycline. A comparative genomics analysis of virulence genes showed acquisition of novel virulence genes involved in secretion system and adherence in cluster M2. We showed that some of these genes were acquired by horizontal gene transfer from closely related Morganellaceae species and propose that novel virulence genes could be responsible for expansion of tissue tropism in M. morganii. Finally, we detected variability in copy number and high sequence divergence in toxin genes and provided evidence for positive selection in insecticidal toxins genes, likely reflecting host-related adaptations. Conclusions In summary, this study describes i) the first isolation and characterization of M. morganii from goose and turkey, ii) a large-scale genetic analysis of M. morganii and an attempt to generate a global picture of the M. morganii intraspecific phylogenetic structure.

Published
2020
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7. Foraging Honeybees (Apis mellifera ligustica) as Biocenosis Monitors of Pollution in Areas Affected by Cement Industry Emissions

Author

Bartolomeo Sebastiani, Sara Mariucci, and Nicola Palmieri

Subjects
honeybees, biomonitors, polyciclic aromatic compounds (PACs), polyciclcic aromatic hydrocarbons (PAHs), polycyclic aromatic sulfur heterocycles (PASHs), n-alkanes, Environmental technology. Sanitary engineering, TD1-1066
Abstract

Two areas affected by cement plant emissions, in an industrial district of Central Italy, were investigated by foraging honeybees (Apis mellifera ligustica) on the return to their hives, as an in situ biomonitor. The contamination was compared with that of a background reference area on the Central Apennine Mountains, quite far from the contamination sources. At all the sites, the bee colonies were stationary. One hundred seventy-seven compounds belonging to the class of polycyclic aromatic compounds (PACs) were positively identified by gas chromatographic and mass spectrometric techniques. For the first time, the presence of several unusual compounds on bee samples is highlighted. These include polycyclic aromatic sulfur heterocycles (PASHs), 1.55–35.63 ng/g d.w., compounds that, like polycyclic aromatic hydrocarbons (PAHs), 67.50–129.95 ng d.w., are classified as carcinogenic and/or mutagenic. In an attempt to identify the contribution of different and specific sources of these pollutants to the total pollution profile, the composition of aliphatic linear hydrocarbons was also examined.

Published
2023
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8. Comparison of an injectable toltrazuril-gleptoferron (Forceris®) and an oral toltrazuril (Baycox®) + injectable iron dextran for the control of experimentally induced piglet cystoisosporosis

Author

Anja Joachim, Aruna Shrestha, Barbara Freudenschuss, Nicola Palmieri, Barbara Hinney, Hamadi Karembe, and Daniel Sperling

Subjects
Pig, Swine, Coccidiosis, Cystoisospora suis, Isospora suis, Diarrhoea, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Cystoisospora suis causes diarrhoeal disease and reduced weight gain in suckling piglets, and a toltrazuril-based oral suspension is available for treatment. Recently a combinatorial product with toltrazuril plus iron has been developed for parenteral application. In this study we compared the efficacy of the injectable product with the oral suspension against experimentally induced piglet cystoisosporosis. Methods In a randomised controlled study, three groups of piglets (n = 10–13) were treated either with a fixed dose of 45 mg toltrazuril + 200 mg gleptoferron i.m. per piglet (Forceris®) on the second day of life (study day 2; SD 2) or with 20 mg toltrazuril/kg body weight as an oral suspension (Baycox® 5%) on SD 4 or left untreated (Control group). The Baycox® and the Control group received 200 mg of iron dextran/piglet on SD 2. All piglets were infected with 1000 sporulated C. suis oocysts on SD 3. Faecal samples were taken daily from SD 7 to SD 20 to determine faecal consistency, oocyst shedding and other diarrhoeal pathogens. Body weight was recorded on SD 1 and then weekly until SD 29. Animals were observed daily for general health and after treatment for possible adverse events. Results In the Control group all animals shed oocysts for 3.1 days on average and all animals showed diarrhoea for an average of five days. Excretion peaked on SD 9 (max. 48,618 oocysts per gram of faeces). Treatment with Forceris® completely suppressed oocyst excretion. In the Baycox® group, low levels of excretion could be detected. Diarrhoea was reduced to single piglets in the treated groups. Body weight development was reduced in the Control group compared to the treated groups. Enteropathogenic bacteria (Escherichia coli, Clostridium perfringens) could be detected. All parameters related to oocyst excretion, faecal consistency and weight gain were significantly improved in the treated groups compared to the Control group without significant differences between the treated groups. Both products were safe to use. Conclusions Treatment with both the injectable (Forceris®) and the oral (Baycox®) formulation of toltrazuril in the prepatent period were safe and highly effective against experimental infection with C. suis in newborn piglets.

Published
2018
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9. Microsatellite Analysis of Geographically Close Isolates of Cystoisospora suis

Author

Anja Joachim, Bärbel Ruttkowski, and Nicola Palmieri

Subjects
swine, coccidian, population genetics, capillary electrophoresis, short repetitive elements, Isospora suis, Veterinary medicine, SF600-1100
Abstract

Microsatellites are short repetitive DNA sequences of 2–6 repeats interspersed in the genome that display a rapid mutation rate and consequently show high variation between individuals or populations. They have been used to characterize population diversity and structure and the level of variation between different isolates of a number of different organisms, including apicomplexan protozoa. Currently nothing is known about the genetic variability and population structure of Cystoisospora suis (Apicomplexa: Coccidia), the causative agent of piglet coccidiosis, and we made use of the recently available genome of C. suis (strain Wien-I) to amplify microsatellite regions (ca. 300–550 bp) and evaluate the applicability of fluorescence-labeled primers to investigate amplicon length variation at high resolution using capillary electrophoresis (CE). Two phenotypically characterized isolates (Wien-I, toltrazuril susceptible; Holl 1 toltrazuril resistant) and six field isolates from Europe were compared by conventional PCR followed by agar-gel electrophoresis, Sanger sequencing, and CE (fluorescence labeling and fragment length analysis) to evaluate the applicability of the method. Four primer pairs could be identified that amplified bands of the expected size and were labeled for CE analysis. High resolution CE for size determination of PCR amplicons proved to be a reliable and simple method. It revealed high diversity of the analyzed strains, with marked differences even between two strains from neighboring swine farms. In follow-up studies, adaptation of the PCR assay to multiplexing and amplification of small DNA quantities will provide a cost-effective tool to analyse field strains to reveal geographic diversity that could be mapped to phenotypic traits.

Published
2019
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10. The life cycle of Drosophila orphan genes

Author

Nicola Palmieri, Carolin Kosiol, and Christian Schlötterer

Subjects
gene gain, gene loss, sex-biased expression, evolutionary rate, D. pseudoobscura, pseudogenes, Medicine, Science, Biology (General), QH301-705.5
Abstract

Orphans are genes restricted to a single phylogenetic lineage and emerge at high rates. While this predicts an accumulation of genes, the gene number has remained remarkably constant through evolution. This paradox has not yet been resolved. Because orphan genes have been mainly analyzed over long evolutionary time scales, orphan loss has remained unexplored. Here we study the patterns of orphan turnover among close relatives in the Drosophila obscura group. We show that orphans are not only emerging at a high rate, but that they are also rapidly lost. Interestingly, recently emerged orphans are more likely to be lost than older ones. Furthermore, highly expressed orphans with a strong male-bias are more likely to be retained. Since both lost and retained orphans show similar evolutionary signatures of functional conservation, we propose that orphan loss is not driven by high rates of sequence evolution, but reflects lineage-specific functional requirements.

Published
2014
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11. Evaluation of different reference based annotation strategies using RNA-Seq - a case study in Drososphila pseudoobscura.

Author

Nicola Palmieri, Viola Nolte, Anton Suvorov, Carolin Kosiol, and Christian Schlötterer

Subjects
Medicine, Science
Abstract

RNA-Seq is a powerful tool for the annotation of genomes, in particular for the identification of isoforms and UTRs. Nevertheless, several software tools exist and no standard strategy to obtain a reliable annotation is yet established. We tested different combinations of the most commonly used reference-based alignment tools (TopHat, GSNAP) in combination with two frequently used reference-based assemblers (Cufflinks, Scripture) and evaluated the potential of RNA-Seq to improve the annotation of Drosophila pseudoobscura. While GSNAP maps a higher proportion of reads, TopHat resulted in a more accurate annotation when used in combination with Cufflinks. Scripture had the lowest sensitivity. Interestingly, after subsampling to the same coverage for GSNAP and TopHat, we find that both mappers have similar performance, implying that the advantage of TopHat is mainly an artifact of the lower coverage. Overall, we observed a low concordance among the different approaches tested both at junction and isoform levels. Using data from both sexes of two adult strains of D. pseudoobscura we detected alternative splicing for about 30% of the FlyBase multiple-exon genes. Moreover, we extended the boundaries for 6523 genes (about 40%). We annotated 669 new genes, 45% of them with splicing evidence. Most of the new genes are located on unassembled contigs, reflecting their incomplete annotation. Finally, we identified 99 additional new genes that are not represented in the current genome contigs of D. pseudoobscura, probably due to location in genomic regions that are difficult to assemble (e.g. heterochromatic regions).

Published
2012
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12. Mapping accuracy of short reads from massively parallel sequencing and the implications for quantitative expression profiling.

Author

Nicola Palmieri and Christian Schlötterer

Subjects
Medicine, Science
Abstract

BACKGROUND:Massively parallel sequencing offers an enormous potential for expression profiling, in particular for interspecific comparisons. Currently, different platforms for massively parallel sequencing are available, which differ in read length and sequencing costs. The 454-technology offers the highest read length. The other sequencing technologies are more cost effective, on the expense of shorter reads. Reliable expression profiling by massively parallel sequencing depends crucially on the accuracy to which the reads could be mapped to the corresponding genes. METHODOLOGY/PRINCIPAL FINDINGS:We performed an in silico analysis to evaluate whether incorrect mapping of the sequence reads results in a biased expression pattern. A comparison of six available mapping software tools indicated a considerable heterogeneity in mapping speed and accuracy. Independently of the software used to map the reads, we found that for compact genomes both short (35 bp, 50 bp) and long sequence reads (100 bp) result in an almost unbiased expression pattern. In contrast, for species with a larger genome containing more gene families and repetitive DNA, shorter reads (35-50 bp) produced a considerable bias in gene expression. In humans, about 10% of the genes had fewer than 50% of the sequence reads correctly mapped. Sequence polymorphism up to 9% had almost no effect on the mapping accuracy of 100 bp reads. For 35 bp reads up to 3% sequence divergence did not affect the mapping accuracy strongly. The effect of indels on the mapping efficiency strongly depends on the mapping software. CONCLUSIONS/SIGNIFICANCE:In complex genomes, expression profiling by massively parallel sequencing could introduce a considerable bias due to incorrectly mapped sequence reads if the read length is short. Nevertheless, this bias could be accounted for if the genomic sequence is known. Furthermore, sequence polymorphisms and indels also affect the mapping accuracy and may cause a biased gene expression measurement. The choice of the mapping software is highly critical and the reliability depends on the presence/absence of indels and the divergence between reads and the reference genome. Overall, we found SSAHA2 and CLC to produce the most reliable mapping results.

Published
2009
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14. Epidemic of cutaneous fowlpox in a naïve population of chickens and turkeys in Austria: Detailed phylogenetic analysis indicates co‐evolution of fowlpox virus with reticuloendotheliosis virus

Author

Miguel Matos, Ivana Bilic, Nicola Palmieri, Peter Mitsch, Franz Sommer, Jana Tvarogová, Dieter Liebhart, and Michael Hess

Subjects
Turkeys, Fowlpox virus, Reticuloendotheliosis virus, General Veterinary, General Immunology and Microbiology, Austria, Animals, Dust, General Medicine, Chickens, Fowlpox, Phylogeny, Poultry Diseases
Abstract

Cutaneous fowlpox is a disease of chickens and turkeys caused by the fowlpox virus (FWPV), characterized by the development of proliferative lesions and scabs on unfeathered areas. FWPVs regularly carry an integrated, active copy of the reticuloendotheliosis virus (REV), and it has been hypothesized that such FWPVs are more problematic in the field. Extensive outbreaks are usually observed in tropical and sub-tropical climates, where biting insects are more difficult to control. Here, we report an epidemic of 65 cutaneous fowlpox cases in Austria in layer chickens (91% of the cases) and broiler breeders and turkeys, all of them unvaccinated against the disease, from October 2018 to February 2020. The field data revealed appearance in flocks of different sizes ranging from less than 5000 birds up to more than 20,000 animals, with the majority raised indoors in a barn system. The clinical presentation was characterized by typical epithelial lesions on the head of the affected birds, with an average decrease of 6% in egg production and an average weekly mortality of 1.2% being observed in the flocks. A real-time multiplex polymerase chain reaction (PCR) confirmed the presence of FWPV-REV DNA, not only in the lesions but also in the environmental dust from the poultry houses. The integration of the REV provirus into the FWPV genome was confirmed by PCR, and revealed different FWPV genome populations carrying either the REV long terminal repeats (LTRs) or the full-length REV genome, reiterating the instability of the inserted REV. Two selected samples were fully sequenced by next generation sequencing (NGS), and the whole genome phylogenetic analysis revealed a regional clustering of the FWPV genomes. The extensive nature of these outbreaks in host populations naïve for the virus is a remarkable feature of the present report, highlighting new challenges associated with FWPV infections that need to be considered.

