41 Works

Lipid mediators detected in COVID-19 patients and healthy controls

Cindy McReynolds, Irene Cortes_Puch, Resmi Ravindran, Imran Khan, Pei-An Betty Shih, Bruce D. Hammock, Jun Yang & Bruce G. Hammock
Polyunsaturated fatty acids are metabolized into regulatory lipids important for initiating inflammatory responses in the event of disease or injury and for signaling the resolution of inflammation and return to homeostasis. The epoxides of linoleic acid (leukotoxins) regulate skin barrier function, perivascular and alveolar permeability and have been associated with poor outcomes in burn patients and in sepsis. It was later reported that blocking metabolism of leukotoxins into the vicinal diols ameliorated the deleterious effects...

Antimicrobials from a feline skin commensal bacterium inhibit skin colonization and infection by drug-resistant S. pseudintermedius

Alan O'Neill
Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is an important emerging zoonotic pathogen that causes severe skin infections. To combat infections from drug-resistant bacteria, the transplantation of commensal antimicrobial bacteria as a therapeutic has shown clinical promise. We screened a collection of diverse staphylococcus species from domestic dogs and cats for antimicrobial activity against MRSP. A unique strain (S. felis C4) was isolated from feline skin that inhibited MRSP and multiple gram-positive pathogens. Competition experiments in mice showed...

Amplicon sequence variant tables of Donax gouldii microbiomes from Scripps Pier, La Jolla, CA, USA

Alexander Neu
Predicting how populations and communities of organisms will respond to anthropogenic change is of paramount concern in ecology today. For communities of microorganisms, however, these predictions remain challenging, primarily due to data limitations. Information about long-term dynamics of host-associated microbial communities, in particular, are lacking. In this study, we use well-preserved and freshly collected samples of soft tissue from a marine bivalve host, Donax gouldii, at a single site to quantify the diversity and composition...

Data from: Chimpanzees behave prosocially in a group-specific manner

Edwin J. C. Van Leeuwen, Sarah E. DeTroy, Stephan P. Kaufhold, Clara Dubois, Sebastian Schütte, Josep Call & Daniel B. M. Haun
Chimpanzees act cooperatively in the wild, but whether they afford benefits to others, and whether their tendency to act prosocially varies across communities is unclear. Here, we show that chimpanzees from neighboring communities provide valuable resources to group members at personal cost, and that the magnitude of their prosocial behavior is group specific. Provided with a resource-donation experiment allowing for free (partner) choice, we observed an increase in prosocial acts across the study period in...

Data from: Precisely timed theta oscillations are selectively required during the encoding phase of memory

Stefan Leutgeb, Jill K Leutgeb, Clare R Quirk, Ipshita Zutshi, Sunandha Srikanth, Maylin L Fu, Naomie Devico Marciano, Morgan K Wright, Darian F Parsey, Stanley Liu, Rachel E Siretskiy & Tiffany L Huynh
Brain oscillations have been hypothesized to support cognitive function by coordinating spike timing within and across brain regions, yet it is often not known when timing is either critical for neural computations or an epiphenomenon. The entorhinal cortex and hippocampus are necessary for learning and memory and exhibit prominent theta oscillations (6–9 Hz), which are controlled by pacemaker cells in the medial septal area. Here we show that entorhinal and hippocampal neuronal activity patterns were...

Iron sulfides and anomalous electrical resistivity in cratonic environments: electrical resistivity data set

Anne Pommier
The interpretation of low-resistivity anomalies in the lithospheric mantle of several cratonic regions has invoked hydrogen, or connected networks of graphite with iron-rich silicates, and/or metal sulfides. Electrical laboratory measurements are a powerful approach for exploring these alternatives. We report electrical measurements of two xenoliths (pyroxenite and dunite) from Tanzania; two metal sulfides (FeS and Fe-S-Ni); and several mixtures of metal sulfides (3.4–18.2 vol.%) with xenolith. A multi- anvil press was employed to maintain a...

