103 Works

MS_Lumos_2020_May

Madlen Hotze
PRM Yang Zhang on Orbitrap Fusion Lumos + NanoU3000Proteomics Yang Zhang with Orbitrap Fusion Lumos + NanoU3000AcylCoAs Alienke van Pijkeren Obitrap Fusion Lumos + Vanquish Flex

MS_Lumos_2020_March

Madlen Hotze
MS Raw Data collected at Obitrap Fusion Lumos in March 2020 at the Institute of Biochemistry, University of InnsbruckThis record contains Proteomics of Yang Zhang (UIBK) and Metabolite measurements (M. Hotze, UIBK) and Acyl-CoA measurements (M. Hotze, UIBK).

Data from: Effects of prey quality and predator body size on prey DNA detection success in a centipede predator

Bernhard Eitzinger, Einar Michael Unger, Michael Traugott & Stefan Scheu
Predator body size and prey quality are important factors driving prey choice and consumption rates. Both factors might affect prey detection success in PCR-based gut content analysis, potentially resulting in over- or underestimation of feeding rates. Experimental evidence, however, is scarce. We examined how body size and prey quality affect prey DNA detection success in centipede predators. Due to metabolic rates increasing with body size, we hypothesized that prey DNA detection intervals will be significantly...

Data from: Habitat heterogeneity induces rapid changes in the feeding behaviour of generalist arthropod predators

Karin Staudacher, Oskar Rennstam Rubbmark, Klaus Birkhofer, Gerard Malsher, Daniela Sint, Mattias Jonsson & Michael Traugott
1. The “habitat heterogeneity hypothesis” predicts positive effects of structural complexity on species coexistence. Increasing habitat heterogeneity can change the diversity (number of species, abundances) and the functional roles of communities. The latter, however, is not well understood as species and individuals may respond very differently and dynamically to a changing environment. 2. Here, we experimentally test how habitat heterogeneity affects generalist arthropod predators, including epigaeic spiders, carabid and staphylinid beetles, under natural conditions by...

Data from: Does hybridization with a widespread congener threaten the long-term persistence of the Eastern Alpine rare local endemic Knautia carinthiaca?

Martin Čertner, Filip Kolář, Peter Schönswetter & Božo Frajman
Interspecific hybridization, especially when regularly followed by backcrossing (i.e., introgressive hybridization), conveys a substantial risk for many endangered organisms. This is particularly true for narrow endemics occurring within distributional ranges of widespread congeners. An excellent example is provided by the plant genus Knautia (Caprifoliaceae): Locally endemic K. carinthiaca is reported from two isolated populations in southern Austria situated within an area predominantly occupied by widespread K. arvensis. While K. carinthiaca usually inhabits low-competition communities on...

Data from: Rapid evolution of antioxidant defense in a natural population of Daphnia magna

Sarah Oexle, Mieke Jansen, Kevin Pauwels, Ruben Sommaruga, Luc De Meester & Robby Stoks
Natural populations can cope with rapid changes in stressors by relying on sets of physiological defense mechanisms. Little is known onto what extent these physiological responses reflect plasticity and/or genetic adaptation, evolve in the same direction and result in an increased defense ability. Using resurrection ecology, we studied how a natural Daphnia magna population adjusted its antioxidant defense to ultraviolet radiation (UVR) during a period with increasing incident UVR reaching the water surface. We demonstrate...

Data from: Evidence for a recent horizontal transmission and spatial spread of Wolbachia from endemic Rhagoletis cerasi (Diptera: Tephritidae) to invasive Rhagoletis cingulata in Europe

Hannes Schuler, Coralie Bertheau, Scott P. Egan, Jeffrey L. Feder, Markus Riegler, Birgit C. Schlick-Steiner, Florian M. Steiner, Jes Johannesen, Peter Kern, Katalin Tuba, Ferenc Lakatos, Kirsten Köppler, Wolfgang Arthofer & Christian Stauffer
The widespread occurrence of Wolbachia in arthropods and nematodes suggests that this intracellular, maternally inherited endosymbiont has the ability to cross species boundaries. However, direct evidence for such a horizontal transmission of Wolbachia in nature is scarce. Here, we compare the well-characterized Wolbachia infection of the European cherry fruit fly, Rhagoletis cerasi, with that of the North American eastern cherry fruit fly, Rhagoletis cingulata, recently introduced to Europe. Molecular genetic analysis of Wolbachia based on...

