60 Works

Data from: The telomeric DNA damage response occurs in the absence of chromatin decompaction

Aleksandra Vancevska, Kyle M. Douglass, Verena Pfeiffer, Suliana Manley & Joachim Lingner
Telomeres are specialized nucleoprotein structures that protect chromosome ends from DNA damage response (DDR) and DNA rearrangements. The telomeric shelterin protein TRF2 suppresses the DDR, and this function has been attributed to its abilities to trigger t-loop formation or prevent massive decompaction and loss of density of telomeric chromatin. Here, we applied stochastic optical reconstruction microscopy (STORM) to measure the sizes and shapes of functional human telomeres of different lengths and dysfunctional telomeres that elicit...

Data from: On the (un)predictability of a large intragenic fitness landscape

Claudia Bank, Sebastian Matuszewski, Ryan T. Hietpas & Jeffrey D. Jensen
The study of fitness landscapes, which aims at mapping genotypes to fitness, is receiving ever-increasing attention. Novel experimental approaches combined with next-generation sequencing (NGS) methods enable accurate and extensive studies of the fitness effects of mutations, allowing us to test theoretical predictions and improve our understanding of the shape of the true underlying fitness landscape and its implications for the predictability and repeatability of evolution. Here, we present a uniquely large multiallelic fitness landscape comprising...

Phenotypic plasticity versus ecotypic differentiation under recurrent summer drought in two drought-tolerant pine species

Christoph Bachofen, Anouchka Perret-Gentil, Tom Wohlgemuth, Pierre Vollenweider & Barbara Moser
1. Despite worldwide reports of high tree mortality, growing evidence indicates that many tree species are well adapted to survive repeated dry spells. The drought resilience of trees is related to their phenotypic plasticity and ecotypic differentiation. Whether these two mechanisms act at the same organisational level of a tree and involve similar plant traits is still unknown. 2. We assessed phenotypic plasticity and ecotypic differentiation across four populations of Pinus sylvestris and Pinus nigra...

CrossLoc Benchmark Datasets

Iordan Doytchinov, Qi Yan, Jianhao Zheng, Simon Reding & Shanci Li
To study the data-scarcity mitigation for learning-based visual localization methods via sim-to-real transfer, we curate and now present the CrossLoc benchmark datasets—a multimodal aerial sim-to-real data available for flights above nature and urban terrains. Unlike the previous computer vision datasets focusing on localization in a single domain (mostly real RGB images), the provided benchmark datasets include various multimodal synthetic cues paired to all real photos. Complementary to the paired real and synthetic data, we offer...

Data from: Male competition and the evolution of mating and life history traits in experimental populations of Aedes aegypti

Alima Qureshi, Andrew Aldersley, Brian Hollis, Alongkot Ponlawat & Lauren J. Cator
Aedes aegypti is an important disease vector and a major target of reproductive control efforts. We manipulated the opportunity for sexual selection in populations of Ae. aegypti by controlling the number of males competing for a single female. Populations exposed to higher levels of male competition rapidly evolved higher male competitive mating success relative to populations evolved in the absence of competition, with an evolutionary response visible after only five generations. We also detected correlated...

Data from: Intraneural stimulation elicits discrimination of textural features by artificial fingertip in intact and amputee humans

Calogero Maria Oddo, Stanisa Raspopovic, Fiorenzo Artoni, Alberto Mazzoni, Giacomo Spigler, Francesco Petrini, Giambattistelli Federica, Vecchio Fabrizio, Miraglia Francesca, Zollo Loredana, Giovanni Di Pino, Domenico Camboni, Maria Chiara Carrozza, Eugenio Guglielmelli, Paolo Maria Rossini, Ugo Faraguna & Silvestro Micera
Restoration of touch after hand amputation is a desirable feature of ideal prostheses. Here, we show that texture discrimination can be artificially provided in human subjects by implementing a neuromorphic real-time mechano-neuro-transduction (MNT), which emulates to some extent the firing dynamics of SA1 cutaneous afferents. The MNT process was used to modulate the temporal pattern of electrical spikes delivered to the human median nerve via percutaneous microstimulation in four intact subjects and via implanted intrafascicular...

