29 Works

Data from: Accounting for variation in temperature and oxygen availability when quantifying marine ecosystem metabolism

Matthew Bracken, Luke Miller, Sarah Mastroni, Stephany Lira & Cascade Sorte
Given human modification of Earth’s ecosystems, it is essential to understand how these changes are influencing ecosystem functioning, including net and gross community production and community respiration. These responses are often estimated by measuring oxygen production in the light (net community production) and consumption in the dark (community respiration). These values can then be combined to estimate gross community production. However, the method used to create “dark” conditions – either experimental darkening during the day...

A hierarchy of global ocean models coupled to CESM1

Tien-Yiao Hsu, Francois Primeau & Gudrun Magnusdottir
Data associated with the following publication: Hsu, T. Y., Primeau, F. W., & Magnusdottir, G. (2022). A Hierarchy of Global Ocean Models Coupled to CESM1. Paper Abstract: We develop a hierarchy of simplified ocean models for coupled ocean, atmosphere, and sea ice climate simulations using the Community Earth System Model version 1 (CESM1). The hierarchy has four members: a slab ocean model, a mixed-layer model with entrainment and detrainment, an Ekman mixed-layer model, and an...

Global Ocean particulate organic phosphorus, carbon, oxygen for respiration, and nitrogen (GO-POPCORN) data from Bio-GO-SHIP cruises

Tatsuro Tanioka, Alyse Larkin, Allison Moreno, Catherine Garcia, Nathan Garcia, Jenna Lee, Adam Fagan, Melissa Brock, Skylar Gerace & Adam Martiny
Here, we present the Global Ocean Particulate Organic Phosphorus, Carbon, Oxygen for Respiration, and Nitrogen (GO-POPCORN) dataset from recent Bio-GO-SHIP cruises between 2011 and 2020. The combined dataset contains 2109 paired surface measurements of particulate organic carbon, nitrogen, and phosphorus from 70°S to 55°N across all major ocean basins. The dataset also includes 933 measurements of oxygen demand for organic carbon respiration. This new dataset is valuable for improving our understanding of how biological elemental...

Surface CO2 variability from the stratosphere, or not

Michael Prather
Fluctuations in atmospheric CO2 can be measured with great precision and are used to identify human-driven sources as well as natural cycles of ocean and land carbon. One source of variability is the stratosphere, where the influx of aged CO2-depleted air can produce fluctuations at the surface. This process has been speculated a potential source of interannual variability (IAV) in CO2 that might obscure the quantification of other sources of IAV. Given the recent success...

Data set for: Experimentally reduced feather microbial loads improve reproductive performance in captive Zebra Finches

Nancy Burley
We performed a laboratory experiment on caged, domesticated zebra finches to assess the effects of antimicrobial treatment applied to birds' plumage on the feather microbial loads of breeding pairs and their associated reproductive performance. Treatments included an experimental group that experienced frequent misting with a broad-spectrum antimicrobial, as well as two control groups. Microbial loads sampled from the belly feathers of breeders were higher post-hatching than pre-hatching, and experimental pairs had lower loads than controls...

Dataset for: Vibrometry as a noncontact alternative to dynamic and viscoelastic mechanical testing in cartilage

Gabriela Espinosa, Gaston Otarola, Jerry Hu & Kyriacos Athanasiou
Physiological loading of knee cartilage is highly dynamic and may contribute to the progression of osteoarthritis. Thus, an understanding of cartilage’s dynamic mechanical properties is crucial in cartilage research. In this study, vibrometry was used as a fast (2 hours), noncontact, and novel alternative to the slower (30 hours), traditional mechanical and biochemical assays for characterization of cartilage from the condyle, patella, trochlear groove, and meniscus. Finite-element models predicted tissue resonant frequencies and bending modes,...

