45 Works

Data from: Post-Turing tissue pattern formation: advent of mechanochemistry

Felix Brinkmann, Moritz Mercker, Thomas Richter & Anna Marciniak-Czochra
Chemical and mechanical pattern formation is fundamental during embryogenesis and tissue development. Yet, the underlying molecular and cellular mechanisms are still elusive in many cases. Most current theories assume that tissue development is driven by chemical processes: either as a sequence of chemical patterns each depending on the previous one, or by patterns spontaneously arising from specific chemical interactions (such as “Turing-patterns”). Within both theories, mechanical patterns are usually regarded as passive by-products of chemical...

Data from: A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

, Anne Bruneau, Nasim Azani, Marielle Babineau, Edeline Gagnon, Carole Sinou, Royce Steeves, Erin Zimmerman, C. Donovan Bailey, Lynsey Kovar, Madhugiri Nageswara-Rao, Hannah Banks, RuthP. Clark, Manuel De La Estrella, Peter Gasson, GeoffreyC. Kite, BenteB. Klitgaard, GwilymP. Lewis, Danilo Neves, Gerhard Prenner, María De Lourdes Rico-Arce, ArianeR. Barbosa, Maria Cristina López-Roberts, Luciano Paganucci De Queiroz, PétalaG. Ribeiro … & Tingshuang Yi
The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most...

Data from: Ethanol abolishes vigilance-dependent astroglia network activation in mice by inhibiting norepinephrine release

Martin Paukert, Liang Ye, Murat Orynbayev, Xiangyu Zhu, Eunice Lim, Ram Dereddi, Amit Agarwal, Dwight Bergles & Manzoor Bhat
This collection of data sets was obtained during a study of the effect of acute ethanol intoxication on vigilance-dependent astroglia network activation in mice. The main findings have been that ethanol inhibits astroglia activation by inhibiting vigilance-dependent norepinephrine release. This leads to a failure of activation of alpha1A-adrenergic receptors on astroglia. Further, this study has revealed that ethanol inhibition of cerebellar Bergmann glia Ca2+ activation does not account for ataxic motor behavior, but may rather...

Survey of Core Facilities Raw Data

Isabelle Kos-Braun, Bjoern Gerlach & Claudia Pitzer
Recently, it has become evident that academic research faces issues with the reproducibility of research data. As Core Facilities (CFs) have a central position in the research infrastructure they are able to promote and disseminate good research standards through their users. To identify the most important factors for research quality, we polled 253 CFs across Europe about their practices and analysed in detail the interaction process between CFs and their users, from the first contact...

Evolutionary footprints of a cold relic in a rapidly warming world

Marcus Koch & Eva Wolf
With accelerating global warming, understanding the evolutionary dynamics of plant adaptation to environmental change is increasingly urgent. Here we reveal the enigmatic history of the genus Cochlearia (Brassicaceae), a Pleistocene relic that originated from a drought-adapted Mediterranean sister genus during the Miocene. Cochlearia rapidly diversified and adapted to circum-Arctic regions and other cold-characterized habitat types during the Pleistocene. This sudden change in ecological preferences was accompanied by a highly complex, reticulate polyploid evolution, which was...

Data from: Intracontinental plant invader shows matching genetic and chemical profiles and might benefit from high defence variation within populations

Lisa Johanna Tewes, Florian Michling, Marcus A. Koch & Caroline Müller
1. Whereas many studies have revealed mechanisms driving plant invasions between continents, research on intracontinental range-expanders is scarce. Therefore, we studied genetic, chemical and ecological traits of a range-expanding Brassicaceae, assuming that high genetic diversity should maintain chemical variation, which potentially benefits the invasion success. Moreover, we expected that within-individual defence diversity plays an essential role in biotic interactions. 2. We compared Bunias orientalis plants from 16 populations of native, invasive or exotic non-invasive origin....

Data from: Monophyletic origin and evolution of the largest crucifer genomes

Terezie Mandáková, Petra Hloušková, Dmitry A. German & Martin A. Lysak
Clade E, or the Hesperis-clade is one of the major Brassicaceae (Crucifereae) clades comprising some 48 genera and 351 species classified into seven tribes and is predominantly distributed across arid and montane regions of Asia. Several taxa have socio-economic significance, being important ornamental but also weedy and invasive species. From the comparative genomic perspective, the clade is noteworthy as it harbors species with the largest crucifer genomes but low numbers of chromosomes (n = 5...