Data from: Mitotic chromosome binding predicts transcription factor properties in interphase

Mahé Raccaud, Elias T. Friman, Andrea B. Alber, Harsha Agarwal, Cédric Deluz, Timo Kuhn, J. Christof M. Gebhardt & David M. Suter
Mammalian transcription factors (TFs) differ broadly in their nuclear mobility and sequence-specific/non-specific DNA binding. How these properties affect their ability to occupy specific genomic sites and modify the epigenetic landscape is unclear. The association of TFs with mitotic chromosomes observed by fluorescence microscopy is largely mediated by non-specific DNA interactions and differs broadly between TFs. Here we combine quantitative measurements of mitotic chromosome binding (MCB) of 501 TFs, TF mobility measurements by fluorescence recovery after...

Data from: Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers

George H. Perry, Matthieu Foll, Jean-Christophe Grenier, Etienne Patin, Yohann Nédélec, Alain Pacis, Maxime Barakatt, Simon Gravel, Xiang Zhou, Sam L. Nsobya, Laurent Excoffier, Lluis Quintana-Murci, Nathaniel J. Dominy & Luis B. Barreiro
The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions that are significantly associated with the pygmy phenotype in the Batwa, a rainforest hunter-gatherer population from Uganda (east central Africa). The identified genomic regions have multiple attributes that provide supporting evidence of genuine association with the pygmy phenotype, including...

Data from: Light availability impacts structure and function of phototrophic stream biofilms across domains and trophic levels

Mia M. Bengtsson, Karoline Wagner, Clarissa Schwab, Tim Urich & Tom J. Battin
Phototrophic biofilms are ubiquitous in freshwater and marine environments where they are critical for biogeochemical cycling, food webs and in industrial applications. In streams, phototrophic biofilms dominate benthic microbial life and harbor an immense prokaryotic and eukaryotic microbial biodiversity with biotic interactions across domains and trophic levels. Here, we examine how community structure and function of these biofilms respond to varying light availability, as the crucial energy source for phototrophic biofilms. Using metatranscriptomics, we found...

Data from: Computer assisted detection of axonal bouton structural plasticity in in vivo time-lapse images

Rohan Gala, Daniel Lebrecht, Daniela A. Sahlender, Anne Jorstad, Graham Knott, Anthony Holtmaat & Armen Stepanyants
The ability to measure minute structural changes in neural circuits is essential for long-term in vivo imaging studies. Here, we propose a methodology for detection and measurement of structural changes in axonal boutons imaged with time-lapse two-photon laser scanning microscopy (2PLSM). Correlative 2PLSM and 3D electron microscopy (EM) analysis, performed in mouse barrel cortex, showed that the proposed method has low fractions of false positive/negative bouton detections (2/0 out of 18), and that 2PLSM-based bouton...

Data from: The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards

Stefan Laurent, Susanne P. Pfeifer, Matthew Settles, Samuel S. Hunter, Kayla M. Hardwick, Louise Ormond, Vitor C. Sousa, Jeffrey D. Jensen, Erica Bree Rosenblum & Matthew L. Settles
Understanding the process of adaptation during rapid environmental change remains one of the central focal points of evolutionary biology. The recently formed White Sands system of southern New Mexico offers an outstanding example of rapid adaptation, with a variety of species having rapidly evolved blanched forms on the dunes that contrast with their close relatives in the surrounding dark soil habitat. In this study, we focus on two of the White Sands lizard species, Sceloporus...

Data from: Sexual selection shapes development and maturation rates in Drosophila

Brian Hollis, Laurent Keller & Tadeusz J. Kawecki
Explanations for the evolution of delayed maturity usually invoke trade-offs mediated by growth, but processes of reproductive maturation often continue long after growth has ceased. Here, we tested whether sexual selection shapes the rate of post-eclosion maturation in the fruit fly Drosophila melanogaster. We found that populations maintained for more than 100 generations under a short generation time and polygamous mating system evolved faster post-eclosion maturation and faster egg-to-adult development of males, when compared to...

Comparative analysis of time-based and quadrat sampling in seasonal population dynamics of intermediate hosts of human schistosomes

Francisco Javier Perez-Saez, Theophile Mande, Dramane Zongo & Andrea Rinaldo
Background Despite their importance for designing and evaluating schistosomiasis control trials, little attention in the literature has been dedicated to sampling protocols for the parasite's snail intermediate hosts since their first development. We propose a comparative analysis of time-based and quadrat sampling protocols to quantify the seasonal variations in the abundance of these aquatic snail species of medical importance. Methodology/Principal Findings Snail populations were monitored during 42 consecutive months in three types of habitats (ephemeral...

