35 Works

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...

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...

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...

Data from: The genomic signature of ecological divergence along the benthic-limnetic axis in allopatric and sympatric threespine stickleback

Andreas Härer, Daniel Bolnick & Diana Rennison
The repeated occurrence of similar phenotypes in independent lineages (i.e., parallel evolution) in response to similar ecological conditions can provide compelling insights into the process of adaptive evolution. An intriguing question is to what extent repeated phenotypic changes are underlain by repeated changes at the genomic level and whether patterns of genomic divergence differ with the geographic context in which populations evolve. Here, we combine genomic, morphological and ecological datasets to investigate the genomic signatures...

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...

No state change in pelagic fish production and biodiversity during the Eocene-Oligocene Transition

Elizabeth Sibert, Michelle Zill, Ella Frigyik & Richard Norris
The Eocene-Oligocene (E/O) boundary ~33.9 million years ago, has been described as a state change in the Earth system marked by the permanent glaciation of Antarctica and a proposed increase in oceanic productivity. Here we quantified the response of fish production and biodiversity to this event using microfossil fish teeth (ichthyoliths) in seven deep-sea sediment cores from around the world. Ichthyolith accumulation rate (a proxy for fish biomass production) shows no synchronous trends across the...

Data from: Stressed connections: cortisol levels following acute psychosocial stress disrupt affiliative mimicry in humans

Jonas P. Nitschke, Cecile S. Sunahara, Evan W. Carr, Piotr Winkielman, Jens C. Pruessner & Jennifer A. Bartz
Mimicry, and especially spontaneous facial mimicry, is a rudimentary element of social–emotional experience that is well-conserved across numerous species. Although such mimicry is thought to be a relatively automatic process, research indicates that contextual factors can influence mimicry, especially in humans. Here, we extend this work by investigating the effect of acute psychosocial stress on spontaneous facial mimicry. Participants performed a spontaneous facial mimicry task with facial electromyography (fEMG) at baseline and approximately one month...

Uneven substrates constrain walking speed in ants through modulation of stride frequency more than stride length

Glenna Clifton, David Holway & Nick Gravish
Natural terrain is rarely flat. Substrate irregularities challenge walking animals to maintain stability, yet we lack quantitative assessments of walking performance and limb kinematics on naturally uneven ground. We measured how continually uneven 3D-printed substrates influence walking performance of Argentine ants by measuring walking speeds of workers from lab colonies and by testing colony-wide substrate preference in field experiments. Tracking limb motion in over 8,000 videos, we used statistical models that associate walking speed with...

Replication Files for Nutrition and the Gut Microbiota in 10–18-Month Old Children Living in Urban Slums of Mumbai, India

Samantha Huey, Aparna Thorat, Varsha Thakker, Julia L. Finkelstein, Lingjing Jiang, Marcus Fedarko, Daniel McDonald, Cameron Martino, Farhana Ali, David G. Russell, Harsha Chopra, Kripa Rajagopalan, Jere Douglas Haas, Rob Knight, S.A. Udipi & P. Ghugre

Efficacy of metabarcoding for identification of fish eggs evaluated with mock communities

Elena Duke & Ron Burton
There is urgent need for effective and efficient monitoring of marine fish populations. Monitoring eggs and larval fish may be more informative that traditional fish surveys since ichthyoplankton surveys reveal the reproductive activities of fish populations, which directly impact their population trajectories. Ichthyoplankton surveys have turned to molecular methods (DNA barcoding & metabarcoding) for identification of eggs and larval fish due to challenges of morphological identification. In this study we examine the effectiveness of using...

Data from: Nutrient availability controls the impact of mammalian herbivores on soil carbon and nitrogen pools in grasslands

Judith Sitters, E.R. Jasper Wubs, Elisabeth S. Bakker, Thomas W. Crowther, Peter B. Adler, Sumanta Bagchi, Jonathan D. Bakker, Lori Biederman, Elizabeth T. Borer, Elsa E. Cleland, Nico Eisenhauer, Jennifer Firn, Laureano Gherardi, Nicole Hagenah, Yann Hautier, Sarah E. Hobbie, Johannes M.H. Knops, Andrew S. MacDougall, Rebecca L. McCulley, Joslin L. Moore, Brent Mortensen, Pablo L. Peri, Suzanne M. Prober, Charlotte Riggs, Anita C. Risch … &
Grasslands have been subject to considerable alteration due to human activities globally, including widespread changes in populations and composition of large mammalian herbivores and elevated supply of nutrients. Grassland soils remain important reservoirs of carbon (C) and nitrogen (N). Herbivores may affect both C and N pools and these changes likely interact with increases in soil nutrient availability. Given the scale of grassland soil fluxes, such changes can have striking consequences for atmospheric C concentrations...

