230 Works

Fibrin fiber fluctuation

Qingda Hu & Elliot Botvinick
Understanding force propagation through the fibrous extracellular matrix can elucidate how cells interact mechanically with their surrounding tissue. Presumably, due to elastic nonlinearities of the constituent filaments and their random connection topology, force propagation in fiber networks is quite complex, and the basic problem of force propagation in structurally heterogeneous networks remains unsolved. We report on a new technique to detect displacements through such networks in response to a localized force, using a fibrin hydrogel...

Environmental drivers of adult locomotion and reproduction in a symbiont-hosting sea anemone

Samuel Bedgood
This data was collected from the sea anemone species Exaiptasia diaphana collected in the Florida Keys in January 2016. Anemones were brought into the lab where they were exposed to feeding treatments (fed or starved) and algal symbiont manipulations (high or low symbiont denisties). We collected data on movement via time lapse photography, reproduction via counting of pedal lacerates, and anemone size via photography and analysis in the program ImageJ. We found that feeding treatments...

Grounding line of Denman Glacier, East Antarctica from satellite radar interferometry

Virginia Brancato, Eric Rignot, Pietro Milillo, Mathieu Morlighem, Jeremie Mouginot, Lu An, Bernd Scheuchl, Seong Su Jeong, Paola Rizzoli, Jose Luiz Bueso Bello & Pau Prats-Iraola
Grounding line, elevation changes, and melt rates maps of Denman Glacier, East Antarctica. Using satellite radar interferometry from the COSMO-SkyMed mission we map the grounding line of Denman Glacier, East Antarctica. We complement these data with some historical interferometric radar acquisition from the European satellite ERS-1/2. We present new maps of elevation changes on the grounded and floating portions of Denman Glacier obtained by temporally differencing TanDEM-X Digital Elevation Models.

Data from: Fine-mapping nicotine resistance loci in Drosophila using a multiparent advanced generation inter-cross population

Tara N. Marriage, Elizabeth G. King, Anthony D. Long & Stuart J. Macdonald
Animals in nature are frequently challenged by toxic compounds, from those that occur naturally in plants as a defense against herbivory, to pesticides used to protect crops. On exposure to such xenobiotic substances, animals mount a transcriptional response, generating detoxification enzymes and transporters that metabolize and remove the toxin. Genetic variation in this response can lead to variation in the susceptibility of different genotypes to the toxic effects of a given xenobiotic. Here we use...

Data from: Extensive transcriptional response associated with seasonal plasticity of butterfly wing patterns

Emily V. Daniels, Rabi Murad, Ali Mortazavi & Robert D. Reed
In the eastern United States the buckeye butterfly, Junonia coenia, shows seasonal wing color plasticity where adults emerging in the spring are tan, while those emerging in the autumn are dark red. This variation can be artificially induced in laboratory colonies, thus making J. coenia a useful model system to examine the mechanistic basis of plasticity. To better understand the developmental basis of seasonal plasticity we used RNA-seq to quantify transcription profiles associated with development...

Data from: Transcriptome-wide differential gene expression in Bicyclus anynana butterflies: female vision-related genes are more plastic

Aide Macias-Muñoz, Gilbert Smith, Antónia Monteiro & Adriana D. Briscoe
cave-adapted species down-regulate the expression of vision genes or even lose their eyes and associated eye genes entirely. Alternatively, organisms that live in fluctuating environments, with different requirements for vision at different times, may evolve phenotypic plasticity for expression of vision genes. Here we use a global transcriptomic and candidate gene approach to compare gene expression in the heads of a polyphenic butterfly. Bicyclus anynana have two seasonal forms that display sexual dimorphism and plasticity...

Data from: Pollution-tolerant invertebrates enhance greenhouse gas flux in urban wetlands

Andrew S. Mehring, Perran L.M. Cook, Victor Evrard, Stanley B. Grant, Lisa A. Levin & Perran L. M. Cook
One of the goals of urban ecology is to link community structure to ecosystem function in urban habitats. Pollution-tolerant wetland invertebrates have been shown to enhance greenhouse gas (GHG) flux in controlled laboratory experiments, suggesting that they may influence urban wetland roles as sources or sinks of GHG. However, it is unclear if their effects can be detected in highly variable conditions in a field setting. Here we use an extensive dataset on carbon dioxide...