Data from: Molecular prey identification in Central European piscivores

Bettina Thalinger, Johannes Oehm, Hannes Mayr, Armin Obwexer, Christiane Zeisler & Michael Traugott
Diet analysis is an important aspect when investigating the ecology of fish-eating animals and essential for assessing their functional role in food webs across aquatic and terrestrial ecosystems. The identification of fish remains in dietary samples, however, can be time-consuming and unsatisfying using conventional morphological analysis of prey remains. Here, we present a two-step multiplex PCR system, comprised of six assays, allowing for rapid, sensitive and specific detection of fish DNA in dietary samples. This...

Data from: \"De novo transcriptome assembly of the mountain fly Drosophila nigrosparsa using short RNA-seq reads\" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014

Wolfgang Arthofer, Francesco Cicconardi, Nicola Palmieri, Viola Nolte, Christian Schlötterer, Birgit C. Schlick-Steiner, Florian M. Steiner, Marcelo Vallinoto, David A. Weese, B. L. Banbury, R. B. Harris, David S. Kang, Cheolho Sim, Thomas F. Duda, A. D. Leaché, Miguel Carneiro, Coralie Nourisson & Fernando Sequeira
Drosophila (Drosophila) nigrosparsa is a habitat specialist restricted to the European montane/alpine zone (Bächli 2008). Mountain biodiversity is considered highly vulnerable to ongoing climate warming (IPCC 2013), and organisms at high altitudes have only limited possibility to shift to cooler habitats at elevations above (Pertoldi & Bach 2007). For such species, rapid evolution may offer a solution for long-term survival. We are establishing D. nigrosparsa as a model system to test the extent and tempo...

Data from: \"You are not what you eat: massive parallel sequencing reveals that gut microbiome is not diet-related in larval Dilophus febrilis (Diptera: Bibionidae)\" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015

Alexander Rief, Wolfgang Arthofer, Birgit C. Schlick-Steiner, Florian M. Steiner & Julia Seeber
This article documents the public availability of metagenome sequence data from 454 amplicon sequencing of larval dipteran gut (Dilophus febrilis) and their potential food sources dwarf shrub litter (Vaccinium gaultheroides), grass litter (Dactylis glomerata), and cow dung (Bos primigenius taurus).

Data from: \"NGS based generation of expressed sequence tags for Lymantria dispar and Lymantria monacha, two closely related lepidopteran species with different responses to parasitism by Glyptapanteles liparidis\" in Genomic Resources Notes accepted 1 December 2013 to 31 January 2014

Wolfgang Arthofer, Birgit C. Schlick-Steiner, Florian M. Steiner, Christa Schafellner, Gregor A. Wachter, Anthony R. Clarke, Nagalingam Kumaran & Peter J. Prentis
Introduction: The gypsy moth, Lymantria dispar, and the nun moth, Lymantria monacha, are closely related species (Lepidoptera, Lymantriidae), co-seasonal and economically important forest pests on broadleaf and coniferous trees. In Central Europe, gypsy moth larvae are frequently parasitized by the gregarious, endoparasitic wasp Glyptapanteles liparidis (Hymenoptera, Braconidae). At oviposition, the female wasp injects between 10 and up to 100 eggs into the hemocoel of a single host larva, together with venom and calyx fluid containing...

Data from: Biogeography of plant root-associated fungal communities in the North-Atlantic region mirrors climatic variability

Synnøve Smebye Botnen, Marie L. Davey, Anders B. Aas, Tor Carlsen, Ella Thoen, Einar Heegaard, Unni Vik, Philipp Dresch, Sunil Mundra, Ursula Peintner, Andy F.S. Taylor & Håvard Kauserud
Aim Polar and alpine ecosystems appear to be particularly sensitive to increasing temperatures and the altered precipitation patterns linked to climate change. However, little is currently known about how these environmental drivers may affect edaphic organisms within these ecosystems. In this study, we examined communities of plant root-associated fungi (RAF) over large biogeographic scales and along climatic gradients in the North Atlantic region in order to gain insights into the potential effects of climate variability...

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...

