41 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...

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: 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: 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: 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...

Data from: Rapid morphological changes, admixture and invasive success in populations of Ring-necked parakeets (Psittacula krameri) established in Europe

Ariane Le Gros, Sarah Samadi, Dario Zuccon, Raphaël Cornette, Michael P. Braun, Juan Carlos Senar & Philippe Clergeau
The Ring-necked parakeet (Psittacula krameri), native of Asia and Africa, is a very successful invasive species in Europe: it has been present there for over 50 years. A recent study showed that European invasive populations occupy a colder climatic niche than in their native range but the establishment of this tropical species in temperate regions remains unexplained. Two main hypotheses may explain the success of Ring-necked parakeet in Europe: admixture between individuals from different origins...

Data from: Brassicales phylogeny inferred from 72 plastid genes: a reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses

Patrick P. Edger, Jocelyn C. Hall, Alex Harkess, Michelle Tang, Jill Coombs, Setareh Mohammadin, M. Eric Schranz, Zhiyong Xiong, James Leebens-Mack, Blake C. Meyers, Kenneth J. Systma, Marcus A. Koch, Ihsan A. Al-Shehbaz, J. Chris Pires & Kenneth J. Sytsma
PREMISE OF THE STUDY - Previous phylogenetic studies employing molecular markers have yielded various insights into the evolutionary history across Brassicales, but many relationships between families remain poorly supported or unresolved. A recent phylotranscriptomic approach utilizing 1155 nuclear markers obtained robust estimates for relationships among 14 of 17 families. Here we report a complete family‐level phylogeny estimated using the plastid genome. METHODS - We conducted phylogenetic analyses on a concatenated data set comprising 44,926 bp...

Data from: Identification, visualization and clonal analysis of intestinal stem cells in fish

Narges Aghaallaei, Franziska Gruhl, Colin Q. Schaefer, Tobias Wernet, Venera Weinhardt, Lázaro Centanin, Felix Loosli, Tilo Baumbach & Joachim Wittbrodt
Recently, a stochastic model of symmetrical stem cell division followed by neutral drift has been proposed for intestinal stem cells (ISCs). This division mode has been suggested to represent the predominant mode of stem cell progression in mammals. In contrast, stem cells in the retina of teleost fish show a preferential asymmetric division mode. To address whether the mode of stem cell division is following phylogenetic or ontogenetic routes we characterized and analysed the entire...

Data from: Molecular resources from transcriptomes in the Brassicaceae family

Lua Lopez, Eva M. Wolf, J. Chris Pires, Patrick P. Edger & Marcus A. Koch
The rapidly falling costs and the increasing availability of large DNA sequence data sets facilitate the fast and affordable mining of large molecular markers data sets for comprehensive evolutionary studies. The Brassicaceae (mustards) are an important species-rich family in the plant kingdom with taxa distributed worldwide and a complex evolutionary history. We performed Simple Sequence Repeats (SSRs) mining using de novo assembled transcriptomes from 19 species across the Brassicaceae in order to study SSR evolution...

Data from: A multilocus molecular phylogeny for the avian genus Liocichla (Passeriformes: Leiothrichidae: Liocichla)

Herman L. Mays, Bailey D. McKay, Dieter Thomas Tietze, Cheng-Te Yao, Lindsey N. Miller, Kathleen N. Moreland & Fumin Lei
Background: Historically the babblers have been assigned to the family Timaliidae but several recent studies have attempted to rest the taxonomy of this diverse passerine assemblage on a more firm evolutionary footing. The result has been a major rearrangement of the group. A well-supported and comprehensive phylogeny for this widespread avian group is an important part of testing evolutionary and biogeographic hypotheses, especially in Asia where the babblers are a key component of many forest...

Data from: How weather instead of urbanity measures affects song trait variability in three European passerine bird species

Julia E. Schäfer, Marcel M. Janocha, Sebastian Klaus & Dieter Thomas Tietze
Previous studies detected an influence of urban characteristics on song traits in passerine birds, that is, song adjustments to ambient noise in urban areas. Several studies already described the effect of weather conditions on the behavior of birds, but not the effect on song traits. We investigate, if song trait variability changes along a continuous urbanity gradient in Frankfurt am Main, Germany. We examined, for the first time on a larger scale, the influence of...

Data from: Resting-state gamma-band power alterations in schizophrenia reveal E/I-balance abnormalities across illness-stages

Tineke Grent-'T-Jong, Joachim Gross, Jozien Goense, Michael Wibral, Ruchika Gajwani, Andrew I. Gumley, Stephen M. Lawrie, Matthias Schwannauer, Frauke Schultze-Lutter, Tobias Navarro Schröder, Dagmar Koethe, F. Markus Leweke, Wolf Singer & Peter J. Uhlhaas
We examined alterations in E/I-balance in schizophrenia (ScZ) through measurements of resting-state gamma-band activity in participants meeting clinical high-risk (CHR) criteria (n = 88), 21 first episode (FEP) patients and 34 chronic ScZ-patients. Furthermore, MRS-data were obtained in CHR-participants and matched controls. Magnetoencephalographic (MEG) resting-state activity was examined at source level and MEG-data were correlated with neuropsychological scores and clinical symptoms. CHR-participants were characterized by increased 64–90 Hz power. In contrast, FEP- and ScZ-patients showed...

Knowledge and attitude of infection prevention and control practices among health care workers caring for patients with suspected or confirmed COVID-19

Eman H. Elsebaie, Amany A. Salem, Amal S. Sedrak, Ahmed Ayad, Bassante A. El Razik, Sahar A. Ahmed & Noha M Abu Bakr Elsaid
Background: COVID-19 pandemic is growing rapidly, accounting for an increasing proportion of cases worldwide. Infection in healthcare facilities enhances very likely the local outbreaks, impacting mainly the elderly and vulnerable populations. All activities used to minimize the risk of infection spread are referred to as infection control measures. Therefore, this study aimed to; determine the proportion of SARS-COV2 infection among heath care workers (HCWs) caring for patients with suspected or confirmed COVID-19, assess their knowledge...

Toba Caldera geochronological and modelling dataset

Adonara Mucek, Martin Danisik, Shanaka De Silva, Daniel Miggins, Axel Schmitt, Indyo Pratomo, Anthony Koppers & Jack Gillespie
Bayesian statistical analysis and inverse thermal history modeling of feldspar 40Ar/39Ar and zircon (U-Th)/He ages reveal that post-caldera dome eruptions at Toba Caldera, Sumatra occurred up to ca. 13.6 kyr later than indicated by 40Ar/39Ar feldspar ages. This discordance implies cold storage of feldspar antecrysts prior to eruption for a maximum duration of ca. 5 and 13 kyr at between 280°C and 500°C. These findings connote that the solidified carapace of remnant magma after the...

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: 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...

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: 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...

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