Published
2022

15. Symptom Burden before and after Dialysis Initiation in Older Patients

Author

de Rooij, Esther N. M., Yvette, Meuleman, de Fijter, Johan W., Jager, Kitty J., Chesnaye, Nicholas C., Marie, Evans, Caskey, Fergus J., Claudia, Torino, Gaetana, Porto, Maciej, Szymczak, Christiane, Drechsler, Christoph, Wanner, Dekker, Friedo W., Hoogeveen, Ellen K., Andreas, Schneider, Anke, Torp, Beate, Iwig, Boris, Perras, Christian, Marx, Christof, Blaser, Claudia, Emde, Detlef, Krieter, Dunja, Fuchs, Ellen, Irmler, Eva, Platen, Hans, Schmidt-Gürtler, Hendrik, Schlee, Holger, Naujoks, Ines, Schlee, Sabine, Cäsar, Joachim, Beige, Jochen, Röthele, Justyna, Mazur, Kai, Hahn, Katja, Blouin, Katrin, Neumeier, Kirsten, Anding-Rost, Lothar, Schramm, Monika, Hopf, Nadja, Wuttke, Nikolaus, Frischmuth, Pawlos, Ichtiaris, Petra, Kirste, Petra, Schulz, Sabine, Aign, Sandra, Biribauer, Sherin, Manan, Silke, Röser, Stefan, Heidenreich, Stephanie, Palm, Susanne, Schwedler, Sylke, Delrieux, Sylvia, Renker, Sylvia, Schättel, Theresa, Stephan, Thomas, Schmiedeke, Thomas, Weinreich, Til, Leimbach, Torsten, Stövesand, Udo, Bahner, Wolfgang, Seeger, Cupisti, Adamasco, Adelia, Sagliocca, Alberto, Ferraro, Alessandra, Mele, Alessandro, Naticchia, Alex, Còsaro, Andrea, Ranghino, Andrea, Stucchi, Angelo, Pignataro, Antonella De Blasio, Antonello, Pani, Aris, Tsalouichos, Bellasi, Antonio, Biagio Raffaele Di Iorio, Butti, Alessandra, Cataldo, Abaterusso, Chiara, Somma, Claudia, D’Alessandro, Claudia, Zullo, Claudio, Pozzi, Daniela, Bergamo, Daniele, Ciurlino, Daria, Motta, Domenico, Russo, Enrico, Favaro, Federica, Vigotti, Ferruccio, Ansali, Ferruccio, Conte, Francesca, Cianciotta, Francesca, Giacchino, Francesco, Cappellaio, Francesco, Pizzarelli, Gaetano, Greco, Giada, Bigatti, Giancarlo, Marinangeli, Gianfranca, Cabiddu, Giordano, Fumagalli, Giorgia, Caloro, Giorgina, Piccoli, Giovanbattista, Capasso, Giovanni, Gambaro, Giuliana, Tognarelli, Giuseppe, Bonforte, Giuseppe, Conte, Giuseppe, Toscano, Goffredo Del Rosso, Irene, Capizzi, Ivano, Baragetti, Lamberto, Oldrizzi, Loreto, Gesualdo, Luigi, Biancone, Manuela, Magnano, Marco, Ricardi, Maria Di Bari, Maria, Laudato, Maria Luisa Sirico, Martina, Ferraresi, Michele, Provenzano, Moreno, Malaguti, Nicola, Palmieri, Paola, Murrone, Pietro, Cirillo, Pietro, Dattolo, Pina, Acampora, Rita, Nigro, Roberto, Boero, Roberto, Scarpioni, Rosa, Sicoli, Rosella, Malandra, Silvana, Savoldi, Silvio, Bertoli, Silvio, Borrelli, Stefania, Maxia, Stefano, Maffei, Stefano, Mangano, Teresa, Cicchetti, Tiziana, Rappa, Valentina, Palazzo, Walter De Simone, Anita, Schrander, Bastiaan van Dam, Carl, Siegert, Carlo, Gaillard, Charles, Beerenhout, Cornelis, Verburgh, Cynthia, Janmaat, Ellen, Hoogeveen, Ewout, Hoorn, Friedo, Dekker, Johannes, Boots, Henk, Boom, Jan-Willem, Eijgenraam, Jeroen, Kooman, Joris, Rotmans, Kitty, Jager, Liffert, Vogt, Maarten, Raasveld, Marc, Vervloet, Marjolijn van Buren, Merel van Diepen, Nicholas, Chesnaye, Paul, Leurs, Pauline, Voskamp, Peter, Blankestijn, Sadie van Esch, Siska, Boorsma, Stefan, Berger, Constantijn, Konings, Zeynep, Aydin, Aleksandra, Musiała, Anna, Szymczak, Ewelina, Olczyk, Hanna, Augustyniak-Bartosik, Ilona, Miśkowiec-Wiśniewska, Jacek, Manitius, Joanna, Pondel, Kamila, Jędrzejak, Katarzyna, Nowańska, Łukasz, Nowak, Magdalena, Durlik, Szyszkowska, Dorota, Teresa, Nieszporek, Zbigniew, Heleniak, Andreas, Jonsson, Anna-Lena, Blom, Björn, Rogland, Carin, Wallquist, Denes, Vargas, Emöke, Dimény, Fredrik, Sundelin, Fredrik, Uhlin, Gunilla, Welander, Isabel Bascaran Hernandez, Knut-Christian, Gröntoft, Maria, Stendahl, Maria, Svensson, Olof, Heimburger, Pavlos, Kashioulis, Stefan, Melander, Tora, Almquist, Ulrika, Jensen, Alistair, Woodman, Anna, Mckeever, Asad, Ullah, Barbara, Mclaren, Camille, Harron, Carla, Barrett, Charlotte, O'Toole, Christina, Summersgill, Colin, Geddes, Deborah, Glowski, Deborah, Mcglynn, Dympna, Sands, Fergus, Caskey, Geena, Roy, Gillian, Hirst, Hayley, King, Helen, Mcnally, Houda, Masri-Senghor, Hugh, Murtagh, Hugh, Rayner, Jane, Turner, Joanne, Wilcox, Jocelyn, Berdeprado, Jonathan, Wong, Joyce, Banda, Kirsteen, Jones, Lesley, Haydock, Lily, Wilkinson, Margaret, Carmody, Maria, Weetman, Martin, Joinson, Mary, Dutton, Michael, Matthews, Neal, Morgan, Nina, Bleakley, Paul, Cockwell, Paul, Roderick, Phil, Mason, Philip, Kalra, Rincy, Sajith, Sally, Chapman, Santee, Navjee, Sarah, Crosbie, Sharon, Brown, Sheila, Tickle, Suresh, Mathavakkannan, Ying, Kuan., Medical Informatics, APH - Aging & Later Life, APH - Quality of Care, APH - Methodology, APH - Global Health, APH - Health Behaviors & Chronic Diseases, and ACS - Pulmonary hypertension & thrombosis

Subjects
Transplantation, chronic kidney disease, dialysis, elderly, end stage kidney disease, epidemiology and outcomes, Nephrology, Epidemiology, Critical Care and Intensive Care Medicine
Abstract

Background and objectives For older patients with kidney failure, lowering symptom burden may be more important than prolonging life. Dialysis initiation may affect individual kidney failure-related symptoms differently, but the change in symptoms before and after start of dialysis has not been studied. Therefore, we investigated the course of total and individual symptom number and burden before and after starting dialysis in older patients.Design, setting, participants, & measurements The European Quality (EQUAL) study is an ongoing, prospective, multicenter study in patients >= 65 years with an incident eGFR

Published
2022

16. Complete genomes of the eukaryotic poultry parasite Histomonas meleagridis: linking sequence analysis with virulence / attenuation

Author

Ivana Bilic, Marcelo de Jesus Ramires, Nicola Palmieri, and Michael Hess

Subjects
Turkey, Sequence analysis, Genomics, QH426-470, Genome, Histomonas meleagridis, Poultry, Illumina, Genetics, Coding region, Animals, Parasites, Indel, Gene, Leucine rich repeat protein, Whole genome sequencing, biology, Virulence, Eukaryota, biology.organism_classification, Chicken, Oxford Nanopore technology (ONT), Virulent, Attenuated, Histomonosis, Sequence Analysis, TP248.13-248.65, Research Article, Biotechnology
Abstract

Background Histomonas meleagridis is a protozoan parasite and the causative agent of histomonosis, an important poultry disease whose significance is underlined by the absence of any treatment and prophylaxis. The recent successful in vitro attenuation of the parasite urges questions about the underlying mechanisms. Results Whole genome sequence data from a virulent and an attenuated strain originating from the same parental lineage of H. meleagridis were recruited using Oxford Nanopore Technology (ONT) and Illumina platforms, which were combined to generate megabase-sized contigs with high base-level accuracy. Inspecting the genomes for differences identified two substantial deletions within a coding sequence of the attenuated strain. Additionally, one single nucleotide polymorphism (SNP) and indel targeting coding sequences caused the formation of premature stop codons, which resulted in the truncation of two genes in the attenuated strain. Furthermore, the genome of H. meleagridis was used for characterizing protein classes of clinical relevance for parasitic protists. The comparative analysis with the genomes of Trichomonas vaginalis, Tritrichomonas foetus and Entamoeba histolytica identified ~ 2700 lineage-specific gene losses and 9 gene family expansions in the H. meleagridis lineage. Conclusions Taken as a whole, the obtained data provide the first hints to understand the molecular basis of attenuation in H. meleagridis and constitute a genomics platform for future research on this important poultry pathogen.

Published
2021

17. Predicting Kidney Failure, Cardiovascular Disease and Death in Advanced CKD Patients

Author

Chava L. Ramspek, Rosemarijn Boekee, Marie Evans, Olof Heimburger, Charlotte M. Snead, Fergus J. Caskey, Claudia Torino, Gaetana Porto, Maciej Szymczak, Magdalena Krajewska, Christiane Drechsler, Christoph Wanner, Nicholas C. Chesnaye, Kitty J. Jager, Friedo W. Dekker, Maarten G.J. Snoeijs, Joris I. Rotmans, Merel van Diepen, Adamasco Cupisti, Adelia Sagliocca, Alberto Ferraro, Aleksandra Musiała, Alessandra Mele, Alessandro Naticchia, Alex Còsaro, Alistair Woodman, Andrea Ranghino, Andrea Stucchi, Andreas Jonsson, Andreas Schneider, Angelo Pignataro, Anita Schrander, Anke Torp, Anna McKeever, Anna Szymczak, Anna-Lena Blom, Antonella De Blasio, Antonello Pani, Aris Tsalouichos, Asad Ullah, Barbara McLaren, Bastiaan van Dam, Beate Iwig, Bellasi Antonio, Biagio Raffaele Di Iorio, Björn Rogland, Boris Perras, Butti Alessandra, Camille Harron, Carin Wallquist, Carl Siegert, Carla Barrett, Carlo Gaillard, Carlo Garofalo, Cataldo Abaterusso, Charles Beerenhout, Charlotte O'Toole, Chiara Somma, Christian Marx, Christina Summersgill, Christof Blaser, Claudia D'alessandro, Claudia Emde, Claudia Zullo, Claudio Pozzi, Colin Geddes, Cornelis Verburgh, Daniela Bergamo, Daniele Ciurlino, Daria Motta, Deborah Glowski, Deborah McGlynn, Denes Vargas, Detlef Krieter, Domenico Russo, Dunja Fuchs, Dympna Sands, Ellen Hoogeveen, Ellen Irmler, Emöke Dimény, Enrico Favaro, Eva Platen, Ewelina Olczyk, Ewout Hoorn, Federica Vigotti, Ferruccio Ansali, Ferruccio Conte, Francesca Cianciotta, Francesca Giacchino, Francesco Cappellaio, Francesco Pizzarelli, Fredrik Sundelin, Fredrik Uhlin, Gaetano Greco, Geena Roy, Giada Bigatti, Giancarlo Marinangeli, Gianfranca Cabiddu, Gillian Hirst, Giordano Fumagalli, Giorgia Caloro, Giorgina Piccoli, Giovanbattista Capasso, Giovanni Gambaro, Giuliana Tognarelli, Giuseppe Bonforte, Giuseppe Conte, Giuseppe Toscano, Goffredo Del Rosso, Gunilla Welander, Hanna Augustyniak-Bartosik, Hans Boots, Hans Schmidt-Gürtler, Hayley King, Helen McNally, Hendrik Schlee, Henk Boom, Holger Naujoks, Houda Masri-Senghor, Hugh Murtagh, Hugh Rayner, Ilona Miśkowiec-Wiśniewska, Ines Schlee, Irene Capizzi, Isabel Bascaran Hernandez, Ivano Baragetti, Jacek Manitius, Jane Turner, Jan-Willem Eijgenraam, Jeroen Kooman, Joachim Beige, Joanna Pondel, Joanne Wilcox, Jocelyn Berdeprado, Jochen Röthele, Jonathan Wong, Joris Rotmans, Joyce Banda, Justyna Mazur, Kai Hahn, Kamila Jędrzejak, Katarzyna Nowańska, Katja Blouin, Katrin Neumeier, Kirsteen Jones, Kirsten Anding-Rost, Knut-Christian Gröntoft, Lamberto Oldrizzi, Lesley Haydock, Liffert Vogt, Lily Wilkinson, Loreto Gesualdo, Lothar Schramm, Luigi Biancone, Łukasz Nowak, Maarten Raasveld, Magdalena Durlik, Manuela Magnano, Marc Vervloet, Marco Ricardi, Margaret Carmody, Maria Di Bari, Maria Laudato, Maria Luisa Sirico, Maria Stendahl, Maria Svensson, Maria Weetman, Marjolijn van Buren, Martin Joinson, Martina Ferraresi, Mary Dutton, Michael Matthews, Michele Provenzano, Monika Hopf, Moreno Malaguti, Nadja Wuttke, Neal Morgan, Nicola Palmieri, Nikolaus Frischmuth, Nina Bleakley, Paola Murrone, Paul Cockwell, Paul Leurs, Paul Roderick, Pauline Voskamp, Pavlos Kashioulis, Pawlos Ichtiaris, Peter Blankestijn, Petra Kirste, Petra Schulz, Phil Mason, Philip Kalra, Pietro Cirillo, Pietro Dattolo, Pina Acampora, Rincy Sajith, Rita Nigro, Roberto Boero, Roberto Scarpioni, Rosa Sicoli, Rosella Malandra, Sabine Aign, Sabine Cäsar, Sadie van Esch, Sally Chapman, Sandra Biribauer, Santee Navjee, Sarah Crosbie, Sharon Brown, Sheila Tickle, Sherin Manan, Silke Röser, Silvana Savoldi, Silvio Bertoli, Silvio Borrelli, Siska Boorsma, Stefan Heidenreich, Stefan Melander, Stefania Maxia, Stefano Maffei, Stefano Mangano, Stephanie Palm, Stijn Konings, Suresh Mathavakkannan, Susanne Schwedler, Sylke Delrieux, Sylvia Renker, Sylvia Schättel, Szyszkowska Dorota, Teresa Cicchetti, Teresa Nieszporek, Theresa Stephan, Thomas Schmiedeke, Thomas Weinreich, Til Leimbach, Tiziana Rappa, Tora Almquist, Torsten Stövesand, Udo Bahner, Ulrika Jensen, Valentina Palazzo, Walter De Simone, Wolfgang Seeger, Ying Kuan, Zbigniew Heleniak, Zeynep Aydin, Vascular Surgery, MUMC+: MA Med Staf Spec Vaatchirurgie (9), RS: Carim - V03 Regenerative and reconstructive medicine vascular disease, Ramspek, C. L., Boekee, R., Evans, M., Heimburger, O., Snead, C. M., Caskey, F. J., Torino, C., Porto, G., Szymczak, M., Krajewska, M., Drechsler, C., Wanner, C., Chesnaye, N. C., Jager, K. J., Dekker, F. W., Snoeijs, M. G. J., Rotmans, J. I., van Diepen, M., Cupisti, A., Sagliocca, A., Ferraro, A., Musiala, A., Mele, A., Naticchia, A., Cosaro, A., Woodman, A., Ranghino, A., Stucchi, A., Jonsson, A., Schneider, A., Pignataro, A., Schrander, A., Torp, A., Mckeever, A., Szymczak, A., Blom, A. -L., De Blasio, A., Pani, A., Tsalouichos, A., Ullah, A., Mclaren, B., van Dam, B., Iwig, B., Antonio, B., Di Iorio, B. R., Rogland, B., Perras, B., Alessandra, B., Harron, C., Wallquist, C., Siegert, C., Barrett, C., Gaillard, C., Garofalo, C., Abaterusso, C., Beerenhout, C., O'Toole, C., Somma, C., Marx, C., Summersgill, C., Blaser, C., D'Alessandro, C., Emde, C., Zullo, C., Pozzi, C., Geddes, C., Verburgh, C., Bergamo, D., Ciurlino, D., Motta, D., Glowski, D., Mcglynn, D., Vargas, D., Krieter, D., Russo, D., Fuchs, D., Sands, D., Hoogeveen, E., Irmler, E., Dimeny, E., Favaro, E., Platen, E., Olczyk, E., Hoorn, E., Vigotti, F., Ansali, F., Conte, F., Cianciotta, F., Giacchino, F., Cappellaio, F., Pizzarelli, F., Sundelin, F., Uhlin, F., Greco, G., Roy, G., Bigatti, G., Marinangeli, G., Cabiddu, G., Hirst, G., Fumagalli, G., Caloro, G., Piccoli, G., Capasso, G., Gambaro, G., Tognarelli, G., Bonforte, G., Conte, G., Toscano, G., Del Rosso, G., Welander, G., Augustyniak-Bartosik, H., Boots, H., Schmidt-Gurtler, H., King, H., Mcnally, H., Schlee, H., Boom, H., Naujoks, H., Masri-Senghor, H., Murtagh, H., Rayner, H., Miskowiec-Wisniewska, I., Schlee, I., Capizzi, I., Hernandez, I. B., Baragetti, I., Manitius, J., Turner, J., Eijgenraam, J. -W., Kooman, J., Beige, J., Pondel, J., Wilcox, J., Berdeprado, J., Rothele, J., Wong, J., Rotmans, J., Banda, J., Mazur, J., Hahn, K., Jedrzejak, K., Nowanska, K., Blouin, K., Neumeier, K., Jones, K., Anding-Rost, K., Grontoft, K. -C., Oldrizzi, L., Haydock, L., Vogt, L., Wilkinson, L., Gesualdo, L., Schramm, L., Biancone, L., Nowak, L., Raasveld, M., Durlik, M., Magnano, M., Vervloet, M., Ricardi, M., Carmody, M., Di Bari, M., Laudato, M., Sirico, M. L., Stendahl, M., Svensson, M., Weetman, M., van Buren, M., Joinson, M., Ferraresi, M., Dutton, M., Matthews, M., Provenzano, M., Hopf, M., Malaguti, M., Wuttke, N., Morgan, N., Palmieri, N., Frischmuth, N., Bleakley, N., Murrone, P., Cockwell, P., Leurs, P., Roderick, P., Voskamp, P., Kashioulis, P., Ichtiaris, P., Blankestijn, P., Kirste, P., Schulz, P., Mason, P., Kalra, P., Cirillo, P., Dattolo, P., Acampora, P., Sajith, R., Nigro, R., Boero, R., Scarpioni, R., Sicoli, R., Malandra, R., Aign, S., Casar, S., van Esch, S., Chapman, S., Biribauer, S., Navjee, S., Crosbie, S., Brown, S., Tickle, S., Manan, S., Roser, S., Savoldi, S., Bertoli, S., Borrelli, S., Boorsma, S., Heidenreich, S., Melander, S., Maxia, S., Maffei, S., Mangano, S., Palm, S., Konings, S., Mathavakkannan, S., Schwedler, S., Delrieux, S., Renker, S., Schattel, S., Dorota, S., Cicchetti, T., Nieszporek, T., Stephan, T., Schmiedeke, T., Weinreich, T., Leimbach, T., Rappa, T., Almquist, T., Stovesand, T., Bahner, U., Jensen, U., Palazzo, V., De Simone, W., Seeger, W., Kuan, Y., Heleniak, Z., Aydin, Z., Medical Informatics, APH - Aging & Later Life, APH - Methodology, APH - Quality of Care, Nephrology, ACS - Microcirculation, APH - Health Behaviors & Chronic Diseases, APH - Global Health, ACS - Pulmonary hypertension & thrombosis, ACS - Diabetes & metabolism, and Internal Medicine