Relationships between plant-soil feedbacks and functional traits

Nianxun Xi, Peter Adler, Dongxia Chen, Hangyu Wu, Jane Catford, Peter Van Bodegom, Michael Bahn, Kerri Crawford & Chengjin Chu
Plant-soil feedbacks (PSF) and functional traits are two active but not well theoretically integrated areas of research. However, PSF and traits are both affected by life history evolution, so the two should theoretically be related. We provide a conceptual framework to link plant functional traits to two types of PSF metrics, and hypothesize that individual PSF (plant performance in conspecific versus heterospecific soil) should be related to the fast-slow trait spectrum, while pairwise PSF (the...

Data from: On the objectivity, reliability, and validity of deep learning enabled bioimage analyses

Dennis Segebarth, Matthias Griebel, Nikolai Stein, Cora R. Von Collenberg, Corinna Martin, Dominik Fiedler, Lucas B. Comeras, Anupam Sah, Victoria Schoeffler, Theresa Lüffe, Alexander Dürr, Rohini Gupta, Manju Sasi, Christina Lillesaar, Maren D. Lange, Ramon O. Tasan, Nicolas Singewald, Hans-Christian Pape, Christoph M. Flath & Robert Blum
Bioimage analysis of fluorescent labels is widely used in the life sciences. Recent advances in deep learning (DL) allow automating time-consuming manual image analysis processes based on annotated training data. However, manual annotation of fluorescent features with a low signal-to-noise ratio is somewhat subjective. Training DL models on subjective annotations may be instable or yield biased models. In turn, these models may be unable to reliably detect biological effects. An analysis pipeline integrating data annotation,...

Terrestrial green algae show higher tolerance to dehydration than do their aquatic sister-species: Raw data and analysis files

Elizaveta Terlova, Andreas Holzinger & Louise Lewis
Diverse algae possess the ability to recover from extreme desiccation without forming specialized resting structures. Green algal genera such as Tetradesmus (Sphaeropleales, Chlorophyceae) contain temperate terrestrial, desert, and aquatic species, providing an opportunity to compare physiological traits associated with the transition to land in closely related taxa. We subjected six species from distinct habitats to three dehydration treatments varying in relative humidity (RH 5%, 65%, 80%) followed by short- and long-term rehydration. We tested the...

Wolbachia affect behavior and possibly reproductive compatibility but not thermoresistance, fecundity, and morphology in a novel transinfected host, Drosophila nigrosparsa

Matsapume Detcharoen, Wolfgang Arthofer, Francis Jiggins, Florian Steiner & Birgit Schlick-Steiner
Wolbachia, intracellular endosymbionts, are estimated to infect about half of all arthropod species. These bacteria manipulate their hosts in various ways for their maximum benefits. The rising global temperature may accelerate species migration and, thus, horizontal transfer of Wolbachia may occur across species previously not in contact. We transinfected and then cured the alpine fly Drosophila nigrosparsa with Wolbachia strain wMel to study its effects on this species. We found low Wolbachia titer, possibly cytoplasmic...

MS_Lumos_2019_August

Hotze
MS Raw Data collected at Obitrap Fusion Lumos in August 2019 at the Institute of Biochemistry, University of InnsbruckThis record contains Proteomics for A. Mödelhammer (UIBK), Secretome Data, HeLa QCs and Standards, TSC Proteome Data (M. Hotze, UIBK) and Metabolite measurements (M. Hotze, UIBK) related to the TSC Proteome Data.

Data from: Ecological differentiation, lack of hybrids involving diploids, and asymmetric gene flow between polyploids in narrow contact zones of Senecio carniolicus (syn. Jacobaea carniolica, Asteraceae)

Karl Hülber, Michaela Sonnleitner, Jan Suda, Jana Krejčíková, Peter Schönswetter, Gerald M. Schneeweiss & Manuela Winkler
Areas of immediate contact of different cytotypes offer a unique opportunity to study evolutionary dynamics within heteroploid species and to assess isolation mechanisms governing coexistence of cytotypes of different ploidy. The degree of reproductive isolation of cytotypes, i.e., the frequency of heteroploid crosses and subsequent formation of viable and (partly) fertile hybrids, plays a crucial role for the long-term integrity of lineages in contact zones. Here, we assessed fine-scale distribution, spatial clustering and ecological niches...

