45 Works

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...

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...

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: 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: PCR duplication: a one-step cloning-free method to generate duplicated chromosomal loci and interference-free expression reporters in yeast

Florian Huber, Matthias Meurer, Daria Bunina, Ilia Kats, Céline I. Maeder, Martin Štefl, Cyril Mongis & Michael Knop
Here, we report on a novel PCR targeting-based strategy called ‘PCR duplication’ that enables targeted duplications of genomic regions in the yeast genome using a simple PCR-based approach. To demonstrate its application we first duplicated the promoter of the FAR1 gene in yeast and simultaneously inserted a GFP downstream of it. This created a reporter for promoter activity while leaving the FAR1 gene fully intact. In another experiment, we used PCR duplication to increase the...

Data from: Visual landmarks sharpen grid cell metric and confer context specificity to neurons of the medial entorhinal cortex

José Antonio Pérez-Escobar, Olga Kornienko, Patrick Latuske, Laura Kohler & Kevin Allen
Neurons of the medial entorhinal cortex (MEC) provide spatial representations critical for navigation. In this network, the periodic firing fields of grid cells act as a metric element for position. The location of the grid firing fields depends on interactions between self-motion information, geometrical properties of the environment and nonmetric contextual cues. Here, we test whether visual information, including nonmetric contextual cues, also regulates the firing rate of MEC neurons. Removal of visual landmarks caused...

Data from: Contrasting heterozygosity-fitness correlations across life in a long-lived seabird

Coraline Bichet, Oscar Vedder, Hedwig Sauer-Gürth, Peter H. Becker, Michael Wink & Sandra Bouwhuis
Selection is a central force underlying evolutionary change and can vary in strength and direction, for example across time and space. The fitness consequences of individual genetic diversity have often been investigated by testing for multi-locus heterozygosity-fitness correlations (HFCs), but few studies have been able to assess HFCs across life stages and in both sexes. Here, we test for HFCs using a 26-year longitudinal individual-based dataset from a large population of a long-lived seabird (the...

Data from: Are the radiations of temperate lineages in tropical alpine ecosystems pre-adapted?

Nicolai M. Nürk, Florian Michling & Hans Peter Linder
Aim: Tropical mountains around the world harbour an extraordinarily rich pool of plant species and are hotspots of biodiversity. Climatically, they can be zoned into montane climates at mid-altitudes and tropical alpine climates above the tree line. Around half of the tropical alpine species belong to plant lineages with a temperate ancestry, although these regions are often geographically distant. We test the hypothesis that these temperate lineages are pre-adapted to the tropical alpine climate. Location:...

Data from: Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants

Lua Lopez, Rodolfo Barreiro, Markus Fischer & Marcus A. Koch
Background: Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest. Methods: Here, we explored the use of publicly available ESTs (GenBank at the National...

Data from: Single-molecule imaging and quantification of the immune-variant adhesin VAR2CSA on knobs of Plasmodium falciparum-infected erythrocytes

Cecilia P. Sanchez, Christos Karathanasis, Rodrigo Sanchez, Marek Cyrklaff, Julia Jäger, Bernd Buchholz, Ulrich S. Schwarz, Mike Heilemann & Michael Lanzer
PfEMP1 (erythrocyte membrane protein 1) adhesins play a pivotal role in the pathophysiology of falciparum malaria, by mediating sequestration of Plasmodium falciparum-infected erythrocytes in the microvasculature. PfEMP1 variants are expressed by var genes and are presented on membrane elevations, termed knobs. However, the organization of PfEMP1 on knobs is largely unclear. Here, we use super-resolution microscopy and genetically altered parasites expressing a modified var2csa gene in which the coding sequence of the photoactivatable mEOS2 was...

Data from: Frequency and characteristics of MODY 1 (HNF4A mutation) and MODY 5 (HNF1B mutation) - Analysis from the DPV database

Katharina Warncke, Sebastian Kummer, Klemens Raile, Jürgen Grulich-Henn, Joachim Woelfle, Elisabeth Steichen, Nicole Prinz & Reinhard W. Holl
Objective. To characterize initial presentation and clinical course of patients with hepatocyte nuclear factor (HNF) 4A- and HNF1B-MODY in a multinational registry. Design, setting and participants. Within the Diabetes Patienten Verlaufsdokumentation (DPV) registry, 44 patients with HNF4A- and 35 patients with HNF1B-MODY were characterized and compared with patients < 20years old with type 1 diabetes (T1D)/type 2 diabetes (T2D). Main outcome measure. Clinical and laboratory parameters, therapy, metabolic control, and extrapancreatic symptoms in patients with...

Data from: Out of the Mediterranean? post-glacial colonisation pathways varied among cold-water coral species

Joana Boavida, Ronan Becheler, Marvin Choquet, Norbert Frank, Marco Taviani, Jean-Francois Bourillet, Anne-Leila Meistertzheim, Anthony Grehan, Alessandra Savini & Sophie Arnaud-Haond
Aim. To infer cold-water corals' post-glacial phylogeography and assess the role of Mediterranean Sea glacial refugia as origins for the recolonisation of the northeastern Atlantic Ocean. Location. Northeastern Atlantic Ocean and Mediterranean Sea. Taxon. Lophelia pertusa, Madrepora oculata. Methods. We sampled cold-water corals using remotely operated vehicles and one sediment core for coral and sediment dating. We characterized spatial genetic patterns (microsatellites and a nuclear gene fragment) using networks, clustering and measures of genetic differentiation....

Data from: Taming the wild: resolving the gene pools of non-model Arabidopsis lineages

Nora Hohmann, Roswitha Schmickl, Tzen-Yuh Chiang, Magdalena Lučanová, Filip Kolář, Karol Marhold & Marcus A. Koch
Background: Wild relatives in the genus Arabidopsis are recognized as useful model systems to study traits and evolutionary processes in outcrossing species, which are often difficult or even impossible to investigate in the selfing and annual Arabidopsis thaliana. However, Arabidopsis as a genus is littered with sub-species and ecotypes which make realizing the potential of these non-model Arabidopsis lineages problematic. There are relatively few evolutionary studies which comprehensively characterize the gene pools across all of...

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...

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...

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...

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