131 Works

Toxic Y-chromosome in D. miranda

Kevin Wei
Large portions of eukaryotic genomes consist of transposable elements (TEs), and the establishment of transcription-repressing heterochromatin during early development safeguards genome integrity. Repeat-rich Y chromosomes can act as reservoirs for TEs (toxic Y effect), and TEs may exploit vulnerabilities associated with incomplete genomic defenses during early development. Here, we contrast the dynamics of early TE activation in two Drosophila species with vastly different Y chromosomes of different age. Zygotic TE expression is elevated in male...

Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene

Augusto Berrocal, Nicholas Lammers, Hernan Garcia & Michael Eisen
We used live imaging to visualize the transcriptional dynamics of the Drosophila melanogaster even-skipped gene at single-cell and high temporal resolution as its seven stripe expression pattern forms, and developed tools to characterize and visualize how transcriptional bursting varies over time and space. We find that despite being created by the independent activity of five enhancers, even-skipped stripes are sculpted by the same kinetic phenomena: a coupled increase of burst frequency and amplitude. By tracking...

Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology

Sean Wu, Penny Hancock, Arnaud Le Menach, Tanya Russell, Thomas Burkot, , Derek Cummings, Kelly Compton, Daniel Citron, John Marshall, Biyonka Liang, Catherine Moyes, Qian Zhang, David Smith, Samson Kiware, Anne Wilson, Thomas Scott, John Henry, Steven Lindsay, Amit Verma & Hector Sanchez C.
Mosquitoes are important vectors for pathogens that infect humans and other vertebrate animals. Some aspects of adult mosquito behavior and mosquito ecology play an important role in determining the capacity of vector populations to transmit pathogens. Here, we re-examine factors affecting the transmission of pathogens by mosquitoes using a new approach. Unlike most previous models, this framework considers the behavioral states and state transitions of adult mosquitoes through a sequence of activity bouts. We developed...

Data from: Enriched East Asian oxygen isotope of precipitation indicates reduced summer seasonality in regional climate and westerlies

John Chiang, Michael Herman, Kei Yoshimura & Inez Fung
This archive contain the isoGSM2 model output used in the publication Chiang, J. C. H., M. J. Herman, K. Yoshimura, and I. Y. Fung: Enriched East Asian oxygen isotope of precipitation indicates reduced summer seasonality in regional climate and westerlies. In press for Proceedings of the National Academy of Sciences, April 2020

Data from: Spatial phylogenetics of the North American flora

Brent Mishler, Robert Guralnick, Pamela Soltis, Stephen Smith, Douglas Soltis, Narayani Barve, Julie Allen & Shawn Laffan
North America is a large continent with extensive climatic, geological, soil, and biological diversity. That biota is under threat from habitat destruction and climate change, making a quantitative assessment of biodiversity of critical importance. Rapid digitization of plant specimen records and accumulation of DNA sequence data enable a much-needed broad synthesis of species occurrences with phylogenetic data. Here we attempted the first such synthesis of a flora from such a large and diverse part of...

Temporal dynamics of migration-linked genetic variation are driven by streamflows and riverscape permeability

Suzanne Kelson, Michael Miller, Tasha Thompson, Sean O'Rourke & Stephanie Carlson
The permeability of landscapes is often explored spatially, but may also vary across time. For example, highways are more passable with low traffic, and mountain landscapes are more passable once snow-free. Landscape permeability especially influences migratory animals. Partial barriers are features that are passable in some conditions. Partial barriers are common in rivers due to the two-dimensional nature of river networks: aquatic organisms cannot circumvent in-river barriers. Barriers in river networks include waterfalls, logjams, or...

Behavioral, morphological, and ecological trait evolution in two clades of New World sparrows (Aimophila and Peucaea, Passerellidae)

Carla Cicero, Nicholas Mason, Lauryn Benedict & James Rising
The New World sparrows (Passerellidae) are a large and diverse group of songbirds that have been the subject of many studies on ecology, behavior, and evolutionary relationships. Here, we studied two clades of sparrows (Aimophila, Peucaea) to examine the evolution of behavioral, morphological, and ecological traits in a phylogenetic framework. Specifically, we inferred phylogenetic relationships in these clades, conducted ancestral state reconstructions, and asked whether patterns of trait evolution extend more broadly to New World...