Data from: How generalist herbivores exploit belowground plant diversity in temperate grasslands

Corinna Wallinger, Karin Staudacher, Nikolaus Schallhart, Evi Mitterutzner, Eva-Maria Steiner, Anita Juen, Michael Traugott & Evi Mitterrutzner
Belowground herbivores impact plant performance, thereby inducing changes in plant community composition, which potentially leads to cascading effects onto higher trophic levels and ecosystem processes and productivity. Amongst soil-living insects, external root-chewing generalist herbivores have the strongest impact on plants. However, the lack of knowledge on their feeding behaviour under field conditions considerably hampers achieving a comprehensive understanding of how they affect plant communities. Here, we address this gap of knowledge by investigating the feeding...

Data from: A novel method to infer the origin of polyploids from AFLP data reveals that the Alpine polyploid complex of Senecio carniolicus (Asteraceae) evolved mainly via autopolyploidy

Manuela Winkler, Pedro Escobar García, Andreas Gattringer, Michaela Sonnleitner, Karl Hülber, Peter Schönswetter & Gerald M. Schneeweiss
Despite its evolutionary and ecological relevance the mode of polyploid origin has been notoriously difficult to be reconstructed from molecular data. Here, we present a method to identify the putative parents of polyploids and thus to infer the mode of their origin (auto- versus allopolyploidy) from Amplified Fragment Length Polymorphism (AFLP) data. To this end, we use Cohen's d of distances between in silico polyploids, generated within a priori defined scenarios of origin from a...

Data from: Is the incidence of survival in interior Pleistocene refugia (nunataks) underestimated? Phylogeography of the high mountain plant Androsace alpina (Primulaceae) in the European Alps revisited

Peter Schönswetter & Gerald M. Schneeweiss
Temperate mountain ranges such as the European Alps have been strongly affected by the Pleistocene glaciations. Glacial advances forced biota into refugia, which were situated either at the periphery of mountain ranges or in their interior. Whereas in the Alps peripheral refugia have been repeatedly and congruently identified, support for the latter scenario, termed “nunatak hypothesis”, is still limited and no general pattern is recognizable yet. Here, we test the hypothesis of nunatak survival for...

Data from: Hypoxia-inducible factor-1 mediates adaptive developmental plasticity of hypoxia tolerance in zebrafish, Danio rerio

Cayleih E. Robertson, Patricia A. Wright, Louise Köblitz, Nicholas J. Bernier & L. Koblitz
In recent years, natural and anthropogenic factors have increased aquatic hypoxia the world over. In most organisms, the cellular response to hypoxia is mediated by the master regulator hypoxia-inducible factor-1 (HIF-1). HIF-1 also plays a critical role in the normal development of the cardiovascular system of vertebrates. We tested the hypothesis that hypoxia exposures which resulted in HIF-1 induction during embryogenesis would be associated with enhanced hypoxia tolerance in subsequent developmental stages. We exposed zebrafish...

Data from: \"454 sequencing of reduced representation libraries to discover single nucleotide polymorphisms (SNPs) in Megabunus harvestmen\" in Genomic Resources Notes accepted 1 December 2013 to 31 January 2014

Gregor Wachter, Birgit Schlick-Steiner, Florian Steiner & Wolfgang Arthofer
Harvestmen or daddy longlegs (Opiliones) are the third-largest and one of the oldest arachnid groups, and in recent years, there has been an increasing interest in this order. Here we use next-generation sequencing of reduced representation libraries to establish nuclear DNA markers. To the best of our knowledge this dataset represents the largest genomic resource for Megabunus harvestmen available to date.

Data from: Evolution at two time frames: polymorphisms from an ancient singular divergence event fuel contemporary parallel evolution

Steven M. Van Belleghem, Carl Vangestel, Katrien De Wolf, Zoë De Corte, Markus Möst, Pasi Rastas, Luc De Meester & Frederik Hendrickx
When environments change, populations may adapt surprisingly fast, repeatedly and even at microgeographic scales. There is increasing evidence that such cases of rapid parallel evolution are fueled by standing genetic variation, but the source of this genetic variation remains poorly understood. In the saltmarsh beetle Pogonus chalceus, short-winged ‘tidal’ and long-winged ‘seasonal’ ecotypes have diverged in response to contrasting hydrological regimes and can be repeatedly found along the Atlantic European coast. By analyzing genomic variation...

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