29 Works

Data from: Opposing effects of allogrooming on disease transmission in ant societies

Fabian J. Theis, Line V. Ugelvig, Carsten Marr & Sylvia Cremer
To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system...

Additional file 4 of H3K18 lactylation marks tissue-specific active enhancers

Eva Galle, Chee-Wai Wong, Adhideb Ghosh, Thibaut Desgeorges, Kate Melrose, Laura C. Hinte, Daniel Castellano-Castillo, Magdalena Engl, Joao Agostinho de Sousa, Francisco Javier Ruiz-Ojeda, Katrien De Bock, Jonatan R. Ruiz & Ferdinand von Meyenn
Additional file 4: Table S2: Genes whose promoters lie in state 8 from the mouse H3K18la ChromHMM. Data used in Fig. 2E.

Acute radiation syndrome-related gene expression in irradiated peripheral blood cell populations

Patrick Ostheim, Alan Don Mallawaratchy, Thomas Müller, Simone Schüle, Cornelius Hermann, Tanja Popp, Stefan Eder, Stephanie E. Combs, Matthias Port & Michael Abend
In a nuclear or radiological event, an early diagnostic tool is needed to distinguish the worried well from those individuals who may later develop life-threatenFing hematologic acute radiation syndrome. We examined the contribution of the peripheral blood's cell populations on radiation-induced gene expression (GE) changes. EDTA-whole-blood from six healthy donors was X-irradiated with 0 and 4Gy and T-lymphocytes, B-lymphocytes, NK-cells and granulocytes were separated using immunomagnetic methods. GE were examined in cell populations and whole...

Additional file 3 of H3K18 lactylation marks tissue-specific active enhancers

Eva Galle, Chee-Wai Wong, Adhideb Ghosh, Thibaut Desgeorges, Kate Melrose, Laura C. Hinte, Daniel Castellano-Castillo, Magdalena Engl, Joao Agostinho de Sousa, Francisco Javier Ruiz-Ojeda, Katrien De Bock, Jonatan R. Ruiz & Ferdinand von Meyenn
Additional file 3: Table S1: Quality Control metrics. For each sample included in this study, the following data is provided: tissue of origin, hPTM profiled, biological replicate, reads (million), GC content (%), aligned fraction of reads (%), number of called peaks.

Additional file 5 of H3K18 lactylation marks tissue-specific active enhancers

Eva Galle, Chee-Wai Wong, Adhideb Ghosh, Thibaut Desgeorges, Kate Melrose, Laura C. Hinte, Daniel Castellano-Castillo, Magdalena Engl, Joao Agostinho de Sousa, Francisco Javier Ruiz-Ojeda, Katrien De Bock, Jonatan R. Ruiz & Ferdinand von Meyenn
Additional file 5: Table S3: GO categories of genes whose promoters lie in state 8 from the mouse H3K18la ChromHMM. Data used in Fig. 2E. The following data is provided: GO ontology category, GO identifier number, GO term description, GO gene ratio, GO background ratio, p-value, adjusted p-value, q-value, gene entrez ids, gene count.

Additional file 2 of Network reconstruction for trans acting genetic loci using multi-omics data and prior information

Johann S. Hawe, Ashis Saha, Melanie Waldenberger, Sonja Kunze, Simone Wahl, Martina Müller-Nurasyid, Holger Prokisch, Harald Grallert, Christian Herder, Annette Peters, Konstantin Strauch, Fabian J. Theis, Christian Gieger, John Chambers, Alexis Battle & Matthias Heinig
Additional file 2 Supplementary tables, large supporting tables with table titles as tabs.

Additional file 2 of Network reconstruction for trans acting genetic loci using multi-omics data and prior information

Johann S. Hawe, Ashis Saha, Melanie Waldenberger, Sonja Kunze, Simone Wahl, Martina Müller-Nurasyid, Holger Prokisch, Harald Grallert, Christian Herder, Annette Peters, Konstantin Strauch, Fabian J. Theis, Christian Gieger, John Chambers, Alexis Battle & Matthias Heinig
Additional file 2 Supplementary tables, large supporting tables with table titles as tabs.

Data from: Association of in utero persistent organic pollutant exposure with placental thyroid hormones

Zhong-Min Li, David Hernandez-Moreno, Katharina Maria Main, Niels Erik Skakkebæk, Hannu Kiviranta, Jorma Toppari, Ulla Feldt-Rasmussen, Heqing Shen, Karl-Werner Schramm & Meri De Angelis
In utero exposure to persistent organic pollutants (POPs) can result in thyroid function disorder, leading to concerns about their impact on fetal and neonatal development. The present study was performed to investigate the associations between placental levels of various POPs and thyroid hormones (THs). In a prospective Danish study initially established for assessing congenital cryptorchidism, 58 placenta samples were collected from mothers of boys born with (28) and without (30) cryptorchidism. The concentrations of polybrominated...

