69 Works

Data from: Airway bacteria drive a progressive COPD-like phenotype in mice with polymeric immunoglobulin receptor deficiency

Bradley W. Richmond, Robert M. Brucker, Wei Han, Rui-Hong Du, Yongqin Zhang, Dong-Sheng Cheng, Linda Gleaves, Rasul Abdolrasulnia, Dina Polosukhina, Peter E. Clark, Seth R. Bordenstein, Timothy S. Blackwell & Vasiliy V. Polosukhin
Mechanisms driving persistent airway inflammation in chronic obstructive pulmonary disease (COPD) are incompletely understood. As secretory immunoglobulin A (SIgA) deficiency in small airways has been reported in COPD patients, we hypothesized that immunobarrier dysfunction resulting from reduced SIgA contributes to chronic airway inflammation and disease progression. Here we show that polymeric immunoglobulin receptor-deficient (pIgR−/−) mice, which lack SIgA, spontaneously develop COPD-like pathology as they age. Progressive airway wall remodelling and emphysema in pIgR−/− mice are...

Data from: Phylosymbiosis: relationships and functional effects of microbial communities across host evolutionary history

Andrew W. Brooks, Kevin D. Kohl, Robert M. Brucker, Edward J. Van Opstal & Seth R. Bordenstein
Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern whereby the ecological relatedness of host-associated microbial communities parallels the phylogeny of related host species. Here, we analyze the prevalence of phylosymbiosis and its functional significance under highly controlled conditions by characterizing the microbiota of 24 animal species from four different groups (Peromyscus deer mice, Drosophila flies, mosquitoes, Nasonia wasps) and re-evaluate the phylosymbiotic relationships of seven species of wild hominids. We demonstrate three key findings....

Data from: Specificity in the symbiotic association between fungus-growing ants and protective Pseudonocardia bacteria

Matías J. Cafaro, Michael Poulsen, Ainslie E. F. Little, Shauna L. Price, Nicole M. Gerardo, Bess Wong, Alison E. Stuart, Bret Larget, Patrick Abbot & Cameron R. Currie
Fungus-growing ants (tribe Attini) engage in a mutualism with a fungus that serves as the ants' primary food source, but successful fungus cultivation is threatened by microfungal parasites (genus Escovopsis). Actinobacteria (genus Pseudonocardia) associate with most of the phylogenetic diversity of fungus-growing ants; are typically maintained on the cuticle of workers; and infection experiments, bioassay challenges and chemical analyses support a role of Pseudonocardia in defence against Escovopsis through antibiotic production. Here we generate a...

Amyloid PET imaging in self-identified non-Hispanic Blacks from the Anti-Amyloid in Asymptomatic Alzheimer’s Disease (A4) Study – Supplementary Data

Kacie Deters, Valerio Napolioni, Reisa Sperling, Gabriel Kennedy, Michael Greicius, Richard Mayeux, Timothy Hohman & Elizabeth Mormino
The goal of the manuscript was to examine whether amyloid PET in CN individuals that were screened for the Anti-Amyloid in Asymptomatic AD (A4) study differed across self-identified, non-Hispanic White and Black (NHW and NHB) groups. We examined 3685 NHW and 144 NHB that passed initial screening for the A4 study and underwent amyloid PET. The effect of race on amyloid PET was examined using logistic (dichotomous groups) and linear (continuous values) regression controlling for...

Raw isotope values from fossil herbivore enamel from sites located below 37° latitude within the contiguous United States

Melissa Pardi & Larisa DeSantis
Paleoecological interpretations are based on our understanding of dietary and habitat preferences of fossil taxa. While morphology provides approximations of diets, stable isotope proxies provide insights into the realized diets of animals. We present a synthesis of the isotopic ecologies (δ13C from tooth enamel) of North American mammalian herbivores since ~7 Ma. We ask: 1) Do morphological interpretations of dietary behavior agree with stable isotope proxy data?; 2) Are grazing taxa specialists, or is grazing...

Data from: Evidence for structure and variable recombination rates among Dutch populations of the opportunistic human pathogen Aspergillus fumigatus

Corné H. W. Klaassen, John G. Gibbons, Natalie D. Fedorova, Jacques S. Meis & Antonis Rokas
As the frequency of antifungal drug resistance continues to increase, understanding the genetic structure of fungal populations, where resistant isolates have emerged and spread, is of major importance. Aspergillus fumigatus is an ubiquitously distributed fungus and the primary causative agent of invasive aspergillosis (IA), a potentially lethal infection in immunocompromised individuals. In the last few years, an increasing number of A. fumigatus isolates has evolved resistance to triazoles, the primary drugs for treating IA infections....

Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence

Xiaofan Zhou, Sarah Lutteropp, Lucas Czech, Alexandros Stamatakis, Moritz Von Looz & Antonis Rokas
Incongruence, or topological conflict, is prevalent in genome-scale data sets. Internode certainty (IC) and related measures were recently introduced to explicitly quantify the level of incongruence of a given internal branch among a set of phylogenetic trees and complement regular branch support measures (e.g., bootstrap, posterior probability) that instead assess the statistical confidence of inference. Since most phylogenomic studies contain data partitions (e.g., genes) with missing taxa and IC scores stem from the frequencies of...

Data from: The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes

Dimitrios Floudas, Manfred Binder, Robert Riley, Kerrie Barry, Robert A. Blanchette, Bernard Henrissat, Angel T. Martínez, Robert Ortillar, Joseph W. Spatafora, Jagjit S. Yadav, Andrea Aerts, Isabelle Benoit, Alex Boyd, Alexis Carlson, Alex Copeland, Pedro M. Coutinho, Ronald P. De Vries, Patricia Ferreira, Keisha Findley, Brian Foster, Jill Gaskell, Dylan Glotzer, Paweł Górecki, Joseph Heitman, Cedar Hesse … & David S. Hibbett
Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non–lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as...

Data from: Patterns of cyto-nuclear linkage disequilibrium in Silene latifolia: genomic heterogeneity and temporal stability

Peter D. Fields, David E. McCauley, Edward V. McAssey & Douglas R. Taylor
Non-random association of alleles in the nucleus and cytoplasmic organelles, or cyto-nuclear linkage disequilibrium (LD), is both an important component of a number of evolutionary processes and a statistical indicator of others. The evolutionary significance of cyto-nuclear LD will depend on both its magnitude and how stable those associations are through time. Here, we use a longitudinal population genetic data set to explore the magnitude and temporal dynamics of cyto-nuclear disequilibria through time. We genotyped...

Data from: Assessing niche conservatism using a multiproxy approach: dietary ecology of extinct and extant spotted hyenas

Larisa R. G. DeSantis, Zhijie Jack Tseng, Jinyi Liu, Aaron Hurst, Blaine Schubert & Qigao Jiangzuo
A central premise of bioclimatic envelope modeling is the assumption of niche conservatism. Whereas such assumptions are testable in modern populations, it is unclear if niche conservatism holds over deeper time spans and over very large geographic ranges. Hyaenids occupied a diversity of ecological niches over time and space, and until the end-Pleistocene they occurred in Europe and most of Asia, with Asian populations of Crocuta suggested as being genetically distinct from their closest living...

Data from: Inference of facultative mobility in the enigmatic Ediacaran organism Parvancorina

Simon A.F. Darroch, Imran A. Rahman, Brandt Gibson, Rachel A. Racicot, Marc Laflamme & Simon A. F. Darroch
Establishing how Ediacaran organisms moved and fed is critical to deciphering their ecological and evolutionary significance, but has long been confounded by their non-analogue body plans. Here, we use computational fluid dynamics to quantitatively analyze water flow around the Ediacaran taxon Parvancorina, thereby testing between competing models for feeding mode and mobility. The results show that flow was not distributed evenly across the organism, but was directed towards localized areas; this allows us to reject...

Data from: Three-dimensional simulation for fast forward flight of a calliope hummingbird

Jialei Song, Bret W. Tobalske, Donald R. Powers, Tyson L. Hedrick & Haoxiang Luo
We present a computational study of flapping-wing aerodynamics of a calliope hummingbird (Selasphorus calliope) during fast forward flight. Three-dimensional wing kinematics were incorporated into the model by extracting time-dependent wing position from high-speed videos of the bird flying in a wind tunnel at 8.3 m s−1. The advance ratio, i.e. the ratio between flight speed and average wingtip speed, is around one. An immersed-boundary method was used to simulate flow around the wings and bird...

Data from: Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

Marcin J. Skwark, Nicholas J. Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Ying Ying Xu, Paul Turner, Simon R. Harris, Stephen B. Beres, James M. Musser, Julian Parkhill, Stephen D. Bentley, Erik Aurell & Jukka Corander
Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and...

