94 Works

Data from: How habitat-modifying organisms structure the food web of two coastal ecosystems

Els M. Van Der Zee, Christine Angelini, Laura L. Govers, Marjolijn J. A. Christianen, Andrew H. Altieri, Karin J. Van Der Reijden, Brian R. Silliman, Johan Van De Koppel, Matthijs Van Der Geest, Jan A. Van Gils, Henk W. Van Der Veer, Theunis Piersma, Peter C. De Ruiter, Han Olff & Tjisse Van Der Heide
The diversity and structure of ecosystems has been found to depend both on trophic interactions in food webs and on other species interactions such as habitat modification and mutualism that form non-trophic interaction networks. However, quantification of the dependencies between these two main interaction networks has remained elusive. In this study, we assessed how habitat-modifying organisms affect basic food web properties by conducting in-depth empirical investigations of two ecosystems: North American temperate fringing marshes and...

Data from: Corrections for rooting volume and plant size reveal negative effects of neighbour presence on root allocation in pea

Bin J. W. Chen, Heinjo J. During, Peter J. Vermeulen, Hans De Kroon, Hendrik Poorter & Niels P. R. Anten
Plants are able to detect the presence of their neighbours belowground. The associated root responses may affect plant performance, plant-plant interactions and community dynamics, but the extent and direction of these responses is heavily debated. Some studies suggest that plants will over-proliferate roots in response to neighbours at the expense of reproduction, which was framed as a “tragedy of the commons”. Others proposed an “ideal free distribution” hypothesis, stating that plants produce roots simply as...

Data from: Peatland vascular plant functional types affect methane dynamics by altering microbial community structure

Bjorn J. M. Robroek, Vincent E. J. Jassey, Martine A. R. Kox, Roeland L. Berendsen, Robert T. E. Mills, Lauric Cécillon, Jéremy Puissant, Marion Meima–Franke, Peter A. H. M. Bakker, Paul L. E. Bodelier & Marion Meima-Franke
1. Peatlands are natural sources of atmospheric methane (CH4), an important greenhouse gas. It is established that peatland methane dynamics are controlled by both biotic and abiotic conditions, yet the interactive effect of these drivers is less studied and consequently poorly understood. 2. Climate change affects the distribution of vascular plant functional types (PFTs) in peatlands. By removing specific PFTs, we assessed their effects on peat organic matter chemistry, microbial community composition and on potential...

Data from: Transgenerational effects of mild heat in Arabidopsis thaliana show strong genotype specificity that is explained by climate at origin

Maartje P. Groot, Alexander Kubisch, N. Joop Ouborg, Joern Pagel, Karl J. Schmid, Philippine Vergeer & Christian Lampei
Transgenerational environmental effects can trigger strong phenotypic variation. However, it is unclear how cues from different preceding generations interact. Also, little is known about genetic variation for these life-history-traits. Here we present effects of grandparental and parental mild heat, and their combination, on four traits of the third-generation phenotype of 14 Arabidopsis thaliana genotypes. We tested for correlations of these effects with climate and constructed a conceptual model to identify the environmental conditions that favour...

Data from: Thermal limits in native and alien freshwater peracarid Crustacea: the role of habitat use and oxygen limitation

Wilco C.E.P. Verberk, Rob S.E.W. Leuven, Gerard Van Der Velde & Friederike Gabel
1. In order to predict which species can successfully cope with global warming and how other environmental stressors modulate their vulnerability to climate related environmental factors, an understanding of the ecophysiology underpinning thermal limits is essential for both conservation biology a nd invasion biology. 2. Heat tolerance and the extent to which heat tolerance differed with oxygen availability were examined for four native and four alien freshwater peracarid crustacean species, with differences in habitat use...

