89 Works

Data deposition for Complex electrophysiological remodeling in postinfarction ischemic heart failure

Bence Hegyi & Ye Chen-Izu
Heart failure (HF) following myocardial infarction (MI) is associated with high incidence of cardiac arrhythmias. Development of therapeutic strategy requires detailed understanding of electrophysiological remodeling. However, changes of ionic currents in ischemic HF remain incompletely understood, especially in translational large animal models. Here, we systematically measure the major ionic currents in ventricular myocytes from the infarct border and remote zones in a porcine model of post-MI HF. We recorded eight ionic currents during the cell’s...

INCREASING CORAL RESILIENCE TO BLEACHING THROUGH MICROBIOME MANIPULATION

Raquel Peixoto, Phillipe Rosado, Deborah Leite, Gustavo Duarte, Ricardo Chaloub, Guillaume Jospin, Jonathan Eisen, David Bourne, Ulisses Da Rocha, João Saraiva & Francisco Dini-Andreote
Although the early coral reef-bleaching warning system (NOAA/USA) is established, there is no feasible treatment that can minimize temperature bleaching and/or disease impacts on corals in the field. Here, we present the first attempts to extrapolate the widespread and well-established use of bacterial consortia to protect or improve health in other organisms (e.g., humans and plants) to corals. Manipulation of the coral-associated microbiome was facilitated through addition of a consortium of native (isolated from Pocillopora...

Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris)

Paul Gepts
Progress in common bean breeding requires the exploitation of genetic variation among market classes, races and gene pools. The present study was conducted to determine the amount of genetic variation and the degree of relatedness among 192 selected common bean advanced cultivars using 58 simple-sequence-repeat markers (SSR) evenly distributed along the 11 linkage groups of the Phaseolus reference map. All the lines belonged to commercial seed type classes that are widely grown in the USA...

Temperature-Dependent Dynamics of Molecular Dopant in Conjugated Polymer

Jun Li, Tucker Murrey, Souleymane Diallo & Adam Moule
Understanding the nature of dopant dynamics in the solid state is critical for improving the longevity and stability of organic electronic devices and for optimizing the dopinginduced solubility control (DISC) patterning method. In this work, we use quasi-elastic neutron scattering (QENS) to study the dynamics of the soluble p-type molecular dopant tetrafluoromethyloxycarbonyltricyanoquinodimethane (F4MCTCNQ) in the semiconductive polymer poly(3-hexylthiophene-2,5-diyl) (P3HT). Specifically, fast dynamics (ps−ns) of the dopant, such as the methyl and the methoxycarbonyl group rotations,...

Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia

Cassandra Ettinger, Laetitia Wilkins, Guillaume Jospin & Jonathan Eisen
Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and...

Data from: Prolific fruit output by the invader Bellucia pentamera (Melastomataceae) is enhanced by selective logging disturbance

Christopher Dillis, Andrew J. Marshall, Campbell O. Webb & Mark N. Grote
Selective logging in tropical rain forests may promote population growth of invasive plants. The ability of invaders to respond, specifically in reproductive traits, to increases in resource abundance may allow them to increase their presence in the seed rain of recipient communities. The invasive pioneer tree Bellucia pentamera (Melastomataceae) is currently spreading within Gunung Palung National Park in West Kalimantan, Indonesia. The park has also experienced periods of illegal, small-scale, selective logging that seem to...

Data from: The spectre of too many species

Adam D. Leache, Tianqi Zhu, Bruce Rannala & Ziheng Yang
Recent simulation studies examining the performance of Bayesian species delimitation as implemented in the BPP program have suggested that BPP may detect population splits but not species divergences and that it tends to over-split when data of many loci are analyzed. Here we confirm these results and provide the mathematical justifications. We point out that the distinction between population and species splits made in the protracted speciation model has no influence on the generation of...

Data from: Sex-dependent effects of 2,2′,3,5′,6-pentachlorobiphenyl (PCB 95) on dendritic arborization of primary mouse neurons

Kimberly P. Keil, Sunjay Sethi & Pamela J. Lein
Early life exposures to environmental contaminants are implicated in the pathogenesis of many neurodevelopmental disorders (NDDs). These disorders often display sex biases, but whether environmental neurotoxicants act in a sex-dependent manner to modify neurodevelopment is largely unknown. Since altered dendritic morphology is associated with many NDDs, we tested the hypothesis that male and female primary mouse neurons are differentially susceptible to the dendrite promoting activity of 2,2′,3,5′,6-pentachlorobiphenyl (PCB 95). Hippocampal and cortical neuron-glia co-cultures were...