Long term irrigation experiment

Arun Bose, Andreas Rigling, Arthur Gessler, Frank Hagedorn, Ivano Brunner, Linda Feichtinger, Christof Bigler, Simon Egli, Sophia Etzold, Martin Gossner, Claudia Guidi, Mathieu Lévesque, Katrin Meusburger, Martina Peter, Matthias Saurer, Daniel Scherrer, Patrick Schleppi, Leonie Schönbeck, Michael Vogel, Georg Von Arx, Beat Wermelinger, Thomas Wohlgemuth, Roman Zweifel & Marcus Schaub
Climate change exposes ecosystems to strong and rapid changes in their environmental boundary conditions mainly due to the altered temperature and precipitation patterns. It is still poorly understood how fast interlinked ecosystem processes respond to altered environmental conditions, if these responses occur gradually or suddenly when thresholds are exceeded, and if the patterns of the responses will reach a stable state. We conducted an irrigation experiment in the Pfynwald, Switzerland from 2003-2018. A naturally dry...

Allometric escape from acoustic constraints in frog calls is rare

Joao Filipe Tonini, Diogo Provete, Natan Maciel, Alessandro Morais, Sandra Goutte, Felipe Toledo & R. Alexander Pyron
Allometric constraint is a product of natural selection, particularly with respect to body size and traits constrained by physical properties thereof, such as metabolism, longevity, and vocal frequency. Parameters describing allometric relationships are conserved across most lineages, indicating that physical constraints dictate scaling patterns in deep time, despite substantial genetic and ecological divergence among organisms. Acoustic allometry (sound frequency ~ body size) is conserved across frogs, in defiance of massive variation in both body size...

Warming may extend tree growing seasons and compensate for reduced carbon uptake during dry periods

Charlotte Grossiord, Christoph Bachofen, Jonas Gisler, Eugenie Mas, Yann Vitasse & Margaux Didion-Gency
1. Warming and drought alter plant phenology, photosynthesis and growth with important consequences for the global carbon cycle and the earth’s climate. Yet, few studies have attempted to tease apart their effects on tree phenology, particularly leaf senescence, and on source and sink activity. 2. We experimentally assessed the single and combined effects of warming and reduced soil moisture on the phenology (leaf-out and senescence date, growing season length) and aboveground sink (height and diameter...

Synthetic self-affine topography scanned with a virtual spherical probe

Tevis D. B. Jacobs, Till Junge & Lars Pastewka
This surface contains a self-affine topography that has been scanned with a spherical virtual probe of radius 40 nm. The probe was lowered normal to the surface on each point of the reference topography (that is also included here) and the center of the probe was taken as the "measured" value of the topography. The reference topography has a Hurst exponent of 0.8 and was generated with a Fourier-filtering algorithm. This surface was used to...

Data from: Cell proliferation and migration during early development of a symbiotic scleractinian coral

Agathe Lecointe, Isabelle Domart-Coulon, Paris Alain & Anders Meibom
In scleractinian reef-building corals, patterns of cell self-renewal, migration and death remain virtually unknown, limiting our understanding of cellular mechanisms underlying initiation of calcification, and ontogenesis of the endosymbiotic dinoflagellate relationship. In this study we pulse-labeled the coral Stylophora pistillata for 24 h with BrdU at four life stages (planula, early metamorphosis, primary polyp, and adult colony) to investigate coral and endosymbiont cell proliferation during development, while simultaneously recording TUNEL-positive, i.e. apoptotic, nuclei. In the...

Data from: Experimental evolution of slowed cognitive aging in Drosophila melanogaster

Martyna K. Zwoinska, Alexei A. Maklakov, Tadeusz J. Kawecki & Brian Hollis
Reproductive output and cognitive performance decline in parallel during aging, but it is unknown whether this reflects a shared genetic architecture or merely the declining force of natural selection acting independently on both traits. We used experimental evolution in Drosophila melanogaster to test for the presence of genetic variation for slowed cognitive aging, and assess its independence from that responsible for other traits’ decline with age. Replicate experimental populations experienced either joint selection on learning...