Data from: Mutation in the intracellular chloride channel CLCC1 associated with autosomal recessive retinitis pigmentosa

Lin Li, Xiaodong Jiao, Ilaria D’Atri, Fumihito Ono, Ralph Nelson, Chi-Chao Chan, Naoki Nakaya, Zhiwei Ma, Yan Ma, Xiaoying Cai, Longhua Zhang, Siying Lin, Abdul Hameed, Barry A. Chioza, Holly Hardy, Gavin Arno, Sarah Hull, Muhammad Imran Khan, James Fasham, V. Gaurav Harlalka, Michel Michaelides, Anthony T. Moore, Zeynep Hande Coban Akdemir, Shalini Jhangiani, James R. Lupski … & Frans P. M. Cremers
We identified a homozygous missense alteration (c.75C>A, p.D25E) in CLCC1, encoding a presumptive intracellular chloride channel highly expressed in the retina, associated with autosomal recessive retinitis pigmentosa (arRP) in eight consanguineous families of Pakistani descent. The p.D25E alteration decreased CLCC1 channel function accompanied by accumulation of mutant protein in granules within the ER lumen, while siRNA knockdown of CLCC1 mRNA induced apoptosis in cultured ARPE-19 cells. TALEN KO in zebrafish was lethal 11 days post...

Data from: A quantitative theory of gamma synchronization in macaque V1

Eric Lowet, Mark Jonathan Roberts, Alina Peter, Bart Gips & Peter De Weerd
Gamma-band synchronization coordinates brief periods of excitability in oscillating neuronal populations to optimize information transmission during sensation and cognition. Commonly, a stable, shared frequency over time is considered a condition for functional neural synchronization. Here, we demonstrate the opposite: instantaneous frequency modulations are critical to regulate phase relations and synchronization. In monkey visual area V1, nearby local populations driven by different visual stimulation showed different gamma frequencies. When similar enough, these frequencies continually attracted and...

Data from: Are acute and acclimated thermal effects on metabolic rate modulated by cell size? A comparison between diploid and triploid zebrafish larvae

Adam Hermaniuk, Iris L.E. Van De Pol & Wilco Verberk
Being composed of small cells may carry energetic costs related to maintaining ionic gradients across cell membranes as well as benefits related to diffusive oxygen uptake. Here we test the hypothesis that these costs and benefits of cell size in ectotherms are temperature dependent. To study the consequences of cell size for whole-organism metabolic rate we compared diploid and triploid zebrafish larvae differing in cell size. A fully factorial design was applied combining three different...

Changes in plant species richness due to land use and nitrogen deposition across the globe

Juan Gallego-Zamorano, Mark Huijbregts & Aafke Schipper
Data and scripts corresponding to the article "Combined effects of land use and nitrogen deposition on plant species richness worldwide". In the article, we quantified the combined effects of land use and nitrogen deposition on terrestrial plant species richness at a 0.25º spatial resolution across the globe. We first determined the proportional changes in plant species richness for different land-use types and N deposition values through meta-analyses of local monitoring data obtained from the literature....

Data from: Warming and eutrophication interactively drive changes in the methane-oxidizing community of shallow lakes

Thomas P.A. Nijman, Thomas A. Davidson, Stefan T.J. Weideveld, Joachim Audet, Chiara Esposito, Eti E. Levi, Adrian Ho, Leon P.M. Lamers, Erik Jeppesen & Annelies J. Veraart
Freshwater ecosystems are the largest natural source of the greenhouse gas methane (CH4), with shallow lakes a particular hot spot. Eutrophication and warming generally increase lake CH4 emissions but their impacts on the sole biological methane sink - methane oxidation - and methane-oxidizer community dynamics are poorly understood. We used the world’s longest-running freshwater climate-change mesocosm experiment to determine how methane-oxidizing bacterial (MOB) abundance and composition, and methane oxidation potential in the sediment respond to...

The metabolic hormone adiponectin affects the correlation between nutritional status and pneumococcal vaccine response in vulnerable indigenous children

Kris E. Siegers, Antonius E. Van Herwaarden, Jacobus H. De Waard, Berenice Del Nogal, Peter W.M. Hermans, Doorlène Van Tienoven, Guy A.M. Berbers, Marien I. De Jonge & Lilly M. Verhagen
Background: Almost 200 million children worldwide are either undernourished or overweight. Only a few studies have addressed the effect of variation in nutritional status on vaccine response. We previously demonstrated an association between stunting and an increased post-vaccination 13-valent pneumococcal conjugate vaccine (PCV13) response. In this prospective study, we assessed to what extent metabolic hormones may be a modifier in the association between nutritional status and PCV13 response. Methods: Venezuelan children aged 6 weeks to...

