163 Works

Data from: Gradual loading ameliorates maladaptation in computational simulations of vein graft growth and remodelling

Abhay Bangalore Ramachandra, Jay D. Humphrey & Alison L. Marsden
Vein graft failure is a prevalent problem in vascular surgeries, including bypass grafting and arteriovenous fistula procedures in which veins are subjected to severe changes in pressure and flow. Animal and clinical studies provide significant insight, but understanding the complex underlying coupled mechanisms can be advanced using computational models. Towards this end, we propose a new model of venous growth and remodelling (G&R) based on a constrained mixture theory. First, we identify constitutive relations and...

Data from: A phylogenomic resolution of the sea urchin tree of life

Nicolás Mongiardino Koch, Simon E. Coppard, Harilaos A. Lessios, Derek E.G. Briggs, Rich Mooi & Greg W. Rouse
Background: Echinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1,000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a...

Data from: Limited trophic partitioning among sympatric delphinids off a tropical oceanic atoll

Hillary Young, Katherine Nigro, Douglas J. McCauley, Lisa T. Ballance, Erin M. Oleson & Simone Baumann-Pickering
Understanding trophic relationships among marine predators in remote environments is challenging, but it is critical to understand community structure and dynamics. In this study, we used stable isotope analysis of skin biopsies to compare the isotopic, and thus, trophic niches of three sympatric delphinids in the waters surrounding Palmyra Atoll, in the Central Tropical Pacific: the melon-headed whale (Peponocephala electra), Gray’s spinner dolphin (Stenella longirostris longirostris), and the common bottlenose dolphin (Tursiops truncatus). δ15N values...

Data from: Evaluating the impact of domestication and captivity on the horse gut microbiome

Jessica L. Metcalf, Se Jin Song, James T. Morton, Sophie Weiss, Andaine Seguin-Orlando, Frédéric Joly, Claudia Feh, Pierre Taberlet, Eric Coissac, Amnon Amir, Eske Willerslev, Rob Knight, Valerie McKenzie & Ludovic Orlando
The mammal gut microbiome, which includes host microbes and their respective genes, is now recognized as an essential second genome that provides critical functions to the host. In humans, studies have revealed that lifestyle strongly influences the composition and diversity of the gastrointestinal microbiome. We hypothesized that these trends in humans may be paralleled in mammals subjected to anthropogenic forces such as domestication and captivity, in which diets and natural life histories are often greatly...

Data from: The Nearctic Nedubini: the most basal lineage of katydids is resolved among the paraphyletic “Tettigoniinae” (Orthoptera: Tettigoniidae)

Jeffrey A. Cole & Bo Huey Chiang
This study investigated the systematics of the Nearctic shield-back katydids (“Tettigoniinae”), a paraphyletic group thought to include genera from a distinctive Gondwanan tribe, the Nedubini, among an otherwise Holarctic fauna. From exemplars of five genera of Nedubini and the majority of other genera of Nearctic “Tettigoniinae,” five gene regions were sequenced, aligned with publicly available sequence data that represent diverse subfamilies of Tettigoniidae, and subjected to phylogenetic analysis under Bayesian and likelihood criteria. Our results...

Data from: The effect of keystone individuals on collective outcomes can be mediated through interactions or behavioral persistence

Noa Pinter-Wollman, Carl Nick Keiser, Roy Wollman & Jonathan Pruitt
Collective behavior emerges from interactions among group members who often vary in their behavior. The presence of just one or a few keystone individuals, such as leaders or tutors, may have a large effect on collective outcomes. These individuals can catalyze behavioral changes in other group members, thus altering group composition and collective behavior. The influence of keystone individuals on group function may lead to trade-offs between ecological situations, because the behavioral composition they facilitate...

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...

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...

Heterogeneity in the Dynamic Effects of Uncertainty on Investment

Sungje Byun & Soojin Jo
How does aggregate profit uncertainty influence investment activity at the firm level? We propose a parsimonious adaptation of a factor-autoregressive conditional heteroscedasticity model to exploit information in a subindustry sales panel for an efficient and tractable estimation of aggregate volatility. The resulting uncertainty measure is then included in an investment forecasting model interacted with firm-specific coefficients. We find that higher profit uncertainty induces firms to lower capital expenditure on average, yet to a considerably different...

A parallel accumulator model accounts for decision randomness when deciding on risky prospects with different expected value

Jonathon Howlett & Martin Paulus
In decision-making situations individuals rarely have complete information available to select the best option and often show decisional randomness, i.e. given the same amount of knowledge individuals choose different options at different times. Dysfunctional processes resulting in altered decisional randomness can be considered a target process for psychiatric disorders, yet these processes remain poorly understood. Advances in computational modeling of decision-making offer a potential explanation for decisional randomness by positing that decisions are implemented in...