Subjects
SDG 3 - Good Health and Well-being, external validation, Nephrology, cardiovascular disease, death, CKD, kidney failure, prognostic model
Abstract

Introduction: Predicting the timing and occurrence of kidney replacement therapy (KRT), cardiovascular events, and death among patients with advanced chronic kidney disease (CKD) is clinically useful and relevant. We aimed to externally validate a recently developed CKD G4+ risk calculator for these outcomes and to assess its potential clinical impact in guiding vascular access placement. Methods: We included 1517 patients from the European Quality (EQUAL) study, a European multicentre prospective cohort study of nephrology-referred advanced CKD patients aged ≥65 years. Model performance was assessed based on discrimination and calibration. Potential clinical utility for timing of referral for vascular access placement was studied with diagnostic measures and decision curve analysis (DCA). Results: The model showed a good discrimination for KRT and “death after KRT,” with 2-year concordance (C) statistics of 0.74 and 0.76, respectively. Discrimination for cardiovascular events (2-year C-statistic: 0.70) and overall death (2-year C-statistic: 0.61) was poorer. Calibration was fairly accurate. Decision curves illustrated that using the model to guide vascular access referral would generally lead to less unused arteriovenous fistulas (AVFs) than following estimated glomerular filtration rate (eGFR) thresholds. Conclusion: This study shows moderate to good predictive performance of the model in an older cohort of nephrology-referred patients with advanced CKD. Using the model to guide referral for vascular access placement has potential in combating unnecessary vascular surgeries.

Published
2022

18. Kidney failure prediction models

Author

Ramspek, Chava L, Evans, Marie, Wanner, Christoph, Drechsler, Christiane, Chesnaye, Nicholas C, Szymczak, Maciej, Krajewska, Magdalena, Torino, Claudia, Porto, Gaetana, Hayward, Samantha, Caskey, Fergus, Dekker, Friedo W, Jager, Kitty J, van Diepen, Merel, EQUAL Study Investigators: Adamasco Cupisti, Adelia Sagliocca, Alberto Ferraro, Aleksandra Musiała, Alessandra Mele, Alessandro Naticchia, Alex Còsaro, Alistair Woodman, Andrea Ranghino, Andrea Stucchi, Andreas Jonsson, Andreas Schneider, Angelo Pignataro, Anita Schrander, Anke Torp, Anna McKeever, Anna Szymczak, Anna-Lena Blom, Antonella De Blasio, Antonello Pani, Aris Tsalouichos, Asad Ullah, Barbara McLaren, Bastiaan van Dam, Beate Iwig, Bellasi Antonio, Biagio Raffaele Di Iorio, Björn Rogland, Boris Perras, Butti Alessandra, Camille Harron, Carin Wallquist, Carl Siegert, Carla Barrett, Carlo Gaillard, Carlo Garofalo, Cataldo Abaterusso, Charles Beerenhout, Charlotte O'Toole, Chiara Somma, Christian Marx, Christina Summersgill, Christof Blaser, Claudia D'alessandro, Claudia Emde, Claudia Zullo, Claudio Pozzi, Colin Geddes, Cornelis Verburgh, Daniela Bergamo, Daniele Ciurlino, Daria Motta, Deborah Glowski, Deborah McGlynn, Denes Vargas, Detlef Krieter, Domenico Russo, Dunja Fuchs, Dympna Sands, Ellen Hoogeveen, Ellen Irmler, Emöke Dimény, Enrico Favaro, Eva Platen, Ewelina Olczyk, Ewout Hoorn, Federica Vigotti, Ferruccio Ansali, Ferruccio Conte, Francesca Cianciotta, Francesca Giacchino, Francesco Cappellaio, Francesco Pizzarelli, Fredrik Sundelin, Fredrik Uhlin, Gaetano Greco, Geena Roy, Gaetana Porto, Giada Bigatti, Giancarlo Marinangeli, Gianfranca Cabiddu, Gillian Hirst, Giordano Fumagalli, Giorgia Caloro, Giorgina Piccoli, Giovanbattista Capasso, Giovanni Gambaro, Giuliana Tognarelli, Giuseppe Bonforte, Giuseppe Conte, Giuseppe Toscano, Goffredo Del Rosso, Gunilla Welander, Hanna Augustyniak-Bartosik, Hans Boots, Hans Schmidt-Gürtler, Hayley King, Helen McNally, Hendrik Schlee, Henk Boom, Holger Naujoks, Houda Masri-Senghor, Hugh Murtagh, Hugh Rayner, Ilona Miśkowiec-Wiśniewska, Ines Schlee, Irene Capizzi, Isabel Bascaran Hernandez, Ivano Baragetti, Jacek Manitius, Jane Turner, Jan-Willem Eijgenraam, Jeroen Kooman, Joachim Beige, Joanna Pondel, Joanne Wilcox, Jocelyn Berdeprado, Jochen Röthele, Jonathan Wong, Joris Rotmans, Joyce Banda, Justyna Mazur, Kai Hahn, Kamila Jędrzejak, Katarzyna Nowańska, Katja Blouin, Katrin Neumeier, Kirsteen Jones, Kirsten Anding-Rost, Knut-Christian Gröntoft, Lamberto Oldrizzi, Lesley Haydock, Liffert Vogt, Lily Wilkinson, Loreto Gesualdo, Lothar Schramm, Luigi Biancone, Łukasz Nowak, Maarten Raasveld, Magdalena Durlik, Manuela Magnano, Marc Vervloet, Marco Ricardi, Margaret Carmody, Maria Di Bari, Maria Laudato, Maria Luisa Sirico, Maria Stendahl, Maria Svensson, Maria Weetman, Marjolijn van Buren, Martin Joinson, Martina Ferraresi, Mary Dutton, Merel van Diepen, Michael Matthews, Michele Provenzano, Monika Hopf, Moreno Malaguti, Nadja Wuttke, Neal Morgan, Nicola Palmieri, Nikolaus Frischmuth, Nina Bleakley, Paola Murrone, Paul Cockwell, Paul Leurs, Paul Roderick, Pauline Voskamp, Pavlos Kashioulis, Pawlos Ichtiaris, Peter Blankestijn, Petra Kirste, Petra Schulz, Phil Mason, Philip Kalra, Pietro Cirillo, Pietro Dattolo, Pina Acampora, Rincy Sajith, Rita Nigro, Roberto Boero, Roberto Scarpioni, Rosa Sicoli, Rosella Malandra, Sabine Aign, Sabine Cäsar, Sadie van Esch, Sally Chapman, Sandra Biribauer, Santee Navjee, Sarah Crosbie, Sharon Brown, Sheila Tickle, Sherin Manan, Silke Röser, Silvana Savoldi, Silvio Bertoli, Silvio Borrelli, Siska Boorsma, Stefan Heidenreich, Stefan Melander, Stefania Maxia, Stefano Maffei, Stefano Mangano, Stephanie Palm, Stijn Konings, Suresh Mathavakkannan, Susanne Schwedler, Sylke Delrieux, Sylvia Renker, Sylvia Schättel, Szyszkowska Dorota, Teresa Cicchetti, Teresa Nieszporek, Theresa Stephan, Thomas Schmiedeke, Thomas Weinreich, Til Leimbach, Tiziana Rappa, Tora Almquist, Torsten Stövesand, Udo Bahner, Ulrika Jensen, Valentina Palazzo, Walter De Simone, Wolfgang Seeger, Ying Kuan, Zbigniew Heleniak, Zeynep Aydin, Internal Medicine, Chava L, Ramspek, Marie, Evan, Christoph, Wanner, Christiane, Drechsler, Nicholas C, Chesnaye, Maciej, Szymczak, Magdalena, Krajewska, Claudia, Torino, Gaetana, Porto, Samantha, Hayward, Fergus, Caskey, Friedo W, Dekker, Kitty J, Jager, Merel, van Diepen, Study Investigators: Adamasco Cupisti, Equal, Sagliocca, Adelia, Ferraro, Alberto, Musiała, Aleksandra, Mele, Alessandra, Naticchia, Alessandro, Còsaro, Alex, Woodman, Alistair, Ranghino, Andrea, Stucchi, Andrea, Jonsson, Andrea, Schneider, Andrea, Pignataro, Angelo, Schrander, Anita, Torp, Anke, Mckeever, Anna, Szymczak, Anna, Blom, Anna-Lena, De Blasio, Antonella, Pani, Antonello, Tsalouichos, Ari, Ullah, Asad, Mclaren, Barbara, van Dam, Bastiaan, Iwig, Beate, Antonio, Bellasi, Raffaele Di Iorio, Biagio, Rogland, Björn, Perras, Bori, Alessandra, Butti, Harron, Camille, Wallquist, Carin, Siegert, Carl, Barrett, Carla, Gaillard, Carlo, Garofalo, Carlo, Abaterusso, Cataldo, Beerenhout, Charle, O'Toole, Charlotte, Somma, Chiara, Marx, Christian, Summersgill, Christina, Blaser, Christof, D'Alessandro, Claudia, Emde, Claudia, Zullo, Claudia, Pozzi, Claudio, Geddes, Colin, Verburgh, Corneli, Bergamo, Daniela, Ciurlino, Daniele, Motta, Daria, Glowski, Deborah, Mcglynn, Deborah, Vargas, Dene, Krieter, Detlef, Russo, Domenico, Fuchs, Dunja, Sands, Dympna, Hoogeveen, Ellen, Irmler, Ellen, Dimény, Emöke, Favaro, Enrico, Platen, Eva, Olczyk, Ewelina, Hoorn, Ewout, Vigotti, Federica, Ansali, Ferruccio, Conte, Ferruccio, Cianciotta, Francesca, Giacchino, Francesca, Cappellaio, Francesco, Pizzarelli, Francesco, Sundelin, Fredrik, Uhlin, Fredrik, Greco, Gaetano, Roy, Geena, Porto, Gaetana, Bigatti, Giada, Marinangeli, Giancarlo, Cabiddu, Gianfranca, Hirst, Gillian, Fumagalli, Giordano, Caloro, Giorgia, Piccoli, Giorgina, Capasso, Giovanbattista, Gambaro, Giovanni, Tognarelli, Giuliana, Bonforte, Giuseppe, Conte, Giuseppe, Toscano, Giuseppe, Del Rosso, Goffredo, Welander, Gunilla, Augustyniak-Bartosik, Hanna, Boots, Han, Schmidt-Gürtler, Han, King, Hayley, Mcnally, Helen, Schlee, Hendrik, Boom, Henk, Naujoks, Holger, Masri-Senghor, Houda, Murtagh, Hugh, Rayner, Hugh, Miśkowiec-Wiśniewska, Ilona, Schlee, Ine, Capizzi, Irene, Bascaran Hernandez, Isabel, Baragetti, Ivano, Manitius, Jacek, Turner, Jane, Eijgenraam, Jan-Willem, Kooman, Jeroen, Beige, Joachim, Pondel, Joanna, Wilcox, Joanne, Berdeprado, Jocelyn, Röthele, Jochen, Wong, Jonathan, Rotmans, Jori, Banda, Joyce, Mazur, Justyna, Hahn, Kai, Jędrzejak, Kamila, Nowańska, Katarzyna, Blouin, Katja, Neumeier, Katrin, Jones, Kirsteen, Anding-Rost, Kirsten, Gröntoft, Knut-Christian, Oldrizzi, Lamberto, Haydock, Lesley, Vogt, Liffert, Wilkinson, Lily, Gesualdo, Loreto, Schramm, Lothar, Biancone, Luigi, Nowak, Łukasz, Raasveld, Maarten, Durlik, Magdalena, Magnano, Manuela, Vervloet, Marc, Ricardi, Marco, Carmody, Margaret, Di Bari, Maria, Laudato, Maria, Luisa Sirico, Maria, Stendahl, Maria, Svensson, Maria, Weetman, Maria, van Buren, Marjolijn, Joinson, Martin, Ferraresi, Martina, Dutton, Mary, van Diepen, Merel, Matthews, Michael, Provenzano, Michele, Hopf, Monika, Malaguti, Moreno, Wuttke, Nadja, Morgan, Neal, Palmieri, Nicola, Frischmuth, Nikolau, Bleakley, Nina, Murrone, Paola, Cockwell, Paul, Leurs, Paul, Roderick, Paul, Voskamp, Pauline, Kashioulis, Pavlo, Ichtiaris, Pawlo, Blankestijn, Peter, Kirste, Petra, Schulz, Petra, Mason, Phil, Kalra, Philip, Cirillo, Pietro, Dattolo, Pietro, Acampora, Pina, Sajith, Rincy, Nigro, Rita, Boero, Roberto, Scarpioni, Roberto, Sicoli, Rosa, Malandra, Rosella, Aign, Sabine, Cäsar, Sabine, van Esch, Sadie, Chapman, Sally, Biribauer, Sandra, Navjee, Santee, Crosbie, Sarah, Brown, Sharon, Tickle, Sheila, Manan, Sherin, Röser, Silke, Savoldi, Silvana, Bertoli, Silvio, Borrelli, Silvio, Boorsma, Siska, Heidenreich, Stefan, Melander, Stefan, Maxia, Stefania, Maffei, Stefano, Mangano, Stefano, Palm, Stephanie, Konings, Stijn, Mathavakkannan, Suresh, Schwedler, Susanne, Delrieux, Sylke, Renker, Sylvia, Schättel, Sylvia, Dorota, Szyszkowska, Cicchetti, Teresa, Nieszporek, Teresa, Stephan, Theresa, Schmiedeke, Thoma, Weinreich, Thoma, Leimbach, Til, Rappa, Tiziana, Almquist, Tora, Stövesand, Torsten, Bahner, Udo, Jensen, Ulrika, Palazzo, Valentina, De Simone, Walter, Seeger, Wolfgang, Kuan, Ying, Heleniak, Zbigniew, Aydin, Zeynep, Medical Informatics, ACS - Pulmonary hypertension & thrombosis, APH - Aging & Later Life, APH - Health Behaviors & Chronic Diseases, APH - Methodology, APH - Quality of Care, and APH - Global Health