Data from: Platelet GPIIb supports initial pulmonary retention but inhibits subsequent proliferation of melanoma cells during hematogenic metastasis

Christian Schulz, Katrin Echtler, Ildiko Konrad, Michael Lorenz, Simon Schneider, Sebastian Hofmaier, Florian Plenagl, Konstantin Stark, Thomas Czermak, Anca Tirniceriu, Martin Eichhorn, Axel Walch, Georg Enders & Steffen Massberg
Platelets modulate the process of cancer metastasis. However, current knowledge on the direct interaction of platelets and tumor cells is mostly based on findings obtained in vitro. We addressed the role of the platelet fibrinogen receptor glycoprotein IIb (integrin αIIb) for experimental melanoma metastasis in vivo. Highly metastatic B16-D5 melanoma cells were injected intravenously into GPIIb-deficient (GPIIb-/-) or wildtype (WT) mice. Acute accumulation of tumor cells in the pulmonary vasculature was assessed in real-time by...

Data from: Effect of plant chemical variation and mutualistic ants on the local population genetic structure of an aphid herbivore

Sharon E. Zytynska, Yasemin Guenay, Sarah Sturm, Mary V. Clancy, Matthias Senft, Joerg-Peter Schnitzler, Saurabh Dilip Pophaly, Christine Wurmser & Wolfgang W. Weisser
1.Plants exhibit impressive genetic and chemical diversity, not just between species but also within species, and the importance of plant intraspecific variation for structuring ecological communities is well known. When there is variation at the local population level, this can create a spatially‐heterogeneous habitat for specialized herbivores potentially leading to non‐random distribution of individuals across host‐plants. 2.Plant variation can affect herbivores directly and indirectly via a third species, resulting in variable herbivore growth rates across...

Carbohydrate depletion in roots impedes phosphorus nutrition of forest trees

Simon Clausing, Rodica Pena, Bin Song, Karolin Müller, Paula Mayer-Gruner, Sven Marhan, Martin Grafe, Stefanie Schulz, Jaane Krüger, Friederike Lang, Michael Schloter, Ellen Kandeler & Andrea Polle
The aim of the study was to determine the effect of belowground plant-derived carbohydrates on P uptake, P concentrations and enzymes activities related to P mobilization in roots, ectomycorrhizas and soil and on the abundances of P-related genes in soil bacteria. We report data from a girdling experiment in two temperate beech forest with contrasting soil phosphorus concentrations. We used soil cores and the fractions of the organic layer and mineral topsoil separately one and...

Data from: Disentangling the aging network of a termite queen

José Manuel Monroy Kuhn, Karen Meusemann & Judith Korb
Background: Most insects are relatively short-lived, with a maximum lifespan of a few weeks, like the aging model organism, the fruit-fly Drosophila melanogaster. By contrast, the queens of many social insects (termites, ants and some bees) can live from a few years to decades. This makes social insects promising models in aging research providing insights into how a long reproductive life can be achieved. Yet, aging studies on social insect reproductives are hampered by a...

Data from: Responses of native and invasive woody seedlings to combined competition and drought are species-specific

Judy Simon, Andrea Bueno & Karin Pritsch
A greenhouse experiment was conducted to evaluate the effects of drought on the interactions between native and invasive tree species. Organic and inorganic net N uptake capacity and total soluble protein as well as total soluable amino acid contents were quantified in leaves and fine roots of the native species Fagus sylvatica L., Quercus robur L. and Pinus sylvestris L.) and the invasive species Prunus serotina Ehrh. and Robinia pseudoacacia L.. We used a fully...

Acute Radiation Syndrome-related gene expression in irradiated peripheral blood cell populations

Patrick Ostheim, Alan Don Mallawaratchy, Thomas Müller, Simone Schüle, Cornelius Hermann, Tanja Popp, Stefan Eder, Stephanie E. Combs, Matthias Port & Michael Abend
In a nuclear or radiological event, an early diagnostic or prognostic tool is needed to distinguish the worried well from low-exposed and those individuals who may later develop life-threatening hematologic acute radiation syndrome (H-ARS). In previous studies, we identified and validated genes in peripheral blood for this purpose. To gain a deeper understanding and to make methodological improvements, we examined the contribution of the peripheral blood´s cell populations on radiation-induced gene expression changes. EDTA whole...

