64 Works

Reduction of elevated proton leak rejuvenates mitochondria in the aged cardiomyocyte

Huiliang Zhang, Nathan Alder, Wang Wang, Hazel Szeto, David Marcinek & Peter Rabinovitch
Aging-associated diseases, including cardiac dysfunction, are increasingly common in the population. However, the mechanisms of physiologic aging in general, and cardiac aging in particular, remain poorly understood. Age-related heart impairment is lacking a clinically effective treatment. Using the model of naturally aging mice and rats, we show direct evidence of increased proton leak in the aged heart mitochondria. Moreover, our data suggested ANT1 as the most likely site of mediating increased mitochondrial proton permeability in...

Colorectal cancer scRNA-seq 10xG-format data matrix

Christopher Lausted, Raymond Yeung, Xiaowei Yan, Neda Jabbari, Qiang Tian, Heidi Kenerson, Changting Meng, Dani Bergey, Venu Pillarisetty, Kevin Sullivan, Priyanka Baloni & Leroy Hood
Metastatic colorectal cancer (CRC) is a major cause of cancer-related death and incidence is rising in the younger population (<50 years). Current chemotherapies can achieve response rates above 50%, but immunotherapies have limited value for patients with microsatellite-stable (MSS) cancers. The present study investigates the impact of chemotherapy on the tumor immune microenvironment. We treat human liver metastases slices with 5-Fluorouracil (5FU) plus either irinotecan or oxaliplatin, then perform single-cell transcriptome analyses. Results from eight...

Data from Cretaceous-Paleogene plant extinction and recovery in Patagonia

Elena Stiles, Peter Wilf, Ari Iglesias, María Alejandra Gandolfo & N. Rubén Cúneo
The Cretaceous-Paleogene (K/Pg) extinction appears to have been geographically heterogeneous for some organismal groups. Southern Hemisphere K/Pg palynological records have shown lower extinction and faster recovery than in the Northern Hemisphere, but no comparable, well-constrained Southern Hemisphere macrofloras spanning this interval had been available. Here, macrofloral turnover patterns are addressed for the first time in the Southern Hemisphere, using over 3,500 dicot leaves from the latest Cretaceous (Maastrichtian) and the earliest Paleocene (Danian) of Argentine...

Upper Columbia River Steelhead Capture-Recapture-Recovery data (2008-2018)

Quinn Payton & Nathaniel Hostetter
In the Columbia River basin, USA, predation by Caspian terns (Hydroprogne caspia) on U.S. Endangered Species Act (ESA)-listed juvenile salmonids (smolts; Oncorhynchus spp.) has led to predator management actions to reduce predation; however, the assumption that reduced predation translates into greater salmonid survival, either within the life stage where predation occurs or across their lifetime, has remained untested. To address this critical uncertainty, we analyzed a long-term (2008-2018) mark-recapture-recovery dataset of ESA-listed steelhead trout (O....

The Rhododendron genome and chromosomal organization provide insight into shared whole-genome duplications across the heath family (Ericaceae)

Valerie L. Soza, Dale Lindsley, Adam Waalkes, Elizabeth Ramage, Rupali P. Patwardhan, Joshua N. Burton, Andrew Adey, Akash Kumar, Ruolan Qiu, Jay Shendure & Benjamin Hall
The genus Rhododendron (Ericaceae), which includes horticulturally important plants such as azaleas, is a highly diverse and widely distributed genus of >1,000 species. Here, we report the chromosome-scale de novo assembly and genome annotation of Rhododendron williamsianum as a basis for continued study of this large genus. We created multiple short fragment genomic libraries, which were assembled using ALLPATHS-LG. This was followed by contiguity preserving transposase sequencing (CPT-seq) and fragScaff scaffolding of a large fragment...

Tree seedling trait optimization and growth in response to local-scale soil and light variability

Maria Natalia Umaña, Gabriel Arellano, Nathan Swenson & Jenny Zambrano
At local scales, it has been suggested that high levels of resources lead to increased tree growth via trait optimization (highly peaked trait distribution). However, this contrasts with (i) theories that suggest that trait optimization and high growth occur in the most common resource level and (ii) empirical evidence showing that high trait optimization can be also found at low resource levels. This raises the question of how are traits and growth optimized in highly...

