154 Works

Data from: Regional environmental pressure influences population differentiation in turbot (Scophthalmus maximus)

S. G. Vandamme, G. E. Maes, J. A. M. Raeymaekers, K. Cottenie, A. K. Imsland, B. Hellemans, G. Lacroix, E. Mac Aoidh, J. T. Martinsohn, P. Martínez, J. Robbens, R. Vilas & F. A. M. Volckaert
Unravelling the factors shaping the genetic structure of mobile marine species is challenging due to the high potential for gene flow. However, genetic inference can be greatly enhanced by increasing the genomic, geographic or environmental resolution of population genetic studies. Here we investigated the population structure of turbot (Scophthalmus maximus) by screening 17 random and gene-linked markers in 999 individuals at 290 geographical locations throughout the Northeast Atlantic Ocean. A seascape genetics approach with the...

Data from: The evolutionary history of Afrocanarian blue tits inferred from genome-wide SNPs

Jostein Gohli, Erica Leder, Eduardo Garcia-Del-Rey, Lars Erik Johannessen, Arild Johnsen, Terje Laskemoen, Magnus Popp, Jan T. Lifjeld & Erica H. Leder
A common challenge in phylogenetic reconstruction is to find enough suitable genomic markers to reliably trace splitting events with short internodes. Here we present phylogenetic analyses based on genome-wide single-nucleotide polymorphisms (SNPs) of an enigmatic avian radiation, the subspecies complex of Afrocanarian blue tits (Cyanistes teneriffae). The two sister species, the Eurasian blue tit (Cyanistes caeruleus) and the azure tit (Cyanistes cyanus), constituted the outgroup. We generated a large data set of SNPs for analysis...

Data from: Quantification of population sizes of large herbivores and their long-term functional role in ecosystems using dung fungal spores

Ambroise G. Baker, Perry Cornelissen, Shonil Bhagwat, Fransciscus W. M. Vera, Katherine J. Willis & Shonil A. Bhagwat
The relationship between large herbivore numbers and landscape cover over time is poorly understood. There are two schools of thought: one views large herbivores as relatively passive elements upon the landscape and the other as ecosystem engineers driving vegetation succession. The latter relationship has been used as an argument to support reintroductions of large herbivores onto many landscapes in order to increase vegetation heterogeneity and biodiversity through local-scale disturbance regimes. Most of the research examining...

Data from: Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities

Jessica L. Ray, Julia Althammer, Katrine S. Skaar, Paolo Simonelli, Aud Larsen, Diane Stoecker, Andrey Sazhin, Umer Z. Ijaz, Christopher Quince, Jens C. Nejstgaard, Marc Frischer, Georg Pohnert & Christofer Troedsson
In order to characterize copepod feeding in relation to microbial plankton community dynamics, we combined metabarcoding and metabolome analyses during a 22-day seawater mesocosm experiment. Nutrient amendment of mesocosms promoted the development of haptophyte (Phaeocystis pouchetii)- and diatom (Skeletonema marinoi)-dominated plankton communities in mesocosms, in which Calanus sp. copepods were incubated for 24 h in flow-through chambers to allow access to prey particles (<500 μm). Copepods and mesocosm water sampled six times spanning the experiment...

Data from: Xenacoelomorpha is the sister group to Nephrozoa

Johanna Taylor Cannon, Bruno Cossermelli Vellutini, Julian Smith, Fredrik Ronquist, Ulf Jondelius & Andreas Hejnol
The position of Xenacoelomorpha in the tree of life remains a major unresolved question in the study of deep animal relationships. Xenacoelomorpha, comprising Acoela, Nemertodermatida, and Xenoturbella, are bilaterally symmetrical marine worms that lack several features common to most other bilaterians, for example an anus, nephridia, and a circulatory system. Two conflicting hypotheses are under debate: Xenacoelomorpha is the sister group to all remaining Bilateria (= Nephrozoa, namely protostomes and deuterostomes) or is a clade...

