490 Works

Multiple Benefits from Agricultural and Natural Land Covers in the Central Valley, CA

Caitlin Peterson, Elias Marvinney & Kristen Dybala
The data and code provided in this repository are associated with the technical report on the "Multiple Benefits from Agricultural and Natural Land Covers" project and were prepared by the authors for the Migratory Bird Conservation Partnership. MBCP partner organizations include The Nature Conservancy, California Audubon, and Point Blue Conservation Science. Executive Summary The Central Valley of California is one of the most heavily modified landscapes in the world, with millions of acres of semi-arid...

Lignification of tomato (Solanum lycopersicum) pericarp tissue during blossom-end rot development

Nicholas Reitz
Blossom-end rot is a physiological disorder causing significant losses in the produce industry each year. Accumulation of reactive oxygen species has been established as a key characteristic of blossom-end rot development. An increase in peroxidase activity and lignin precursor content are also associated with blossom-end rot symptoms, leading to the hypothesis that lignification may be occurring during blossom-end rot development. To investigate the potential involvement of lignification, hydrogen peroxide content, catalase activity, and peroxidase activity...

Data for: Genetic architecture modulates diet induced hepatic mRNA and miRNA expression profiles

Excel Que, Kristen L. James, Alisha R. Coffey, Tangi L. Smallwood, Jody Albright, M. Nazmul Huda, Daniel Pomp, Praveen Sethupathy & Brian J. Bennett
Genetic approaches in model organisms have consistently demonstrated that molecular traits such as gene expression are under genetic regulation, similar to clinical traits. The resulting expression quantitative trait loci (eQTL) have revolutionized our understanding of genetic regulation and identified numerous candidate genes for clinically-relevant traits. More recently, these analyses have been extended to other molecular traits such as protein abundance, metabolite levels, and miRNA expression. Here we performed global hepatic eQTL and miRNA expression quantitative...

Pesticide and resource stressors additively impair wild bee reproduction

Clara Stuligross & Neal Williams
Bees and other beneficial insects experience multiple stressors within agricultural landscapes that act together to impact their health and diminish their ability to deliver the ecosystem services on which human food supplies depend. Disentangling the effects of coupled stressors is a primary challenge for understanding how to promote their populations and ensure robust pollination and other ecosystem services. We used a crossed design to quantify the individual and combined effects of food resource limitation and...

Dataset: Spatiotemporal analysis of freight patterns in Southern California

Daniel Rivera-Royero, Miguel Jaller, John Harvey, Changmo Kim & Jeremy Lea
There has been general trend to shift the location of warehouses and distribution facilities away from consumer markets (logistics sprawl) in Southern California. This shift has a negative impact on cost and the environment because freight vehicles have to travel longer to reach their destinations. However, during the last decade, this trend has not continued at the same pace, and it may have even reversed. Two main factors potentially explain this phenomenon: the 2008-2009 economic...

Apis mellifera wing images (Africanized honey bees)

Erin Calfee, Marcelo Agra, María Alejandra Palacio, Santiago Ramírez & Graham Coop
Honey bee wing lengths and vein patterns differ between major genetic lineages. In this dataset we publish forewing images for 276 individual honey bees with mixtures of African and European genetic ancestry of varying proportions. In the associated population genomics study, we compared evolutionary outcomes of the Africanized honey bee invasion in North and South America (California and Argentina). Samples from Argentina were provided by the National Institute of Agricultural Technology (INTA), Argentina.

Global human influence maps reveal clear opportunities in conserving Earth’s remaining intact terrestrial ecosystems

Jason Riggio, Jonathan E. M. Baillie, Steven Brumby, Erle Ellis, Christina M. Kennedy, James R. Oakleaf, Alex Tait, Therese Tepe, David M. Theobald, Oscar Venter, James E.M. Watson & Andrew P. Jacobson
Leading up to the 2020 Convention on Biological Diversity there is momentum around setting bold conservation targets. Yet it remains unclear how much of Earth’s land area remains without significant human influence and where this land is located. We compare four recent global maps of human influences across Earth’s land, Anthromes, Global Human Modification, Human Footprint, and Low Impact Areas, to answer these questions. Despite using various methodologies and data, these different spatial assessments independently...

Pathogen genetic control of transcriptome variation in the Arabidopsis thaliana – Botrytis cinerea pathosystem

Nicole Soltis, Celine Caseys, Wei Zhang, Jason Corwin, Susanna Atwell & Daniel Kliebenstein
In plant-pathogen relations, disease symptoms arise from the interaction of the host and pathogen genomes. Host-pathogen functional gene interactions are well described while little is known about how the pathogen genetic variation modulates both organisms’ transcriptomes. To model and generate hypotheses on a generalist pathogen control of gene expression regulation, we used the Botrytis cinerea - Arabidopsis thaliana pathosystem and the genetic diversity of a collection of 96 B. cinerea isolates. We performed expression-based genome-wide...