Subjects
Male, progression of chronic renal failure, medicine.medical_specialty, Time Factors, epidemiology and outcome, 030232 urology & nephrology, Risk Assessment, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Older patients, external validation, Predictive Value of Tests, medicine, Humans, Failure risk, Clinical Epidemiology, In patient, comprehensive external validation, 030212 general & internal medicine, Statistic, Aged, Aged, 80 and over, Kidney, Models, Statistical, business.industry, External validation, General Medicine, prediction, kidney failure, Europe, prediction model, medicine.anatomical_structure, chronic kidney disease, epidemiology and outcomes, prognosis, Nephrology, Emergency medicine, Disease Progression, Kidney Failure, Chronic, Female, business, prognostic, Predictive modelling, prognosi, Cohort study
Abstract

Background Various prediction models have been developed to predict the risk of kidney failure in patients with CKD. However, guideline-recommended models have yet to be compared head to head, their validation in patients with advanced CKD is lacking, and most do not account for competing risks. Methods To externally validate 11 existing models of kidney failure, taking the competing risk of death into account, we included patients with advanced CKD from two large cohorts: the European Quality Study (EQUAL), an ongoing European prospective, multicenter cohort study of older patients with advanced CKD, and the Swedish Renal Registry (SRR), an ongoing registry of nephrology-referred patients with CKD in Sweden. The outcome of the models was kidney failure (defined as RRT-treated ESKD). We assessed model performance with discrimination and calibration. Results The study included 1580 patients from EQUAL and 13,489 patients from SRR. The average c statistic over the 11 validated models was 0.74 in EQUAL and 0.80 in SRR, compared with 0.89 in previous validations. Most models with longer prediction horizons overestimated the risk of kidney failure considerably. The 5-year Kidney Failure Risk Equation (KFRE) overpredicted risk by 10%-\18%. The four- and eight-variable 2-year KFRE and the 4-year Grams model showed excellent calibration and good discrimination in both cohorts. Conclusions Some existing models can accurately predict kidney failure in patients with advanced CKD. KFRE performed well for a shorter time frame (2 years), despite not accounting for competing events. Models predicting over a longer time frame (5 years) overestimated risk because of the competing risk of death. The Grams model, which accounts for the latter, is suitable for longer-term predictions (4 years).

Published
2021

19. Infection dynamics of Salmonella Infantis strains displaying different genetic backgrounds – with or without pESI-like plasmid – vary considerably

Author

Nicola Palmieri, Michael Hess, Victoria Drauch, Claudia Hess, and Christian Kornschober

Subjects
Serotype, Salmonella, Epidemiology, Immunology, Virulence, General Medicine, Biology, medicine.disease_cause, Microbiology, Infectious Diseases, Plasmid, Virology, Drug Discovery, medicine, Parasitology, Infection dynamics, human activities, Salmonella infantis
Abstract

Food-borne infections with Salmonella are among the most common causes of human diseases worldwide, and infections with the serovar Infantis are becoming increasingly important. So far, diverse phe...

Published
2021

20. MO808: Indoxyl-Sulphate and Cresyl Sulphate are Respectively Linked to Calcium-Phosphate Metabolism Variables and to Cardiovascular Morbidity in Hemodialysed Patients

Author

Arianna Bologna, Nadia Edvige Foligno, Monica Avino, Teresa Del Mastro, Ferruccio Conte, Nicola Palmieri, Sergio Bisegna, Giorgio Slaviero, Teresa Arcidiacono, and Giuseppe Vezzoli

Subjects
Transplantation, Nephrology
Abstract

BACKGROUND AND AIMS Indoxyl sulphate (IS) and Cresyl sulphate (CS) are uremic toxins generated by the intestinal amino acid catabolism. Blood levels of these toxins increase in patients with CKD and are linked to cardiovascular events. Therefore, we studied the relationship between serum levels of free IS and CS and divalent ion metabolism variables and cardiovascular morbidity (stroke, heart failure, angor and myocardial infarction) in 139 haemodialysis patients (age 68 + 13 years, weight 65 + 13 kg, dialysis vintage 69 + 71 months). METHOD We divided patients according to tertiles of free serum IS and CS. RESULTS Patients in the highest tertile of serum free IS showed shorter dialysis vintage and higher body weight gain between dialysis sessions than patients in the other two tertiles. Patients in the highest tertile of IS showed lower body weight and serum concentrations of alkaline phosphatase, 1,25(OH)2D and PTH compared with the lowest tertile. Serum PTH was also measured during 2 years after the baseline; it was higher in patients in the lowest than those in the highest tertile of serum free IS. No relationships of serum free CS concentrations with phosphate and calcium metabolism variables were observed. Kaplan–Meier survival analysis shows an increased cardiovascular morbidity in patients in the CS highest tertile (blue line in the figure) compared with those in the lowest and middle tertiles taken together (red line; P = 0.01). This association was not found considering IS tertiles. CONCLUSION Our findings suggest that serum free IS may be associated with PTH and 1,25(OH)2D secretion, whereas free PCS may predict cardiovascular risk in haemodialysis patients. A point for future investigation could be the relationship between IS and adynamic bone disease.

Published
2022

21. A novel Chaphamaparvovirus is the etiological agent of hepatitis outbreaks in pheasants (Phasianus colchicus) characterized by high mortality

Author

Miguel Matos, Ivana Bilic, Nicolas Viloux, Nicola Palmieri, Olivier Albaric, Xavier Chatenet, Jana Tvarogová, Nora Dinhopl, Sarah Heidl, Dieter Liebhart, and Michael Hess

Subjects
Parvoviridae Infections, Parvovirus, General Veterinary, General Immunology and Microbiology, Animals, General Medicine, Quail, Disease Outbreaks, Hepatitis
Abstract

In the present study, we report the occurrence of several outbreaks of hepatitis in flocks of young pheasants in France, between 2017 and 2021. The disease was characterized by prostration, apathy and a median cumulative mortality of 12%, with the birds presenting multifocal to coalescing necrotizing hepatitis on necropsy. Severe extensive areas of degeneration and necrosis were observed in the liver, with degenerative hepatocytes presenting large amphophilic to acidophilic intranuclear inclusion bodies. Transmission electron microscopy examination of liver samples showed the presence of parvovirus-like virions of 21-24 nm, a finding already reported decades ago. Further investigations by Next Generation Sequencing and PCR revealed the complete genome of a novel species of parvovirus, here designated Phasianus chaphamaparvovirus 1 (PhChPV-1), that belongs to the new genus Chaphamaparvovirus in the Hamaparvovirinae subfamily. In situ hybridization and real-time PCR confirmed the etiology of the outbreaks, demonstrating the viral genome in the lesions. The findings establish the etiology of a pathology first described in pheasants 50 years ago and pave the way for a targeted protection strategy.

Published
2022

22. Sequencing of five poultry strains elucidates phylogenetic relationships and divergence in virulence genes in Morganella morganii

Author

Michael Hess, Claudia Hess, Nicola Palmieri, and Merima Alispahic

Subjects
0106 biological sciences, lcsh:QH426-470, lcsh:Biotechnology, Virulence, beta-Lactams, Antimicrobial resistance, 01 natural sciences, Genome, beta-Lactamases, Poultry, 03 medical and health sciences, Morganella, Phylogenetics, lcsh:TP248.13-248.65, Genetics, polycyclic compounds, Animals, Humans, MALDI-TOF MS, Phylogeny, 030304 developmental biology, Comparative genomics, Morganella morganii, 0303 health sciences, NGS data, biology, Phylogenetic tree, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Anti-Bacterial Agents, lcsh:Genetics, Virulence genes, Horizontal gene transfer, bacteria, Research Article, 010606 plant biology & botany, Biotechnology
Abstract

Background M. morganii is a bacterium frequently associated with urinary infections in humans. While many human strains are sequenced, only the genomes of few poultry strains are available. Here, we performed a detailed characterization of five highly resistant Morganella morganii strains isolated in association with Escherichia coli from diseased domestic Austrian poultry flocks, namely geese, turkeys and chicken layers. Additionally, we sequenced the genomes of these strains by NGS and analyzed phylogenetic clustering, resistance and virulence genes in the context of host-specificity. Results Two strains were identified to be Extended Spectrum Beta Lactamase (ESBL) and one as AmpC beta-lactamases (AMP-C) phenotype, while two were ESBL negative. By integrating the genome sequences of these five poultry strains with all the available M. morganii genomes, we constructed a phylogenetic tree that clearly separates the Morganella genus into two clusters (M1 and M2), which approximately reflect the proposed subspecies classification (morganii and sibonii). Additionally, we found no association between phylogenetic structure and host, suggesting interspecies transmission. All five poultry strains contained genes for resistance to aminocoumarins, beta-lactams, colistin, elfamycins, fluoroquinolones, phenicol, rifampin and tetracycline. A comparative genomics analysis of virulence genes showed acquisition of novel virulence genes involved in secretion system and adherence in cluster M2. We showed that some of these genes were acquired by horizontal gene transfer from closely related Morganellaceae species and propose that novel virulence genes could be responsible for expansion of tissue tropism in M. morganii. Finally, we detected variability in copy number and high sequence divergence in toxin genes and provided evidence for positive selection in insecticidal toxins genes, likely reflecting host-related adaptations. Conclusions In summary, this study describes i) the first isolation and characterization of M. morganii from goose and turkey, ii) a large-scale genetic analysis of M. morganii and an attempt to generate a global picture of the M. morganii intraspecific phylogenetic structure.