Data from: Coupling between motor cortex and striatum increases during sleep over long-term skill learning

Stefan Lemke, Dhakshin Ramanathan, David Darevsky, Dan Egert, Josh Berke & Karunesh Ganguly
The strength of cortical connectivity to the striatum influences the balance between behavioral variability and stability. Learning to consistently produce a skilled action requires plasticity in corticostriatal connectivity associated with repeated training of the action. However, it remains unknown whether such corticostriatal plasticity occurs during training itself or “offline” during time away from training, such as sleep. Here, we monitor the corticostriatal network throughout long-term skill learning in rats and find that non-REM (NREM) sleep...

Drivers and projections of global surface temperature anomalies at the local scale

Susanne Benz, Steven Davis & Jennifer Burney
More than half of the world’s population now lives in urban areas, and trends in rural-to-urban migration are expected to continue through the end of the century. Although cities create efficiencies that drive innovation and economic growth, they also alter the local surface energy balance, resulting in urban temperatures that can differ dramatically from surrounding areas. Here we introduce a global 1-km resolution data set of seasonal and diurnal anomalies in urban surface temperatures relative...

Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment-dependent

Ken Thompson, Catherine Peichel, Diana Rennison, Matthew McGee, Arianne Albert, Timothy Vines, Anna Greenwood, Abigail Wark, Yaniv Brandvain, Molly Schumer & Dolph Schluter
Hybrid incompatibilities occur when interactions between opposite-ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are 'intrinsic', meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus...

Data accompanying manuscript: Allometric analysis of brain cell number in Hymenoptera suggests ant brains diverge from general trends

R Keating Godfrey, Mira Swartzlander & Gronenberg Wulfila
Many comparative neurobiological studies seek to connect sensory or behavioral attributes across taxa with differences in their brain composition. Such studies can only be interpreted in a meaningful way if the general brain-body relationships are known on a larger taxonomic scale. Recent studies in vertebrates suggest cell number and density may be better correlated with behavioral ability than brain mass or volume, but few estimates of such figures exist for insects. Here we use the...

Response diversity in corals: hidden differences in bleaching mortality among cryptic Pocillopora species

Scott Burgess, Erika Johnston, Alex Wyatt, James Leichter & Peter Edmunds
Variation among functionally similar species in their response to environmental stress buffers ecosystems from changing states. Functionally similar species may often be cryptic species representing evolutionarily distinct genetic lineages that are morphologically indistinguishable. However, the extent to which cryptic species differ in their response to stress, and could therefore provide a source of response diversity, remains unclear because they are often not identified or are assumed to be ecologically equivalent. Here, we uncover differences in...

Introgressive hybridization erodes morphological divergence between lentic and lotic habitats in an endangered minnow

Henry Baker, Danielle C. Hankins & Jonathan Shurin
Introgressive hybridization may erode phenotypic divergence along environmental gradients, collapsing locally adapted populations into a hybrid swarm. Alternatively, introgression may promote phenotypic divergence by providing variation on which natural selection can act. In freshwater fishes, water flow often selects for divergent morphological traits in lake versus stream habitats. We tested the effects of introgression on lake-stream morphological divergence in the minnow Owens Tui Chub (Siphateles bicolor snyderi), which has been rendered endangered by introgression from...

Supplementary data for: Reproductive deficits induced by prenatal anti-Mullerian hormone exposure require androgen receptor in kisspeptin cells

Karen Tonsfeldt, Emily Ho, Chengxian Shi, Michelle He, Ryan Nguyen, Genevieve Ryan & Pamela Mellon
Polycystic ovary syndrome (PCOS) is a common reproductive disorder characterized by elevated androgens and anti-Mullerian hormone (AMH). These hormones remain elevated throughout pregnancy, and potential effects of hormone exposure on offspring from women with PCOS remain largely unexplored. Expanding on recent reports of prenatal AMH exposure in mice, we have fully characterized the reproductive consequences of prenatal AMH (pAMH) exposure throughout the lifespan of first- and second-generation offspring of both sexes. We also sought to...