Data from: Naïve domestic Bos Taurus calves recognize the scent of a canine predator

Sarah J. J. Adcock & Cassandra B. Tucker
Wild ungulates can recognize certain predators without previous experience, but this innate ability may be relaxed under domestication. Using naïve dairy calves, Bos taurus, we examined the effects of exposure to a predator odour (coyote, Canis latrans, urine) and two control odours (deer urine and water) on (1) latency to approach a milk food reward, (2) exploration, vigilance and locomotor play, (3) magnitude of the startle response to a sudden noise delivered upon arrival at...

Phylogenies of fungi isolated from the seagrass, Zostera marina

Cassandra Ettinger & Jonathan Eisen
Fungi in the marine environment are often neglected, despite that they having critical roles on land as decomposers, pathogens or beneficial endophytes. We used culture-dependent methods to survey the fungi associated with the seagrass, Zostera marina, and then placed these sequences in the fungal tree of life. Four different sequence alignments were generated, (1) an alignment to investigate seagrass isolates in the Basidiomycota and Zygomycota phyla, (2) an alignment to investigate seagrass isolates in the...

Data from: Using an arbitrary moment predictor to investigate the optimal choice of prognostic moments in bulk cloud microphysics schemes

Adele A. Igel
Most bulk cloud microphysics schemes predict up to three standard properties of hydrometeor size distributions, namely, the mass mixing ratio, number concentration, and reflectivity factor in order of increasing scheme complexity. However, it is unclear whether this combination of properties is optimal for obtaining the best simulation of clouds and precipitation in models. In this study, a bin microphysics scheme has been modified to act like a bulk microphysics scheme. The new scheme can predict...

Functional variants of DOG1 control seed chilling responses and variation in seasonal life history strategies in Arabidopsis thaliana

Alejandra Martinez-Berdeja, Michelle Stitzer, Mark A. Taylor, Miki Okada, Exequiel Ezcurra, Daniel E. Runcie & Johanna Schmitt
The seasonal timing of seed germination determines a plant's realized environmental niche, and is important for adaptation to climate. The timing of seasonal germination depends on patterns of seed dormancy release or induction by cold and interacts with flowering time variation to construct different seasonal life histories. To characterize the genetic basis and climatic associations of natural variation in seed chilling responses and associated life history syndromes, we selected 559 fully-sequenced accessions of the model...

Impacts of caudal autotomy on personality

Marcus Michelangeli, Brooke Melki-Wegner, Kate Laskowski, Bob Wong & David Chapple
Caudal autotomy, the voluntary shedding of a tail, is a last-ditch strategy used by many lizard species to escape from predators. There are several costs associated with caudal autotomy that may cause lizards to make behavioral adjustments during tail regeneration. These behavioral changes may be dependent upon individual differences in response to autotomy (e.g. trait or state-dependent differences) and/or the degree of tail loss, as many lizards have the capacity to only partially shed their...

Data from: Habitat primarily structures seagrass epifaunal communities: a regional-scale assessment in the Chesapeake Bay

Claire Murphy, Jonathan Lefcheck & Robert Orth
Epifaunal invertebrates play an important role in seagrass systems, both by grazing epiphytic algae from seagrass blades and by acting as a major food source for higher trophic levels. However, while many studies have described epifaunal community properties at small spatial scales (1 – 10 m2) and across very large gradients (from continental coastlines to the entire globe), few have examined regional-scale (100 ­– 1000 km2) patterns or, more importantly, disentangled the drivers of these...

Phylogenomic species delimitation in the ants of the Temnothorax salvini Group (Hymenoptera: Formicidae): An integrative approach

Matthew Prebus
The members of the Temnothorax salvini species group are rarely collected, arboreally nesting ants of Central American forests. Previously thought to consist of two broadly dispersed species, recent collections have revealed a diversity of specimens that defy the two-species salvini group concept, but these are difficult to distinguish from each other based solely on morphology. I contrast several model-based approaches to species delimitation based on target-enriched genomic data. With molecular data from thousands of ultraconserved...

Data from: Injury alters motivational trade-offs in calves during the healing period

Cassandra Tucker & Sarah Adcock
Injury can produce long-lasting motivational changes that may alter decisions made under risk. Our objective was to determine whether a routine painful husbandry procedure, hot-iron disbudding, affects how calves trade off risk avoidance against a competing motivation (i.e., feeding), and whether this response depends on time since injury. We used a startle test to evaluate this trade-off in calves disbudded 0 or 21 days previously and non-injured control calves. For 3 days, calves were individually...

