25 Works

Dataset for: Molecular diversity of dragonflies in high altitude Andean lakes through DNA barcoding

Alonzo Alfaro-Núñez, Rodrigo Chiriboga-Ortega, Christine Van Der Heyden, Maria Eugenia Sulen Burgos, Sania Ortega, Tania Oña, Elizabeth Velarde & Peter Goethals
Genetic and morphological identification of dragonflies’ larvae species in three high elevation Andean tropical lakes was done using DNA barcoding of the cytochrome oxidase 1 gene (COI). Phylogeny allowed inferring the evolutionary relationships of at least 5 species (from 74 samples) that belong to two different families within the Odonata order.

Additional file 1 of Multi-omics to predict changes during cold pressor test

Lisette J. A. Kogelman, Madeleine Ernst, Katrine Falkenberg, Gianluca Mazzoni, Julie Courraud, Li Peng Lundgren, Susan Svane Laursen, Arieh Cohen, Jes Olesen & Thomas Folkmann Hansen
Additional file 1. Annotation of identified metabolites.

Data from: Re-examination of species limits in Aspergillus section Flavipedes using advanced species delimitation methods and description of four new species

František Sklenář, Željko Jurjević, Jos Houbraken, Miroslav Kolařík, Maiken Cavling Arendrup, Karin Meinike Jørgensen, Joao Paulo Zen Siqueira, Josepa Gené, Takashi Yaguchi, Chibundu Ngozi Ezekiel, Cristina Silva Pereira & Vít Hubka
Since the last revision in 2015, the taxonomy of section Flavipedes evolved rapidly along with the availability of new species delimitation techniques. This study aims to re-evaluate the species boundaries of section Flavipedes members using modern delimitation methods applied to an extended set of strains (n=90) collected from various environments. The analysis used DNA sequences of three house-keeping genes (benA, CaM, RPB2) and consisted of two steps: application of several single-locus (GMYC, bGMYC, PTP, bPTP)...

Additional file 2 of A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)

Jacob Agerbo Rasmussen, Kasper Rømer Villumsen, Madeleine Ernst, Martin Hansen, Torunn Forberg, Shyam Gopalakrishnan, M. Thomas P. Gilbert, Anders Miki Bojesen, Karsten Kristiansen & Morten Tønsberg Limborg
Additional file 1 Supplementary information.

A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)

Jacob Agerbo Rasmussen, Kasper Rømer Villumsen, Madeleine Ernst, Martin Hansen, Torunn Forberg, Shyam Gopalakrishnan, M. Thomas P. Gilbert, Anders Miki Bojesen, Karsten Kristiansen & Morten Tønsberg Limborg
Abstract Background Animal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. Here, we investigate the functional effects of bacteria-based pro- and synbiotic feed additives on microbiome-associated functions in relation to growth performance in the commercially important rainbow trout (Oncorhynchus mykiss). We combine complementary insights from multiple omics datasets from gut content samples, including 16S bacterial profiling, whole...

Additional file 1 of Multi-omics to predict changes during cold pressor test

Lisette J. A. Kogelman, Madeleine Ernst, Katrine Falkenberg, Gianluca Mazzoni, Julie Courraud, Li Peng Lundgren, Susan Svane Laursen, Arieh Cohen, Jes Olesen & Thomas Folkmann Hansen
Additional file 1. Annotation of identified metabolites.

Data from: Unravelling the immune signature of Plasmodium falciparum transmission-reducing immunity

Will J. R. Stone, Joseph J. Campo, André Lin Ouédraogo, Lisette Meerstein-Kessel, Isabelle Morlais, Dari Da, Anna Cohuet, Sandrine Nsango, Colin J. Sutherland, Marga Van De Vegte-Bolmer, Rianne Siebelink-Stoter, Geert-Jan Van Gemert, Wouter Graumans, Kjerstin Lanke, Adam D. Shandling, Jozelyn V. Pablo, Andy A. Teng, Sophie Jones, Roos M. De Jong, Amanda Fabra-García, John Bradley, Will Roeffen, Edwin Lasonder, Giuliana Gremo, Evelin Schwarzer … & Matthijs M. Jore
Infection with Plasmodium can elicit antibodies that inhibit parasite survival in the mosquito, when they are ingested in an infectious blood meal. Here, we determine the transmission-reducing activity (TRA) of naturally acquired antibodies from 648 malaria-exposed individuals using lab-based mosquito-feeding assays. Transmission inhibition is significantly associated with antibody responses to Pfs48/45, Pfs230, and to 43 novel gametocyte proteins assessed by protein microarray. In field-based mosquito-feeding assays the likelihood and rate of mosquito infection are significantly...

