20 Works

Data from: Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Hollis Dahn, Jacquelyn Mountcastle, Jennifer Balacco, Sylke Winkler, Iliana Bista, Anthony Schmitt, Olga Vinnere Pettersson, Giulio Formenti, Karen Oliver, Michelle Smith, Wenhua Tan, Anne Kraus, Stephen Mac, Lisa Komoroske, Tanya Lama, Andrew Crawford, Robert Murphy, Samara Brown, Alan Scott, Phillip Morin, Erich Jarvis & Olivier Fedrigo
Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different...

Data from: A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture

Hernán Morales-Navarrete, Fabián Segovia-Miranda, Piotr Klukowski, Kirstin Meyer, Hidenori Nonaka, Giovanni Marsico, Mikhail Chernykh, Alexander Kalaidzidis, Marino Zerial & Yannis Kalaidzidis
A prerequisite for the systems biology analysis of tissues is an accurate digital three-dimensional reconstruction of tissue structure based on images of markers covering multiple scales. Here, we designed a flexible pipeline for the multi-scale reconstruction and quantitative morphological analysis of tissue architecture from microscopy images. Our pipeline includes newly developed algorithms that address specific challenges of thick dense tissue reconstruction. Our implementation allows for a flexible workflow, scalable to high-throughput analysis and applicable to...

Data from: Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon

Anne C. Roulin, Christoph Stritt, Michele Wyler, Elena L. Gimmi & Martin Pippel
Transposable elements (TEs) are the main reason for the high plasticity of plant genomes, where they occur as communities of diverse evolutionary lineages. Because research has typically focused on single abundant families or summarized TEs at a coarse taxonomic level, our knowledge about how these lineages differ in their effects on genome evolution is still rudimentary. Here we investigate the community composition and dynamics of 32 long terminal repeat retrotransposon (LTR-RT) families in the 272...

Dataset for: A condensate dynamic instability orchestrates actomyosin cortex activation

Victoria Tianjing Yan & Arjun Narayanan
:unav

Drosophila wing disc cell morphology in timelapse

Natalie Dye & Marko Popovic
Here we provide measurements of cell morphology in the proliferating Drosophila larval wing disc, specifically the wing disc pouch, as it grows in ex vivo culture. The tables provided here include measurements of cell morphology (area and elongation) at each timepoint in each of 5 wing disc samples. For cell elongation, we report the elongation values for each of its component triangles (formed by connecting the cell to the center of its neighbors). We also...

Data from: The comparative genomic landscape of adaptive radiation in Crater Lake cichlid fishes

Peiwen Xiong, C. Darrin Hulsey, Carmelo Fruciano, Wai Y. Wong, Alexander Nater, Andreas F. Kautt, Oleg Simakov, Martin Pippel, Shigehiro Kuraku, Axel Meyer & Paolo Franchini
Factors ranging from ecological opportunity to genome composition might explain why only some lineages form adaptive radiations. While being rare, particular systems can provide natural experiments within an identical ecological setting where the factors promoting increased species numbers and phenotypic divergence in two closely related lineages is notably different. We investigated one such natural experiment using two de novo assembled and 40 re-sequenced genomes and asked why two closely related Neotropical cichlid fish lineages, the...

Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

João P. L. Castro, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, Ronald Naumann, Isabella Skuplik, John Cobb, Nick H. Barton, Campbell Rolian & Yingguang Frank Chan
Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory,...

Pleurodeles waltl genome assembly

Thomas Brown
Genome assembly and annotation of the Iberian ribbed newt, Pleurodeles waltl

Data from: A tunable refractive index matching medium for live imaging cells, tissues and model organisms

Tobias Boothe, Lennart Hilbert, Michael Heide, Lea Berninger, Wieland B. Huttner, Vasily Zaburdaev, Nadine L. Vastenhouw, Eugene W. Myers, David N. Drechsel & Jochen C. Rink
In light microscopy, refractive index mismatches between media and sample cause spherical aberrations that often limit penetration depth and resolution. Optical clearing techniques can alleviate these mismatches, but they are so far limited to fixed samples. We present Iodixanol as a non-toxic medium supplement that allows refractive index matching in live specimens and thus a substantial improvement of the live-imaging of primary cell cultures, planarians, zebrafish and human cerebral organoids.

