308 Works

Steele/Burnand Anza-Borrego Desert Research Center

Information Manager UCNRS
MISSION STATEMENT: The UC Natural Reserve System is a network of protected natural areas throughout California. Its 39 sites include more than 756,000 acres, making it the largest university-administered reserve system in the world. Most major state ecosystems are represented, from coastal tidepools to inland deserts, and lush wetlands to Sierra Nevada forests. The reserves also serve as a gateway to more than a million acres of public lands. Founded in 1965 to provide undisturbed...

Data for analysis of snowmelt timing as a determinant of inflow mixing in Lake Tahoe

Derek Roberts, Shohei Watanabe & S. Geoffrey Schladow
This dataset includes data files pertinent to the manuscript, "Snowmelting timing as a determinant of inflow mixing," accepted for publication in Water Resources Research in January 2018. Included data were used for an analysis of relative stream-lake conditions as they pertain to winter climate conditions and the subsequent mixing of snowmelt inflows into the lake. Included with each of the six files listed below is a [FILENAME]_Reference.txt file with details on data collection, curation, and...

Coastal dune invasion and restoration at Point Reyes: the ecology of European sea rocket, Cakile maritime

Shay McGraw, Jay Luce Nelson, Yuxin Shen & Aidé Villegas
California coastal dune ecosystems are prime targets for conservation and restoration efforts due to their high native plant diversity and rates of endemism. Invasive dune species such as European sea rocket (Cakile maritima) may disrupt key ecosystem processes by altering dune physical processes and outcompeting native species, decreasing the success of the endangered species beach layia (Layia carnosa) and Tidestrom's lupine (Lupinus tidestromii) at Point Reyes National Seashore in Marin County, California. We investigated potential...

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...

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...

Through space and time: Vertebrate coexistence through circadian changes in community composition

Mark Arenas, Danielle Davis, Mikala Haptonstall, Brendan Kyle & Eric Stubbs
Many mechanisms of biodiversity exist in nature. Temporal niche partitioning is an overlooked mechanism that could explain how species coexist in the same space. We hypothesized that different vertebrate communities would be using a shared habitat space (rock bars) at different times of day. To test this hypothesis, we surveyed the total number of vertebrates present on six different rock bars during morning, midday, and night. We documented strong differences between vertebrate communities by time...

The fungus among us: Ecological succession within decomposer communities

Marta Alvarez, Ashlyn Bahrychuk, Kellie Cutsinger, Alexander Gallandt & Thomas Lenihan
The process of succession can be a major driving force in sculpting ecological communities over time. Decomposers play a crucial role in forest succession, recycling nutrients from fallen logs back into the ecosystem. In this study, we examined the community of plants, fungi, and invertebrates living in fallen log microhabitats across decomposition stages in a mixed conifer forest. We predicted there would be a shift in species composition among decomposer communities in Douglas fir logs...

Life on the edge: Abiotic stress and competitive exclusion affect plant communities across a subalpine edaphic gradient

, Willem Schep, Hanan Abels-Sullivan & Casey Kwok
Abiotic stress and heavy competition each limit the assemblages of plant communities, defining their composition as well as their boundaries. One plant community governed by stress and another by competition may abut one another, forming a biotic gradient called an ecotone. In California’s White Mountains, this gradient occurs across the meeting point between a calcareous (dolomite) and non-calcareous (quartzite) soil types. In this study, we tested the effects of this gradient on plant community compositions...

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...

Is the USDA core collection of common bean representative of genetic diversity of the species, as assessed by SNP diversity?

Paul Gepts, Saarah Kuzay & Paige Hamilton
Core collections are envisioned to be a representative subset of larger germplasm collections. They were introduced to facilitate the characterization and use of these germplasm collections. The common bean (Phaseolus vulgaris) core collection of the USDA Western Regional Plant Introduction Station was one of the first ones to be established in the early 1990s. Here, we evaluate the representativity of this common bean collection in light of the availability of a SNP platform and new...

Effects of predation risk on rodent foraging behavior in the Colorado Desert

, Jessica Du, Anass Malabeh & Caitlyn N. Rich
The survival of animals often depends on a tenuous balance between the rewards of food acquisition and the risks associated with predation. In desert environments where resources are incredibly limited, it is imperative for organisms to optimize physiological and behavioral traits in order to maximize nutritional reward while minimizing risks of predation. In this study, we examined the effects of simulated predation risk on the foraging behavior of granivorous desert rodents. We predicted that rodents...

Supporting data for the manuscript: Observations and modeling of the surface seiches of Lake Tahoe, USA

Derek Roberts, S. Geoffrey Schladow & Alexander Forrest
This data set was created to make the data associated with the manuscript Observations and modeling of the surface seiches of Lake Tahoe, USA, accepted for publication in Aquatic Sciences, publically available per journal convention. The publication abstract is shown below: A rich array of spatially complex surface seiche modes exists in lakes. While the amplitude of these oscillations is often small, knowledge of their spatio-temporal characteristics is valuable for understanding when they might be...

Effect of Drought Stress on the Genetic Architecture of Photosynthate Allocation and Remobilization in Pods of Common Bean (Phaseolus vulgaris L.), a Key Species for Food Security

Paul Gepts, Jorge Carlos Berny Mier Y Teran, Enéas R. Konzen, Antonia Palkovic, Siu M. Tsai, Idupulapati M. Rao & Stephen Beebe
Background: Common bean is the most important staple grain legume for direct human consumption and nutrition. It complements major sources of carbohydrates, including cereals, root crop, or plantain, as a source of dietary proteins. It is also a significant source of vitamins and minerals like iron and zinc. To fully play its nutritional role, however, its robustness against stresses needs to be strengthened. Foremost among these is drought, which commonly affects its productivity and seed...