Data from: Diversification patterns in the CES clade (Brassicaceae tribes Cremolobeae, Eudemeae, Schizopetaleae) in Andean South America

Diego Leonel Salariato, Fernando O. Zuloaga, Andreas Franzke, Klaus Mummenhoff & Ihsan A. Al-Shehbaz
Dated molecular phylogenetic trees show that the Andean uplift had a major impact on South American biodiversity. For many Andean groups, accelerated diversification (radiation) has been documented. However, not all Andean lineages appear to have diversified following the model of rapid radiation, particularly in the central and southern Andes. Here, we investigated the diversification patterns for the largest South American-endemic lineage of Brassicaceae, composed of tribes Cremolobeae, Eudemeae and Schizopetaleae (CES clade). Species of this...

Data from: Phylogeny and new taxonomy of the Booted Eagles (Accipitriformes: Aquilinae)

Heather R. L. Lerner, Les Christidis, Anita Gamauf, Carole Griffiths, Elisabeth Haring, Christopher J. Huddleston, Sonia Kabra, Annett Kocum, Meade Krosby, Kirsti Kvaloy, David Mindell, Pamela Rasmussen, Nils Rov, Rachel Wadleigh, Michael Wink & Jan Ove Gjershaug
We present a phylogeny of all booted eagles (38 extant and one extinct species) based on analysis of published sequences from seven loci. We find molecular support for five major clades within the booted eagles: Nisaetus (10 species), Spizaetus (4 species), Clanga (3 species), Hieraaetus (6 species) and Aquila (11 species), requiring generic changes for 14 taxa. Additionally, we recommend that the Long-crested Eagle (Lophaetus occipitalis) and the Black Eagle (Ictinaetus malaiensis) remain in their...

Data from: Non-rhythmic head-direction cells in the parahippocampal region are not constrained by attractor network dynamics

Olga Kornienko, Patrick Latuske, Mathis Bassler, Laura Kohler & Kevin Allen
Computational models postulate that HD cells are part of an attractor network integrating angular head turns. This network requires inputs from visual landmarks to anchor the HD signal to the external world. We investigated whether information about HD and visual landmarks is integrated in the medial entorhinal cortex and parasubiculum, resulting in neurons expressing a conjunctive code for HD and visual landmarks. We found that parahippocampal HD cells could be divided into two classes based...

Data from: Wnt/PCP controls spreading of Wnt/β-catenin signals by cytonemes in vertebrates

Benjamin Mattes, Yonglong Dang, Gediminas Greicius, Lilian Tamara Kaufmann, Benedikt Prunsche, Jakob Rosenbauer, Johannes Stegmaier, Ralf Mikut, Suat Özbek, Gerd Ulrich Nienhaus, Alexander Schug, David M. Virshup & Steffen Scholpp
Signaling filopodia, termed cytonemes, are dynamic actin-based membrane structures that regulate the exchange of signaling molecules and their receptors within tissues. However, how cytoneme formation is regulated remains unclear. Here, we show that Wnt/PCP autocrine signaling controls the emergence of cytonemes, and that cytonemes subsequently control paracrine Wnt/β-catenin signal activation. Upon binding of the Wnt family member Wnt8a, the receptor tyrosine kinase Ror2 gets activated. Ror2/PCP signaling leads to induction of cytonemes, which mediate transport...

Exploring whole-genome duplicate gene retention with complex genetic interaction analysis

Elena Kuzmin, Benjamin VanderSluis, Alex N. Nguyen Ba, Wen Wang, Elizabeth N. Koch, Matej Usaj, Anton Khmelinskii, Mojca Mattiazzi Usaj, Jolanda Van Leeuwen, Oren Kraus, Amy Tresenrider, Michael Pryszlak, Ming-Che Hu, Brenda Varriano, Michael Costanzo, Michael Knop, Alan Moses, Chad L. Myers, Brenda J. Andrews & Charles Boone
Whole-genome duplication has played a central role in genome evolution of many organisms, including the human genome. Most duplicated genes are eliminated and factors that influence the retention of persisting duplicates remain poorly understood. Here, we describe a systematic complex genetic interaction analysis with yeast paralogs derived from the whole-genome duplication event. Mapping digenic interactions for a deletion mutant of each paralog and trigenic interactions for the double mutant provides insight into their roles and...

Data from: Sex differentiation in grayling (Salmonidae) goes through an all-male stage and is delayed in genetic males who instead grow faster

Diane Maitre, Oliver M. Selmoni, Anshu Uppal, Lucas Marques Da Cunha, Laetitia G. E. Wilkins, Julien Roux, Kenyon B. Mobley, Isabelle Castro, Susanne Knörr, Marc Robinson-Rechavi & Claus Wedekind
Fish populations can be threatened by distorted sex ratios that arise during sex differentiation. Here we describe sex differentiation in a wild grayling (Thymallus thymallus) population that suffers from distorted sex ratios. We verified that sex determination is linked to the sex determining locus (sdY) of salmonids. This allowed us to study sex-specific gene expression and gonadal development. Sex-specific gene expression could be observed during embryogenesis and was strong around hatching. About half of the...