Data from: Gene flow improves fitness at a range edge under climate change

Megan Bontrager & Amy L. Angert
Populations at the margins of a species' geographic range are often thought to be poorly adapted to their environment. According to theoretical predictions, gene flow can inhibit these range edge populations if it disrupts adaptation to local conditions. Alternatively, if range edge populations are small or isolated, gene flow can provide beneficial genetic variation, and may facilitate adaptation to environmental change. We tested these competing predictions in the annual wildflower Clarkia pulchella using greenhouse crosses...

Data from: Moving in the Anthropocene: global reductions in terrestrial mammalian movements

Marlee A. Tucker, Katrin Böhning-Gaese, William F. Fagan, John M. Fryxell, Bram Van Moorter, Susan C. Alberts, Abdullahi H. Ali, Andrew M. Allen, Nina Attias, Tal Avgar, Hattie Bartlam-Brooks, Buuveibaatar Bayarbaatar, Jerrold L. Belant, Alessandra Bertassoni, Dean Beyer, Laura Bidner, Floris M. Van Beest, Stephen Blake, Niels Blaum, Chloe Bracis, Danielle Brown, P. J. Nico De Bruyn, Francesca Cagnacci, Justin M. Calabrese, Constança Camilo-Alves … & Thomas Mueller
Animal movement is fundamental for ecosystem functioning and species survival, yet the effects of the anthropogenic footprint on animal movements have not been estimated across species. Using a unique GPS-tracking database of 803 individuals across 57 species, we found that movements of mammals in areas with a comparatively high human footprint were on average one-half to one-third the extent of their movements in areas with a low human footprint. We attribute this reduction to behavioral...

Data from: Urbanization and anticoagulant poisons promote immune dysfunction in bobcats

Laurel E.K. Serieys, Amanda J. Lea, Marta Epeldegui, Tiffany C. Armenta, Joanne Moriarty, Sue Vandewoude, Scott Carver, Janet Foley, Robert K. Wayne, Seth P.D. Riley, Christel H. Uittenbogaart, Laurel E. K. Serieys & Seth P. D. Riley
Understanding how human activities influence immune response to environmental stressors can support biodiversity conservation across increasingly urbanizing landscapes. We studied a bobcat (Lynx rufus) population in urban southern California that experienced a rapid population decline from 2002–2005 due to notoedric mange. Because anticoagulant rodenticide (AR) exposure was an underlying complication in mange deaths, we aimed to understand sublethal contributions of urbanization and ARs on 65 biochemical markers of immune and organ function. Variance in immunological...

Data from: Verbalizing phylogenomic conflict: representation of node congruence across competing reconstructions of the neoavian explosion

Nico M. Franz, Lukas J. Musher, Joseph W. Brown, Yu Shizhuo & Bertram Ludäscher
Phylogenomic research is accelerating the publication of landmark studies that aim to resolve deep divergences of major organismal groups. Meanwhile, systems for identifying and integrating the products of phylogenomic inference–such as newly supported clade concepts–have not kept pace. However, the ability to verbalize node concept congruence and conflict across multiple, in effect simultaneously endorsed phylogenomic hypotheses, is a prerequisite for building synthetic data environments for biological systematics and other domains impacted by these conflicting inferences....

Data from: Systemic thyroid hormone status during levothyroxine therapy in hypothyroidism: a systematic review and meta-analysis

Elizabeth A. McAninch, Kumar B. Rajan, Corinne H. Miller & Antonio C. Bianco
CONTEXT: The standard of care for overt hypothyroidism is levothyroxine at doses that normalize serum TSH levels. Whether this approach universally restores thyroid hormone signaling is unknown. OBJECTIVE: To review studies of overt hypothyroidism in which participants were treated with levothyroxine to normalize serum TSH levels and measured other objective markers of thyroid hormone signaling. DESIGN: Databases were searched for studies that reported objective markers of thyroid hormone signaling (serum low-density lipoprotein (LDL), total cholesterol...