It's a wormy world: Meta-analysis reveals several decades of change in the global abundance of the parasitic nematodes Anisakis spp. and Pseudoterranova spp. in marine fishes and invertebrates

Evan Fiorenza, Catrin Wendt, Katie Dobkowski, Teri King, Marguerite Pappaionou, Peter Rabinowitz, Jameal Samhouri & Chelsea Wood
The Anthropocene has brought substantial change to ocean ecosystems, but whether this age will bring more or less marine disease is unknown. In recent years, the accelerating tempo of epizootic and zoonotic disease events has made it seem as if disease is on the rise. Is this apparent increase in disease due to increased observation and sampling effort, or to an actual rise in the abundance of parasites and pathogens? We examined the literature to...

Cryptic and extensive hybridization between ancient lineages of American crows

David L. Slager, Kevin L. Epperly, Renee R. Ha, Sievert Rohwer, Chris Wood, Caroline Van Hemert & John Klicka
Most species and therefore most hybrid zones have historically been defined using phenotypic characters. However, both speciation and hybridization can occur with negligible morphological differentiation. Recently developed genomic tools provide the means to better understand cryptic speciation and hybridization. The Northwestern Crow (Corvus caurinus) and American Crow (Corvus brachyrhynchos) are continuously distributed sister taxa that lack reliable traditional characters for identification. In this first population genomic study of Northwestern and American crows, we use genomic...

Data from: Assessing cetacean populations using integrated population models: an example with Cook Inlet beluga whales

Eiren Jacobson, Charlotte Boyd, Tamara McGuire, Kim Shelden, Gina Himes Boor & André Punt
Effective conservation and management of animal populations requires knowledge of abundance and trends. For many species, these quantities are estimated using systematic visual surveys. Additional individual-level data are available for some species. Integrated population modelling (IPM) offers a mechanism for leveraging these datasets into a single estimation framework. IPMs that incorporate both population- and individual-level data have previously been developed for birds, but have rarely been applied to cetaceans. Here, we explore how IPMs can...

Spatial-temporal growth, distribution, and diffusion of marine microplastic research and national plastic policies

Lyda Harris
Plastic accounts for 80% of material waste in the ocean. The field of marine microplastic research is relatively new and is growing rapidly, in terms of published papers as well as institutions and countries conducting research. To combat plastic pollution, there is sufficient evidence that policies can lead to reduced plastic production and consumption both locally and globally. We aim to understand how marine plastics research and policies have grown and spread. Specifically, we used...

Cold-induced hyperphagia requires AgRP-neuron activation in mice

Jennifer Deem
To maintain energy homeostasis during cold exposure, the increased energy demands of thermogenesis must be counterbalanced by increased energy intake. To investigate the neurobiological mechanisms underlying this cold-induced hyperphagia, we asked whether agouti-related peptide (AgRP) neurons are activated when animals are placed in a cold environment and, if so, whether this response is required for the associated hyperphagia. We report that AgRP-neuron activation occurs rapidly upon acute cold exposure, as do increases of both energy...

Symbiotic moss-cyanobacteria associations as a novel source of biological N2-fixation in temperate grasslands

Lalita Calabria, Kate Peterson, Amanda Bidwell & Sarah Hamman
Aims. Terrestrial mosses contribute significantly to nitrogen budgets in boreal forests through symbiotic associations with N2-fixing cyanobacteria, but few studies have considered these interactions in temperate systems. We investigated how N2-fixation by moss-cyanobacterial associations contribute spatio-temporally to site-level N dynamics in a western North American prairie ecosystem. Methods. We first tested for the presence of N2-fixing cyanobacteria on six moss species using epi-fluorescence light microscopy. We then used an acetylene reduction assay to estimate monthly...

Changes in taxonomic and phylogenetic diversity in the Anthropocene

Daijiang Li, Julian Olden, Julie Lockwood, Sydne Record, Michael McKinney & Benjamin Baiser
To better understand how ecosystems are changing, a multifaceted approach to measuring biodiversity that considers species richness and evolutionary history across spatial scales is needed. Here we compiled 162 datasets for fish, bird, and plant assemblages across the globe and measured how taxonomic and phylogenetic diversity changed at different spatial scales (within site α diversity and between sites spatial β diversity). Biodiversity change is measured from these datasets in three ways: across land use gradients,...