Spatially compartmentalized phase regulation of a Ca2+-cAMP-PKA oscillatory circuit

Brian Tenner
Signaling networks are spatiotemporally organized in order to sense diverse inputs, process information, and carry out specific cellular tasks. In pancreatic β cells, Ca2+, cyclic adenosine monophosphate (cAMP), and Protein Kinase A (PKA) exist in an oscillatory circuit characterized by a high degree of feedback. Here, we describe a mode of regulation within this circuit involving a spatial dependence of the relative phase between cAMP, PKA, and Ca2+. We show that nanodomain clustering of Ca2+-sensitive...

Bacteriophage lambda overcomes a perturbation in its host‐viral genetic network through mutualism and evolution of life history traits

Animesh Gupta, Anechelle N. Soto, Sarah J. Medina, Katherine L. Petrie & Justin R. Meyer
An important driver of viral evolution is natural selection to optimize the use of their hosts’ genetic network. To learn how viruses respond to this pressure, we disrupted the genetic network of Escherichia coli to inhibit replication of its virus, bacteriophage lambda, and then observed how λ evolved to compensate. We deleted E. coli's dnaJ gene, which lambda uses to initiate DNA replication. Lambda partially restored its ability to reproduce with just two adaptive mutations...

Experiencing Cancer in Appalachian Kentucky

Melanie McComsey, David Ahern, Robin C. Vanderpool, Timothy W. Mullett, Ming-Yuan Chih, Meghan Johnson, Michele Ellison, Karen Onyeije, Bradford W. Hesse & Eliah Aronoff-Spencer
Nothing tells the story of people working together better than a community quilt. A diversity of talents, colors, and materials brought together through skill and shared purpose. Perhaps never before have we as Americans needed a stronger reminder that many hands make short work of big problems. The work presented here by the L.A.U.N.C.H. Collaborative offers a new framework for health care that could be compared to a digital quilt, powered by community-based participatory design,...

Dynamic post-translational modification profiling of M. tuberculosis-infected primary macrophages

Jonathan M Budzik, Danielle L Swaney, David Jimenez-Morales, Jeffrey R Johnson, Nicholas E Garelis, Teresa Repasy, Allison W Roberts, Lauren M Popov, Trevor J Parry, Dexter Pratt, Trey Ideker, Nevan J Krogan & Jeffery S Cox
Macrophages are highly plastic cells with critical roles in immunity, cancer, and tissue homeostasis, but how these distinct cellular fates are triggered by environmental cues is poorly understood. To uncover how primary murine macrophages respond to bacterial pathogens, we globally assessed changes in post-translational modifications of proteins during infection with Mycobacterium tuberculosis, a notorious intracellular pathogen. We identified hundreds of dynamically regulated phosphorylation and ubiquitylation sites, indicating that dramatic remodeling of multiple host pathways, both...

Data from: High-throughput molecular identification of fish eggs using multiplex suspension bead arrays

Lani U Gleason & Ronald S Burton
The location and abundance of fish eggs provide information concerning the timing and location of spawning activities and can provide fishery-independent estimates of spawning biomass. However, the full value of egg and larval surveys is severely restricted because many species’ eggs and larvae are morphologically similar, making species-level identification difficult. Recent efforts have shown that nearly all species of fish may be identified by mitochondrial DNA (mtDNA) sequences (e.g., via “DNA barcoding”). By taking advantage...

Data from: Underlying mechanisms and ecological context of variation in exploratory behavior of the Argentine ant, Linepithema humile

Hannah Page, Andrew Sweeney, Anna Pilko & Noa Pinter-Wollman
Uncovering how and why animals explore their environment is fundamental for understanding population dynamics, the spread of invasive species, species interactions, etc. In social animals, individuals within a group can vary in their exploratory behavior, and the behavioral composition of the group can determine its collective success. Workers of the invasive Argentine ant (Linepithema humile) exhibit individual variation in exploratory behavior, which affects the colony’s collective nest selection behavior. Here, we examine the mechanisms underlying...

Data from: Age, gender, neck circumference, and Epworth sleepiness scale do not predict obstructive sleep apnea (OSA) in moderate to severe chronic obstructive pulmonary disease (COPD): the challenge to predict OSA in advanced COPD

Xavier Soler, S.Y. Liao, J.M. Marin, G. Lorenzi-Filho, R. Jen, P. DeYoung, R.L. Owens, A.L. Ries & A. Malhotra
The combination of chronic obstructive pulmonary disease (COPD) and obstructive sleep apnea (OSA) is associated with substantial morbidity and mortality. We hypothesized that predictors of OSA among patients with COPD may be distinct from OSA in the general population. Therefore, we investigated associations between traditional OSA risk factors (e.g. age), and sleep questionnaires [e.g. Epworth Sleepiness Scale] in 44 patients with advanced COPD. As a second aim we proposed a pilot, simplified screening test for...

Data from: Acquisition of obligate mutualist symbionts during the larval stage is not beneficial for a coral host

Aaron Hartmann, Kristen Marhaver, Anke Klueter, Michael Lovci, Collin Closek, Erika Diaz Almeyda, Valerie Chamberland, Frederick Archer, Dimitri Deheyn, Mark Vermeij & Monica Medina
Theory suggests that the direct transmission of endosymbionts from parents to offspring (vertical transmission) in animal hosts is advantageous and evolutionarily stable, yet many host species instead acquire their symbionts from the environment (horizontal acquisition). An outstanding question in marine biology is why some scleractinian corals do not provision their eggs and larvae with the endosymbiotic dinoflagellates that are necessary for a juvenile’s ultimate survival. We tested whether the acquisition of photosynthetic endosymbionts (family Symbiodiniaceae)...