Data from: Nationwide prevalence and incidence study of neuromyelitis optica spectrum disorder in Denmark

Viktoria Papp, Zsolt Illes, Melinda Magyari, Nils Koch-Henriksen, Matthias Kant, Claudia Christina Pfleger, Shanu Faerch Roemer, Michael Broksgaard Jensen, Annett Evelyn Petersen, Helle Hvilsted Nielsen, Lene Rosendahl, Zsolt Mezei, Tove Christensen, Kristina Svendsen, Poul Erik Hyldgaard Jensen, Magnus Christian Lydolph, Niels Heegaard, Jette Lautrup Frederiksen, Finn Thorup Sellebjerg, Egon Stenager & Thor Petersen
Objectives: To estimate the nationwide population-based incidence, prevalence, and geographical distribution of neuromyelitis optica spectrum disorder in Denmark based on the 2015 International Panel for NMO Diagnosis (IPND) criteria Methods: We conducted a multicentre, historically prospective study. Data were sourced from the Danish National Patient Registry, the Danish Multiple Sclerosis Registry, departments of neurology and laboratories providing aquaporin 4 (AQP4) antibody test. Cases were selected based on the 2006 Wingerchuk and the 2015 IPND criteria...

Additional file 4 of A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)

Jacob Agerbo Rasmussen, Kasper Rømer Villumsen, Madeleine Ernst, Martin Hansen, Torunn Forberg, Shyam Gopalakrishnan, M. Thomas P. Gilbert, Anders Miki Bojesen, Karsten Kristiansen & Morten Tønsberg Limborg
Additional file 3

Multi-omics to predict changes during cold pressor test

Lisette J. A. Kogelman, Madeleine Ernst, Katrine Falkenberg, Gianluca Mazzoni, Julie Courraud, Li Peng Lundgren, Susan Svane Laursen, Arieh Cohen, Jes Olesen & Thomas Folkmann Hansen
Abstract Background The cold pressor test (CPT) is a widely used pain provocation test to investigate both pain tolerance and cardiovascular responses. We hypothesize, that performing multi-omic analyses during CPT gives the opportunity to home in on molecular mechanisms involved. Twenty-two females were phenotypically assessed before and after a CPT, and blood samples were taken. RNA-Sequencing, steroid profiling and untargeted metabolomics were performed. Each ‘omic level was analyzed separately at both single-feature and systems-level (principal...

Data from: Progressive genome-wide introgression in agricultural Campylobacter coli

Samuel K. Sheppard, Xavier Didelot, Keith A. Jolley, Aaron E. Darling, David J. Kelly, Alison Cody, Frances M. Colles, Norval J.C. Strachan, Iain D. Ogden, Ken Forbes, Nigel P. French, Philip Carter, William G. Miller, Noel D. McCarthy, Robert Owen, Eva Litrup, Michael Egholm, Stephen D. Bentley, Julian Parkhill, Martin C. J. Maiden, Daniel Falush, Jason P. Affourtit, Norval J. C. Strachan, Ben Pascoe & Guillaume Meric
Hybridization between distantly related organisms can facilitate rapid adaptation to novel environments, but is potentially constrained by epistatic fitness interactions among cell components. The zoonotic pathogens Campylobacter coli and C. jejuni differ from each other by around 15% at the nucleotide level, corresponding to an average of nearly 40 amino acids per protein-coding gene. Using whole genome sequencing, we show that a single C. coli lineage, which has successfully colonized an agricultural niche, has been...