Published
2020

23. Associations between depressive symptoms and disease progression in older patients with chronic kidney disease

Author

Eveleens Maarse, Boukje C., Chesnaye, Nicholas C., Robbert, Schouten, Michels, Wieneke M., Bos, Willem Jan W., Maciej, Szymczak, Magdalena, Krajewska, Marie Evans, Olof Heimburger, Caskey, Fergus J., Christoph, Wanner, Jager, Kitty J., Dekker, Friedo W., Yvette, Meuleman, Andreas, Schneider, Anke, Torp, Beate, Iwig, Boris, Perras, Christian, Marx, Christiane, Drechsler, Christof, Blaser, Claudia, Emde, Detlef, Krieter, Dunja, Fuchs, Ellen, Irmler, Eva, Platen, Hans, Schmidt-Gürtler, Hendrik, Schlee, Holger, Naujoks, Ines, Schlee, Sabine, Cäsar, Joachim, Beige, Jochen, Röthele, Justyna, Mazur, Kai, Hahn, Katja, Blouin, Katrin, Neumeier, Kirsten, Anding-Rost, Lothar, Schramm, Monika, Hopf, Nadja, Wuttke, Nikolaus, Frischmuth, Pawlos, Ichtiaris, Petra, Kirste, Petra, Schulz, Sabine, Aign, Sandra, Biribauer, Sherin, Manan, Silke, Röser, Stefan, Heidenreich, Stephanie, Palm, Susanne, Schwedler, Sylke, Delrieux, Sylvia, Renker, Sylvia, Schättel, Theresa, Stephan, Thomas, Schmiedeke, Thomas, Weinreich, Til, Leimbach, Torsten, Stövesand, Udo, Bahner, Wolfgang, Seeger, Cupisti, Adamasco, Adelia, Sagliocca, Alberto, Ferraro, Alessandra, Mele, Alessandro, Naticchia, Alex, Còsaro, Andrea, Ranghino, Andrea, Stucchi, Angelo, Pignataro, Antonella De Blasio, Antonello, Pani, Aris, Tsalouichos, Bellasi, Antonio, Biagio Raffaele Di Iorio, Butti, Alessandra, Cataldo, Abaterusso, Chiara, Somma, Claudia, D'Alessandro, Claudia, Torino, Claudia, Zullo, Claudio, Pozzi, Daniela, Bergamo, Daniele, Ciurlino, Daria, Motta, Domenico, Russo, Enrico, Favaro, Federica, Vigotti, Ferruccio, Ansali, Ferruccio, Conte, Francesca, Cianciotta, Francesca, Giacchino, Francesco, Cappellaio, Francesco, Pizzarelli, Gaetano, Greco, Gaetana, Porto, Giada, Bigatti, Giancarlo, Marinangeli, Gianfranca, Cabiddu, Giordano, Fumagalli, Giorgia, Caloro, Giorgina, Piccoli, Giovanbattista, Capasso, Giovanni, Gambaro, Giuliana, Tognarelli, Giuseppe, Bonforte, Giuseppe, Conte, Giuseppe, Toscano, Goffredo Del Rosso, Irene, Capizzi, Ivano, Baragetti, Lamberto, Oldrizzi, Loreto, Gesualdo, Luigi, Biancone, Manuela, Magnano, Marco, Ricardi, Maria Di Bari, Maria, Laudato, Maria Luisa Sirico, Martina, Ferraresi, Maurizio, Postorino, Michele, Provenzano, Moreno, Malaguti, Nicola, Palmieri, Paola, Murrone, Pietro, Cirillo, Pietro, Dattolo, Pina, Acampora, Rita, Nigro, Roberto, Boero, Roberto, Scarpioni, Rosa, Sicoli, Rosella, Malandra, Silvana, Savoldi, Silvio, Bertoli, Silvio, Borrelli, Stefania, Maxia, Stefano, Maffei, Stefano, Mangano, Teresa, Cicchetti, Tiziana, Rappa, Valentina, Palazzo, Walter De Simone, Anita, Schrander, Bastiaan van Dam, Carl, Siegert, Carlo, Gaillard, Charles, Beerenhout, Cornelis, Verburgh, Cynthia, Janmaat, Ellen, Hoogeveen, Ewout, Hoorn, Friedo, Dekker, Johannes, Boots, Henk, Boom, Jan-Willem, Eijgenraam, Jeroen, Kooman, Joris, Rotmans, Kitty, Jager, Liffert, Vogt, Maarten, Raasveld, Marc, Vervloet, Marjolijn van Buren, Merel van Diepen, Nicholas, Chesnaye, Paul, Leurs, Pauline, Voskamp, Peter, Blankestijn, Sadie van Esch, Siska, Boorsma, Stefan, Berger, Constantijn, Konings, Zeynep, Aydin, Aleksandra, Musiała, Anna, Szymczak, Ewelina, Olczyk, Hanna, Augustyniak-Bartosik, Ilona, Miśkowiec-Wiśniewska, Jacek, Manitius, Joanna, Pondel, Kamila, Jędrzejak, Katarzyna, Nowańska, Łukasz, Nowak, Magdalena, Durlik, Szyszkowska, Dorota, Teresa, Nieszporek, Zbigniew, Heleniak, Andreas, Jonsson, Anna-Lena, Blom, Björn, Rogland, Carin, Wallquist, Denes, Vargas, Emöke, Dimény, Fredrik, Sundelin, Fredrik, Uhlin, Gunilla, Welander, Isabel Bascaran Hernandez, Knut-Christian, Gröntoft, Maria, Stendahl, Maria, Svensson, Marie, Evans, Olof, Heimburger, Pavlos, Kashioulis, Stefan, Melander, Tora, Almquist, Ulrika, Jensen, Alistair, Woodman, Anna, Mckeever, Asad, Ullah, Barbara, Mclaren, Camille, Harron, Carla, Barrett, Charlotte, O'Toole, Christina, Summersgill, Colin, Geddes, Deborah, Glowski, Deborah, Mcglynn, Dympna, Sands, Fergus, Caskey, Geena, Roy, Gillian, Hirst, Hayley, King, Helen, Mcnally, Houda, Masri-Senghor, Hugh, Murtagh, Hugh, Rayner, Jane, Turner, Joanne, Wilcox, Jocelyn, Berdeprado, Jonathan, Wong, Joyce, Banda, Kirsteen, Jones, Lesley, Haydock, Lily, Wilkinson, Margaret, Carmody, Maria, Weetman, Martin, Joinson, Mary, Dutton, Michael, Matthews, Neal, Morgan, Nina, Bleakley, Paul, Cockwell, Paul, Roderick, Phil, Mason, Philip, Kalra, Rincy, Sajith, Sally, Chapman, Santee, Navjee, Sarah, Crosbie, Sharon, Brown, Sheila, Tickle, Suresh, Mathavakkannan, Ying, Kuan, Internal medicine, Nephrology, ACS - Diabetes & metabolism, Medical Informatics, APH - Methodology, APH - Aging & Later Life, Graduate School, APH - Quality of Care, ACS - Microcirculation, APH - Health Behaviors & Chronic Diseases, APH - Global Health, ACS - Pulmonary hypertension & thrombosis, Eveleens Maarse, B. C., Chesnaye, N. C., Schouten, R., Michels, W. M., Bos, W. J. W., Szymczak, M., Krajewska, M., Evans, M., Heimburger, O., Caskey, F. J., Wanner, C., Jager, K. J., Dekker, F. W., Meuleman, Y., Schneider, A., Torp, A., Iwig, B., Perras, B., Marx, C., Drechsler, C., Blaser, C., Emde, C., Krieter, D., Fuchs, D., Irmler, E., Platen, E., Schmidt-Gurtler, H., Schlee, H., Naujoks, H., Schlee, I., Casar, S., Beige, J., Rothele, J., Mazur, J., Hahn, K., Blouin, K., Neumeier, K., Anding-Rost, K., Schramm, L., Hopf, M., Wuttke, N., Frischmuth, N., Ichtiaris, P., Kirste, P., Schulz, P., Aign, S., Biribauer, S., Manan, S., Roser, S., Heidenreich, S., Palm, S., Schwedler, S., Delrieux, S., Renker, S., Schattel, S., Stephan, T., Schmiedeke, T., Weinreich, T., Leimbach, T., Stovesand, T., Bahner, U., Seeger, W., Cupisti, A., Sagliocca, A., Ferraro, A., Mele, A., Naticchia, A., Cosaro, A., Ranghino, A., Stucchi, A., Pignataro, A., De Blasio, A., Pani, A., Tsalouichos, A., Antonio, B., Raffaele Di Iorio, B., Alessandra, B., Abaterusso, C., Somma, C., D'Alessandro, C., Torino, C., Zullo, C., Pozzi, C., Bergamo, D., Ciurlino, D., Motta, D., Russo, D., Favaro, E., Vigotti, F., Ansali, F., Conte, F., Cianciotta, F., Giacchino, F., Cappellaio, F., Pizzarelli, F., Greco, G., Porto, G., Bigatti, G., Marinangeli, G., Cabiddu, G., Fumagalli, G., Caloro, G., Piccoli, G., Capasso, G., Gambaro, G., Tognarelli, G., Bonforte, G., Conte, G., Toscano, G., Del Rosso, G., Capizzi, I., Baragetti, I., Oldrizzi, L., Gesualdo, L., Biancone, L., Magnano, M., Ricardi, M., Di Bari, M., Laudato, M., Luisa Sirico, M., Ferraresi, M., Postorino, M., Provenzano, M., Malaguti, M., Palmieri, N., Murrone, P., Cirillo, P., Dattolo, P., Acampora, P., Nigro, R., Boero, R., Scarpioni, R., Sicoli, R., Malandra, R., Savoldi, S., Bertoli, S., Borrelli, S., Maxia, S., Maffei, S., Mangano, S., Cicchetti, T., Rappa, T., Palazzo, V., De Simone, W., Schrander, A., Van Dam, B., Siegert, C., Gaillard, C., Beerenhout, C., Verburgh, C., Janmaat, C., Hoogeveen, E., Hoorn, E., Boots, J., Boom, H., Eijgenraam, J. -W., Kooman, J., Rotmans, J., Vogt, L., Raasveld, M., Vervloet, M., Van Buren, M., Van Diepen, M., Leurs, P., Voskamp, P., Blankestijn, P., Van Esch, S., Boorsma, S., Berger, S., Konings, C., Aydin, Z., Musiala, A., Szymczak, A., Olczyk, E., Augustyniak-Bartosik, H., Miskowiec-Wisniewska, I., Manitius, J., Pondel, J., Jedrzejak, K., Nowanska, K., Nowak, L., Durlik, M., Dorota, S., Nieszporek, T., Heleniak, Z., Jonsson, A., Blom, A. -L., Rogland, B., Wallquist, C., Vargas, D., Dimeny, E., Sundelin, F., Uhlin, F., Welander, G., Bascaran Hernandez, I., Grontoft, K. -C., Stendahl, M., Svensson, M., Kashioulis, P., Melander, S., Almquist, T., Jensen, U., Woodman, A., Mckeever, A., Ullah, A., Mclaren, B., Harron, C., Barrett, C., O'Toole, C., Summersgill, C., Geddes, C., Glowski, D., Mcglynn, D., Sands, D., Roy, G., Hirst, G., King, H., Mcnally, H., Masri-Senghor, H., Murtagh, H., Rayner, H., Turner, J., Wilcox, J., Berdeprado, J., Wong, J., Banda, J., Jones, K., Haydock, L., Wilkinson, L., Carmody, M., Weetman, M., Joinson, M., Dutton, M., Matthews, M., Morgan, N., Bleakley, N., Cockwell, P., Roderick, P., Mason, P., Kalra, P., Sajith, R., Chapman, S., Navjee, S., Crosbie, S., Brown, S., Tickle, S., Mathavakkannan, S., and Kuan, Y.

Subjects
Transplantation, prospective cohort study, depressive symptoms, nephrology care, Nephrology, clinical outcome, chronic kidney disease, clinical trial, epidemiology, joint model, survival analysis, depressive symptom
Abstract

Background Depressive symptoms are associated with adverse clinical outcomes in patients with end-stage kidney disease; however, few small studies have examined this association in patients with earlier phases of chronic kidney disease (CKD). We studied associations between baseline depressive symptoms and clinical outcomes in older patients with advanced CKD and examined whether these associations differed depending on sex. Methods CKD patients (≥65 years; estimated glomerular filtration rate ≤20 mL/min/1.73 m2) were included from a European multicentre prospective cohort between 2012 and 2019. Depressive symptoms were measured by the five-item Mental Health Inventory (cut-off ≤70; 0–100 scale). Cox proportional hazard analysis was used to study associations between depressive symptoms and time to dialysis initiation, all-cause mortality and these outcomes combined. A joint model was used to study the association between depressive symptoms and kidney function over time. Analyses were adjusted for potential baseline confounders. Results Overall kidney function decline in 1326 patients was –0.12 mL/min/1.73 m2/month. A total of 515 patients showed depressive symptoms. No significant association was found between depressive symptoms and kidney function over time (P = 0.08). Unlike women, men with depressive symptoms had an increased mortality rate compared with those without symptoms [adjusted hazard ratio 1.41 (95% confidence interval 1.03–1.93)]. Depressive symptoms were not significantly associated with a higher hazard of dialysis initiation, or with the combined outcome (i.e. dialysis initiation and all-cause mortality). Conclusions There was no significant association between depressive symptoms at baseline and decline in kidney function over time in older patients with advanced CKD. Depressive symptoms at baseline were associated with a higher mortality rate in men.

Published
2022

24. The association between TMAO, CMPF and clinical outcomes in advanced CKD; results from the EQUAL study

Author

Dai, Lu, Ziad, A Massy, Peter, Stenvinkel, Nicholas, C Chesnaye, Islam Amine Larabi, Jean Claude Alvarez, Fergus, J Caskey, Claudia, Torino, Gaetana, Porto, Maciej, Szymczak, Magdalena, Krajewska, Christiane, Drechsler, Christoph, Wanner, Kitty, J Jager, Friedo, W Dekker, Pieter, Evenepoel, Marie, Evans, Andreas, Schneider, Anke, Torp, Beate, Iwig, Boris, Perras, Christian, Marx, Christof, Blaser, Claudia, Emde, Detlef, Krieter, Dunja, Fuchs, Ellen, Irmler, Eva, Platen, Hans, Schmidt-Gürtler, Hendrik, Schlee, Holger, Naujoks, Ines, Schlee, Sabine, Cäsar, Joachim, Beige, Jochen, Röthele, Justyna, Mazur, Kai, Hahn, Katja, Blouin, Katrin, Neumeier, Kirsten, Anding-Rost, Lothar, Schramm, Monika, Hopf, Nadja, Wuttke, Nikolaus, Frischmuth, Pawlos, Ichtiaris, Petra, Kirste, Petra, Schulz, Sabine, Aign, Sandra, Biribauer, Sherin, Manan, Silke, Röser, Stefan, Heidenreich, Stephanie, Palm, Susanne, Schwedler, Sylke, Delrieux, Sylvia, Renker, Sylvia, Schättel, Theresa, Stephan, Thomas, Schmiedeke, Thomas, Weinreich, Til, Leimbach, Torsten, Stövesand, Udo, Bahner, Wolfgang, Seeger, Cupisti, Adamasco, Adelia, Sagliocca, Alberto, Ferraro, Alessandra, Mele, Alessandro, Naticchia, Alex, Còsaro, Andrea, Ranghino, Andrea, Stucchi, Angelo, Pignataro, Antonella De Blasio, Antonello, Pani, Aris, Tsalouichos, Bellasi, Antonio, Biagio Raffaele Di Iorio, Butti, Alessandra, Cataldo, Abaterusso, Chiara, Somma, Claudia, D'Alessandro, Claudia, Zullo, Claudio, Pozzi, Daniela, Bergamo, Daniele, Ciurlino, Daria, Motta, Domenico, Russo, Enrico, Favaro, Federica, Vigotti, Ferruccio, Ansali, Ferruccio, Conte, Francesca, Cianciotta, Francesca, Giacchino, Francesco, Cappellaio, Francesco, Pizzarelli, Gaetano, Greco, Giada, Bigatti, Giancarlo, Marinangeli, Gianfranca, Cabiddu, Giordano, Fumagalli, Giorgia, Caloro, Giorgina, Piccoli, Giovanbattista, Capasso, Giovanni, Gambaro, Giuliana, Tognarelli, Giuseppe, Bonforte, Giuseppe, Conte, Giuseppe, Toscano, Goffredo Del Rosso, Irene, Capizzi, Ivano, Baragetti, Lamberto, Oldrizzi, Loreto, Gesualdo, Luigi, Biancone, Manuela, Magnano, Marco, Ricardi, Maria Di Bari, Maria, Laudato, Maria Luisa Sirico, Martina, Ferraresi, Michele, Provenzano, Moreno, Malaguti, Nicola, Palmieri, Paola, Murrone, Pietro, Cirillo, Pietro, Dattolo, Pina, Acampora, Rita, Nigro, Roberto, Boero, Roberto, Scarpioni, Rosa, Sicoli, Rosella, Malandra, Silvana, Savoldi, Silvio, Bertoli, Silvio, Borrelli, Stefania, Maxia, Stefano, Maffei, Stefano, Mangano, Teresa, Cicchetti, Tiziana, Rappa, Valentina, Palazzo, Walter De Simone, Anita, Schrander, Bastiaan van Dam, Carl, Siegert, Carlo, Gaillard, Charles, Beerenhout, Cornelis, Verburgh, Cynthia, Janmaat, Ellen, Hoogeveen, Ewout, Hoorn, Friedo, Dekker, Johannes, Boots, Henk, Boom, Jan-Willem, Eijgenraam, Jeroen, Kooman, Joris, Rotmans, Kitty, Jager, Liffert, Vogt, Maarten, Raasveld, Marc, Vervloet, Marjolijn van Buren, Merel van Diepen, Nicholas, Chesnaye, Paul, Leurs, Pauline, Voskamp, Sadie van Esch, Siska, Boorsma, Stefan, Berger, Constantijn, Konings, Zeynep, Aydin, Aleksandra, Musiała, Anna, Szymczak, Ewelina, Olczyk, Hanna, Augustyniak-Bartosik, Ilona, Miśkowiec-Wiśniewska, Jacek, Manitius, Joanna, Pondel, Kamila, Jędrzejak, Katarzyna, Nowańska, Łukasz, Nowak, Magdalena, Durlik, Szyszkowska, Dorota, Teresa, Nieszporek, Zbigniew, Heleniak, Andreas, Jonsson, Björn, Rogland, Carin, Wallquist, Denes, Vargas, Emöke, Dimény, Fredrik, Sundelin, Fredrik, Uhlin, Gunilla, Welander, Isabel Bascaran Hernandez, Knut-Christian, Gröntoft, Maria, Stendahl, Maria Eriksson Svensson, Olof, Heimburger, Pavlos, Kashioulis, Stefan, Melander, Tora, Almquist, Alistair, Woodman, Anna, Mckeever, Asad, Ullah, Barbara, Mclaren, Camille, Harron, Carla, Barrett, Charlotte, O'Toole, Christina, Summersgill, Colin, Geddes, Deborah, Glowski, Deborah, Mcglynn, Dympna, Sands, Fergus, Caskey, Geena, Roy, Gillian, Hirst, Hayley, King, Helen, Mcnally, Houda, Masri-Senghor, Hugh, Murtagh, Hugh, Rayner, Jane, Turner, Joanne, Wilcox, Jocelyn, Berdeprado, Jonathan, Wong, Joyce, Banda, Kirsteen, Jones, Lesley, Haydock, Lily, Wilkinson, Margaret, Carmody, Maria, Weetman, Martin, Joinson, Mary, Dutton, Michael, Matthews, Neal, Morgan, Nina, Bleakley, Paul, Cockwell, Paul, Roderick, Phil, Mason, Philip, Kalra, Rincy, Sajith, Sally, Chapman, Santee, Navjee, Sarah, Crosbie, Sharon, Brown, Sheila, Tickle, Suresh, Mathavakkannan, and Ying, Kuan

Subjects
3-carboxy-4-methyl-5-propyl-2-furanpropionate, CKD, fish intake, kidney replacement therapy, mortality, red meat, trimethylamine N-oxide, uremic toxins
Published
2022

25. Serum concentrations of free indoxyl and p-cresyl sulfate are associated with mineral metabolism variables and cardiovascular risk in hemodialysis patients

Author

Teresa Arcidiacono, Lorenza Macrina, Simone Premaschi, Arianna Bologna, Giulia Magni, Nadia Foligno, Monica Avino, Cristina Belloni, Nicola Palmieri, Ferruccio Conte, Sergio Bisegna, Marco Simonini, Giorgio Slaviero, Massimo Locatelli, and Giuseppe Vezzoli

Subjects
Minerals, Indoles, Sulfates, Sulfuric Acid Esters, Phosphates, Cresols, Nephrology, Cardiovascular Diseases, Heart Disease Risk Factors, Renal Dialysis, Risk Factors, Humans, Calcium, Indican, Biomarkers
Abstract

Indoxyl sulfate (IS) and p-cresyl sulfate (PCS) are uremic toxins associated with cardiovascular outcome in CKD patients. The present work is an analysis of the association of serum free, total IS and PCS with cardiovascular events and calcium-phosphate metabolism variables in hemodialysis patients.Serum levels of total and free IS and PCS were measured in 139 hemodialysis patients. Their relationship with calcium-phosphate metabolism variables were tested in an observational cohort study. In addition, their association with cardiovascular events was investigated during a 4-year follow-up.Patients in the highest tertile (T3) of serum free IS showed lower serum 1,25(OH)Serum free IS may be associated with PTH and 1,25(OH)

Published
2021

26. Infection dynamics of

Author

Victoria, Drauch, Christian, Kornschober, Nicola, Palmieri, Michael, Hess, and Claudia, Hess

Subjects
Salmonella Infections, Animal, Virulence, Salmonella Infantis, Antibodies, Bacterial, pESI-like plasmid, infection, experimental study, virulence, broiler chicken, Salmonella, Animals, Chickens, Genetic Background, Poultry Diseases, Plasmids, Research Article
Abstract

Food-borne infections with Salmonella are among the most common causes of human diseases worldwide, and infections with the serovar Infantis are becoming increasingly important. So far, diverse phenotypes and genotypes of S. Infantis have been reported. Therefore, the present study aimed to investigate the infection dynamics of two different S. Infantis strains in broilers. For this purpose, 15 birds were infected on day 2 of life with 108 CFU/ml of a pESI+ or a pESI– S. Infantis strain, respectively. Ten uninfected birds served as in-contact birds to monitor transmission. In both groups, an increase of infection was observed from 7 days of age onwards, reaching its peak at 28 days. However, the pESI+ strain proved significantly more virulent being re-isolated from most cloacal swabs and organs by direct plating. In contrast, the pESI– strain could be re-isolated from cloacal swabs and caeca only when enrichment was applied. Although the excretion of this strain was limited, the transmission level to in-contact birds was similar to the pESI+ strain. Differences in infection dynamics were also reflected in the antibody response: whereas the pESI+ strain provoked a significant increase in antibodies, antibody levels following infection with the pESI– strain remained in the range of negative control birds. The actual findings provide for the first time evidence of S. Infantis strain-specific infectivity in broilers and confirm previous observations in the field regarding differences in persistence on farms and resistance against disinfectants.