Data from: Evolution of the exclusively human-pathogen Neisseria gonorrhoeae: human-specific engagement of immunoregulatory Siglecs

Corinna S. Landig, Ashley Hazel, Benjamin P. Kellman, Jerry J. Fong, Flavio Schwarz, Sarika Agarwal, Nissi Varki, Paola Massari, Nathan E. Lewis, Sanjay Ram & Ajit Varki
Neisseria gonorrhoeae causes the sexually transmitted disease gonorrhea exclusively in humans and uses multiple strategies to infect, including acquisition of host sialic acids that cap and mask lipooligosaccharide termini, while restricting complement activation. We hypothesized that gonococci selectively target human anti-inflammatory sialic acid-recognizing Siglec receptors on innate immune cells to blunt host responses, and that pro-inflammatory Siglecs and SIGLEC pseudogene polymorphisms represent host evolutionary adaptions to counteract this interaction. N. gonorrhoeae can indeed engage multiple...

Data from: The curious case of Hermodice carunculata (Annelida: Amphinomidae): evidence for genetic homogeneity throughout the Atlantic Ocean and adjacent basins

Joseph B. Ahrens, Elizabeth Borda, Rômulo Barroso, Paulo C. Paiva, Alexandra M. Campbell, Alexander Wolf, Maggy M. Nugues, Greg W. Rouse & Anja Schulze
Over the last few decades, advances in molecular techniques have led to the detection of strong geographic population structure and cryptic speciation in many benthic marine taxa, even those with long-lived pelagic larval stages. Polychaete annelids, in particular, generally show a high degree of population divergence, especially in mitochondrial genes. Rarely have molecular studies confirmed the presence of ‘cosmopolitan’ species. The amphinomid polychaete Hermodice carunculata was long considered the sole species within its genus, with...

Data from: When should we expect early bursts of trait evolution in comparative data? Predictions from an evolutionary food web model

Travis Ingram, Luke J. Harmon & Jonathan B. Shurin
Conceptual models of adaptive radiation predict that competitive interactions among species will result in an early burst of speciation and trait evolution followed by a slowdown in diversification rates. Empirical studies often show early accumulation of lineages in phylogenetic trees, but usually fail to detect early bursts of phenotypic evolution. We use an evolutionary simulation model to assemble food webs through adaptive radiation, and examine patterns in the resulting phylogenetic trees and species' traits (body...

Data from: Olfaction contributes to pelagic navigation in a coastal shark

Andrew P. Nosal, Yi Chao, John D. Farrara, Fei Chai & Philip A. Hastings
How animals navigate the constantly moving and visually uniform pelagic realm, often along straight paths between distant sites, is an enduring mystery. The mechanisms enabling pelagic navigation in cartilaginous fishes are particularly understudied. We used shoreward navigation by leopard sharks (Triakis semifasciata) as a model system to test whether olfaction contributes to pelagic navigation. Leopard sharks were captured alongshore, transported 9 km offshore, released, and acoustically tracked for approximately 4 h each until the transmitter...

Data from: Expanding the described metabolome of the marine cyanobacterium Moorea producens JHB through orthogonal natural products workflows

Paul D. Boudreau, Emily A. Monroe, Suneet Mehrotra, Shane Desfor, Anton Korobeynikov, David H. Sherman, Thomas F. Murray, Lena Gerwick, Pieter C. Dorrestein & William H. Gerwick
Moorea producens JHB, a Jamaican strain of tropical filamentous marine cyanobacteria, has been extensively studied by traditional natural products techniques. These previous bioassay and structure guided isolations led to the discovery of two exciting classes of natural products, hectochlorin (1) and jamaicamides A (2) and B (3). In the current study, mass spectrometry-based ‘molecular networking’ was used to visualize the metabolome of Moorea producens JHB, and both guided and enhanced the isolation workflow, revealing additional...

Data from: Ecological speciation of bacteriophage lambda in allopatry and sympatry

Justin R. Meyer, Devin T. Dobias, Sarah J. Medina, Lisa Servilio, Animesh Gupta & Richard E. Lenski
Understanding the conditions that allow speciation to occur is difficult because most research has focused on either long-lived organisms or asexual microorganisms. We propagated bacteriophage λ, a virus with rapid generations and frequent recombination, on two Escherichia coli host genotypes that expressed either the LamB or OmpF receptor. When supplied with either single host (allopatry), λ improved its binding to the available receptor while losing its ability to use the alternative. When evolving on both...

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  • University of California, San Diego
  • University of Kentucky
  • Yale University
  • Scripps Institution of Oceanography
  • University of California, Santa Barbara
  • Columbia University
  • University of Minnesota
  • Southwest Fisheries Science Center
  • University of Toronto
  • University of British Columbia