Application of radiation omics in the development of adverse outcome pathway networks: an example of radiation-induced cardiovascular disease

Omid Azimzadeh, Simone Moertl, Raghda Ramadan, Bjorn Baselet, Evagelia C. Laiakis, Soji Sebastian, Danielle Beaton, Jaana M. Hartikainen, Jan Christian Kaiser, Afshin Beheshti, Sisko Salomaa, Vinita Chauhan & Nobuyuki Hamada
Epidemiological studies have indicated that exposure of the heart to doses of ionizing radiation as low as 0.5 Gy increases the risk of cardiac morbidity and mortality with a latency period of decades. The damaging effects of radiation to myocardial and endothelial structures and functions have been confirmed radiobiologically at high dose, but much less are known at low dose. Integration of radiation biology and epidemiology data is a recommended approach to improve the radiation...

Application of radiation omics in the development of adverse outcome pathway networks: an example of radiation-induced cardiovascular disease

Omid Azimzadeh, Simone Moertl, Raghda Ramadan, Bjorn Baselet, Evagelia C. Laiakis, Soji Sebastian, Danielle Beaton, Jaana M. Hartikainen, Jan Christian Kaiser, Afshin Beheshti, Sisko Salomaa, Vinita Chauhan & Nobuyuki Hamada
Epidemiological studies have indicated that exposure of the heart to doses of ionizing radiation as low as 0.5 Gy increases the risk of cardiac morbidity and mortality with a latency period of decades. The damaging effects of radiation to myocardial and endothelial structures and functions have been confirmed radiobiologically at high dose, but much less are known at low dose. Integration of radiation biology and epidemiology data is a recommended approach to improve the radiation...

Data from: Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses

Daniel Penselin, Martin Muensterkoetter, Susanne Kirsten, Marius Felder, Stefan Taudien, Matthias Platzer, Kevin Ashelford, Konrad H. Paskiewicz, Richard J. Harrison, David J. Hughes, Thomas Wolf, Ekaterina Shelest, Jenny Graap, Jan Hoffmann, Claudia Wenzel, Nadine Woeltje, Kevin M. King, Bruce D. L. Fitt, Ulrich Gueldener, Anna Avrova & Wolfgang Knogge
Background: The Rhynchosporium species complex consists of hemibiotrophic fungal pathogens specialized to different sweet grass species including the cereal crops barley and rye. A sexual stage has not been described, but several lines of evidence suggest the occurrence of sexual reproduction. Therefore, a comparative genomics approach was carried out to disclose the evolutionary relationship of the species and to identify genes demonstrating the potential for a sexual cycle. Furthermore, due to the evolutionary very young...

Data from: Additive effects of plant chemotype, mutualistic ants and predators on aphid performance and survival

Matthias Senft, Mary V. Clancy, Wolfgang W. Weisser, Joerg-Peter Schnitzler & Sharon E. Zytynska
1. Cascading effects in ecological systems acting across three or more trophic levels can be either of a resource-based (bottom-up) or natural enemy-based (top-down) nature. But, due to their complexity these effects are often considered separately and their relative strength, acting simultaneously, remains unknown. 2. In a semi-natural field experiment using tansy (Tanacetum vulgare L.) and the specialised tansy aphid Metopeurum fuscoviride Stroyan as a model system, we compared the effects of four distinct plant...

Data from: Epigenome-wide association study of lung function level and its change

Medea Imboden, Matthias Wielscher, Faisal I Rezwan, Andre F S Amaral, Emmanuel Schaffner, Ayoung Jeong, Anna Beckmeyer-Borowko, Sarah E Harris, John M Starr, Ian J Deary, Claudia Flexeder, Melanie Waldenberger, Annette Peters, Holger Schulz, Su Chen, Shadia KHan Sunny, Wilfried J J Karmaus, Yu Jiang, Gertraud Erhart, Florian Kronenberg, Ryan Arathimos, Gemma C Sharp, Alexander John Henderson, Yu Fu, Paivi Piirila … & Nicole M Probst-Hensch
Previous reports link differential DNA methylation (DNAme) to environmental exposures which are associated with lung function. Direct evidence on lung function DNAme is however limited. We undertook an agnostic epigenome-wide association study (EWAS) on pre-bronchodilation lung function and its change in adults. In a discovery-replication EWAS design, DNAme in blood and spirometry were measured twice, six-to-15 years apart, in the same participants of three adult population-based discovery cohorts (n=2,043). Associated DNAme markers (P<5x10-7) were tested...