Data from: Links between blood parasites, blood chemistry, and the survival probability of nestling American crows

Andrea K. Townsend, Sarah S. Wheeler, David Freund, Ravinder N.M. Sehgal, Walter M. Boyce & Ravinder N. M. Sehgal
1. Many studies have used the avian haemosporidians (Leucocytozoon, Plasmodium, and Haemoproteus) to test hypotheses of host-parasite co-evolution, yet documented health and survival consequences of these blood parasites vary among studies and generalizations about their pathogenicity are debatable. In general, the negative effects of the haemosporidians are likely to be greatest during acute infections of young birds, yet most previous studies in wild passerines have examined chronic effects in adults. 2. Here, we evaluated responses...

Data from: The telomere bouquet is a hub where meiotic double-strand breaks, synapsis, and stable homolog juxtaposition are coordinated in the zebrafish, Danio rerio

Yana P. Blokhina, An D. Nguyen, Bruce W. Draper & Sean M. Burgess
Meiosis is a cellular program that generates haploid gametes for sexual reproduction. While chromosome events that contribute to reducing ploidy (homologous chromosome pairing, synapsis, and recombination) are well conserved, their execution varies across species and even between sexes of the same species. The telomere bouquet is a conserved feature of meiosis that was first described nearly a century ago, yet its role is still debated. Here we took advantage of the prominent telomere bouquet in...

Data from: The origin of the odorant receptor gene family in insects

Philipp Brand, Hugh M. Robertson, Wei Lin, Ratnasri Pothula, William E. Klingeman, Juan Luis Jurat-Fuentes & Brian R. Johnson
The origin of the insect odorant receptor (OR) gene family has been hypothesized to have coincided with the evolution of terrestriality in insects. Missbach et al. (2014) suggested that ORs instead evolved with an ancestral OR co-receptor (Orco) after the origin of terrestriality and the OR/Orco system is an adaptation to winged flight in insects. We investigated genomes of the Collembola, Diplura, Archaeognatha, Zygentoma, Odonata, and Ephemeroptera, and find ORs present in all insect genomes...

Data from: Soil microbial communities alter conspecific and congeneric competition consistent with patterns of field coexistence in three Trifolium congeners

Andrew Siefert, Kenneth W. Zillig, Maren L. Friesen & Sharon Y. Strauss
1. Coexistence and diversity in plant communities depend upon outcomes of plant competition. Competition and coexistence can be mediated by abiotic soil nutrient differences as well as by soil microbial communities. The latter effects occur through various mechanisms including negative plant-soil feedbacks, when plants foster the build-up of specialized pathogenic microbes, which ultimately reduce conspecific, but not heterospecific, densities. Microbial mutualists can have generalized associations with host plants, and by associating with multiple species might...

Data from: The effect of rhizosphere microbes outweighs host plant genotype in reducing insect herbivory

Charley J. Hubbard, Baohua Li, Robby McMinn, Marcus T. Brock, Lois Maignien, Brent E. Ewers, Daniel Kliebenstein & Cynthia Weinig
Rhizosphere microbes affect plant performance, including plant resistance against insect herbivores; yet, a direct comparison of the relative influence of rhizosphere microbes vs. plant genotype on herbivory levels and on metabolites related to defense is lacking. In the crucifer Boechera stricta, we tested the effects of rhizosphere microbes and plant genotype on herbivore resistance, the primary metabolome, and select secondary metabolites. Plant populations differed significantly in the concentrations of 6 glucosinolates (GLS), secondary metabolites known...

Data from: Effects of experimental anthropogenic noise on avian settlement patterns and reproductive success

Allison S. Injaian, Lauren Poon, Gail L. Patricelli & Lauren Y Poon
The acoustic footprints of factories, roadways, etc. reach far beyond their physical infrastructure because high amplitude, low frequency noise can propagate many kilometers. Previous studies found that noise exposure decreases habitat quality and reproductive success for some species. However, few studies have linked the reduction in perceived habitat quality due to noise exposure to effects on avian settlement patterns and reproductive success. Here, we experimentally investigate the impacts of noise pollution during settlement on adult...