Succession and soil development of Pleistocene glacial remnants in a sagebrush steppe

Sophie Borison, Charlotte Bruggeman & Sam Steuart
Following glacial retreat, soils and plant communities often undergo drastic changes as succession occurs. As bare soil is colonized, the plant community shifts and drives future succession patterns. The aim of this study was to assess the modern stage of succession on different-aged glaciated areas by sampling a Tahoe-era glaciation (130 to 70 ka) lateral moraine, a Tioga-era glaciation (28 to 13 ka) lateral moraine, a flat which the Tahoe-era glacier covered, and a flat...

Low coverage whole genomes of Calypte anna across California, USA

Nicole Adams, Ruta Bandivadekar, Michael Clark, Lisa Tell & Rachael Bay
Recently, it was suggested that North America has lost nearly 30% of its avifauna since the 1970s. To mitigate such avian population declines, many birds in California are protected under the Migratory Bird Treaty Act and California Fish and Game Code. Avian presence, therefore, at Caltrans infrastructure projects, especially bridge construction, has caused costly delays. To avoid this conflict and understand population-specific migration and nesting patterns, we used Anna’s hummingbird, Calypte anna, (a species whose...

Genital morphology and the mechanics of copulation in the millipede genus Pseudopolydesmus (Diplopoda: Polydesmida: Polydesmidae)

Xavier Zahnle, Petra Sierwald, Stephanie Ware & Jason Bond
Mate choice, copulation, genital morphology, and sperm storage are not very well understood in millipedes. The use of three-dimensional x-ray computed tomography (µCT) provides new morphological data regarding millipede reproductive systems in both the female and male, including chitinous sclerites and membranes, muscles, glands, oviducts, and sperm conduits. Here we present a complete integrated account of the morphology and function of the female genital organs in the family Polydesmidae (Diplopoda: Polydesmida) using µCT, UV fluorescence...

Optimal foraging behavior in desert harvester ants (Veromessor pergandei)

Carlee Bowen, George Eskander, Brian Lai & Mariam Samy
Optimal foraging behavior is exhibited when individuals in a species maximize their nutritional intake, while minimizing their energy expenditure during the foraging process. In this study, we explored the foraging behavior of Black Harvester Ants (Veromessor pergandei) to assess if their foraging habits coincided with optimal foraging theory. We observed 35 Veromessor colonies in Anza Borrego State Park in a controlled experiment where piles of large and small pumpkin and oat seeds were placed on...

Patterns of vegetative reproduction and distribution of Cylindropuntia

Ryan Fong, Lucy Johnson & Joseph Saucedo
Cylindropuntia can reproduce sexually, asexually, or both ways, highlighting the spectrum of reproductive strategies within a single genus. This diversity in reproduction provided an excellent framework for better understanding the distributive differences between sexually and asexually reproducing species within the same habitat. The sole use of asexual reproduction in C. bigelovii is not well studied, despite being such an iconic desert species. We investigated factors that might affect vegetative reproduction, such as water content and...

Employee airline travel preferences survey data, UC Davis GreenFLY project

Annamaria Amenta & Angela Sanguinetti
This survey data is from a study exploring the potential to promote lower-emissions air travel by providing consumers with information about the carbon emissions of possible flight choices in the context of online flight search and booking. We surveyed over 450 faculty, researchers, and staff at the University of California, Davis, and asked them to choose among hypothetical flight options for a domestic and an international university-related business trip. Emissions estimates for different flight alternatives...

Domestic Well Vulnerability to Drought Duration and Unsustainable Groundwater Management in California's Central Valley

Richard Pauloo, Helen Dahlke, Graham Fogg, Herve Guillon, Amanda Fencl & Alvar Escriva-Bou
Millions of Californians access drinking water via domestic wells, which are vulnerable to drought and unsustainable groundwater management. Groundwater overdraft and the possibility of longer drought duration under climate change threatens domestic well reliability, yet we lack tools to assess the impact of such events. Here, we leverage 943,469 well completion reports and 20 years of groundwater elevation data to develop a spatially-explicit domestic well failure model covering California's Central Valley. Our model successfully reproduces...

Bicycling comfort video experiment

Dillon Fitch, Jane Carlen & Susan Handy
This tabular data can be used to evaluate perceived bicycling comfort on distinct state highways in California. The highway settings are primarily urban, but vary in traffic conditions, lane configurations, speeds, and bicycling infrastructure. The data include survey responses to video clips of these state highways along with a series of additional survey data that co-varies with the video survey responses.

Channel types predictions for the South Fork Eel River basin

Hervé Guillon, Colin F. Byrne, Belize A. Lane, Samuel Sandoval Solis & Gregory B. Pasternack
Hydrologic and geomorphic classifications have gained traction in response to the increasing need for basin-wide water resources management. Regardless of the selected classification scheme, an open scientific challenge is how to extend information from limited field sites to classify tens of thousands to millions of channel reaches across a basin. To address this spatial scaling challenge, we leveraged machine learning to predict reach-scale geomorphic channel types using publicly available geospatial data.

Evolution of the Greater Caucasus basement and formation of the Main Caucasus Thrust, Georgia

Dylan Vasey, Eric Cowgill, Sarah Roeske, Nathan Niemi, Tea Godoladze, Irakli Skhirtladze & Salome Gogoladze
Along the northern margin of the Arabia-Eurasia collision zone in the western Greater Caucasus, the Main Caucasus Thrust (MCT) juxtaposes Paleozoic crystalline basement to the north against Mesozoic metasedimentary and volcaniclastic rocks to the south. The MCT is commonly assumed to be the trace of an active plate-boundary scale structure that accommodates Arabia-Eurasia convergence, but field data supporting this interpretation are equivocal. Here we investigate the deformation history of the rocks juxtaposed across the MCT...

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