Genesis locations of the costliest atmospheric rivers impacting the Western United States (insurance claim data)

Hamish Prince
Atmospheric rivers (ARs) are responsible for the vast majority (approximately 88%) of flood damage in the Western U.S, an annual average of USD$1.1 billion. Here, using historical flood insurance data, we investigate the genesis characteristics of damaging ARs in the Western U.S. ARs exceeding USD$20 million in damage (90th percentile), are shown to travel further across the Pacific Ocean, with median genesis locations 8° to 27° further westward compared to typical ARs. Identifying regions of...

Efficient light‐harvesting of mesophotic corals is facilitated by coral optical traits

Netanel Kramer, Raz Tamir, Or Ben Zvi, Steven Jacques, Yossi Loya & Daniel Wangpraseurt
Sustained light-dependent coral reef communities can be found at a wide range of light environments, extending from the sea level to as deep as 150 m (i.e., mesophotic). How mesophotic corals thrive despite extremely limited light conditions still requires further investigation. Here, we undertook a comprehensive ecophysiological and bio-optical study on four depth-generalist coral species aiming to delineate the functional role that optical trait-properties have in light-harvesting, at contrasting light regimes. We show that the...

Timing the SARS-CoV-2 index case in Hubei Province

Jonathan Pekar & Joel Wertheim
Understanding when SARS-CoV-2 emerged is critical to evaluating our current approach to monitoring novel zoonotic pathogens and understanding the failure of early containment and mitigation efforts for COVID-19. We employed a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how long SARS-CoV-2 could have circulated prior to the time of the most recent common ancestor. Our results define the period between mid-October and mid-November 2019 as the plausible interval...

Mapfile and ASV table of whole-body and shell-surface samples from geminate species of gastropods separated by the Isthmus of Panama

Alexander Neu
The rise of the Isthmus of Panama ~3.5 mya separated populations of many marine organisms, which then diverged into new geminate sister species currently living in the Eastern Pacific Ocean and Caribbean Sea. However, we know very little about how such evolutionary divergences of host species have shaped their microbiomes. Here, we compared the microbiomes of whole-body and shell-surface samples of geminate species of marine gastropods in the genera Cerithiumand Cerithideopsis to those of congeneric...

Pico-phytoplankton abundance, growth and grazing rates along 110°E in the eastern Indian Ocean

Michael Landry & Selph Karen
Dilution experiments were conducted on R/V Investigator cruise IN2019v03 (17 May to 5 June 2019) on a south-to-north transect along longitude 110°E, west of Australia. Population abundances were measured by flow cytometry. Instantaneous rates of growth and grazing mortality were calculated from 2-treatment dilution incubations at six light levels.

Accuracy in near-perfect virus phylogenies

Joel Wertheim
Phylogenetic trees from real-world data often include short edges with very few substitutions per site, which can lead to partially resolved trees and poor accuracy. Theory indicates that the number of sites needed to accurately reconstruct a fully resolved tree grows at a rate proportional to the inverse square of the length of the shortest edge. However, when inferred trees are partially resolved due to short edges, "accuracy" should be defined as the rate of...

Large mitochondrial DNA deletions in HIV sensory neuropathy

Ricardo Roda, David Bargiela, Weiran Chen, Ken Perry, Ronald J. Ellis, David B. Clifford, Ajay Bharti, Asha Kallianpur, Michelli F Oliveira, Monica M. Diaz, Leah H. Rubin, Christina Gavegnano, Justin C. McArthur, Ahmet Hoke & Michael Polydefkis
Objective: The primary objective of this study was to evaluate the correlation of large mitochondrial DNA deletions in skin samples of people with HIV with measure of neuropathy and prior exposure to therapy. We hypothesized that deletions would be associated with the presence of neuropathy. As secondary objectives we determined the correlation of deletion burden with demographic data and neuropathy measures. Methods: In this retrospective cohort study we measured the accumulation of large mtDNA deletions...