Published
2021

27. High-resolution characterisation of ESBL/pAmpC-producing Escherichia coli isolated from the broiler production pyramid

Author

Alessandra Piccirillo, Claudia Feudi, Nicola Palmieri, Inga Eichhorn, Luca Fasolato, Ilias Apostolakos, and Stefan Schwarz

Subjects
0301 basic medicine, 600 Technik, Medizin, angewandte Wissenschaften::630 Landwirtschaft::630 Landwirtschaft und verwandte Bereiche, Molecular biology, Cephalosporin, lcsh:Medicine, medicine.disease_cause, Genome, e. coli, EMERGENCE, molecular characterization, Plasmid, polycyclic compounds, Animal Husbandry, lcsh:Science, Phylogeny, Genetics, Multidisciplinary, food-producing animals, FOOD-PRODUCING ANIMALS, MOLECULAR CHARACTERIZATION, ANTIMICROBIAL RESISTANCE, E. COLI, PLASMIDS, VIRULENCE, IDENTIFICATION, CEPHALOSPORINS, SEQUENCES, plasmids, medicine.drug_class, 030106 microbiology, Virulence, Biology, Microbiology, beta-Lactam Resistance, beta-Lactamases, Article, 03 medical and health sciences, Antibiotic resistance, Bacterial Proteins, medicine, Escherichia coli, Animals, antimicrobial resistance, Gene, Whole genome sequencing, Whole Genome Sequencing, lcsh:R, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, virulence, 030104 developmental biology, Genes, Bacterial, cephalosporins, identification, lcsh:Q, Chickens, Genome, Bacterial
Abstract

The presence of extended-spectrum β-lactamase (ESBL) or plasmid-mediated AmpC β-lactamase (pAmpC)-producing Escherichia coli (ESBL/pAmpC-EC) in livestock is a public health risk given the likelihood of their transmission to humans via the food chain. We conducted whole genome sequencing on 100 ESBL/pAmpC-EC isolated from the broiler production to explore their resistance and virulence gene repertoire, characterise their plasmids and identify transmission events derived from their phylogeny. Sequenced isolates carried resistance genes to four antimicrobial classes in addition to cephalosporins. Virulence gene analysis assigned the majority of ESBL/pAmpC-EC to defined pathotypes. In the complex genetic background of ESBL/pAmpC-EC, clusters of closely related isolates from various production stages were identified and indicated clonal transmission. Phylogenetic comparison with publicly available genomes suggested that previously uncommon ESBL/pAmpC-EC lineages could emerge in poultry, while others might contribute to the maintenance and dissemination of ESBL/pAmpC genes in broilers. The majority of isolates from diverse E. coli lineages shared four dominant plasmids (IncK2, IncI1, IncX3 and IncFIB/FII) with identical ESBL/pAmpC gene insertion sites. These plasmids have been previously reported in diverse hosts, including humans. Our findings underline the importance of specific plasmid groups in the dissemination of cephalosporin resistance genes within the broiler industry and across different reservoirs.

Published
2020
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28. Glucagon-like peptide-1 receptor and sarcoglycan delta genetic variants can affect cardiovascular risk in chronic kidney disease patients under hemodialysis

Author

Ferruccio Conte, Annalisa Terranegra, Sara Tomei, Giuseppe Vezzoli, Alessandro Rubinacci, Teresa Arcidiacono, Francesca Pivari, Nicola Palmieri, Lee Silcock, Mario Cozzolino, Laura Soldati, Lorenza Macrina, Marcella Sirtori, Massimo Mezzavilla, Alessandra Mingione, Caterina Brasacchio, Terranegra, Annalisa, Arcidiacono, Teresa, Macrina, Lorenza, Brasacchio, Caterina, Pivari, Francesca, Mingione, Alessandra, Tomei, Sara, Mezzavilla, Massimo, Silcock, Lee, Cozzolino, Mario, Palmieri, Nicola, Conte, Ferruccio, Sirtori, Marcella, Rubinacci, Alessandro, Soldati, Laura, and Vezzoli, Giuseppe

Subjects
Oncology, medicine.medical_specialty, gene polymorphism, Population, 030232 urology & nephrology, Single-nucleotide polymorphism, 03 medical and health sciences, 0302 clinical medicine, cardiovascular disease, Internal medicine, Chronic kidney disease, Genotype, medicine, Genetics, genetics, Cardiovascular disease, Gene polymorphism, Hemodialysis, Allele, AcademicSubjects/MED00340, education, Genotyping, 030304 developmental biology, 0303 health sciences, Transplantation, education.field_of_study, hemodialysis, business.industry, Original Articles, medicine.disease, Nephrology, Genetic marker, business, chronic kidney disease, Kidney disease
Abstract

Background Chronic kidney disease (CKD) patients under hemodialysis show a higher risk of cardiovascular (CV) mortality and morbidity than the general population. This study aims to identify genetic markers that could explain the increased CV risk in hemodialysis. Methods A total of 245 CKD patients under hemodialysis were recruited and followed up for 5 years to record CV events. Genetic analysis was performed using single-nucleotide polymorphisms (SNPs) genotyping by Infinium Expanded Multi-Ethnic Genotyping Array (Illumina, San Diego, CA, USA) comparing patients with and without a history of CV events [161 cardiovascular diseases (CVDs) and 84 no CVDs]. The fixation index (Fst) measure was used to identify the most differentiated SNPs, and gene ontology analysis [Protein Analysis THrough Evolutionary Relationships (PANTHER) and Ingenuity Pathway Analysis (IPA)] was applied to define the biological/pathological roles of the associated SNPs. Partitioning tree analysis interrogated the genotype–phenotype relationship between discovered genetic variants and CV phenotypes. Cox regression analysis measured the effect of these SNPs on new CV events during the follow-up (FU). Results Fst analysis identified 3218 SNPs that were significantly different between CVD and no CVD. Gene ontology analysis identified two of these SNPs as involved in cardiovascular disease pathways (Ingenuity Pathway) and heart development (Panther) and belonging to 2 different genes: Glucagon-like peptide-1 receptor (GLP1R) and Sarcoglycan delta (SGCD). The phenotype–genotype analysis found a higher percentage of CVD patients carrying the GLP1R rs10305445 allele A (P = 0.03) and lower percentages of CVD patients carrying the SGCD rs145292439 allele A (P = 0.038). Moreover, SGCD rs145292439 was associated with higher levels of high-density lipoprotein (P = 0.015). Cox analysis confirmed the increased frequency of CV events during the 5-year FU in patients carrying GLP1R rs1035445 allele A but it did not show any significant association with SGCD rs145292439. Conclusions This study identified GLP1R rs10305445 and SCGD rs145292439 as potential genetic markers that may explain the higher risk of CVD in hemodialysis patients.

Published
2020

29. Genomic analysis of extra-intestinal Campylobacter jejuni and Campylobacter coli isolated from commercial chickens

Author

Luca Bano, Ilenia Drigo, Elena Tonon, Andrea Laconi, Alessandra Piccirillo, Nicola Palmieri, Raffaela Franch, and Lisa Carraro

Subjects
Male, Farms, Virulence Factors, Virulence, Campylobacter coli, medicine.disease_cause, Microbiology, Genome, Campylobacter jejuni, 03 medical and health sciences, Liver disease, Campylobacter Infections, medicine, Animals, Colonization, Gene, Poultry Diseases, 030304 developmental biology, 0303 health sciences, Whole Genome Sequencing, General Veterinary, biology, 030306 microbiology, Campylobacter, Genomics, General Medicine, biology.organism_classification, medicine.disease, Intestines, Campylobacter jejuni Campylobacter coli chicken Extra-intestinal spread Whole-genome characterization Virulome Comparison, Female, Chickens, Genome, Bacterial
Abstract

Campylobacter jejuni and Campylobacter coli have commonly been considered harmless commensal inhabitants of the chicken gut; however, these Campylobacter spp. are known to be able to multiply in the gut and invade other tissues, negatively affecting host health and performance. In this study, fourteen Campylobacter spp. were isolated from chickens showing foci of necrosis on the liver surface resembling lesions observed in cases of avian vibrionic hepatitis/spotty liver disease. The whole genome sequences of the fourteen isolates were analysed and their virulomes compared to those of Campylobacter reference sequences, aiming to investigate the possible association between virulence genes and the observed pathological lesions. Nine C. jejuni and five C. coli were studied. These Campylobacter shared twelve virulence factors with other isolates originated from chicken livers and hosted a higher number of virulence-associated genes in comparison to the reference genomes, including genes encoding for factors involved in adherence to and invasion of the intestinal epithelial cells. Our findings seem to point out that these twelve common virulence-associated genes, together with the presence of a high number of virulence factors involved in adherence, invasion and motility, might be responsible for the extra-intestinal spread of our isolates and the colonization of parenchymatous tissues, possibly causing the pathological lesions observed.

Published
2021

30. The genome of the protozoan parasite Cystoisospora suis and a reverse vaccinology approach to identify vaccine candidates

Author

Bärbel Ruttkowski, Aruna Shrestha, Damer P. Blake, Tomas Beck, Nicola Palmieri, Fiona M. Tomley, Anja Joachim, and Claus Vogl

Subjects
Protozoan Vaccines, 0301 basic medicine, Vacceed, Swine, Cystoisospora, Sequence assembly, Antigens, Protozoan, Computational biology, Genome, Article, DNA sequencing, 03 medical and health sciences, parasitic diseases, Animals, Antigens, Gene, ComputingMethodologies_COMPUTERGRAPHICS, Whole genome sequencing, biology, Reverse vaccinology, Illumina sequencing, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, DNA, Protozoan, biology.organism_classification, Virology, Coccidia, 030104 developmental biology, Infectious Diseases, Sarcocystidae, Proteome, Parasitology, Transcriptome, Apicomplexa, Genome, Protozoan
Abstract

Graphical abstract, Highlights • The draft genome of Cystoisospora suis is ∼84 Mb with > 11,000 protein-coding genes. • Vacceed identified 1,168 candidates including apical complex proteins and surface antigens. • 220 of these candidates are specific to apicomplexans and highly expressed in merozoites. • Analysis of a selected C. suis-specific transmembrane protein confirmed the usefulness of reverse vaccinology., Vaccine development targeting protozoan parasites remains challenging, partly due to the complex interactions between these eukaryotes and the host immune system. Reverse vaccinology is a promising approach for direct screening of genome sequence assemblies for new vaccine candidate proteins. Here, we applied this paradigm to Cystoisospora suis, an apicomplexan parasite that causes enteritis and diarrhea in suckling piglets and economic losses in pig production worldwide. Using Next Generation Sequencing we produced an ∼84 Mb sequence assembly for the C. suis genome, making it the first available reference for the genus Cystoisospora. Then, we derived a manually curated annotation of more than 11,000 protein-coding genes and applied the tool Vacceed to identify 1,168 vaccine candidates by screening the predicted C. suis proteome. To refine the set of candidates, we looked at proteins that are highly expressed in merozoites and specific to apicomplexans. The stringent set of candidates included 220 proteins, among which were 152 proteins with unknown function, 17 surface antigens of the SAG and SRS gene families, 12 proteins of the apicomplexan-specific secretory organelles including AMA1, MIC6, MIC13, ROP6, ROP12, ROP27, ROP32 and three proteins related to cell adhesion. Finally, we demonstrated in vitro the immunogenic potential of a C. suis-specific 42 kDa transmembrane protein, which might constitute an attractive candidate for further testing.

Published
2017
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31. Volumetric expression of palynological spectra for nutritional studies

Author

Nicola Palmieri, Mauro Mariotti, Ida Conti, Piotr Medrzycki, and Maria Lucia Piana

Subjects
Palynology, pollen, palynological analysis, volume, volume, Insect Science, Pollen, pollen, Botany, medicine, palynological analysis, Biology, medicine.disease_cause
Abstract

When pollen is studied from nutritional point of view, it would be desirable to correct its raw palynological spectrum in order to express the mass contribution of each pollen type. Different appro...

Published
2019

32. Morphological and molecular identification of nasopharyngeal bot fly larvae infesting red deer (Cervus elaphus) in Austria

Author

Barbara Eigner, Natascha Leitner, Domenico Otranto, Walter Glawischnig, Hans-Peter Fuehrer, Nicola Palmieri, Laurin Schwarzmann, and Carina Zittra

Subjects
0301 basic medicine, Cephenemyia auribarbis, animal structures, Short Communication, 030231 tropical medicine, Cervus elaphus, Zoology, Pharyngomyia picta, Biology, law.invention, Myiasis, 03 medical and health sciences, 0302 clinical medicine, law, Nasopharynx, parasitic diseases, Genetic variation, medicine, Animals, Polymerase chain reaction, Molecular identification, Cytochrome oxidase subunit I, Larva, General Veterinary, Ecology, Deer, Diptera, fungi, General Medicine, medicine.disease, Oestridae, Molecular Typing, Nasopharyngeal Diseases, 030104 developmental biology, Infectious Diseases, Austria, Insect Science, Parasitology, human activities
Abstract

Nasopharyngeal myiases are caused by larvae of bot flies (Diptera: Oestridae), which have evolved a high specificity for their hosts. Bot flies (n = 916) were collected from 137 (57.6 %) out of 238 red deer (Cervus elaphus) hunted in Vorarlberg and Tyrol (Western Austria). After being stored in 75 % ethanol, larvae were identified to species level and developmental stage using morphological and morphometric keys. Larvae were also molecularly characterized by polymerase chain reaction (PCR) amplification and partial sequencing of the mitochondrial cytochrome oxidase subunit I gene. Morphological and molecular analysis allowed identification of larvae as Cephenemyia auribarbis and Pharyngomyia picta. Genetic variations were also examined within the specimens collected in both geographical locations.