Blastocystis SSU rRNA alignment

Zuzana Lhotská, Milan Jirků, Oldřiška Hložková, Kristýna Brožová, Dagmar Jirsová, Dagmar Jirsová, C. Rune Stensvold, Martin Kolísko & Kateřina Jirků Pomajbíková
Blastocystis is a cosmopolitan protist inhabiting the human intestine; which prevalence varies between non-industrial and industrialized countries. Its role in the human gut ecosystem remains unclear due to persisting gaps in knowledge of epidemiology and factors affecting gut colonization. The aim of this study was therefore to expand the knowledge of the epidemiology of Blastocystis in the gut-healthy humans in one of the industrialized European countries, including the distribution of its subtypes, the correlation between...

Data from: Relevance of heterokaryosis for adaptation and azole-resistance development in Aspergillus fumigatus

Jianhua Zhang, Eveline E. Snelders, Bas J. Zwaan, Sijmen E. Schoustra, Ed J. Kuijper, Maiken C. Arendrup, Willem J.G. Melchers, Paul E. Verweij, Alfons J.M. Debets & Alfons J. M. Debets
Aspergillus fumigatus causes a range of diseases in humans, some of which are characterized by fungal persistence. A. fumigatus, being a generalist saprotroph, may initially establish lung colonisation due to its physiological versatility and subsequently adapt through genetic changes to the human lung environment and antifungal treatments. Human lung-adapted genotypes can arise by spontaneous mutation and/or recombination and subsequent selection of the fittest genotypes. Sexual and asexual spores are considered crucial contributors to the genetic...

Additional file 2 of A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)

Jacob Agerbo Rasmussen, Kasper Rømer Villumsen, Madeleine Ernst, Martin Hansen, Torunn Forberg, Shyam Gopalakrishnan, M. Thomas P. Gilbert, Anders Miki Bojesen, Karsten Kristiansen & Morten Tønsberg Limborg
Additional file 1 Supplementary information.

Additional file 3 of A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)

Jacob Agerbo Rasmussen, Kasper Rømer Villumsen, Madeleine Ernst, Martin Hansen, Torunn Forberg, Shyam Gopalakrishnan, M. Thomas P. Gilbert, Anders Miki Bojesen, Karsten Kristiansen & Morten Tønsberg Limborg
Additional file 2

Additional file 4 of A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)

Jacob Agerbo Rasmussen, Kasper Rømer Villumsen, Madeleine Ernst, Martin Hansen, Torunn Forberg, Shyam Gopalakrishnan, M. Thomas P. Gilbert, Anders Miki Bojesen, Karsten Kristiansen & Morten Tønsberg Limborg
Additional file 3

Cardiovascular risk factors, radiation therapy, and myocardial infarction among lymphoma survivors

Talya Salz, Emily C. Zabor, Peter De Nully Brown, Susanne Oksbjerg Dalton, Nirupa J. Raghunathan, Matthew J. Matasar, Richard Steingart, Henrik Hjalgrim, Lena Specht, Andrew J. Vickers, Kevin C. Oeffinger & Christoffer Johansen
Mediastinal radiation is associated with increased risk of myocardial infarction (MI) among non-Hodgkin lymphoma (NHL) survivors. To evaluate how preexisting cardiovascular risk factors (CVRFs) modify the association of mediastinal radiation and MI among a national population of NHL survivors with a range of CVRFs. Using Danish registries, we identified adults diagnosed with lymphoma 2000–2010. We assessed MI from one year after diagnosis through 2016. We ascertained CVRFs (hypertension, dyslipidemia, and diabetes), vascular disease, and intrinsic...

Data from: Safety and immunogenicity of H1/IC31®, an adjuvanted TB subunit vaccine, in HIV-infected adults with CD4+ Lymphocyte counts greater than 350 cells/mm3: a phase II, multi-centre, double-blind, randomized, placebo-controlled trial

Klaus Reither, Lynn Katsoulis, Trevor Beattie, Nicolene Gardiner, Nicole Lenz, Khadija Said, Elirehema Mfinanga, Christian Pohl, Katherine L. Fielding, Hannah Jeffery, Benjamin M. Kagina, Elisabeth J. Hughes, Thomas J. Scriba, Willem A. Hanekom, Søren T. Hoff, Peter Bang, Ingrid Kromann, Claudia Daubenberger, Peter Andersen & Gavin J. Churchyard
Background: Novel tuberculosis vaccines should be safe, immunogenic, and effective in various population groups, including HIV-infected individuals. In this phase II multi-centre, double-blind, placebo-controlled trial, the safety and immunogenicity of the novel H1/IC31 vaccine, a fusion protein of Ag85B-ESAT-6 (H1) formulated with the adjuvant IC31, was evaluated in HIV-infected adults. Methods: HIV-infected adults with CD4+ T cell counts >350/mm3 and without evidence of active tuberculosis were enrolled and followed until day 182. H1/IC31 vaccine or...