Data from: Topographic heterogeneity lengthens the duration of pollinator resources

Rachael Olliff-Yang & David Ackerly
The availability of sufficient and diverse resources across time is important for maintenance of biodiversity and ecosystem functioning. In this study we examine the potential for variation in environmental conditions across topographic gradients to extend floral resource timing. Flowering time on a landscape may vary across topography due to differences in abiotic factors, species turnover, or genotypic differences. However, the extent to which this variation in phenology affects overall flowering duration on a landscape, and...

Snow depth, air temperature, humidity, soil moisture and temperature, and solar radiation data from the basin-scale wireless-sensor network in American River Hydrologic Observatory (ARHO)

Roger Bales, Guotao Cui, Robert Rice, Xiande Meng, Ziran Zhang, Peter Hartsough, Steven Glaser & Martha Conklin
Snow depth, air temperature, humidity, soil moisture and temperature, and solar radiation are measured by a basin-scale wireless-sensor network in the American River Hydrologic Observatory (ARHO). The wireless-sensor network is deployed across the upper, snow-covered areas of the American River basin from 1510 to 2723 m elevation on the western slope of the Sierra Nevada in California. The network comprises 13 sensor clusters (Schneiders, Echo Peak, MT Lincoln, Caples Lake, Alpha, Duncan Peak, Van Vleck,...

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...

A method for probabilistic assessment of tunneling-induced damage to surface structures considering soil-structure interaction effects

Jinyan Zhao, Andrea Franza & Matthew DeJong
Uncertainty in the early stage assessment of surface structure damage caused by tunneling-induced ground movements is analyzed with a Monte-Carlo method and a numerical model for tunnel-soil-structure interaction. The sources of uncertainty in tunneling-induced ground movements are quantified using field monitoring data, and the uncertainties in soil and structure properties are characterized from published experimental tests and empirical analyses. Then, a probabilistic assessment method to analyze structural damage is proposed and demonstrated by two case...

Data from: Impact of cognitive tasks on CO2 and isoprene emissions from humans

Elliott Gall, Asit Mishra, Jiayu Li, Stefano Schiavon & Aurelie Laguerre
The human body emits a wide range of chemicals, including CO2 and isoprene. To examine the impact of cognitive tasks on human emission rates of CO2 and isoprene, we conducted an across subjects, counterbalanced study in a controlled chamber involving 16 adults. The chamber replicated an office environment. In groups of four, participants engaged in 30 minutes each of cognitive tasks (stressed activity) and watching nature documentaries (relaxed activity). Measured biomarkers indicated higher stress levels...

Environmental and ecological correlates of avian field metabolic rate and water flux

Soorim Song & Steven Beissinger
1. The field metabolic rate (FMR) of an endothermic animal represents its energy expenditure in a natural environment, or its energy budget, and its field water flux (FWF) reflects the animal’s water requirements. 2. We examined FMR of 103 species and FWF of 75 species of adult birds from direct field measurements by the doubly-labelled water method, and used the phylogenetic generalised least squares method to conduct a phylogenetically-informed, comprehensive analysis of the relationship between...

Rethinking megafauna

Marcos Moleón, José Sánchez-Zapata, José Donázar, Eloy Revilla, Berta Martín-López, Cayetano Gutiérrez-Cánovas, Wayne Getz, Zebensui Morales-Reyes, Ahimsa Campos-Arceiz, Larry Crowder, Mauro Galetti, Manuela González-Suárez, Fengzhi He, Pedro Jordano, Rebecca Lewison, Robin Naidoo, Norman Owen-Smith, Nuria Selva, Jens-Christian Svenning, José Tella, Christiane Zarfl, Sonja Jähnig, Matt Hayward, Søren Faurby, Nuria García … & Klement Tochner
Concern for megafauna is increasing among scientists and non-scientists. Many studies have emphasized that megafauna play prominent ecological roles and provide important ecosystem services to humanity. But, what precisely are “megafauna”? Here we critically assess the concept of megafauna and propose a goal-oriented framework for megafaunal research. First, we review definitions of megafauna and analyze associated terminology in the scientific literature. Second, we conduct a survey among ecologists and paleontologists to assess the species traits...