Cholesterol depletion sensitizes gallbladder cancer to cisplatin by impairing DNA damage response

Yonglong Zhang, Yanfeng Liu, Jinlin Duan, Hui Wang, Yuchen Zhang, Ke Qiao & Jian Wang
Gallbladder cancer (GBC) is the common malignancy of the bile tract system with extremely poor clinical outcomes, owing to its metastatic property and intrinsic resistance to the first-line drugs. Although it is well-established that cholesterol abnormity contributes to gallstone formation, a leading risk factor for GBC, the link of cholesterol homeostasis with GBC has not been investigated. The present study systematically examined the genes implicated in cholesterol homeostasis, and revealed altered gene expressions of de...

Data from: Evolution of virulence under intensive farming: salmon lice increase skin lesions and reduce host growth in salmon farms

Mathias S. Ugelvik, Arne Skorping, Olav Moberg & Adele Mennerat
Parasites rely on resources from a host and are selected to achieve an optimal combination of transmission and virulence. Human-induced changes in parasite ecology, such as intensive farming of hosts, might not only favor increased parasite abundances, but also alter the selection acting on parasites and lead to life history evolution. The trade-off between transmission and virulence could be affected by intensive farming practices such as high host density and the use of anti-parasitic drugs,...

Data from: Last Glacial Maximum environmental conditions at Andøya, northern Norway; evidence for a northern ice-edge ecological “hotspot”

Inger Alsos, Per Sjögren, Antony Brown, Ludovic Gielly, Marie Merkel, Aage Paus, Youri Lammers, Mary Edwards, Torbjørn Alm, Melanie Leng, Tomasz Goslar, Catherine Langdon, Jostein Bakke & Willem Van Der Bilt
Andøya on the NW coast of Norway is a key site for understanding the Last Glacial Maximum (LGM) in northern Europe. Controversy has arisen concerning the local conditions, especially about the timing and extent of local glacial cover, maximum July temperatures and whether pine and/or spruce could have grown there. We reviewed all existing data and add newly analysed ancient sedimentary DNA, pollen, macrofossils, geochemistry and stable isotopes from three lake sediment cores from Øvre...

Data from: Atlantic bluefin tuna spawn at suboptimal temperatures for their offspring

Patricia Reglero, Aurelio Ortega, Rosa Balbín, Francisco Javier Abascal, Antonio Medina, Edurne Blanco, Fernando De La Gándara, Diego Alvarez-Berastegui, Manuel Hidalgo, Leif Rasmuson, Francisco Alemany & Øyvind Fiksen
Life-history traits such as spawning migrations and timing of reproduction are adaptations to specific environmental constraints and seasonal cycles in many organisms’ annual routines. In this study we analyze how offspring fitness constrains spawning phenology in a large migratory apex predator, the Atlantic bluefin tuna. The reproductive schedule of Atlantic bluefin tuna varies between spawning sites suggesting plasticity to local environmental conditions. Generally, temperature is considered to be the main constraint on tuna spawning phenology....

Data from: Spatial covariance of herbivorous and predatory guilds of forest canopy arthropods along a latitudinal gradient

Ondřej Mottl
In arthropod community ecology, species richness studies tend to be prioritized over those investigating patterns of abundance. Consequently, the biotic and abiotic drivers of arboreal arthropod abundance are still relatively poorly known. In this cross-continental study, we employ a theoretical framework in order to examine patterns of covariance among herbivorous and predatory arthropod guilds. Leaf-chewing and leaf-mining herbivores, and predatory ants and spiders, were censused on > 1,000 trees in nine 0.1 ha forest plots....

Frog tongue segmentation data for a realistic vascular structure in modelling

Ulin Nuha Abdul Qohar, Erik Andreas Hanson, Antonella Zanna Munthe-Kaas & Jan Martin Nordbotten
In the last decade, numerical models have been an increasingly important tool in biological and medical science both for the fundamental understanding of physiology as well as the potential for novel diagnostics and treatments tools in clinical application. In this paper, a nonlinear multi-scale model framework is developed for blood flow distribution in the full vascular system of an organ. We couple a quasi 1D vascular graph model to represent blood flow in larger vessels...