CA1 20-40 Hz oscillatory dynamics reflect trial-specific information processing supporting nonspatial sequence memory

Sandra Gattas, Gabriel Elias, John Janecek, Michael Yassa & Norbert Fortin
The hippocampus is known to play a critical role in processing information about the temporal context in which our experiences occur. However, it remains unclear how hippocampal oscillations are associated with this type of information processing, and how their functional organization is influenced by connectivity gradients. Here we investigate these issues by examining local field potential activity recorded across the proximodistal axis of CA1 as rats performed a complex odor sequence memory task. More specifically,...

Beach wrack ecology at Crystal Cove State Park

Elizabeth Herrmann, Amy Henry, Sarah Kimball, Jennifer Mendez, Tarynn Kimmick & Joseph Basile
Crystal Cove State Park (CCSP) is one of few beaches in southern California that does not remove beach wrack. Beach wrack, marine organic material deposited from other ecosystems, includes algae, seagrass, marine phytoplankton, and carrion and is the key nutrient subsidy to this highly dynamic habitat. Many invasive brown algae species from the genus Sargassum have in some locations outcompeted and replaced native kelp offshore, potentially affecting wrack communities. Anthropogenic impacts such as oil spills,...

Prey naiveté alters the balance of consumptive and non-consumptive predator effects and shapes trophic cascades in freshwater plankton

Henry Baker, Stephanie Li, Stefan Samu, Natalie Jones, Celia Symons & Jonathan Shurin
Predators drive trophic cascades by reducing prey biomass and altering prey traits, selecting for prey that exhibit constitutive and induced anti-predator defenses that decrease susceptibility to consumption. These defense traits are often costly, generating a tradeoff between consumptive (CEs) and non-consumptive predator effects (NCEs). The ecological and evolutionary experience that prey share with a given predator may determine their position along this tradeoff curve, affecting the nature and strength of top-down control of ecosystems. Conceptual...

Microbiome assembly and maintenance across the lifespan of bumble bee workers

Tobin Hammer, August Easton-Calabria & Nancy A. Moran
How a host’s microbiome changes over its lifespan can influence development and aging. As these temporal patterns have only been described in detail for humans and a handful of other hosts, an important next step is to compare microbiome dynamics across a broader array of host-microbe symbioses, and to investigate how and why they vary. Here we characterize the temporal dynamics and stability of the bumblebee worker gut microbiome. Bumblebees are a useful symbiosis model...

Greenland mass trends from airborne and satellite altimetry during 2011–2020

Shfaqat Abbas Khan, Jonathan L. Bamber, Eric Rignot, Veit Helm, Andy Aschwanden, David M. Holland, Michiel R. Van Den Broeke, Michalea King, Brice Noël, Martin Truffer, Angelika Humbert, William Colgan, Saurabh Vijay & Peter Kuipers Munneke
We use satellite and airborne altimetry to estimate annual mass changes of the Greenland Ice Sheet. We estimate ice loss corresponding to a sea-level rise of 6.9±0.4 millimeters from April 2011 to April 2020, with the highest annual ice loss rate of 1.4 mm/yr sea-level equivalent from April 2019 to April 2020. On a regional scale, our annual mass loss timeseries reveals 10-15 m/yr dynamic thickening at the terminus of Jakobshavn Isbræ from April 2016...

Data from: Comparative impacts of long-term trends in snowmelt and species interactions on plant population dynamics

Diane Campbell, Diane Campbell, Mary Price, Nick Waser, Rebecca Irwin & Alison Brody
Climate change can impact plant fitness and population persistence directly through changing abiotic conditions and indirectly through its effects on species interactions. Pollination and seed predation are important biotic interactions that can impact plant fitness, but their impact on population growth rates relative to the role of direct climatic effects is unknown. We combined 13 years of experiments on pollen limitation of seed set and pre-dispersal seed predation in Ipomopsis aggregata, a subalpine wildflower, with...

Distinct colon mucosa microbiomes associated with Tubular Adenomas and Serrated Polyps

Julio Avelar-Barragan
Background: Colorectal cancer is the second most deadly and third most common cancer in the world. Its development is heterogenous, with multiple mechanisms of carcinogenesis. Two distinct mechanisms include the adenoma-carcinoma sequence and the serrated pathway. The gut microbiome has been identified as a key player in the adenoma-carcinoma sequence, but its role in serrated carcinogenesis is less clear. In this study, we characterized the gut microbiome of 140 polyp-free and polyp-bearing individuals using colon...