The target of selection matters: an established resistance – development-time negative genetic trade-off is not found when selecting on development time.

Lewis Bartlett, Elisa Visher, Yazmin Haro, Katherine Roberts & Mike Boots
Trade-offs are fundamental to evolutionary outcomes and play a central role in eco-evolutionary theory. They are often examined by experimentally selecting on one life-history trait and looking for negative correlations in other traits. For example, populations of the moth Plodia interpunctella selected to resist viral infection show a life-history cost with longer development times. However, we rarely examine whether the detection of such negative genetic correlations depends on the trait on which we select. Here...

Work that body: fin and body movements determine herbivore feeding performance within the natural reef environment

Roi Holzman, Christopher H. Martin, Asaph Rivlin & Tal Perevolotsky
Herbivorous fishes form a keystone component of reef ecosystems, yet the functional mechanisms underlying their feeding performance are poorly understood. In water, gravity is counter-balanced by buoyancy, hence fish are recoiled backwards after every bite they take from the substrate. To overcome this recoil and maintain contact with the algae covered substrate, fish need to generate thrust while feeding. However, the locomotory performance of reef herbivores in the context of feeding has hitherto been ignored....

Data from: The genetic architecture of plant defense tradeoffs in a common monkeyflower

Nicholas Kooyers, Benjamin Blackman, Abigail Donofrio & Liza Holeski
Determining how adaptive combinations of traits arose requires understanding the prevalence and scope of genetic constraints. Frequently observed phenotypic correlations between plant growth, defenses, and/or reproductive timing have led researchers to suggest that pleiotropy or strong genetic linkage between variants affecting independent traits is pervasive. Alternatively, these correlations could arise via independent mutations in different genes for each trait and extensive correlational selection. Here we evaluate these alternatives by conducting a QTL mapping experiment involving...

A survey of small-scale waves and wave-like phenomena in Jupiter's atmosphere detected by JunoCam

Glenn Orton, Fachreddin Tabataba-Vakili, Gerald Eichstaedt, John Rogers, Candice Hansen, Thomas Momary, Andrew Ingersoll, Shawn Brueshaber, Michael H. Wong, Amy Simon, Leigh Fletcher, Michael Ravine, Michael Caplinger, Dakota Smith, Scott Bolton, Stephen Levin, James Sinclair, Chloe Thepenier, Hamish Nicholson & Abigail Anthony
In the first 20 orbits of the Juno spacecraft around Jupiter, we have identified a variety of wave-like features in images made by its public-outreach camera, JunoCam. Because of Juno’s unprecedented and repeated proximity to Jupiter’s cloud tops during its close approaches, JunoCam has detected more wave structures than any previous surveys. Most of the waves appear in long wave packets, oriented east-west and populated by narrow wave crests. Spacing between crests were measured as...

Data from: Postwar wildlife recovery in an African savanna: Evaluating patterns and drivers of species occupancy and richness

Kaitlyn Gaynor, Joshua Daskin, Lindsey Rich & Justin Brashares
As local and global disturbances reshape African savannas, an understanding of how animal communities recover and respond to landscape features can inform conservation and restoration. Here, we explored the spatial ecology of a wildlife community in Gorongosa National Park, Mozambique, where conservation efforts have fostered the recovery of large mammal populations after their near‐extirpation during Mozambique’s civil war. We deployed a grid of 60 camera traps and used a hierarchical, multi‐species occupancy modeling approach to...

The rescue effect and inference from isolation-extinction relationships

Nathan Van Schmidt & Steven Beissinger
The rescue effect in metapopulations hypothesizes that less isolated patches are unlikely to go extinct because recolonization may occur between breeding seasons (“recolonization rescue”), or immigrants may sufficiently bolster population size to prevent extinction altogether (“demographic rescue”). These mechanisms have rarely been demonstrated directly, and most evidence of the rescue effect is from relationships between isolation and extinction. We determined the frequency of recolonization rescue for metapopulations of black rails (Laterallus jamaicensis) and Virginia rails...