Data from: Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients

Solveig Tangedal, Marianne Aanerud, Rune Grønseth, Christine Drengenes, Harald G. Wiker, Per S. Bakke & Tomas Eagan
Background: Induced and spontaneous sputum are used to evaluate the airways microbiota. Whether the sputum types can be used interchangeably in microbiota research is unknown. Our aim was to compare microbiota in induced and spontaneous sputum from COPD patients sampled during the same consultation. Methods: COPD patients from Bergen, Norway, were followed between 2006/2010, examined during the stable state and exacerbations. 30 patients delivered 36 sample pairs. DNA was extracted by enzymatic and mechanical lysis...

Data from: Ecological impact assessments of alien species in Norway

Hanno Sandvik, Olga Hilmo, Snorre Henriksen, Reidar Elven, Per Arvid Åsen, Hanne Hegre, Oddvar Pedersen, Per Anker Pedersen, Heidi Solstad, Vigdis Vandvik, Kristine B. Westergaard, Frode Ødegaard, Sandra Åström, Hallvard Elven, Anders Endrestøl, Øivind Gammelmo, Bjørn Arild Hatteland, Halvor Solheim, Björn Nordén, Leif Sundheim, Venche Talgø, Tone Falkenhaug, Bjørn Gulliksen, Anders Jelmert, Eivind Oug … & Lisbeth Gederaas
Due to globalisation, trade and transport, the spread of alien species is increasing dramatically. Some alien species become ecologically harmful by threatening native biota. This can lead to irreversible changes in local biodiversity and ecosystem functioning, and, ultimately, to biotic homogenisation. We risk-assessed all alien plants, animals, fungi and algae, within certain delimitations, that are known to reproduce in Norway. Mainland Norway and the Arctic archipelago of Svalbard plus Jan Mayen were treated as separate...

Exploring protocol bias in airway microbiome studies: One versus two PCR steps and 16S rRNA gene region V3 V4 versus V4

Christine Drengenes, Rune Nielsen, Ingvild Haaland, Harald Wiker & Tomas Eagan
Background: Studies on the airway microbiome have been performed using a wide range of laboratory protocols for high-throughput sequencing of the bacterial 16S ribosomal RNA (16S rRNA) gene. We sought to determine the impact of number of polymerase chain reaction (PCR) steps (1- or 2-steps) and choice of target marker gene region (V3 V4 and V4) on the presentation of the upper and lower airway microbiome. Our analyses included lllumina MiSeq sequencing following three setups:...

Data from: Clitellate worms (Annelida) in lateglacial and Holocene sedimentary DNA records from the Polar Urals and northern Norway

Youri Lammers, Charlotte L. Clarke, Christer Erséus, Antony G. Brown, Mary E. Edwards, Ludovic Gielly, Haflidi Haflidason, Jan Mangerud, Emilia Rota, John Inge Svendsen & Inger Greve Alsos
While there are extensive macro- and microfossil records of a range of plants and animals from Quaternary records, earthworms and their close relatives among annelids are not preserved as fossils, and therefore we have limited knowledge of their Quaternary distributions. This lack of fossils means that clitellate worms (Annelida) are currently underused in palaeoecological research, even though they can provide valuable information about terrestrial and aquatic environmental conditions. Their DNA might be preserved in sediments,...

Data from: Acid-sensing ion channels emerged over 600 MYA and are conserved throughout the deuterostomes

Timothy Lynagh, Yana Mikhaleva, Janne M. Colding, Joel C. Glover & Stephan A. Pless
Acid-sensing ion channels (ASICs) are proton-gated ion channels broadly expressed in the vertebrate nervous system, converting decreased extracellular pH into excitatory sodium current. ASICs were previously thought to be a vertebrate-specific branch of the DEG/ENaC family, a broadly conserved but functionally diverse family of channels. Here, we provide phylogenetic and experimental evidence that ASICs are conserved throughout deuterostome animals, showing that ASICs evolved over 600 million years ago. We also provide evidence of ASIC expression...