Data from: Kinematic trajectories in response to speed perturbations in walking suggest modular task-level control of leg angle and length

M. Janneke Schwaner, Kiisa Nishikawa & Monica Daley
Abstract Navigating complex terrains requires dynamic interactions between the substrate, musculoskeletal and sensorimotor systems. Current perturbation studies have mostly used visible terrain height perturbations, which do not allow us to distinguish among the neuromechanical contributions of feedforward control, feedback-mediated and mechanical perturbation responses. Here, we use treadmill belt speed perturbations to induce a targeted perturbation to foot speed only, and without terrain-induced changes in joint posture and leg loading at stance onset. Based on previous...

Direct measurements of ozone response to emissions perturbations in California

Shenglun Wu, Hyung Joo Lee, Andrea Rohrbacher, Shang Liu, Toshihiro Kuwayama, John Seinfeld & Michael Kleeman
A new technique was used to directly measure O3 response to changes in precursor NOx and VOC concentrations in the atmosphere using three identical Teflon “smog chambers” equipped with UV lights. One chamber served as the baseline measurement for O3 formation, one chamber added NOx, and one chamber added surrogate VOCs (ethylene, m-xylene, n-hexane). Comparing the O3 formation between chambers over a three-hour UV cycle provides a direct measurement of O3 sensitivity to precursor concentrations....

Wildland-urban interface in California using remote sensing data

Shu Li, Vu Dao, Mukesh Kumar, Phu Nguyen & Tirtha Banerjee
Due to the mixed distribution of buildings and vegetation, wildland-urban interface (WUI) areas are characterized by complex fuel distributions and geographical environments. The behavior of wildfires occurring in the WUI often leads to severe hazards and significant damage to man-made structures. Therefore, WUI areas warrant more attention during the wildfire season. Due to the ever-changing dynamic nature of California’s population and housing, the update frequency and resolution of WUI maps that are currently used can...

Is it best to add native shrubs to a coastal sage scrub restoration project as seeds or as seedlings?

Kylie D. F. McGuire, Katharina T. Schmidt, Priscilla Ta, Jennifer J. Long, Matthew Yurko & Sarah Kimball
Ecological restoration frequently involves the addition of native plants, but the effectiveness (in terms of plant growth, plant survival, and cost) of using seeds versus container plants has not been studied in many plant communities. It is also not known if plant success would vary by species or based on functional traits. To answer these questions, we added several shrub species to a coastal sage scrub restoration site as seeds or as seedlings in a...

Monarch (Danaus plexippus) larval records in the western U.S

Nalleli Carvajal Acosta
Species distributions are driven by abiotic and biotic factors, but the importance of variation in the availability and quality of critical resources is poorly understood. Disentangling the relative importance of these factors – abiotic environment, availability of critical resources, and resource quality– will be important to modeling species current distributions and responses to projected climate change. We address these questions using species distribution models (SDMs) for the western monarch butterfly population (Danaus plexippus), whose larvae...

Effects of the VACES particle concentrator on secondary organic aerosol and ambient particle composition

Lisa Wingen, David Herman, Andrew Keebaugh, Geovani Montoya, Samantha Renusch, Barbara Finlayson-Pitts & Michael Kleinman
The effects of concentrating particles using the Versatile Aerosol Concentration Enrichment System (VACES) were investigated with a focus on the organic particle composition. The VACES uses water condensation to grow particles and allow enrichment in particle concentrations by virtual impaction, followed by diffusion drying to remove excess liquid water. Aerosol mass spectrometry was used to compare the submicron organic composition before and after the VACES for laboratory-generated secondary organic aerosol (SOA) from ozonolysis of α-pinene...