Dataset for: Cascading effects of freshwater salinization on plankton communities in the Sierra Nevada

Emma Moffett, Henry Baker, Christine Bonadonna, Jonathan Shurin & Celia Symons
Runoff containing road salt (sodium chloride, NaCl) causes the salinization of inland freshwaters, with potentially severe impacts on aquatic species. We performed a mesocosm experiment to test the effects of salinization on plankton community structure in an oligotrophic mountain lake with a limited history of elevated salt concentrations. We exposed plankton communities to a gradient of 30 salt concentrations ranging from 1-2900 Cl– mg L-1 for six weeks. Adding salt increased zooplankton biomass at concentrations...

Dataset marmoset Snowdrift

Alejandro Sanchez Amaro, Judith Burkart & Federico Rossano
Social primates constantly face situations in which their preferences collide and they need to engineer strategies to overcome conflicts of interest. Studies with chimpanzees have found that they use competitive strategies to overcome social dilemmas, maximizing their own benefits while minimizing the loss of rewards. However, little is known about how other primates that rely more on cooperation would overcome similar dilemmas. We therefore presented male-female pairs of common marmosets (cooperative breeders) with two experiments...

VELB watershed data 2005

Michael Dobbins, Theresa Talley & Marcel Holyoak
The Valley Elderberry Longhorn Beetle (“VELB,” Desmocerus californicus dimorphus) is a rare and cryptic species that is found on or near its host plant, blue elderberry (Sambucus mexicana), and is native to California’s Central Valley. Over the past 100 years, the riparian forests of Central California have shrunk by over 90%, resulting in highly fragmented, and often isolated, remaining VELB habitat patches. This has created the need for robust monitoring and demographic data to assess...

Data from: Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): developing a model system for the evolution of marine bioluminescence

Jessica A. Goodheart, Geetanjali Minsky, Mira N. Brynjegard-Bialik, Michael S. Drummond, J. David Munoz, Timothy R. Fallon, Darrin T. Schultz, Jing-Ke Weng, Elizabeth Torres & Todd H. Oakley
Bioluminescence, or the production of light by living organisms via chemical reaction, is widespread across Metazoa. Laboratory culture of bioluminescent organisms from diverse taxonomic groups is important for determining the biosynthetic pathways of bioluminescent substrates, which may lead to new tools for biotechnology and biomedicine. Some bioluminescent groups may be cultured, including some cnidarians, ctenophores, and brittle stars, but those use luminescent substrates (luciferins) obtained from their diets, and therefore are not informative for determination...

Data from: Training 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...

Data from: Sugar content of diet does not buffer against chronic oral imidacloprid exposure in the alfalfa leafcutting bee, Megachile rotundata (Hymenoptera: Megachilidae)

Jacob Cecala, Danelle Angeline Baronia & Erin Wilson Rankin
Bees are economically critical pollinators, but are declining broadly due to several stressors, including non-target exposure to insecticides and deficiencies in nutrition. Understanding the simultaneous impact of stressors, particularly interactions between them, are critical to effectively conserving bees. While behavioral effects of pesticides like neonicotinoids have received some attention in solitary bees, our understanding of how they are modulated by diet quality is limited. Furthermore, scarce data exist on what concentrations of orally ingested neonicotinoids...

Traits and depth: what do hydroids tell us about morphology and life-history strategies in the deep sea?

Marina Oliveira Fernandez, Allen Collins, Arjan Gittenberger, Roy Kaustuv & Antonio Carlos Marques
Aim: Traits affect the survival and reproduction of individuals in different habitat conditions, ultimately altering their distributions. In the oceans, changes in environmental conditions with bathymetry may influence the occurrence of specific traits. Therefore, characterizing trait variation with depth can illuminate drivers related to the distribution of diversity of forms, functions, and life histories. We aimed to investigate patterns of variation in the diversified life histories and morphologies of hydroids with depth, integrating these patterns...