Data for: Programmable synthetic cell networks regulated by tuneable reaction rates

Dora Tang, Mengfei Gao, Giorgio Fracasso & Adrian Zambrano
:unav

Dataset for: An endosomal tether undergoes an entropic collapse to bring vesicles together

David Murray & Marcus Jahnel
Raw data files from EM rotary shadowing experiments of Early Endosome Antigen 1 (EEA1) under various conditions. The datasets have been obtained for the study of Murray & Jahnel et al., "An endosomal tether undergoes an entropic collapse to bring vesicles together", Nature, 2016. Different datasets correspond to different mutants of EEA1 and different conditions, for example, the presence of the binding partner, the small GTPase Rab5. Each data directory corresponds to a different condition....

Code for manuscript \"Nanog organizes transcription bodies\"

Kuznetsova Ksenia
This directory contains code needed for denoising the images, producing the max projections and normalisation of the signal.

Data from: Contrasting signatures of genomic divergence during sympatric speciation

Andreas Kautt, Claudius Kratochwil, Alexander Nater, Gonzalo Machado-Schiaffino, Melisa Olave, Frederico Henning, Julián Torres-Dowdall, Andreas Härer, Darrin Hulsey, Paolo Franchini, Martin Pippel, Eugene Myers & Axel Meyer
The transition from “well-marked varieties” into “well-defined species” has puzzled evolutionary biologists ever since Darwin — especially when extensive gene flow between incipient species is possible due to the lack of physical barriers (sympatric speciation). Gene flow counteracts the build-up of genome-wide differentiation, which is both a hallmark of speciation and forms the underlying basis of irreversible reproductive barriers (incompatibilities) that ultimately complete the speciation process. Theory predicts that the genetic architecture of divergently selected...

Cell-free gene expression dynamics in synthetic cell populations

David Gonzales
:unav

Data from: Outstanding intraindividual genetic diversity in fissiparous planarians (Dugesia, Platyhelminthes) with facultative sex

Laia Leria, Miquel Vila-Farré, Eduard Solà & Marta Riutort
Background: Predicted genetic consequences of asexuality include high intraindividual genetic diversity (i.e., the Meselson effect) and accumulation of deleterious mutations (i.e., Muller’s Ratchet), among others. These consequences have been largely studied in parthenogenetic organisms, but studies on fissiparous species are scarce. Differing from parthenogens, fissiparous organisms inherit part of the soma of the progenitor, including somatic mutations. Thus, in the long term, fissiparous reproduction may also result in genetic mosaicism, besides the presence of the...

Data for: Bifunctional Monosaccharides Preferentially Localize to Nuclear Subcompartments

Pavel Barahtjan, Annett Lohmann, André Nadler & Juan M. Iglesias-Artola
:unav

Large‐scale genome sampling reveals unique immunity and metabolic adaptations in bats

Diana Daniela Moreno Santillan, Tanya Lama, Yocelyn T Gutierrez Guerrero, Zixia Huang, Graham Hughes, Alexis Brown, Paul Donat, Huabin Zhao, Stephen Rossiter, Laurel Yohe, Joshua Potter, Emma Teeling, Sonja Vernes, Kalina Davies, Eugene Myers, Federico Hoffmann, Angelique Corthals, David Ray & Liliana Davalos
Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species encompassing a large...

Adaptation to environmental temperature in divergent clades of the nematode Pristionchus pacificus

Mark Leaver
Because of ongoing climate change, populations of organisms are being subjected to stressful temperatures more often. This is especially problematic for ectothermic organisms, which are likely to be more sensitive to changes in temperature. Therefore, we need to know if ectotherms have adapted to environmental temperature and, if so, what are the evolutionary mechanisms behind such adaptation. Here, we use the nematode Pristionchus pacificus as a case study to investigate thermal adaptation on the Indian...

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