Hawkmoths use wingstroke-to-wingstroke frequency modulation for aerial recovery to vortex ring perturbations

Jeff Gau, Ryan Gemilere, FM Subteam LDS-VIP, James Lynch, Nick Gravish & Simon Sponberg
Centimetre-scale fliers must contend with the high power requirements of flapping flight. Insects have elastic elements in their thoraxes which may reduce the inertial costs of their flapping wings. Matching wingbeat frequency to a mechanical resonance can be energetically favourable, but also poses control challenges. Many insects use frequency modulation on long timescales, but wingstroke-to-wingstroke modulation of wingbeat frequencies in a resonant spring-wing system is potentially costly because muscles must work against the elastic flight...

Test data from SPCAM for machine learning in moist physics

Guang Zhang, Yilun Han, Xiaomeng Huang & Yong Wang
Current moist physics parameterization schemes in general circulation models (GCMs) are the main source of biases in simulated precipitation and atmospheric circulation. Recent advances in machine learning make it possible to explore data-driven approaches to developing parameterization for moist physics processes such as convection and clouds. This study aims to develop a new moist physics parameterization scheme based on deep learning. We use a residual convolutional neural network (ResNet) for this purpose. It is trained...

Cortex cis-regulatory switches establish scale colour identity and pattern diversity in Heliconius

Luca Livraghi, Joseph J. Hanly, Ling Sheng Loh, Anna Ren, Ian A. Warren, Carolina Concha, Charlotte Wright, Jonah M. Walker, Jessica Foley, Henry Arenas-Castro, Arnaud Martin, William O. McMillan, Chris D. Jiggins, Steven M. Van Bellghem, Gabriela Montejo-Kovacevich, James J. Lewis, Micheal W. Perry, Zachary H. Goldberg, Laura H. Lopez, Riccardo Papa & Eva S.M. Van Der Heijden
In Heliconius butterflies, wing pattern diversity is controlled by a few genes of large effect that regulate colour pattern switches between morphs and species across a large mimetic radiation. One of these genes, cortex, has been repeatedly associated with colour pattern evolution in butterflies. Here we carried out CRISPR knock-outs in multiple Heliconius species and show that cortex is a major determinant of scale cell identity. Chromatin accessibility profiling and introgression scans identified cis-regulatory regions...

Recovery from hybrid breakdown reveals a complex genetic architecture of mitonuclear incompatibilities

Thiago Lima, Ricardo Pereira, Ronald Burton, Tessa Pierce & Lin Chao
Reproductive isolation is often achieved when genes that are neutral or beneficial in their genomic background become functionally incompatible in a foreign genome, causing inviability, sterility or low fitness in hybrids. Recent studies suggest that mitonuclear interactions are among the initial incompatibilities to evolve at early stages of population divergence across taxa. Yet, the genomic architecture of mitonuclear incompatibilities has rarely been elucidated. We employ an experimental evolution approach starting with low-fitness F2 interpopulation hybrids...

DEPP: Deep learning enables extending species trees using single genes

Yueyu Jiang, Metin Balaban, Qiyun Zhu & Siavash Mirarab
Placing new sequences onto reference phylogenies is increasingly used for analyzing environmental samples, especially microbiomes. However, existing placement methods have a fundamental limitation: they assume that query sequences have evolved using specific models directly on the reference phylogeny. Thus, they can place single-gene data (e.g., 16S rRNA amplicons) onto their own gene tree. This practice is a proxy for a more ambitious goal: extending a (genome-wide) species tree given data from individual genes. No algorithm...

Registration Year

  • 2021
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Resource Types

  • Dataset
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Affiliations

  • University of California, San Diego
    41
  • Stanford University
    2
  • Harvard University
    2
  • Emory University School of Medicine
    1
  • Massachusetts General Hospital
    1
  • Rady Children's Hospital-San Diego
    1
  • California State University, Long Beach
    1
  • University of Antwerp
    1
  • Zhejiang University
    1
  • University of Washington
    1