Data for impact of “non-lethal” tarsal clipping on bumble bees (Bombus vosnesenskii) may depend on queen stage and worker size

John Mola, Clara Stuligross, Maureen Page, Danielle Rutkowski & Neal Williams
Recent bumble bee declines have prompted the development of novel population monitoring tools, including the use of putatively non-lethal tarsal clipping to obtain genetic material. However, the potential side effects of tarsal clipping have only been tested in the worker caste of a single domesticated species, prompting the need to more broadly test whether tarsal clipping negatively affects sampled individuals. To determine if tarsal clipping reduces queen survivorship and colony establishment, we collected wild queens...

Compositional variation in early life parenting structures alters oxytocin and vasopressin 1a receptor development in prairie voles (Microtus ochrogaster)

Forrest Rogers, Sara Freeman, Marina Anderson, Michelle Palumbo & Karen Bales
Paternal absence can significantly alter bio-behavioral development in many biparental species. This effect has generally been demonstrated by comparing the development of offspring reared under biparental care with those reared after removal of the father. However, studies employing this design conflate two significant modifications to early life experience: removal of father-specific qualities and the general reduction of offspring-directed care. In the socially monogamous prairie vole (Microtus ochrogaster), the experience of paternal absence without substitution during...

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...

A solitary ground-nesting wasp truncates its parental investment in response to detection of parasites

Jay Rosenheim
1. Parental investment by solitary nest-building wasps and bees is predicted to be plastic, responding to variation in the sex of the offspring, the availability of food used as provisions (‘resource limitation’), the female’s inventory of mature oocytes (‘egg limitation’), and risk imposed by nest parasites. 2. I observed nest provisioning by Ammophila dysmica, a solitary, ground-nesting wasp that provisions its nest with one or two caterpillar prey to evaluate the hypotheses that provisioning is...

Mucilage-binding to ground protects seeds of many plants from harvester ants: a functional investigation

Vincent Pan, Marshall McMunn, Richard Karban, Jake Goidell, Eric LoPresti & Marjorie Weber
The seeds of many plant species produce mucilage on their surfaces that when wetted and dried, firmly adheres seeds to surfaces and substrates. Previous studies have demonstrated that seed anchorage to the ground can reduce seed predation, though only a few species have thus far been tested. Here we investigated whether binding to the ground reduces seed removal by harvester ants (Pogonomyrmex subdentatus), an important granivore, for 53 species with mucilaginous seeds. We also explored...

Phylogenomics and biogeography of leptonetid spiders (Araneae : Leptonetidae)

Jason Bond, Joel Ledford & Marshal Hedin
Leptonetidae are rarely encountered spiders, usually associated with caves and mesic habitats, and are disjunctly distributed across the Holarctic. Data from ultraconserved elements (UCEs) were used in concatenated and coalescent-based analyses to estimate the phylogenetic history of the family. Our taxon sample included close outgroups, and 90% of described leptonetid genera, with denser sampling in North America and Mediterranean Europe. Two data matrices were assembled and analysed; the first ‘relaxed’ matrix includes the maximum number...

Data from: An improved and highly efficient geometry for facemasks

Christopher Cappa, William Ristenpart & Sanziana Roman
The dataset provided here is associated with the work "An improved and highly efficient geometry for facemasks," by Cappa et al, currently submitted for publication. This includes measurements made of the influence of a new cloth mask, designed originally for singing, on the emission of micron-scale aerosols from various expiratory activities (singing, speaking) and on inhalation of ambient particles. The dataset provided here includes *.txt files exported from an Aerodynamic Particle Sizer that contain time-series...

Data from: Early-life experience influences dispersal in coyotes (Canis latrans)

Emily Zepeda, Ashley Wurth, Stanley Gehrt, Eric Payne & Andy Sih
Natal dispersal plays an important role in connecting individual animal behavior with ecological processes at all levels of biological organization. As urban environments are rapidly increasing in extent and intensity, understanding how urbanization influences these long distance movements is critical for predicting the persistence of species and communities. There is considerable variation in the movement responses of individuals within a species, some of which is attributed to behavioral plasticity which interacts with experience to produce...


Varuni Dantanarayana
Conformational and energetic disorder in organic semiconductors reduces charge and exciton transport because of the structural defects, thus reducing the efficiency in devices such as organic photovoltaics and organic light-emitting diodes. The main structural heterogeneity is because of the twisting of the polymer backbone that occurs even in polymers that are mostly crystalline. Here, we explore the relationship between polymer backbone twisting and exciton delocalization by means of transient absorption spectroscopy and density functional theory...

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  • University of California, Davis
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