Ancient life and moving fluids

Brandt M. Gibson, David J. Furbish, Imran A. Rahman, Mark W. Schmeeckle, Marc Laflamme & Simon A.F. Darroch
Over 3.7 billion years of Earth history, life has evolved complex adaptations to help navigate and interact with the fluid environment. Consequently, fluid dynamics has become a powerful tool for studying ancient fossils, providing insights into the paleobiology and -ecology of extinct organisms from across the tree of life. In recent years, this approach has been extended to the Ediacara biota, an enigmatic assemblage of Neoproterozoic soft-bodied organisms that represent the first major radiation of...

Data from: Laminar microcircuitry of visual cortex producing attention-associated electric fields

Jacob Westerberg, Michelle Schall, Alexander Maier, Geoffrey Woodman & Jeffrey Schall
Cognitive operations are widely studied by measuring electric fields through EEG and ECoG. However, despite their widespread use, the component neural circuitry giving rise to these signals remains unknown. Specifically, the functional architecture of cortical columns which results in attention-associated electric fields has not been explored. Here we detail the laminar cortical circuitry underlying an attention-associated electric field often measured over posterior regions of the brain in humans and monkeys. First, we identified visual cortical...

Epidermal Growth Factor signaling promotes sleep through a combined series and parallel neural circuit

Jan Konietzka, Maximilian Fritz, Silvan Spiri, Rebecca McWhirter, Andreas Leha, Sierra Palumbos, Wagner Steuer Costa, Alexandra Oranth, Alexander Gottschalk, , Alex Hajnal & Henrik Bringmann
Sleep requires sleep-active neurons that depolarize to inhibit wake circuits. Sleep-active neurons are under the control of homeostatic mechanisms that determine sleep need. However, little is known about the molecular and circuit mechanisms that translate sleep need into the depolarization of sleep-active neurons. During many stages and conditions in C. elegans, sleep requires a sleep-active neuron called RIS. Here, we defined the transcriptome of RIS to discover that genes of the Epidermal Growth Factor Receptor...

Extinction of North American Cuvieronius (Mammalia, Proboscidea, Gomphotheriidae) driven by dietary resource competition with sympatric mammoths and mastodons

Gregory Smith & Larisa DeSantis
The gomphotheres were a diverse and widespread group of proboscideans occupying Eurasia, North America, and South America throughout the Neogene. Their decline was temporally and spatially heterogeneous and the gomphotheres ultimately became extinct during the late Pleistocene; however, the genus Cuvieronius is rarely represented in late Pleistocene assemblages in North America. Two alternative hypotheses have been invoked to explain this phenomenon: (1) competitive exclusion by sympatric mammoths and mastodons, or (2) ecologic displacement due to...

Microbiome reduction and endosymbiont gain from a switch in sea urchin life-history

Tyler Carrier, Brittany Leigh, Dione Deaker, Hannah Devens, Gregory Wray, Seth Bordenstein, Maria Byrne & Adam Reitzel
Animal gastrointestinal tracts harbor a microbiome that is integral to host function, yet species from diverse phyla have evolved a reduced digestive system or lost it completely. Whether such changes are associated with alterations in the diversity and/or abundance of the microbiome remains an untested hypothesis in evolutionary symbiosis. Here, using the life-history transition from planktotrophy (feeding) to lecithotrophy (non-feeding) in the sea urchin Heliocidaris, we demonstrate that the lack of a functional gut corresponds...

Data from: Postmating isolation and genetically variable host use in ecologically divergent host forms of Neochlamisus bebbianae leaf beetles

Scott P Egan, Eric M Janson, Christopher G Brown & Daniel J Funk
Ecological speciation studies have more thoroughly addressed premating than postmating reproductive isolation. This study examines multiple postmating barriers between host forms of Neochlamisus bebbianae leaf beetles that specialize on Acer versus Salix trees. We demonstrate cryptic isolation and reduced hybrid fitness via controlled matings of these host forms. These findings reveal host-associated postmating isolation, although a non-ecological, ‘intrinsic’ basis for these patterns cannot be ruled out. Host preference and performance results among cross types further...

Data from: The application of an oxygen isotope aridity index to terrestrial paleoenvironmental reconstructions in Pleistocene North America

Lindsey T. Yann, Larisa R. G. DeSantis, Ryan J. Haupt, Jennifer L. Romer, Sarah E. Corapi & David J. Ettenson
Geochemical tools, including the analysis of stable isotopes from fossil mammals, are often used to infer regional climatic and environmental differences. We have further developed an oxygen isotope aridity index and used oxygen (δ18O) isotope values and carbon (δ13C) isotope values to assess regional climatic differences between the southeastern and southwestern United States during the Pleistocene. Using data collected from previously published studies, we assigned taxa to evaporation-sensitivity categories by quantifying the frequency and magnitude...