Warming acts through earlier snowmelt to advance but not extend alpine community flowering

Meredith Jabis, Daniel Winkler & Lara Kueppers
Large-scale warming will alter multiple local climate factors in alpine tundra, yet very few experimental studies examine the combined yet distinct influences of earlier snowmelt, higher temperatures and altered soil moisture on alpine ecosystems. This limits our ability to predict responses to climate change by plant species and communities. To address this gap, we used infrared heaters and manual watering in a fully factorial experiment to determine the relative importance of these climate factors on...

Five-years of ocrelizumab in relapsing multiple sclerosis: OPERA studies open-label extension

Stephen L Hauser, Ludwig Kappos, Douglas L Arnold, Amit Bar-Or, Bruno Brochet, Robert T Naismith, Anthony Traboulsee, Jerry S Wolinsky, Shibeshih Belachew, Harold Koendgen, Victoria Levesque, Marianna Manfrini, Fabian Model, Stanislas Hubeaux, Lahar Mehta & Xavier Montalban
Objective To assess over 3 years of follow-up, the effects of maintaining or switching to ocrelizumab (OCR) therapy on clinical and MRI outcomes and safety measures in the open-label extension (OLE) phase of the pooled OPERA studies in relapsing multiple sclerosis. Methods After 2 years of double-blind, controlled treatment, patients continued OCR (600 mg infusions every 24 weeks) or switched from interferon (IFN) β-1a (44 μg 3 times weekly) to OCR when entering the OLE...

Monitoring Data from Pilot-Scale Open-Water Unit Process Wetland Treatment of Reverse Osmosis Concentrate from Water Reuse

Rachel Scholes, Jack King, Michael Vega, Josh Sharp, William Mitch & David Sedlak
This workbook provides monitoring data from a pilot-scale ozone/open-water wetland treatment system for reverse osmosis concentrate from the Silicon Valley Advanced Water Purification Center (San Jose, CA). Water quality analyses included common water quality parameters, nutrients, trace metals, and trace organics. These analyses were performed by UC Berkeley, Stanford University, Valley Water's Water Quality Lab, and a contract lab (Eurofins). Functional gene analyses (qPCR) were conducted at Colorado School of Mines for samples of the...

Data and code for: Microalgae-blend tilapia feed eliminates fishmeal and fish oil, improves growth, and is cost viable

Pallab Sarker, Anne Kapuscinski, Brandi McKuin, Devin Fitzgerald, Hannah Nash & Connor Greenwood
Aquafeed manufacturers have reduced, but not fully eliminated, fishmeal and fish oil and are seeking cost competitive replacements. We combined two commercially available microalgae, to produce a high-performing fish-free feed for Nile tilapia (Oreochromis niloticus) —the world’s second largest group of farmed fish. We substituted protein-rich defatted biomass of Nannochloropsis oculata (leftover after oil extraction for nutraceuticals) for fishmeal and whole cells of docosahexaenoic acid (DHA)-rich Schizochytrium sp. as substitute for fish oil. Here, we...

Data from: Complex interactions between temperature, sexual signals, and mate choice in a desert-dwelling jumping spider

Erin Brandt, Malcolm Rosenthal & Damian Elias
Environmental context is a crucial factor that influences sexual communication systems. Particularly in ectotherms, which cannot metabolically regulate their body temperature, temperature has an outsized effect on these intraspecific interactions. Using a desert-dwelling jumping spider Habronattus clypeatus, we assessed how temperature impacts various parts of the male signal and female mate choice for the signal. These spiders have multimodal, temporally-structured courtship displays that begin with visual-only “sidling” displays and proceed to multimodal visual and vibratory...

Registration Year

  • 2020
    131

Resource Types

  • Dataset
    129
  • Text
    2

Affiliations

  • University of California, Berkeley
    130
  • University of California, Davis
    11
  • University of Minnesota
    5
  • Cornell University
    5
  • University of Washington
    3
  • Stanford University
    3
  • Duke University
    3
  • University of Georgia
    3
  • Ehime University
    3
  • University of Pennsylvania
    2