Pollen-chemistry variations along elevation gradients and their implications for a proxy for UV-B radiation in the plant-fossil record

Alistair Seddon, Daniela Festi, Mayke Nieuwkerk, Ragnhild Gya, Børge Hamre, Linn Cecilie Krüger, Silje Östman & T. Matthew Robson
1. Research indicates that the phenolic compounds (e.g. para-coumaric acid) found within pollen grains may be useful as a proxy to reconstruct the UV-B radiation received at the Earth’s surface in the geological past. However, application of this method to the plant-fossil record currently relies on a series of untested assumptions surrounding the ecological factors driving the response of pollen grains in the contemporary environment. 2. Here, we investigate the relationship of Pinus spp. pollen...

Data from: Trophic interactions and abiotic factors drive functional and phylogenetic structure of vertebrate herbivore communities across the Arctic tundra biome

James D.M. Speed, Ina A. Skjelbred, Isabel C. Barrio, Michael D. Martin, Dominique Berteaux, C. Guillermo Bueno, Katie S. Christie, Bruce C. Forbes, Jennifer Forbey, Daniel Fortin, Jon-Arvid Grytnes, Katrine S. Hoset, Nicolas Lecomte, Bryndis Marteinsdottir, Jesper B. Mosbacher, Åshild O. Pedersen, Virve Ravolainen, Eileen C. Rees, Anna Skarin, Natalya Sokolova, Andrew H. Thornhill, Ingunn Tombre & Eeva M. Soininen
Communities are assembled from species that evolve or colonise a given geographic region, and persist in the face of abiotic conditions and interactions with other species. The evolutionary and colonisation histories of communities are characterised by phylogenetic diversity, while functional diversity is indicative of abiotic and biotic conditions. The relationship between functional and phylogenetic diversity infers whether species functional traits are divergent (differing between related species) or convergent (similar among distantly related species). Biotic interactions...

Data underlying RSOS-210474: Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for Lantern Shark taxonomy (Chondrichthyes: Etmopteridae)

Nicolas Straube
After initial detection of target archival DNA of a 116 year old syntype specimen of the Smooth Lanternshark, Etmopterus pusillus in a single stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4,599 mitochondrial reads were available for the genome...

The lower airways microbiome and antimicrobial peptides in Idiopathic Pulmonary Fibrosis differ from Chronic Obstructive Pulmonary Disease

Tomas Eagan, Kristel Knudsen, Sverre Lehmann, Rune Nielsen, Solveig Tangedal, Ingvild Haaland & Pieter Hiemstra
Background: The lower airways microbiome and host immune response in chronic pulmonary diseases are incompletely understood. We aimed to investigate possible microbiome characteristics and key antimicrobial peptides and proteins in idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD). Methods: 12 IPF patients, 12 COPD patients and 12 healthy controls were sampled with oral wash (OW), protected bronchoalveolar lavage (PBAL) and right lung protected sterile brushings (rPSB). The antimicrobial peptides and proteins (AMPs), secretory...

A forest pool as a habitat island for mites in a limestone forest in Southern Norway

Anna Seniczak, Stanislaw Seniczak, Radomir Graczyk, Sławomir Kaczmarek, Bjarte H. Jordal, Jarosław Kowalski, Per Djursvoll, Steffen Roth & Thomas Bolger
Forest water bodies, e.g., pools, constitute ‘environmental islands’ within forests, with specific flora and fauna thus contributing considerably to the landscape biodiversity. The mite communities of Oribatida and Mesostigmata in two distinctive microhabitats, water-soaked Sphagnum mosses at the edge of a pool and other mosses growing on the medium-wet forest floor nearby, were compared in a limestone forest in Southern Norway. In total, 16,189 specimens of Oribatida representing 98 species, and 499 specimens of Mesostigmata,...