Additional file 2 of Infraslow closed-loop brain training for anxiety and depression (ISAD): a protocol for a randomized, double-blind, sham-controlled pilot trial in adult females with internalizing disorders

Tyson M. Perez, Paul Glue, Divya B. Adhia, Muhammad S. Navid, Jiaxu Zeng, Peter Dillingham, Mark Smith, Imran K. Niazi, Calvin K. Young & Dirk De Ridder
Additional file 2. PCC voxelsR1.

Data from: Occipital alpha activity during stimulus processing gates the information flow to object-selective cortex

Johanna M. Zumer, René Scheeringa, Jan-Mathijs Schoffelen, David G. Norris & Ole Jensen
Given the limited processing capabilities of the sensory system, it is essential that attended information is gated to downstream areas, whereas unattended information is blocked. While it has been proposed that alpha band (8–13 Hz) activity serves to route information to downstream regions by inhibiting neuronal processing in task-irrelevant regions, this hypothesis remains untested. Here we investigate how neuronal oscillations detected by electroencephalography in visual areas during working memory encoding serve to gate information reflected...

Data from: The simultaneous inducibility of phytochemicals related to plant direct and indirect defences against herbivores is stronger at low elevation

Loïc Pellissier, Xoaquín Moreira, Holger Danner, Martha Serrano, Nicolas Salamin, Nicole M. Van Dam & Sergio Rasmann
Ecological theory indicates that warmer and more stable climates should result in stronger biotic interactions. Therefore, plant species growing at lower elevations and experiencing greater herbivore pressure, should invest in higher levels of defences than those at higher elevations. Nonetheless, there are a number of studies that have found no effect of elevational gradients on plant defensive traits. Several factors might explain the lack of consistency for the altitude-defence relationships; including 1) the reduction of...

Data from: Recent and dynamic transposable elements contribute to genomic divergence under asexuality

Julie Ferreira De Carvalho, Victor De Jager, Thomas P. Van Gurp, Niels C.A.M. Wagemaker & Koen J.F. Verhoeven
Background: Transposable elements (TEs) are mobile pieces of genetic information with high mutagenic potential for the host genome. Transposition is often neutral or deleterious but may also generate potentially adaptive genetic variation. This additional source of variation could be especially relevant in non-recombining species reproducing asexually. However, evidence is lacking to determine the relevance of TEs in plant asexual genome evolution and their associated effects. Here, we characterize the repetitive fraction of the genome of...

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: A family-based study into penetrance in facioscapulohumeral muscular dystrophy type 1

Mariëlle Wohlgemuth, Richard J. Lemmers, Marianne Jonker, Ely Van Der Kooi, Corinne G. Horlings, Baziel G. Van Engelen, Silvere M. Van Der Maarel, George W. Padberg & Nicol C. Voermans
Objective: An observational cross-sectional study was conducted in a national facioscapulohumeral muscular dystrophy (FSHD) expertise center to estimate the penetrance of FSHD1 and to evaluate phenotype–genotype correlations. Methods: Ten FSHD1 probands carrying 4–9 D4Z4 unit alleles and 140 relatives were examined. All 150 participants were genetically characterized, including D4Z4 methylation levels in the mutation carriers. Mutation carriers were classified as (1) symptomatic: with symptoms of muscle weakness on history and muscle FSHD signs on examination;...

Data from: Belowground complementarity effects in a grassland biodiversity experiment are related to deep-rooting species

Natalie J. Oram, Janneke M. Ravenek, Kathryn E. Barry, Alexandra Weigelt, Hongmei Chen, Arthur Gessler, Annette Gockele, Hans De Kroon, Jan Willem Van Der Paauw, Michael Scherer-Lorenzen, Annemiek Smit-Tiekstra, Jasper Van Ruijven & Liesje Mommer
1. Belowground resource partitioning is often proposed as the underlying mechanism for the positive relationship between plant species richness and productivity. For example, if species have different root distributions, a mixture of plant species may be able to use the available resources more completely than the individual species in a monoculture. However, there is little experimental evidence for differentiation in vertical root distributions among species and its contribution to biodiversity effects. 2. We determined species-specific...