Published
2016

33. Tegaderm™ CHG Dressing Significantly Improves Catheter-related Infection Rate in Hemodialysis Patients

Author

Mario Prencipe, Marco Righetti, Francesca Colombo, Irene Brenna, Ferruccio Conte, Oscar Bracchi, Alfio Scalia, Karen Amar, Francesca Stefani, Elena Bruschetta, and Nicola Palmieri

Subjects
Male, Catheterization, Central Venous, medicine.medical_specialty, Time Factors, Cost-Benefit Analysis, medicine.medical_treatment, 030232 urology & nephrology, Pilot Projects, Drug Costs, law.invention, 03 medical and health sciences, Catheters, Indwelling, 0302 clinical medicine, Randomized controlled trial, Cost Savings, Renal Dialysis, Risk Factors, law, medicine, Central Venous Catheters, Humans, Prospective Studies, 030212 general & internal medicine, Prospective cohort study, Aged, Cross-Over Studies, business.industry, Chlorhexidine, Maintenance hemodialysis, Bandages, Crossover study, Catheter-Related Infections, Surgery, Treatment Outcome, Italy, Nephrology, Anti-Infective Agents, Local, Female, Hemodialysis, business, Central venous catheter, medicine.drug
Abstract

Introduction Catheter-related infections are an important clinical problem in maintenance hemodialysis patients. Catheter-related bloodstream infections have a negative effect on survival, hospitalization and cost of care. Tegaderm™ chlorhexidine gluconate (CHG) dressing may be useful to reduce catheter-related infection rates. Methods We performed a study to assess the efficacy of Tegaderm™ CHG dressing for reducing catheter-related infections. We designed a prospective randomized cross-over study with a scheme of two treatments, Tegaderm™ CHG dressing versus standard dressing, and two periods of six months. Catheter-related infection rate was the primary outcome. We enrolled 59 prevalent hemodialysis patients. Results Catheter-related infection rate per 1000 catheter days was reduced from 1.21 in patients using standard dressing to 0.28 in patients with Tegaderm™ CHG dressing (p = 0.02). Catheter-related bloodstream infection rate per 1000 catheter days was equal to 0.09 in patients with Tegaderm™ CHG dressing versus 0.65 in patients with standard dressing (p = 0.05). Annual total healthcare costs for catheter-related bloodstream infections were estimated equal to EUR62,459 versus EUR300,399, respectively, for patients with Tegaderm™ CHG versus standard dressing. Conclusions This is the first prospective study to show that Tegaderm™ CHG dressing significantly reduces catheter-related infection rates in hemodialysis patients.

Published
2016

34. Comparison of an injectable toltrazuril-gleptoferron (Forceris®) and an oral toltrazuril (Baycox®) + injectable iron dextran for the control of experimentally induced piglet cystoisosporosis

Author

Nicola Palmieri, Anja Joachim, Barbara Freudenschuss, Hamadi Karembe, Aruna Shrestha, Daniel Sperling, and Barbara Hinney

Subjects
Diarrhea, 0301 basic medicine, Drug-Related Side Effects and Adverse Reactions, Efficacy, Swine, Toltrazuril, animal diseases, Administration, Oral, Biology, lcsh:Infectious and parasitic diseases, Isospora suis, Excretion, 03 medical and health sciences, chemistry.chemical_compound, Animal science, Faecal consistency, medicine, Animals, lcsh:RC109-216, Experimental infection, Iron Dextran Complex, Feces, Swine Diseases, Pig, Coccidiosis, Triazines, Research, Body Weight, 030108 mycology & parasitology, medicine.disease, Diarrhoea, Treatment Outcome, Infectious Diseases, Animals, Newborn, chemistry, Sarcocystidae, Coccidiostats, Administration, Intravenous, Iron-Dextran Complex, Parasitology, Cystoisospora suis, medicine.symptom, Weight gain
Abstract

Background Cystoisospora suis causes diarrhoeal disease and reduced weight gain in suckling piglets, and a toltrazuril-based oral suspension is available for treatment. Recently a combinatorial product with toltrazuril plus iron has been developed for parenteral application. In this study we compared the efficacy of the injectable product with the oral suspension against experimentally induced piglet cystoisosporosis. Methods In a randomised controlled study, three groups of piglets (n = 10–13) were treated either with a fixed dose of 45 mg toltrazuril + 200 mg gleptoferron i.m. per piglet (Forceris®) on the second day of life (study day 2; SD 2) or with 20 mg toltrazuril/kg body weight as an oral suspension (Baycox® 5%) on SD 4 or left untreated (Control group). The Baycox® and the Control group received 200 mg of iron dextran/piglet on SD 2. All piglets were infected with 1000 sporulated C. suis oocysts on SD 3. Faecal samples were taken daily from SD 7 to SD 20 to determine faecal consistency, oocyst shedding and other diarrhoeal pathogens. Body weight was recorded on SD 1 and then weekly until SD 29. Animals were observed daily for general health and after treatment for possible adverse events. Results In the Control group all animals shed oocysts for 3.1 days on average and all animals showed diarrhoea for an average of five days. Excretion peaked on SD 9 (max. 48,618 oocysts per gram of faeces). Treatment with Forceris® completely suppressed oocyst excretion. In the Baycox® group, low levels of excretion could be detected. Diarrhoea was reduced to single piglets in the treated groups. Body weight development was reduced in the Control group compared to the treated groups. Enteropathogenic bacteria (Escherichia coli, Clostridium perfringens) could be detected. All parameters related to oocyst excretion, faecal consistency and weight gain were significantly improved in the treated groups compared to the Control group without significant differences between the treated groups. Both products were safe to use. Conclusions Treatment with both the injectable (Forceris®) and the oral (Baycox®) formulation of toltrazuril in the prepatent period were safe and highly effective against experimental infection with C. suis in newborn piglets.

Published
2018

35. Cloning, expression and molecular characterization of a Cystoisospora suis specific uncharacterized merozoite protein

Author

Ahmed Abd-Elfattah, Anja Joachim, Bärbel Ruttkowski, Nicola Palmieri, Aruna Shrestha, and Marc Pagès

Subjects
0301 basic medicine, DNA, Complementary, Swine, In silico, 030231 tropical medicine, Protozoan Proteins, Recombinant antigen, Immunofluorescence, Polymerase Chain Reaction, law.invention, Apicomplexa, Invasion inhibition, 03 medical and health sciences, 0302 clinical medicine, Eimeriidae, law, medicine, Animals, Coding region, Amino Acid Sequence, RNA, Messenger, Cloning, Molecular, Protozoa, Gene, Cloning, Expression vector, Base Sequence, medicine.diagnostic_test, biology, Merozoites, Research, DNA, Protozoan, biology.organism_classification, Virology, Molecular biology, 030104 developmental biology, Infectious Diseases, Gene Expression Regulation, Sporozoites, Recombinant DNA, Cystoisosporosis, Parasitology, RNA, Protozoan
Abstract

Background The genome of the apicomplexan parasite Cystoisospora suis (syn. Isospora suis) has recently been sequenced and annotated, opening the possibility for the identification of novel therapeutic targets against cystoisosporosis. It was previously proposed that a 42 kDa uncharacterized merozoite protein, encoded by gene CSUI_005805, might be a relevant vaccine candidate due to its high immunogenic score, high expression level and species-specificity as determined in silico. Methods The 1170 bp coding sequence of the CSUI_005805 gene was PCR amplified and cloned into the bacterial expression vector pQE-31. The specificity of the expressed recombinant protein was evaluated in an immunoblot, and relative levels of expression in different developmental stages and subcellular localization were determined by quantitative real-time PCR and indirect immunofluorescence assay, respectively. Results The CSUI_005805 gene encoded for a 389 amino acid protein containing a histidine-rich region. Quantitative RT-PCR showed that CSUI_005805 was differentially expressed during the early development of C. suis in vitro, with higher transcript levels in merozoites compared to sporozoites. The recombinant protein was specifically recognized by sera from chicken immunized with recombinant CSUI_005805 protein and sera from piglets experimentally infected with C. suis, all of which suggested that despite prokaryotic expression, the recombinant CSUI_005805 protein maintained antigenic determinants and could elicit an immune response in the host. Immunofluorescence labelling and confocal microscopy revealed localization primarily at the surface of the parasite. Conclusions The results suggest that CSUI_005805 is highly expressed in merozoites and might thus be critical for their survival and establishment inside host cells. Owing to its specificity, localization and expression pattern, CSUI_005805 could be exploited as an attractive candidate for alternative control strategies against C. suis such as vaccines. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2003-1) contains supplementary material, which is available to authorized users.

Published
2017

36. Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions

Author

Leif Andersson, Gottfried Brem, Markus Neuditschko, Julia Metzger, Robert J. Schaefer, Molly E. McCue, Tosso Leeb, Doris Rigler, Jens Tetens, Georg Thaller, Gabriella Lindgren, Thomas Druml, Stefan Rieder, Ruedi Fries, Ottmar Distl, Christian Schlötterer, Carl-Johan Rubin, Elif Bozlak, Vidhya Jagannathan, Claus Vogl, Barbara Wallner, and Nicola Palmieri

Subjects
0301 basic medicine, Male, Lineage (genetic), Biology, Turkoman horse, Y chromosome, General Biochemistry, Genetics and Molecular Biology, Haplogroup, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, Y Chromosome, Animals, Horses, Domestication, Genetics, 630 Agriculture, Haplotype, 0402 animal and dairy science, Horse, Genetic Variation, 04 agricultural and veterinary sciences, 040201 dairy & animal science, Pedigree, Europe, 030104 developmental biology, Haplotypes, Evolutionary biology, 570 Life sciences, biology, 590 Animals (Zoology), General Agricultural and Biological Sciences
Abstract

The Y chromosome directly reflects male genealogies, but the extremely low Y chromosome sequence diversity in horses has prevented the reconstruction of stallion genealogies [1, 2]. Here, we resolve the first Y chromosome genealogy of modern horses by screening 1.46 Mb of the male-specific region of the Y chromosome (MSY) in 52 horses from 21 breeds. Based on highly accurate pedigree data, we estimated the de novo mutation rate of the horse MSY and showed that various modern horse Y chromosome lineages split much later than the domestication of the species. Apart from few private northern European haplotypes, all modern horse breeds clustered together in a roughly 700-year-old haplogroup that was transmitted to Europe by the import of Oriental stallions. The Oriental horse group consisted of two major subclades: the Original Arabian lineage and the Turkoman horse lineage. We show that the English Thoroughbred MSY was derived from the Turkoman lineage and that English Thoroughbred sires are largely responsible for the predominance of this haplotype in modern horses.

Published
2017
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37. Cystoisospora suis - a model of mammalian cystoisosporosis

Author

Aruna Shrestha, Barbara Hinney, Barbara Freudenschuss, Ahmed Abd-Elfattah, Nicola Palmieri, Anja Joachim, and Bärbel Ruttkowski

Subjects
Cystoisospora, Swine, Mini Review, microbiome, Genomics, Disease, piglets, immunology, Immune system, Coccidia, medicine, microbiota, Parasite hosting, Microbiome, coccidian, lcsh:Veterinary medicine, General Veterinary, biology, biology.organism_classification, Diarrhea, Immunology, lcsh:SF600-1100, Veterinary Science, medicine.symptom, Cystoisospora suis
Abstract

Cystoisospora suis is a coccidian species that typically affects suckling piglets. Infections occur by oral uptake of oocysts and are characterized by non-hemorrhagic transient diarrhea resulting in poor weight gain. Apparently, primary immune responses to C. suis cannot readily be mounted by neonates which contributes to the establishment and rapid development of the parasite, while in older pigs age-resistance prevents disease development. However, the presence of extraintestinal stages, although not unequivocally demonstrated, is suspected to enable parasite persistence together with the induction and maintenance of immune response in older pigs, which in turn may facilitate the transfer of C. suis-specific factors from sow to offspring. It is assumed that neonates are particularly prone to clinical disease because infections with C. suis interfere with the establishment of the gut microbiome. Clostridia have been especially inferred to profit from the altered intestinal environment during parasite infection. New tools, particularly in the area of genomics, might illustrate the interactions between C. suis and its host and pave the way for the development of new control methods not only for porcine cystoisosporosis but also for other mammalian Cystoisospora infections. The first reference genome for C. suis is under way and will be a fertile ground to discover new drugs and vaccines. At the same time, the establishment and refinement of an in vivo model and an in vitro culture system, supporting the complete life cycle of C. suis, will underpin the functional characterization of the parasite and shed light on its biology and control. Keywords: swine, piglets, Cystoisospora suis, immunology, microbiome, coccidian

Published
2015

38. The life cycle of Drosophila orphan genes

Author

Carolin Kosiol, Christian Schlötterer, Nicola Palmieri, University of St Andrews. School of Biology, and University of St Andrews. Centre for Biological Diversity

Subjects
Male, 0106 biological sciences, QH301 Biology, pseudogenes, Genes, Insect, 01 natural sciences, Genome, gene gain, Biology (General), R2C, Genetics, D. pseudoobscura, 0303 health sciences, biology, General Neuroscience, A protein, General Medicine, Orphan gene, Medicine, Drosophila, Female, BDC, endocrine system, QH301-705.5, Pseudogene, Science, QH426 Genetics, 010603 evolutionary biology, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, sex-biased expression, 03 medical and health sciences, QH301, Animals, Quantitative Biology - Genomics, Gene, QH426, 030304 developmental biology, Sequence (medicine), Genomics (q-bio.GN), General Immunology and Microbiology, gene loss, biology.organism_classification, FOS: Biological sciences, evolutionary rate, Minimal genome, Gene Deletion
Abstract

Orphans are genes restricted to a single phylogenetic lineage and emerge at high rates. While this predicts an accumulation of genes, the gene number has remained remarkably constant through evolution. This paradox has not yet been resolved. Because orphan genes have been mainly analyzed over long evolutionary time scales, orphan loss has remained unexplored. Here we study the patterns of orphan turnover among close relatives in the Drosophila obscura group. We show that orphans are not only emerging at a high rate, but that they are also rapidly lost. Interestingly, recently emerged orphans are more likely to be lost than older ones. Furthermore, highly expressed orphans with a strong male-bias are more likely to be retained. Since both lost and retained orphans show similar evolutionary signatures of functional conservation, we propose that orphan loss is not driven by high rates of sequence evolution, but reflects lineage specific functional requirements., Comment: 47 pages, 19 figures

Published
2014

40. FO027TEGADERM CHG® DRESSING SIGNIFICANTLY IMPROVES CATHETER RELATED INFECTIONS RATE IN HEMODIALYSIS PATIENTS

Author

Oscar Bracchi, Francesca Colombo, Ferruccio Conte, Karen Amar, Irene Brenna, Marco Righetti, Francesca Stefani, Nicola Palmieri, Alfio Scalia, Mario Prencipe, and Elena Bruschetta

Subjects
Transplantation, medicine.medical_specialty, Nephrology, business.industry, medicine.medical_treatment, medicine, Hemodialysis, business, Catheter-Related Infections, Surgery
Published
2015

41. Estimating the population mutation rate from a de novo assembled Bactrian camel genome and cross-species comparison with dromedary ESTs

Author

Pamela A, Burger and Nicola, Palmieri

Subjects
Expressed Sequence Tags, Male, endocrine system, Comparative Genomic Hybridization, Camelus, Genome, Sequence Analysis, DNA, comparative genomics, single-nucleotide polymorphism, camelidae, nucleotide diversity, Polymorphism, Single Nucleotide, Contig Mapping, Genetics, Population, Mutation Rate, Species Specificity, whole-genome sequencing, Animals, Domestic, Animals, Symposium Article
Abstract

The Bactrian camel (Camelus bactrianus) and the dromedary (Camelus dromedarius) are among the last species that have been domesticated around 3000–6000 years ago. During domestication, strong artificial (anthropogenic) selection has shaped the livestock, creating a huge amount of phenotypes and breeds. Hence, domestic animals represent a unique resource to understand the genetic basis of phenotypic variation and adaptation. Similar to its late domestication history, the Bactrian camel is also among the last livestock animals to have its genome sequenced and deciphered. As no genomic data have been available until recently, we generated a de novo assembly by shotgun sequencing of a single male Bactrian camel. We obtained 1.6 Gb genomic sequences, which correspond to more than half of the Bactrian camel’s genome. The aim of this study was to identify heterozygous single-nucleotide polymorphisms (SNPs) and to estimate population parameters and nucleotide diversity based on an individual camel. With an average 6.6-fold coverage, we detected over 116 000 heterozygous SNPs and recorded a genome-wide nucleotide diversity similar to that of other domesticated ungulates. More than 20 000 (85%) dromedary expressed sequence tags successfully aligned to our genomic draft. Our results provide a template for future association studies targeting economically relevant traits and to identify changes underlying the process of camel domestication and environmental adaptation.