Data from: Alcohol reduces muscle fatigue through atomistic interactions with nicotinic receptors

Hamid R. Noori, Christian Mücksch, Valentina Vengeliene, Kai Schönig, Tatiane T. Takahashi, Nuriya Mukhtasimova, Maryam Bagher Oskouei, Matias Mosqueira, Dusan Bartsch, Rainer Fink, Herbert M. Urbassek, Rainer Spanagel & Steven M. Sine
Alcohol consumption affects many organs and tissues, including skeletal muscle. However, the molecular mechanism of ethanol action on skeletal muscle remains unclear. Here, using molecular dynamics simulations and single channel recordings, we show that ethanol interacts with a negatively charged amino acid within an extracellular region of the neuromuscular nicotinic acetylcholine receptor (nAChR), thereby altering its global conformation and reducing the single channel current amplitude. Charge reversal of the negatively charged amino acid abolishes the...

Data from: Demographic expansion and genetic load of the halophyte model plant Eutrema salsugineum

Xiao-Juan Wang, Quan-Jun Hu, Xin-Yi Guo, Kun Wang, Da-Fu Ru, Dmitry A. German, Elizabeth A. Weretilnyk, Richard J. Abbott, Martin Lascoux & Jian-Quan Liu
Eutrema salsugineum is a widely distributed species, which provide a good model to study long-distance dispersal and accumulation of deleterious mutations. Based on population genomic data, we clarified demographic history of E. salsugineum and showed how deleterious alleles accumulated.

Data from: A global genetic interaction network maps a wiring diagram of cellular function

Michael Costanzo, Benjamin VanderSluis, Elizabeth N. Koch, Anastasia Baryshnikova, Carles Pons, Guihong Tan, Wen Wang, Matej Usaj, Julia Hanchard, Susan D. Lee, Vicent Pelechano, Erin B. Styles, Maximilian Billmann, Jolanda Van Leeuwen, Nydia Van Dyk, Zhen-Yuan Lin, Elena Kuzmin, Justin Nelson, Jeff S. Piotrowski, Tharan Srikumar, Sondra Bahr, Yiqun Chen, Raamesh Deshpande, Christoph F. Kurat, Sheena C. Li … & Charles Boone
INTRODUCTION: Genetic interactions occur when mutations in two or more genes combine to generate an unexpected phenotype. An extreme negative or synthetic lethal genetic interaction occurs when two mutations, neither lethal individually, combine to cause cell death. Conversely, positive genetic interactions occur when two mutations produce a phenotype that is less severe than expected. Genetic interactions identify functional relationships between genes and can be harnessed for biological discovery and therapeutic target identification. They may also...

Data from: The sickle cell trait affects contact dynamics and endothelial cell activation in Plasmodium falciparum-infected erythrocytes

Christine Lansche, Anil K. Dasanna, Katharina Quadt, Benjamin Fröhlich, Dimitris Missirlis, Marilou Tetard, Benoit Gamain, Bernd Buchholz, Cecilia P. Sanchez, Motomu Tanaka, Ulrich S. Schwarz & Michael Lanzer
Sickle cell trait, a common hereditary blood disorder, protects carriers from severe disease in infections with the human malaria parasite Plasmodium falciparum. Protection is associated with a reduced capacity of parasitized erythrocytes to cytoadhere to the microvascular endothelium and cause vaso-occlusive events. However, the underpinning cellular and biomechanical processes are only partly understood and the impact on endothelial cell activation is unclear. Here, we show, by combining quantitative flow chamber experiments with multiscale computer simulations...

Data from: Oligocene niche shift, Miocene diversification - cold tolerance and accelerated speciation rates in the St. John's Worts (Hypericum, Hypericaceae)

Nicolai M. Nürk, Simon Uribe-Convers, Berit Gehrke, David C. Tank & Frank R. Blattner
Background: Our aim is to understand the evolution of species-rich plant groups that shifted from tropical into cold/temperate biomes. It is well known that climate affects evolutionary processes, such as how fast species diversify, species range shifts, and species distributions. Many plant lineages may have gone extinct in the Northern Hemisphere due to Late Eocene climate cooling, while some tropical lineages may have adapted to temperate conditions and radiated; the hyper-diverse and geographically widespread genus...

Data from: A time-calibrated road map of Brassicaceae species radiation and evolutionary history

Nora Hohmann, Eva M. Wolf, Martin A. Lysak & Marcus A. Koch
The Brassicaceae include several major crop plants and numerous important model species in comparative evolutionary research such as Arabidopsis, Brassica, Boechera, Thellungiella, and Arabis species. As any evolutionary hypothesis needs to be placed in a temporal context, reliably dated major splits within the evolution of Brassicaceae are essential. We present a comprehensive time-calibrated framework with important divergence time estimates based on whole-chloroplast sequence data for 29 Brassicaceae species. Diversification of the Brassicaceae crown group started...