Data from: Experimental evaluation of the robustness of the growth-stress tolerance trade-off within the perennial grass Dactylis glomerata

Pauline Bristiel, Lauren Gillespie, Liv Østrem, Jennifer Balachowski, Cyrille Violle & Florence Volaire
1. A core tenet of functional ecology is that the vast phenotypic diversity observed in the plant kingdom could be partly generated by a trade- off between the ability of plants to grow quickly and acquire resources in rich environments vs. the ability to conserve resources and avoid mortality under stress. However, experimental demonstrations remain scarce and potentially blurred by phylogenetic constraints in cross-species analyses. Here we experimentally decoupled growth potential and stress survival by...

Data from: Mutualists stabilize coexistence of congeneric legumes

Andrew Siefert, Kenneth W. Zillig, Maren L. Friesen & Sharon Y. Strauss
Coexistence requires that stabilizing niche differences, which cause species to limit themselves more than others, outweigh relative fitness differences that cause competitive exclusion. Interactions with shared mutualists, which can differentially affect host fitness and change in magnitude with host frequency, can satisfy these conditions for coexistence, yet empirical tests of mutualist effects on relative fitness and stabilizing niche differences are largely lacking within the framework of coexistence theory. Here, we show that N-fixing rhizobial mutualists...

Data from: Can biosecurity and local network properties predict pathogen species richness in the salmonid industry?

Tadaishi Yatabe, Simon J. More, Fiona Geoghegan, Catherine McManus, Ashley E. Hill & Beatriz Martinez-Lopez
Salmonid farming in Ireland is mostly organic, which implies limited disease treatment options. This highlights the importance of biosecurity for preventing the introduction and spread of infectious agents. Similarly, the effect of local network properties on infection spread processes has rarely been evaluated. In this paper, we characterized the biosecurity of salmonid farms in Ireland using a survey, and then developed a score for benchmarking the disease risk of salmonid farms. The usefulness and validity...

Data from: Reef fish functional traits evolve fastest at trophic extremes

Samuel R. Borstein, James A. Fordyce, Brian C. O'Meara, Peter C. Wainwright & Matthew D. McGee
Trophic ecology is thought to exert a profound influence on biodiversity, but the specifics of the process are rarely examined at large spatial and evolutionary scales. We investigate how trophic position and diet breadth influence functional trait evolution in one of the most species-rich and complex vertebrate assemblages, coral reef fishes, within a large-scale phylogenetic framework. We show that, in contrast with established theory, functional traits evolve fastest in trophic specialists with narrow diet breadths...

Data from: Surveying the spatial distribution of feral sorghum (Sorghum bicolor L.) and its sympatry with johnsongrass (S. halepense) in South Texas

Sara Ohadi, Matthew Littlejohn, Mohsen Mesgaran, William Rooney, Muthu Bagavathiannan & Muthukumar Bagavathiannan
Sorghum (Sorghum bicolor) is an important grain and forage crop grown across the US. In some areas, sorghum can become feral along roadsides and other ruderal areas, as a result of seed spill during harvest or transport. In some of these situations, feral sorghum grows in or near established johnsongrass (S. halepense) populations. Johnsongrass, a wild relative of sorghum and an incredibly noxious weed, is capable of hybridizing with cultivated sorghum. Because commercial hybrid sorghum...

Data from: The evolution of floral signals in relation to range overlap in a clade of California Jewelflowers (Streptanthus s.l.)

Marjorie G. Weber, N. Ivalu Cacho, Martin J. Q. Phan, Caprice Disbrow, Santiago R. Ramirez & Sharon Y. Strauss
Because of their function as reproductive signals in plants, floral traits experience distinct selective pressures related to their role in speciation, reinforcement, and prolonged coexistence with close relatives. However, few studies have investigated whether population-level processes translate into detectable signatures at the macroevolutionary scale. Here, we ask whether patterns of floral trait evolution and range overlap across a clade of California Jewelflowers reflect processes hypothesized to shape floral signal differentiation at the population level. We...

Registration Year

  • 2018
    89

Resource Types

  • Dataset
    89

Affiliations

  • University of California, Davis
    89
  • Duke University
    4
  • University of Wyoming
    3
  • Michigan State University
    3
  • Max Planck Institute for Ornithology
    2
  • University of Washington
    2
  • University of Michigan-Ann Arbor
    2
  • University of California System
    2
  • Université Paul-Valéry Montpellier
    2
  • The Ohio State University
    2