Data and code for: Explainable machine learning revealed the conditional response of biogenic isoprene to the changes in environmental factors at an urban site in the Yangtze River Delta, China

Yiming Qin
Biogenic isoprene is highly sensitive to environmental conditions while the confounding factors makes it challenging to identify the causal response. We report here an enhanced isoprene concentration from biogenic source during May to October at an urban site in the Yangtze River Delta, China. Random forest coupled with Shapley additive explanations dependence algorithm was used to determine the conditional response of biogenic isoprene to the changes in environmental factors. The conditional response of isoprene concentration...

Isotopic signatures of methane emissions from dairy farms in California's San Joaquin Valley

Valerie Carranza, Brenna Biggs, Deanne Meyer, Amy Townsend-Small, Ranga Thiruvenkatachari, Akula Venkatram, Marc Fischer & Francesca Hopkins
In this study, we present seasonal atmospheric measurements of δ13CCH4 from dairy farms in the San Joaquin Valley of California. We used δ13CCH4 to characterize emissions from enteric fermentation by measuring downwind of cattle housing (e.g., freestall barns, corrals) and from manure management areas (e.g., anaerobic manure lagoons) with a mobile platform equipped with cavity ring-down spectrometers. Across seasons, the δ13CCH4 from enteric fermentation source areas ranged from -69.7 ± 0.6 per mil (‰) to...

Reductions in California's urban fossil fuel CO2 emissions during the COVID-19 pandemic

Cindy Yañez, Francesca Hopkins, Xiaomei Xu, Joana Tavares, Allison Welch & Claudia Czimczik
Fossil fuel carbon dioxide emissions (ffCO2) constitute the majority of greenhouse gas emissions and are the main determinent of global climate change. The COVID-19 pandemic caused wide-scale disruption to human activity and provided an opportunity to evaluate our capability to detect ffCO2 emission reductions. Quantifying changes in ffCO2 levels is especially challenging in cities, where climate mitigation policies are being implemented but local emissions lead to spatially and temporally complex atmospheric mixing ratios. Here, we...

Data files for simulated advanced adenoma age incidence, under aspirin treatment

Natalia Komarova
Aspirin intake has been shown to lead to significant protection against colorectal cancer, e.g. with an up to two-fold reduction in colorectal adenoma incidence rates at higher doses. The mechanisms contributing to protection are not yet fully understood. While aspirin is an anti-inflammatory drug and can thus influence the tumor microenvironment, in vitro and in vivo experiments have recently shown that aspirin can also have a direct effect on cellular kinetics and fitness. It reduces...

A novel intramandibular joint facilitates feeding versatility in the sixbar distichodus

Christopher Martinez, Angelly Tovar & Peter Wainwright
The intramandibular joint (IMJ) is a secondary point of movement between the two major bones of the lower jaw. It has independently evolved in several groups of teleost fishes, each time representing a departure from related species in which the mandible functions as a single structure rotating only at the quadratomandibular joint (QMJ). In this study, we examine kinematic consequences of the IMJ novelty in a freshwater characiform fish, the herbivorous Distichodus sexfasciatus. We combine...

Data from: Genetic and spatial variation in vegetative and floral traits across a hybrid zone

Diane Campbell, Robert Raguso, Maya Midzik, Mascha Bischoff & Geoffrey Broadhead
Premise: Genetic variation influences potential for evolution to rescue populations from impacts of environmental change. Most studies of genetic variation in fitness-related traits focus on either vegetative or floral traits, with few on floral scent. How vegetative and floral traits compare in potential for adaptive evolution is poorly understood. Results: Vegetative traits SLA and WUE varied greatly among planting sites, while showing weak or no genetic variation among source populations. SLA and trichomes responded plastically...

Registration Year

  • 2022

Resource Types

  • Dataset


  • University of California, Irvine
  • University of California, Riverside
  • University of California, Davis
  • Rocky Mountain Biological Laboratory
  • Indian Institute of Technology Roorkee
  • The University of Texas at Austin
  • Princeton University
  • Meharry Medical College
  • Oregon State University
  • University of Vermont