Data from: Middle Bronze Age land use practices in the north-western Alpine foreland – A multi-proxy study of colluvial deposits, archaeological features and peat bogs

Sascha Scherer, Benjamin Höpfer, Katleen Deckers, Elske Fischer, Markus Fuchs, Ellen Kandeler, Eva Lehndorff, Johanna Lomax, Sven Marhan, Elena Marinova, Julia Meister, Christian Poll, Humay Rahimova, Manfred Rösch, Kristen Wroth, Julia Zastrow, Thomas Knopf, Thomas Scholten & Peter Kühn
This paper aims to reconstruct Middle Bronze Age (MBA) land use practices in the north-western Alpine foreland (SW Germany, Hegau). We used a multi-proxy approach including the biogeochemical proxies from colluvial deposits in the surrounding of the well-documented settlement site of Anselfingen and offsite pollen data from two peat bogs. This approach allowed in-depth insights into the MBA subsistence economy and shows that the MBA in the north-western Alpine foreland was a period of establishing...

A scalable realization of local U(1) gauge invariance in cold atomic mixtures

Fred Jendrzejewski, Markus K. Oberthaler, Alexander Mil, Torsten V. Zache, Apoorva Hedge, Andy Xia, Rohit P. Bhatt, Philipp Hauke & Jürgen Berges
In the fundamental laws of physics, gauge fields mediate the interaction between charged particles. An example is quantum electrodynamics -- the theory of electrons interacting with the electromagnetic field -- based on U(1) gauge symmetry. Solving such gauge theories is in general a hard problem for classical computational techniques. While quantum computers suggest a way forward, it is difficult to build large-scale digital quantum devices required for complex simulations. Here, we propose a fully scalable...

Chironomid assemblages and inferred summer temperature from the Last Glacial Period (ca. 98–46 ka), from Füramoos, Southern Germany

Alexander Bolland, Oliver Kern, Frederik Allstädt, Dorothy Peteet3, Andreas Koutsodendris, Jörg Pross & Oliver Heiri
The data herein presents a new chironomid record and associated chironomid-based temperature reconstruction covering the time interval ca. 98–46 ka from the palaeolake Füramoos, Southern Germany. These data also include non-chironomid invertebrate remains, including Ceratopogonidae, Daphnia and Ephemeroptera as well as Characean oospores.

Genetic admixture despite ecological segregation in a North African sparrow hybrid zone (Aves, Passeriformes, Passer domesticus x Passer hispaniolensis)

Martin Päckert, Abdelkrim Belkacem, Hannes Wolfgramm, Oliver Gast, David Canal, Gabriele Giacalone, Mario Lo Valvo, Melita Vamberger, Michael Wink, Jochen Martens & Heiko Stuckas
Under different environmental conditions hybridization between the same species might result in different patterns of genetic admixture. Particularly, species pairs with large distribution ranges and long evolutionary history may have experienced several independent hybridization events over time in different zones of overlap. In birds, the diverse hybrid populations of the house sparrow (Passer domesticus) and the Spanish sparrow (P. hispaniolensis) provide a striking example. Throughout their range of sympatry, these two species do not regularly...

European soil seed bank communities across a climate and land-cover gradient

Jan Plue, Hans Van Calster, Inger Auestad, Sofia Basto, Reneé M. Bekker, Hans Henrik Bruun, Richard Chevalier, Guillaume Decocq, Ulf Grandin, Martin Hermy, Hans Jacquemyn, Anna Jakobsson, Rein Kalamees, Rob H. Marrs, Bryndis Marteinsdóttir, Per Milberg, Robin J. Pakeman, Gareth Phoenix, Ken Thompson, Vigdis Vandvik, Markus Wagner, Sara A.O. Cousins, Ove Eriksson, Jamshid Ghorbani, Małgorzata Jankowska-Błaszczuk … & Alistair G. Auffret
This is the data set used for the publication Buffering effects of soil seed banks on plant community composition in response to land use and climate, published in the journal Global Ecology and Biogeography. Aim. Climate and land use are key determinants of biodiversity, with past and ongoing changes posing serious threats to global ecosystems. Unlike most other organism groups, plant species can possess dormant life-history stages such as soil seed banks, which may help...

A little damping goes a long way: code and data

Steve Heim, Matthew Millard, Charlotte Le Mouel & Alexander Badri-Spröwitz
It is currently unclear if damping plays a functional role in legged locomotion, and simple models often do not include damping terms. We present a new model with a damping term that is isolated from other parameters: that is, the damping term can be adjusted without retuning other model parameters for nominal motion. We systematically compare how increased damping affects stability in the face of unexpected ground-height perturbations. Unlike most studies, we focus on task-level...

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