Quantification of Bone Marrow Compartments in Histological Sections

Josefine Tratwal & Olaia Naveiras
We report the development of a semi-automated image analysis plug-in, MarrowQuant, which employs the open-source software QuPath, to systematically quantify multiple bone components in H&E sections in an unbiased manner. MarrowQuant discerns and quantifies the areas occupied by bone, adipocyte ghosts, hematopoietic cells and the interstitial/microvascular compartment. A separate feature, AdipoQuant, fragments adipocyte ghosts in H&E-stained sections of extramedullary adipose tissue sections to render adipocyte area and size distribution. Quantification of BM hematopoietic cellularity with...

Data from: The effects of aging on neuropil structure in mouse somatosensory cortex—A 3D electron microscopy analysis of layer 1

Corrado Cali, Marta Wawrzyniak, Carlos Becker, Bohumil Maco, Marco Cantoni, Anne Jorstad, Biagio Nigro, Federico Grillo, Vincenzo De Paola, Pascal Fua & Graham William Knott
This study has used dense reconstructions from serial EM images to compare the neuropil ultrastructure and connectivity of aged and adult mice. The analysis used models of axons, dendrites, and their synaptic connections, reconstructed from volumes of neuropil imaged in layer 1 of the somatosensory cortex. This shows the changes to neuropil structure that accompany a general loss of synapses in a well-defined brain region. The loss of excitatory synapses was balanced by an increase...

Data from: Shifting fitness landscapes in response to altered environments

Ryan T. Hietpas, Claudia Bank, Jeffrey D. Jensen & Daniel N. A. Bolon
The role of adaptation in molecular evolution has been contentious for decades. Here, we shed light on the adaptive potential in Saccharomyces cerevisiae by presenting systematic fitness measurements for all possible point mutations in a region of Hsp90 under four environmental conditions. Under elevated salinity, we observe numerous beneficial mutations with growth advantages up to 7% relative to the wild type. All of these beneficial mutations were observed to be associated with high costs of...

Data from: The fitness landscape of the codon space across environments

Inês Fragata, Sebastian Matuszweski, Mark A. Schmitz, Thomas Bataillon, Jeffrey D. Jensen & Claudia Bank
Fitness landscapes map the relationship between genotypes and fitness. However, most fitness landscape studies ignore the genetic architecture imposed by the codon table and thereby neglect the potential role of synonymous mutations. To quantify the fitness effects of synonymous mutations and their potential impact on adaptation on a fitness landscape, we use a new software based on Bayesian Monte Carlo Markov Chain methods and re-estimate selection coefficients of all possible codon mutations across 9 amino-acid...

Data from: Diffantom: whole-brain diffusion MRI phantoms derived from real datasets of the Human Connectome Project

Oscar Esteban, Emmanuel Caruyer, Alessandro Daducci, Meritxell Bach-Cuadra, María J. Ledesma-Carbayo & Andres Santos
Diffantom is a whole-brain diffusion MRI (dMRI) phantom publicly available through the Dryad Digital Repository (doi:10.5061/dryad.4p080). The dataset contains two single-shell dMRI images, along with the corresponding gradient information, packed following the BIDS standard (Brain Imaging Data Structure, Gorgolewski et al., 2015). The released dataset is designed for the evaluation of the impact of susceptibility distortions and benchmarking existing correction methods. In this Data Report we also release the software instruments involved in generating diffantoms,...

Data from: A novel biomechanical approach for animal behaviour recognition using accelerometers

Pritish Chakravarty, Gabriele Cozzi, Arpat Ozgul & Kamiar Aminian
Data from animal‐borne inertial sensors are widely used to investigate several aspects of an animal's life, such as energy expenditure, daily activity patterns and behaviour. Accelerometer data used in conjunction with machine learning algorithms have been the tool of choice for characterising animal behaviour. Although machine learning models perform reasonably well, they may not rely on meaningful features, nor lend themselves to physical interpretation of the classification rules. This lack of interpretability and control over...

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  • École Polytechnique Fédérale de Lausanne
  • University of Lausanne
  • Swiss Federal Institute for Forest, Snow and Landscape Research
  • Swiss Institute of Bioinformatics
  • Harvard University
  • University of Neuchâtel
  • University of Bern
  • Aarhus University
  • Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA 15261, USA
  • McGill University