Additional file 3 of H3K18 lactylation marks tissue-specific active enhancers

Eva Galle, Chee-Wai Wong, Adhideb Ghosh, Thibaut Desgeorges, Kate Melrose, Laura C. Hinte, Daniel Castellano-Castillo, Magdalena Engl, Joao Agostinho de Sousa, Francisco Javier Ruiz-Ojeda, Katrien De Bock, Jonatan R. Ruiz & Ferdinand von Meyenn
Additional file 3: Table S1: Quality Control metrics. For each sample included in this study, the following data is provided: tissue of origin, hPTM profiled, biological replicate, reads (million), GC content (%), aligned fraction of reads (%), number of called peaks.

Additional file 6 of H3K18 lactylation marks tissue-specific active enhancers

Eva Galle, Chee-Wai Wong, Adhideb Ghosh, Thibaut Desgeorges, Kate Melrose, Laura C. Hinte, Daniel Castellano-Castillo, Magdalena Engl, Joao Agostinho de Sousa, Francisco Javier Ruiz-Ojeda, Katrien De Bock, Jonatan R. Ruiz & Ferdinand von Meyenn
Additional file 6: Table S4: Genes expression changes in MB treated with 10 mM lactate. Data used in Fig. 3H. edgeR outcome from differential expression test of control MBs versus MBs treated with 10 mM sodium-L-lactate (see ‘Materials and methods’). The following data is provided: ensembl gene id, gene entrez id, gene name, logFC, logCPM, p-value, FDR, regulation (up/down/non-significant), and whether the gene has a H3K18la-peak in its promoter region in MTs or MBs.

Acute radiation syndrome-related gene expression in irradiated peripheral blood cell populations

Patrick Ostheim, Alan Don Mallawaratchy, Thomas Müller, Simone Schüle, Cornelius Hermann, Tanja Popp, Stefan Eder, Stephanie E. Combs, Matthias Port & Michael Abend
In a nuclear or radiological event, an early diagnostic tool is needed to distinguish the worried well from those individuals who may later develop life-threatenFing hematologic acute radiation syndrome. We examined the contribution of the peripheral blood's cell populations on radiation-induced gene expression (GE) changes. EDTA-whole-blood from six healthy donors was X-irradiated with 0 and 4Gy and T-lymphocytes, B-lymphocytes, NK-cells and granulocytes were separated using immunomagnetic methods. GE were examined in cell populations and whole...

LSFM-image z-stack of an optically cleared porcine adipose tissue sample

Andreas Blutke
In translational obesity research, objective assessment of adipocyte sizes and numbers is essential to characterize histomorphological alterations linked to obesity, and to evaluate the efficacies of experimental medicinal or dietetic interventions. Design-based quantitative stereological techniques based on the analysis of 2D-histological sections provide unbiased estimates of relevant 3D-parameters of adipocyte morphology, but often involve complex and time-consuming tissue processing and analysis steps. Here we report the application of direct 3D light sheet fluorescence microscopy (LSFM)...

A haplotype-led approach to increase the precision of wheat breeding

Cristobal Uauy, Jemima Brinton, Ricardo Ramirez-Gonzalez, James Simmonds, Luzie Wingen, Simon Orford, Simon Griffiths, Georg Haberer, Manuel Spannagl, Sean Walkowiak & Curtis Pozniak
Crop productivity must increase at unprecedented rates to meet the needs of the growing worldwide population. Exploiting natural variation for the genetic improvement of crops plays a central role in increasing productivity. Although current genomic technologies can be used for high-throughput identification of genetic variation, methods for efficiently exploiting this genetic potential in a targeted, systematic manner are lacking. Here, we developed a haplotype-based approach to identify genetic diversity for crop improvement using genome assemblies...

Data from: Tree species rather than type of mycorrhizal association drives inorganic and organic nitrogen acquisition in tree-tree interactions

Judy Simon, Robert Reuter, Olga Ferlian, Mika Tarkka, Nico Eisenhauer & Karin Pritsch
A field study was conducted to evaluate the effects of associated mycorrhization type on tree-tree interactions using the framework of the MyDiv tree diversity experiment established at the Bad Lauchstädt Experimental Research Station of the Helmholtz Centre for Environmental Research (UFZ) (Saxony-Anhalt, Germany). Inorganic and organic net N uptake capacity was quantified in fine roots of AM (i.e. Acer pseudoplatanus L., Fraxinus excelsior L., and Prunus avium L.) as well as EM associated tree species...

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