Dominant native and non-native graminoids differ in key leaf traits irrespective of nutrient availability

Arthur Broadbent, Jennifer Firn, James McGree, Elizabeth Borer, Yvonne Buckley, W. Stanley Harpole, Kimberly Komatsu, Andrew MacDougall, Kate Orwin, Nicholas Ostle, Eric Seabloom, Jonathan Bakker, Lori Biedermann, Maria Caldeira, Nico Eisenhauer, Nicole Hagenah, Yann Hautier, Joslin Moore, Carla Nogueira, Pablo Peri, Anita Risch, Christiane Roscher, Martin Schuetz & Carly Stevens
Aim Nutrient enrichment is associated with plant invasions and biodiversity loss. Functional trait advantages may predict the ascendancy of invasive plants following nutrient enrichment but this is rarely tested. Here, we investigate 1) whether dominant native and non-native plants differ in important morphological and physiological leaf traits, 2) how their traits respond to nutrient addition, and 3) whether responses are consistent across functional groups. Location Australia, Europe, North America and South Africa Time period 2007...

Data from: Fluid preservation causes minimal reduction of parasite detectability in fish specimens: a new approach for reconstructing parasite communities of the past?

Evan Fiorenza, Katie Leslie, Mark Torchin, Katherine Maslenikov, Luke Tornabene & Chelsea Wood
Long-term datasets are needed to evaluate temporal patterns in wildlife disease burdens, but historical data on parasite abundance are extremely rare. For more than a century, natural history collections have been accumulating fluid-preserved specimens, which should contain the parasites infecting the host at the time of its preservation. However, before this unique data source can be exploited, we must identify the artefacts that are introduced by the preservation process. Here, we experimentally address whether the...

Data from: Genomic and phenotypic effects of inbreeding across two different hatchery management regimes in Chinook salmon

Charles Waters, Jeffrey Hard, David Fast, Curtis Knudsen, William Bosch & Kerry-Ann Naish
Genomic approaches permit direct estimation of inbreeding and its effect on fitness. We used genomic-based estimates of inbreeding to investigate their relationship with eight adult traits in a captive-reared Pacific salmonid that is released into the wild. Estimates were also used to determine whether alternative broodstock management approaches reduced risks of inbreeding. Specifically, 1,100 unlinked restriction-site associated (RAD) loci were used to compare pairwise relatedness, derived from a relationship matrix, and individual inbreeding, estimated by...

Rapamycin rejuvenates oral health in aging mice

Kristopher Kerns
Periodontal disease is an age-associated disorder clinically defined by periodontal bone loss, inflammation of the specialized tissues that surround and support the tooth, and microbiome dysbiosis. Currently, there is no therapy for reversing periodontal disease, and treatment is generally restricted to preventive measures or tooth extraction. The FDA-approved drug rapamycin slows aging and extends lifespan in multiple organisms, including mice. Here we demonstrate that short-term treatment with rapamycin rejuvenates the aged oral cavity of elderly...

Activity niches outperform thermal physiological limits in predicting global ant distributions

Fengyi Guo, Benoit Guénard, Evan Economo, Curtis Deutsch & Timothy Bonebrake
Aim: Thermal physiology is commonly used in mechanistic models to predict species distributions and project distribution change. Such thermal constraints for ants are often measured under laboratory conditions as critical thermal limits (CTmax and CTmin), but have also been observed in the field as foraging thermal limits (FTmin and FTmax). Here we compared distribution projections based on ant physiological and behavioural thermal limits with their realized distributions to assess the validity of using ecophysiological models...

Habitat transitions alter the adaptive landscape and shape phenotypic evolution in needlefishes (Belonidae)

Matthew Kolmann, Michael D. Burns, Justin Y. K. Ng, Nathan R. Lovjoy & Devin D. Bloom
Habitat occupancy can have a profound influence on macroevolutionary dynamics, and a switch in major habitat type may alter the evolutionary trajectory of a lineage. In this study we investigate how evolutionary transitions between marine and freshwater habitats affect macroevolutionary adaptive landscapes, using needlefishes (Belonidae) as a model system. We examined the evolution of body shape and size in marine and freshwater needlefishes and tested for phenotypic change in response to transitions between habitats. Using...