Translation, cultural adaptation, and validation of a screening test for cognitive and behavioural changes in amyotrophic lateral sclerosis

Tina Taule, Annbjørg Spilde Morland, Jörg Aßmus, Ole-Bjørn Tysnes & Tiina Rekand
To describe challenges of translating and culturally adapting the Edinburgh Cognitive and Behavioural Amyotrophic Lateral Sclerosis (ALS) Screen into Norwegian (ECAS-N), evaluate its content validity; provide age- and education-balanced norms for verbal fluency and cut-off values for abnormal performance. Translation to Norwegian and back-translation to English complied with standard methods. Patients and ALS experts evaluated the relevance, comprehensiveness and comprehensibility of the translated ECAS (ECAS-N). Content validity indexes at the item level (I-CVI), scale level...

Size-selective harvesting affects the immunocompetence of guppies exposed to the parasite Gyrodactylus

Vitalija Bartusevičiūtė, Beatriz Diaz-Pauli, Anne Gro Vea Salvanes & Mikko P. Heino
Harvesting is typically positively size-selective, targeting large individuals. This is expected to lead to reduced average body size and earlier maturation, i.e., faster life histories. Such changes can also affect traits seemingly unrelated to harvesting, including immunocompetence. The pace-of-life syndrome predicts that faster life histories are correlated with decreased immunocompetence, i.e., a negative association between positively size-selective harvesting and immunocompetence. However, the energetic trade-off between early growth and immunocompetence suggests the opposite pattern. Here, we...

Circum-Arctic distribution of chemical anti-herbivore compounds arctic shrubs

Elin Lindén, Mariska Te Beest, Ilka Abreu, Thomas Moritz, Maja Sundqvist, Isabel C Barrio, Julia Boike, John Bryant, Kari Anne Bråthen, Agata Buchwal, Guillermo Bueno, Alain Cuerrier, Dagmar Egelkraut, Bruce Forbes, Martin Hallinger, Monique Heijmans, Luise Hermanutz, David S Hik, Annika Hofgaard, Milena Holmgren, Diane C Huebner, Toke Hoye, Ingibjörg Jónsdóttir, Elina Kaarlejärvi, Emilie Kissler … & Johan Olofsson
Spatial variation in plant chemical defence towards herbivores can help us understand variation in herbivore top-down control of shrubs in the Arctic and possibly also shrub responses to global warming. Less defended, non-resinous shrubs could be more influenced by herbivores than more defended, resinous shrubs. However, sparse field measurements limit our current understanding of how much of the circum-Arctic variation in defence compounds is explained by taxa or defence functional groups (resinous/non-resinous). We measured circum-Arctic...

Altered transcriptome-proteome coupling indicates aberrant proteostasis in Parkinson’s disease

Fiona Dick, Guido Werner Alves, Ole-Bjørn Tysnes, Gonzalo S. Nido & Charalampos Tzoulis
Datasets for the analysis of "Altered transcriptome-proteome coupling indicates aberrant proteostasis in Parkinson’s disease"
RNASeq data: gene expression quantification (raw) as output from Salmon (https://combine-lab.github.io/salmon/) Proteomics data: raw data output from MaxQuant in R file format ".rds" (https://www.maxquant.org/).* Metadata: Sample information for RNA ("info_rna_all.rds") and proteomics data ("info.rds") in R file format ".rds"
*Proteomics data includes protein expression of samples that were not included in the analysis. Data is provided to enable the...

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  • University of Bergen
  • Haukeland University Hospital
  • Fudan University
  • Qinghai University Affiliated Hospital
  • North West Agriculture and Forestry University
  • Sun Yat-sen University
  • Zhejiang University
  • Lanzhou Veterinary Research Institute
  • Air Force Medical University
  • Fudan University Shanghai Cancer Center