Closed-loop control of k-space sampling via physiologic feedback for cine MRI

Francisco Contijoch
This dataset accompanies the manuscript outlining a method for closed-loop sampling of k-space in response to physiologic changes. The closed-loop approach enables near-uniform radial sampling in a segmented acquisition approach which was higher than predetermined golden-angle radial sampling. This can be utilized to increase the sampling or decrease the temporal footprint of an acquisition and the closed-loop framework has the potential to be applied to patients with complex heart rhythms. Briefly, Segmented cine cardiac MRI...

Experimental electrical resistivity values and computed thermal conductivities

Anne Pommier, Christopher Davies & Rong Zhang
We present a joint experimental-modeling investigation of core cooling in small terrestrial bodies. Significant amounts of light elements (S, O, Mg, Si) may compose the metallic cores of terrestrial planets and moons. However, the effect of multiple light elements on transport properties, in particular, electrical resistivity and thermal conductivity, is not well constrained. Electrical experiments were conducted at 10 GPa and up to 1850 K on high-purity powder mixtures in the Fe-S-O(+/-Mg, +/-Si) systems using...

Data from: FSHB transcription is regulated by a novel 5’ distal enhancer containing a fertility-associated single nucleotide polymorphism

Stephanie C. Bohaczuk, Varykina G. Thackray, Jia Shen, Dorota Skowronska-Krawczyk & Pamela L. Mellon
The pituitary gonadotropins, follicle-stimulating hormone (FSH) and luteinizing hormone, signal the gonads to regulate male and female fertility. FSH is critical for female fertility as it regulates oocyte maturation, ovulation, and hormone synthesis. Multiple genome-wide association studies (GWAS) link a 130 Kb locus at 11p14.1, which encompasses the FSH beta-subunit (FSHB) gene, with fertility-related traits including polycystic ovary syndrome, age of natural menopause, and dizygotic twinning. The most statistically significant single-nucleotide polymorphism from several GWAS...

Utilizing next-generation sequencing to identify prey DNA in western North Atlantic grey seal (Halichoerus grypus) diet

Kelly Flanders, Zachary Olson & Kathryn Ono
Increasing grey seal (Halichoerus grypus) abundance in coastal New England is leading to social, political, economic, and ecological controversies. We studied grey seal feeding habits through next-generation sequencing of prey DNA using 16S amplicons from seal scat (N = 74) collected from a breeding colony on Monomoy Island in Massachusetts, U.S. and report frequency of occurrence and relative read abundance. We also assigned seal sex to scat samples using a revised PCR assay. In contrast...

Antagonistic effects of temperature and dissolved organic carbon on fish growth in California mountain lakes

Celia C. Symons, Marika A. Schulhof, Hamanda B. Cavalheri & Jonathan B. Shurin
Resources and temperature play major roles in determining biological production in lake ecosystems. Lakes have been warming and ‘browning’ over recent decades due to climate change and increased loading of terrestrial organic matter. Conflicting hypotheses and evidence have been presented about whether these changes will increase or decrease fish growth within lakes. Most studies have been conducted in low-elevation lakes where terrestrially derived carbon tends to dominate over carbon produced within lakes. Understanding how fish...

Dense seismic three-component nodal array at the Ramona Reservation

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High-Resolution imaging and monitoring of the subsurface structure and seismicity at a site along the San Jacinto fault zone using a dense seismic nodal array. The site is located about 6 km northwest of the town of Anza, California. The type of nodal sensor employed is the Fairfield Zland 3-component 5 Hz geophones (records ground velocity continuously at 500 sps). The array consists of 97 sensors, with 65 located along a linear across-fault profile and...

Social trematodes parasites increase standing army size in areas of greater invasion threat

Emlyn Resetarits, Mark Torchin & Ryan Hechinger
Organisms or societies are resource limited, causing important trade-offs between reproduction and defence. Given such trade-offs, optimal allocation theory predicts that, for animal societies with a soldier caste, allocation to soldiers should reflect local external threats. Although both threat intensity and soldier allocation can vary widely in nature, we currently lack strong evidence that spatial variation in threat can drive corresponding variation in soldier allocation. The diverse guild of trematode parasites of the California horn...

Registration Year

  • 2020

Resource Types

  • Dataset


  • University of California, San Diego
  • University of California, Irvine
  • University of Queensland
  • University of California, Berkeley
  • Netherlands Institute of Ecology
  • University of California, Santa Barbara
  • University of California, Riverside
  • Vrije Universiteit Brussel
  • University of Washington
  • University of Pretoria