Data from: Phosphorus limitation does not drive loss of bony lateral plates in freshwater stickleback (Gasterosteus aculeatus)

Sophie L. Archambeault, Daniel J. Durston, Alex Wan, Rana El-Sabaawi, Blake Matthews & Catherine L. Peichel
Connecting the selective forces that drive the evolution of phenotypes to their underlying genotypes is key to understanding adaptation, but such connections are rarely tested experimentally. Threespine stickleback (Gasterosteus aculeatus) are a powerful model for such tests because genotypes that underlie putatively adaptive traits have been identified. For example, a regulatory mutation in the Ectodysplasin (Eda) gene causes a reduction in the number of bony armor plates, which occurs rapidly and repeatedly when marine sticklebacks...

Confronting Sources of Systematic Error to Resolve Historically Contentious Relationships: A Case Study Using Gadiform Fishes (Teleostei, Paracanthopterygii, Gadiformes)

Adela Roa-Varon, Rebecca Dikow, Giorgio Carnevale, Luke Tornabene, Carole Baldwin, Chenhong Li & Eric Hilton
Reliable estimation of phylogeny is central to avoid inaccuracy in downstream macroevolutionary inferences. However, limitations exist in the implementation of concatenated and summary coalescent approaches, and Bayesian and full coalescent inference methods may not yet be feasible for computation of phylogeny using complicated models and large datasets. Here, we explored methodological (e.g., optimality criteria, character sampling, model selection) and biological (e.g., heterotachy, branch length heterogeneity) sources of systematic error that can result in biased or...

Data from - Ecological insights from three decades of animal movement tracking across a changing Arctic

Gil Bohrer, Sarah Davidson, Eliezer Gurarie, Scott LaPoint, Peter Mahoney, Emma Grier, Ophélie Couriot, Allicia Kelly, Bryan Bedrosian, Jerrold Belant, Travis Booms, Bridget Borg, Stan Boutin, Erica Craig, Tracy Davison, Robert Domenech, James Hodson, Kyle Joly, Nicholas Larter, A. David M. Latham, Stephen Lewis, Carol McIntyre, Tricia Miller, Kelsey Russell, Dale Seip … & Judy Williams
We provide here the data used in analysis of 3 test cases, presented in the manuscript "Ecological insights from three decades of animal movement tracking across a changing Arctic". We utilized the new Arctic Animal Movement Archive (AAMA), a growing collection of 201 standardized terrestrial and marine animal tracking studies from 1991–present. The AAMA supports public data discovery, preserves fundamental baseline data for the future, and facilitates efficient, collaborative data analysis. With three AAMA-based case...

Level and spatial pattern of overstory retention impose tradeoffs for regenerating and retained trees

Charles Halpern & Lauren Urgenson
Variable retention (VR) has been adopted globally as an alternative to more intensive forms of regeneration harvest. By retaining live trees within harvest units, VR seeks balance among the commodity, ecological, and aesthetic values of managed forests. Achieving these multiple, often competing objectives requires an understanding of how level and spatial pattern of retention shape the abundance, growth, and mortality of regenerating and retained trees. Using long-term (18-19 yr) data from a regional-scale VR experiment,...

Data from: Gut microbiome critically impacts PCB-induced changes in metabolic fingerprints and the hepatic transcriptome in mice

Joe Lim, Julia Cui, Xueshu Li, Hans-Joachim Lehmler, Dongfang Wang & Haiwei Gu
Polychlorinated biphenyls (PCBs) are ubiquitously detected in the environment and have been linked to metabolic diseases. The liver serves as a central hub for the metabolism of xenobiotics and endogenous metabolites. Gut dysbiosis is recognized as a critical regulator of disease susceptibility, however, little is known regarding how PCBs and gut microbiome interact to modulate the interface between xenobiotic and intermediary metabolism. We hypothesized that the gut microbiome regulates PCBs-mediated changes in the metabolic fingerprints...

Newick trees for \"Within-patient phylogenetic reconstruction reveals early events in Barrett's Esophagus\"

Mary Kuhner & Lucian Smith
Newick format within-patient phylogenetic trees for a Barrett's Esophagus WGS dataset

Registration Year

  • 2020

Resource Types

  • Dataset


  • University of Washington
  • Smithsonian Institution
  • Arizona State University
  • Bangor University
  • University of Pretoria
  • University of Queensland
  • Oregon State University
  • University of Minnesota
  • University of Guelph
  • Monash University