Data from: Integrated molecular imaging reveals tissue heterogeneity driving host-pathogen interactions

James E. Cassat, Jessica L. Moore, Kevin J. Wilson, Zachary Stark, Boone M. Prentice, Raf Van De Plas, William J. Perry, Yaofang Zhang, John Virostko, Daniel C. Colvin, Kristie L. Rose, Audra M. Judd, Michelle L. Reyzer, Jeffrey M. Spraggins, Caroline M. Grunenwald, John C. Gore, Richard M. Caprioli & Eric P. Skaar
All diseases are characterized by distinct changes in tissue molecular distribution. Molecular analysis of intact tissues traditionally requires pre-existing knowledge of, and reagents for, the targets of interest. Conversely, label-free discovery of disease-associated tissue analytes requires destructive processing for downstream identification platforms. Tissue-based analyses therefore sacrifice discovery to gain spatial distribution of known targets, or sacrifice tissue architecture for discovery of unknown targets. To overcome these obstacles, we developed a multi-modality imaging platform for discovery-based...

Data from: The origin and genetic differentiation of the socially parasitic aphid Tamalia inquilinus

Don G. Miller, Sarah P. Lawson, David C. Rinker, Heather Estby & Patrick Abbot
Social and brood parasitisms are nonconsumptive forms of parasitism involving the exploitation of the colonies or nests of a host. Such parasites are often related to their hosts and may evolve in various ecological contexts, causing evolutionary constraints and opportunities for both parasites and their hosts. In extreme cases, patterns of diversification between social parasites and their hosts can be coupled, such that diversity of one is correlated with or even shapes the diversity of...

Data from: Wind turbine blade shear web disbond detection using rotor blade operational sensing and data analysis

Noah J. Myrent, Douglas E. Adams, D. Todd Griffith & N. Myrent
A wind turbine blade's structural dynamic response is simulated and analysed with the goal of characterizing the presence and severity of a shear web disbond. Computer models of a 5 MW offshore utility-scale wind turbine were created to develop effective algorithms for detecting such damage. Through data analysis and with the use of blade measurements, a shear web disbond was quantified according to its length. An aerodynamic sensitivity study was conducted to ensure robustness of...

Data from: A chromosome 5q31.1 locus associates with tuberculin skin test reactivity in HIV-positive individuals from tuberculosis hyper-endemic regions in east Africa

Rafal S. Sobota, Catherine M. Stein, Nuri Kodaman, Isaac Maro, Wendy Wieland-Alter, Robert P. Igo, Albert Magohe, LaShaunda L. Malone, Keith Chervenak, Noemi B. Hall, Mecky Matee, Harriet Mayanja-Kizza, Moses Joloba, Jason H. Moore, William K. Scott, Timothy Lahey, W. Henry Boom, C. Fordham Von Reyn, Scott M. Williams & Giorgio Sirugo
One in three people has been infected with Mycobacterium tuberculosis (MTB), and the risk for MTB infection in HIV-infected individuals is even higher. We hypothesized that HIV-positive individuals living in tuberculosis-endemic regions who do not get infected by Mycobacterium tuberculosis are genetically resistant. Using an "experiment of nature" design that proved successful in our previous work, we performed a genome-wide association study of tuberculin skin test positivity using 469 HIV-positive patients from prospective study cohorts...

Data from: Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting

Nicole A. Doria-Rose, Han R. Altae-Tran, Ryan S. Roark, Stephen D. Schmidt, Matthew S. Sutton, Mark K. Louder, Gwo-Yu Chuang, Robert T. Bailer, Valerie Cortez, Rui Kong, Krisha McKee, Sijy O'Dell, Felicia Wang, Salim S. Abdool Karim, James M. Binley, Mark Connors, Barton F. Haynes, Malcolm A. Martin, David C. Montefiori, Lynn Morris, Julie Overbaugh, Peter D. Kwong, John R. Mascola, Ivelin S. Georgiev & Sijy O’Dell
Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially...

Registration Year

  • 2022
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Resource Types

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  • Vanderbilt University
  • University of Toronto
  • United States Geological Survey
  • Stanford University
  • Columbia University
  • Duke University
  • University of Georgia
  • Oregon State University
  • University of North Carolina
  • University of Cambridge