Data from: Costs and benefits of admixture between foreign genotypes and local populations in the field

Jun Shi, Jasmin Joshi, Katja Tielborger, Koen J. F. Verhoeven & Mirka Macel
Admixture is the hybridization between populations within one species. It can increase plant fitness and population viability by alleviating inbreeding depression and increasing genetic diversity. However, populations are often adapted to their local environments and admixture with distant populations could break down local adaptation by diluting the locally adapted genomes. Thus, admixed genotypes might be selected against and be outcompeted by locally adapted genotypes in the local environments. To investigate the costs and benefits of...

Data from msGBS: A new high-throughput approach to quantify the relative species abundance in root samples of multi-species plant communities

Niels Wagemaker
Plant interactions are as important belowground as aboveground. Belowground plant interactions are however inherently difficult to quantify, as roots of different species are difficult to disentangle. Although for a couple of decades molecular techniques have been successfully applied to quantify root abundance, root identification and quantification in multi-species plant communities remains particularly challenging. Here we present a novel methodology, multi-species Genotyping By Sequencing (msGBS), as a next step to tackle this challenge. First, a multi-species...

Mammal population densities at a global scale are higher in human-modified areas

Marlee A. Tucker, Luca Santini, Chris Carbone & Thomas Mueller
Global landscapes are changing due to human activities with consequences for both biodiversity and ecosystems. For single species, terrestrial mammal population densities have shown mixed responses to human pressure, with both increasing and decreasing densities reported in the literature. How the impacts of human activities on mammal populations translates into altered global density patterns remains unclear. Here we aim to disentangle the effect of human impacts on large-scale patterns of mammal population densities using a...

Data from: Effects of admixture in native and invasive populations of Lythrum salicaria

Jun Shi, Mirka Macel, Katja Tielbörger, Koen J.F. Verhoeven & Koen J. F. Verhoeven
Intraspecific hybridization between diverged populations can enhance fitness via various genetic mechanisms. The benefits of such admixture have been proposed to be particularly relevant in biological invasions, when invasive populations originating from different source populations are found sympatrically. However, it remains poorly understood if admixture is an important contributor to plant invasive success and how admixture effects compare between invasive and native ranges. Here, we used experimental crosses in Lythrum salicaria, a species with well-established...

Data from: Modeling the impact of Plasmodium falciparum sexual stage immunity on the composition and dynamics of the human infectious reservoir for malaria in natural settings

André Lin Ouédraogo, Philip A. Eckhoff, Adrian J. F. Luty, Will Roeffen, Robert W. Sauerwein, Teun Bousema & Edward A. Wenger
Malaria transmission remains high in Sub-Saharan Africa despite large-scale implementation of malaria control interventions. A comprehensive understanding of the transmissibility of infections to mosquitoes may guide the design of more effective transmission reducing strategies. The impact of P. falciparum sexual stage immunity on the infectious reservoir for malaria has never been studied in natural settings. Repeated measurements were carried out at start-wet, peak-wet and dry season, and provided data on antibody responses against gametocyte/gamete antigens...

Data from: Why time-limited individuals can make populations more vulnerable to disturbance

Henk-Jan Van Der Kolk, Bruno Ens, Magali Frauendorf, Eelke Jongejans, Kees Oosterbeek, Willem Bouten & Martijn Van De Pol
Individual variation in disturbance vulnerability (i.e. the likelihood that disturbance negatively affects an individual’s fitness) can affect how disturbance impacts animal populations, as even at low disturbance levels some individuals could be severely affected and die. Individual variation in vulnerability can arise due to different responses to disturbance. We propose a new hypothesis that even when individuals respond similarly to disturbance, time-limited individuals are more at risk that their condition deteriorates since they have limited...

Data from: Species abundance fluctuations over 31 years are associated with plant-soil feedback in a species-rich mountain meadow

, Tomáš Herben, Annelien Van Den Brink, Eric Visser & Hans De Kroon
1. Increasing evidence suggest that plant-soil interactions play an essential role in plant community assembly processes. Empirical investigations show that plant species abundance in the field is often related to plant-soil biota interactions, however, the direction of these relations have yielded inconsistent results. 2. We combined unique 31-year long field data on species abundances from a species-rich mountain meadow with single time point plant-soil feedback greenhouse experiments of 24 co-occurring plant species. We tested whether...

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