Data from: Polyphasic data support the splitting of Aspergillus candidus into two species; proposal of Aspergillus dobrogensis sp. nov.

Vit Hubka, Alena Nováková, Željko Jurjević, František Sklenář, Jens C. Frisvad, Jos Houbraken, Maiken C. Arendrup, João P. Z. Siqueira, Josepa Gené & Miroslav Kolařík
Aspergillus candidus is a species frequently isolated from stored grain, food, indoor environments, soil and occasionally also from clinical material. Recent bioprospecting studies highlighted the potential of using A. candidus and its relatives in various industrial sectors as a result of their significant production of enzymes and bioactive compounds. A high genetic variability was observed among A. candidus isolates originating from various European countries and the USA, that were mostly isolated from indoor environments, caves...

Additional file 3 of A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)

Jacob Agerbo Rasmussen, Kasper Rømer Villumsen, Madeleine Ernst, Martin Hansen, Torunn Forberg, Shyam Gopalakrishnan, M. Thomas P. Gilbert, Anders Miki Bojesen, Karsten Kristiansen & Morten Tønsberg Limborg
Additional file 2

A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)

Jacob Agerbo Rasmussen, Kasper Rømer Villumsen, Madeleine Ernst, Martin Hansen, Torunn Forberg, Shyam Gopalakrishnan, M. Thomas P. Gilbert, Anders Miki Bojesen, Karsten Kristiansen & Morten Tønsberg Limborg
Abstract Background Animal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. Here, we investigate the functional effects of bacteria-based pro- and synbiotic feed additives on microbiome-associated functions in relation to growth performance in the commercially important rainbow trout (Oncorhynchus mykiss). We combine complementary insights from multiple omics datasets from gut content samples, including 16S bacterial profiling, whole...

Tyra Grove Krause: »Svært ved at se, at vi får ny og alvorlig coronavirus-variant«

Tyra Grove Krause

Cardiovascular risk factors, radiation therapy, and myocardial infarction among lymphoma survivors

Talya Salz, Emily C. Zabor, Peter De Nully Brown, Susanne Oksbjerg Dalton, Nirupa J. Raghunathan, Matthew J. Matasar, Richard Steingart, Henrik Hjalgrim, Lena Specht, Andrew J. Vickers, Kevin C. Oeffinger & Christoffer Johansen
Mediastinal radiation is associated with increased risk of myocardial infarction (MI) among non-Hodgkin lymphoma (NHL) survivors. To evaluate how preexisting cardiovascular risk factors (CVRFs) modify the association of mediastinal radiation and MI among a national population of NHL survivors with a range of CVRFs. Using Danish registries, we identified adults diagnosed with lymphoma 2000–2010. We assessed MI from one year after diagnosis through 2016. We ascertained CVRFs (hypertension, dyslipidemia, and diabetes), vascular disease, and intrinsic...

Forskere forklarer: Derfor er re-vaccination effektiv

Mie Gram, Hanne-Dorthe Emborg, Astrid Blicher Schelde, Katrine Finderup Nielsen, palle valentiner-branth & Christian Holm Hansen

Multi-omics to predict changes during cold pressor test

Lisette J. A. Kogelman, Madeleine Ernst, Katrine Falkenberg, Gianluca Mazzoni, Julie Courraud, Li Peng Lundgren, Susan Svane Laursen, Arieh Cohen, Jes Olesen & Thomas Folkmann Hansen
Abstract Background The cold pressor test (CPT) is a widely used pain provocation test to investigate both pain tolerance and cardiovascular responses. We hypothesize, that performing multi-omic analyses during CPT gives the opportunity to home in on molecular mechanisms involved. Twenty-two females were phenotypically assessed before and after a CPT, and blood samples were taken. RNA-Sequencing, steroid profiling and untargeted metabolomics were performed. Each ‘omic level was analyzed separately at both single-feature and systems-level (principal...

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