Published
2013

42. MP657INTRADIALYTIC PARENTERAL NUTRITION AS FIRST CHOICE TREATMENT IN PROTEIN-ENERGY WASTING HEMODIALYSIS PATIENTS

Author

Francesca Stefani, Alfio Scalia, Mario Prencipe, Antonella Di Giacomo, Ferruccio Conte, Nicola Palmieri, Marco Righetti, Oscar Bracchi, and Karen Amar

Subjects
Transplantation, medicine.medical_specialty, Parenteral nutrition, Nephrology, business.industry, medicine.medical_treatment, Medicine, Protein energy wasting, Hemodialysis, business, Intensive care medicine
Published
2016

43. Evaluation of Different Reference Based Annotation Strategies Using RNA-Seq – A Case Study in Drososphila pseudoobscura

Author

Christian Schlötterer, Nicola Palmieri, Viola Nolte, Anton Suvorov, and Carolin Kosiol

Subjects
Sequence analysis, 0206 medical engineering, lcsh:Medicine, 02 engineering and technology, Computational biology, Genome, Transcriptomes, Drosophila pseudoobscura, 03 medical and health sciences, Annotation, Genome Analysis Tools, Animals, FlyBase : A Database of Drosophila Genes & Genomes, lcsh:Science, Gene Prediction, Biology, 030304 developmental biology, Genetics, 0303 health sciences, Expressed sequence tag, Multidisciplinary, Sequence Assembly Tools, biology, Software Tools, Sequence Analysis, RNA, Gene Ontologies, lcsh:R, Intron, Computational Biology, Software Engineering, Genome project, Genomics, Genome Scans, biology.organism_classification, Computer Science, RNA, lcsh:Q, Drosophila, Sequence Analysis, Zoology, Entomology, 020602 bioinformatics, Research Article
Abstract

RNA-Seq is a powerful tool for the annotation of genomes, in particular for the identification of isoforms and UTRs. Nevertheless, several software tools exist and no standard strategy to obtain a reliable annotation is yet established. We tested different combinations of the most commonly used reference-based alignment tools (TopHat, GSNAP) in combination with two frequently used reference-based assemblers (Cufflinks, Scripture) and evaluated the potential of RNA-Seq to improve the annotation of Drosophila pseudoobscura. While GSNAP maps a higher proportion of reads, TopHat resulted in a more accurate annotation when used in combination with Cufflinks. Scripture had the lowest sensitivity. Interestingly, after subsampling to the same coverage for GSNAP and TopHat, we find that both mappers have similar performance, implying that the advantage of TopHat is mainly an artifact of the lower coverage. Overall, we observed a low concordance among the different approaches tested both at junction and isoform levels. Using data from both sexes of two adult strains of D. pseudoobscura we detected alternative splicing for about 30% of the FlyBase multiple-exon genes. Moreover, we extended the boundaries for 6523 genes (about 40%). We annotated 669 new genes, 45% of them with splicing evidence. Most of the new genes are located on unassembled contigs, reflecting their incomplete annotation. Finally, we identified 99 additional new genes that are not represented in the current genome contigs of D. pseudoobscura, probably due to location in genomic regions that are difficult to assemble (e.g. heterochromatic regions).

Published
2012

44. Exploring the gonad transcriptome of two extreme male pigs with RNA-seq

Author

Robert Kofler, Miguel Pérez-Enciso, Giovanni Bussotti, Nicola Palmieri, Anna Esteve-Codina, Cedric Notredame, Ministerio de Educación (España), Ministerio de Ciencia e Innovación (España), CSIC-IRTA-UAB-UB - Centre de Recerca Agrigenómica (CRAG), European Commission, La Caixa, and Austrian Science Fund

Subjects
Male, lcsh:QH426-470, Swine, lcsh:Biotechnology, RNA-Seq, Biology, Polymorphism, Single Nucleotide, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, lcsh:TP248.13-248.65, Testis, Gene expression, Genetics, Animals, Spermatogenesis, Gene, Gene Library, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, 0303 health sciences, Sequence Analysis, RNA, Gene Expression Profiling, Chromosome Mapping, RNA, Lipid Metabolism, Phenotype, Gene expression profiling, lcsh:Genetics, DNA microarray, 030217 neurology & neurosurgery, Research Article, Biotechnology
Abstract

[Background]: Although RNA-seq greatly advances our understanding of complex transcriptome landscapes, such as those found in mammals, complete RNA-seq studies in livestock and in particular in the pig are still lacking. Here, we used high-throughput RNA sequencing to gain insight into the characterization of the poly-A RNA fraction expressed in pig male gonads. An expression analysis comparing different mapping approaches and detection of allele specific expression is also discussed in this study., [Results]: By sequencing testicle mRNA of two phenotypically extreme pigs, one Iberian and one Large White, we identified hundreds of unannotated protein-coding genes (PcGs) in intergenic regions, some of them presenting orthology with closely related species. Interestingly, we also detected 2047 putative long non-coding RNA (lncRNA), including 469 with human homologues. Two methods, DEGseq and Cufflinks, were used for analyzing expression. DEGseq identified 15% less expressed genes than Cufflinks, because DEGseq utilizes only unambiguously mapped reads. Moreover, a large fraction of the transcriptome is made up of transposable elements (14500 elements encountered), as has been reported in previous studies. Gene expression results between microarray and RNA-seq technologies were relatively well correlated (r = 0.71 across individuals). Differentially expressed genes between Large White and Iberian showed a significant overrepresentation of gamete production and lipid metabolism gene ontology categories. Finally, allelic imbalance was detected in ~ 4% of heterozygous sites., [Conclusions]: RNA-seq is a powerful tool to gain insight into complex transcriptomes. In addition to uncovering many unnanotated genes, our study allowed us to determine that a considerable fraction is made up of long non-coding transcripts and transposable elements. Their biological roles remain to be determined in future studies. In terms of differences in expression between Large White and Iberian pigs, these were largest for genes involved in spermatogenesis and lipid metabolism, which is consistent with phenotypic extreme differences in prolificacy and fat deposition between these two breeds., AEC is recipient of a FPI PhD fellowship from Ministry of Education, Spain. Work funded by AGL2010-14822 grant to MPE and by a Consolider grant from Spanish Ministry of Research, CSD2007-00036 "Centre for Research in Agrigenomics". RK and NP were supported by the FWF grant P19467 awarded to C. Schlötterer. CN and GB were co-funded by the Plan Nacional BFU2008-00419, the European Commission, within the 7th Framework Programme, Grant Agreement KBBE-2A-222664 ("Quantomics"), the La Caixa PhD program and the Centre de Regulació Genomica.

Published
2011

45. Epidemiology and outcome - 2

Author

Peter Bárány, F. Lladós, Gisela Sturm, Andrea Remuzzi, Brenda W. Gillespie, John L. Griffith, Abdul Rashid Qureshi, Heinz Jürgen Roth, Peter Stenvinkel, H.C. Rayner, Glenn M. Chertow, Anna Bednarek, Tiziana Di Paolantonio, Patricia de Sequera, Simona Hogas, Ray Krediet, J.A. Kellum, Piero Ruggenenti, F. Nurhan Ozdemir, Maria Concetta Vaccaro, Hiroko Inagaki, Ausilia Maione, Hal Morgenstern, Paolo Parini, Asta Auerbach, Jana Smrzova, Muhammad Shahed Ahmed, Daniel Rajdl, Mônica Viegas Andrade, Emanuel Zitt, Karen Amar, Véronique Joyeux, L. Weissfeld, Cacia Mendes Matos, David M. Kent, Marta Lugo, Marit Jordhoy, A. Martín-Malo, Odilon Vanni de Queiroz, Márcia Tereza Silva Martins, Maurice Alan Brookhart, Navdeep Tangri, A. Casula, Maria Luisa Lozano, Francesco Locatelli, Ursula Caceres, Jorgen Hegbrant, Shouichi Fujimoto, Antonio Nicolucci, Dulce Nicolas, K. Pitcher, Matthew Howse, Isabel Cristina Gomes, X. Cuevas, Nathan W. Levin, J. Fort, Antonio Piccoli, Shigehiro Uezono, Mark R. Marshall, Gordon Prescott, F.K. Port, Keith Simpson, Tomislav Bozek, Taina Lara Campos Cordeiro Valadares, Günter Edenharter, Toril Dammen, Kellie Hunter Campbell, Fabio Pellegrini, J. Lozano, Catherine Vérove, Jennifer Ennis, Claudia Barth, Mostapha Elallam, Michal Vostry, M. Unruh, Jaroslav Racek, Nistor Ionut, Nicole Stankus, Jaromír Eiselt, Milan Petrovic, Bolesław Rutkowski, lle Pechter, Cécile Couchoud, D.J. de Jager, Paul M. Just, R. Pérez-García, Yoav Ben-Shlomo, Lucia Guidotti, Karl Lhotta, Nicola Palmieri, Graciela Voronovitsky, William Dale, Merike Luman, Christoph Wanner, B.M. Robinson, Daniel Resende Faleiros, Paul Stroumza, Robert Mactier, C. Argyropoulos, Ognjenka Djurdjev, Kevan R. Polkinghorne, Juan Nin Ferrari, Bruce G. Robinson, Gelfman Ruben, Naoko Ikeda, Elviira Seppet, David Ansell, Marion Verduijn, Kirsten Haas, Bengt Lindholm, Jan Dulawa, Marcello Tonelli, Olof Heimbürger, E.W. Boeschoten, Juan Jesus Carrero, Adeera Levin, Dina Montasser, Gildete Barreto Lopes, Omar Maoujoud, Agostino Naso, Luminita Voroneanu, Paul Gusbeth-Tatomir, Brian D. Bradbury, Seema Sondhi, Margit Muliin, Valjbona Prelevic, Pierre Donnadieu, Giovanni F.M. Strippoli, Diana C. Grootendorst, Ingrid Os, Bogdan Ene-Iordache, Lada Malanova, Sergio Carminati, Keiko Kodama, J. Gilg, Mario Plebani, Inga Mandac, Sebnem Karakan, Pajica Pavkovic, Seiichiro Hara, Pedro Trinidad, Olga Sergeyeva, Oscar Bracchi, Yassir Zajari, Mohammed Hassani, Jonathan Bazeley, F. Tentori, Hans-Jürgen Schober-Halstenberg, Inger Hilde Nordhus, Mathilde Lassalle, Akira Saito, Marietta Torok, Ingrid Prkacin, Külli Kõlvald, Valjbona Preljevic, Yun Li, Martin Wagner, Ulrich Neyer, Elisabeth Reiss, Alberto Menegotto, Hannelore Sprenger-Mähr, Siiri Mesikepp, Vidojko Djordjevic, Marianna Zsom, Luis Espejo, Siren Sezer, Friedrich K. Port, Naser Tayebi, Mohammed Alayoud, Antonio Alberto Lopes, Simon Sawhney, Ruben Lopez, Augusto Afonso Guerra Junior, R.L. Pisoni, Stephen McDonald, Abdelali Bahadi, Shunichi Fukuhara, Gero von Gersdorff, Bruno Saligari, Zouhir Oualim, Alexandra Kitazawa, Marinella Ruospo, Mohammed Asseraji, Jorge Velez, Mathias Schaller, Lin Tong, Cesar Cruzalegui, Stevan Glogovac, Monserrat Morales, Peter C. Thomson, Alison M. MacLeod, M. Heaton, Nicola D'Ambrosio, Felipe Vazquez, A. Hodsman, Michał Chmielewski, F.W. Dekker, David R. Walker, Ronald L. Pisoni, H. Morgenstern, Martin Gomez, Charles R.V. Tomson, Letizia Gargano, Jamie P. Traynor, Anca Seica, Len A. Usvyat, Michela Sciancalepore, Jun Liu, Rolfdieter Krause, Francisco de Assis Acurcio, M.J. Blayney, M.E. Roumelioti, J. Davies, Bénédicte Stengel, Emmanuel Villar, Alan M. Brookhart, Carolyn Hunter, Catherine Wall, Tone Hortemo sthus, Adrian Covic, Michel Labeeuw, Peter Kotanko, Marco Murgo, P.G. Kerr, Stefan Arver, Moncef Kadiri, Giuseppe Remuzzi, Bertha Martinez, Ulrich Frei, Maria Lucia Sambati, R.T. Krediet, Paul Roderick, Y.Z. Shah, Florian Kronenberg, Taoufiq Aatif, Madis Ilmoja, Liliana Pinelli, Luc Frimat, Giovanni Cancarini, Ferruccio Conte, Wolfgang C. Winkelmayer, F. García, Rinaldo Di Toro Mammarella, Ronan Cunningham, Ermelinda Santiago, Giuseppe Accogli, Luciana Gravellone, Carmen Bonifati, Mihai Onofriescu, Eli Iola Gurgel Andrade, Friederike Lins, Els Boeschoten, A. Cheung, Michel Jadoul, Elaheh Dashti, Dolapo Ayansina, Monica Maria Mion, Edoardo Celia, Julio Gomez, Aleksander Lõhmus, Inger K. Laegreid, Eberechi Sandra Agwa, Ladislav Trefil, Friedo W. Dekker, Anna Casula, Austin G. Stack, Norberto Perico, Brian Bieber, George Mellotte, Mai Rosenberg, Hoang Nguyen, Conrad A. Baldamus, Daniele Araújo Campos Szuster, Abbas Ali Zeraati, Marta Codognotto, Tomáš Urbánek, Otto Freistätter, Alessandra Maciel Almeida, Massih Naghibi, and Stephan Thijssen

Subjects
03 medical and health sciences, Transplantation, medicine.medical_specialty, 0302 clinical medicine, Nephrology, business.industry, Epidemiology, 030232 urology & nephrology, medicine, Intensive care medicine, business, Outcome (game theory)
Published
2009

46. 220 kV Cable Connection in Rome

Author

Pietro Calzolari, Franco Bellucci, Nicola Palmieri, and Giuseppe Bazzi

Subjects
Engineering, Electric power transmission, business.industry, General Engineering, Electrical engineering, Energy Engineering and Power Technology, Electric power, Electrical and Electronic Engineering, business, Electrical conductor, Connection (mathematics), Conductor, Voltage
Abstract

The constantly increasing demand for electric power supply made it necessary to provide with 220 kV voltage feeding two substations in the city of Rome; the connection was obtained by an oil- filled cable-line of a total length of 22 km and conductor cross-section of-1000 to 1800 mm2.

Published
1972

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