Data from: Sexual dimorphism and retinal mosaic diversification following the evolution of a violet receptor in butterflies

Kyle J. McCulloch, Furong Yuan, Ying Zhen, Matthew L. Aardema, Gilbert Smith, Jorge Llorente-Bousquets, Peter Andolfatto & Adriana D. Briscoe
Numerous animal lineages have expanded and diversified the opsin-based photoreceptors in their eyes underlying color vision behavior. However, the selective pressures giving rise to new photoreceptors and their spectral tuning remain mostly obscure. Previously, we identified a violet receptor (UV2) that is the result of a UV opsin gene duplication specific to Heliconius butterflies. At the same time the violet receptor evolved, Heliconius evolved UV-yellow coloration on their wings, due to the pigment 3-hydroxykynurenine (3-OHK)...

Data from: Environmental filtering by pH and soil nutrients drives community assembly in fungi at fine spatial scales

Sydney I. Glassman, Ian J. Wang & Thomas D. Bruns
Whether niche processes, like environmental filtering, or neutral processes, like dispersal limitation, are the primary forces driving community assembly is a central question in ecology. Here, we use a natural experimental system of isolated tree “islands” to test whether environment or geography primarily structures fungal community composition at fine spatial scales. This system consists of isolated pairs of two distantly-related, congeneric pine trees established at varying distances from each other and the forest edge, allowing...

Data from: The evolution of diapause in Rivulus (Laimosemion)

Andrew I. Furness, David N. Reznick, Andrey Tatarenkov & John C. Avise
Annual killifish adapted to life in aquatic habitat that seasonally dries have evolved desiccation resistant eggs capable of undergoing diapause, developmental arrest, at specific stages during embryology. Although noted for their remarkable abilities to live at the land-water interface, species in the genus Rivulus are considered non-annual killifish exhibiting typical teleost development patterns and no embryonic diapause. Here, we combine a molecular phylogeny with embryological study to demonstrate an independent origin of mid-embryonic diapause within...

Data from: Predatory birds and ants partition caterpillar prey by body size and diet breadth

Michael S. Singer, Robert E. Clark, Isaac H. Lichter-Marck, Emily R. Johnson, Kailen A. Mooney & Issac H. Lichter-Marck
1.The effects of predator assemblages on herbivores are predicted to depend critically on predator-predator interactions and the extent to which predators partition prey resources. The role of prey heterogeneity in generating such multiple predator effects has received limited attention. 2.Vertebrate and arthropod insectivores constitute two co-dominant predatory taxa in many ecosystems, and the emergent properties of their joint effects on insect herbivores inform theory on multiple predator effects as well as biological control of insect...

Data from: Traits underlying community consequences of plant intra-specific diversity

Luis Abdala-Roberts, Riley Pratt, Jessica D. Pratt & Kailen A. Mooney
A plant’s performance and interactions with other trophic levels are recorgnized to be contingent upon plant diversity and underlying associational dynamics, but far less is known about the plant traits driving such phenomena. We manipulated diversity in plant traits using pairs of plant and a substitutive design to elucidate the mechanisms underlying diversity effects operating at a fine spatial scale. Specifically, we measured the effects of diversity in sex (sexual monocultures vs. male and female...

Data from: Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy

Natalie M Clark, Elizabeth Hinde, Cara M Winter, Adam P Fisher, Giuseppe Crosti, Ikram Blilou, Enrico Gratton, Philip N Benfey & Rosangela Sozzani
To understand complex regulatory processes in multicellular organisms, it is critical to be able to quantitatively analyze protein movement and protein-protein interactions in time and space. During Arabidopsis development, the intercellular movement of SHORTROOT (SHR) and subsequent interaction with its downstream target SCARECROW (SCR) control root patterning and cell fate specification. However, quantitative information about the spatio-temporal dynamics of SHR movement and SHR-SCR interaction is currently unavailable. Here, we quantify parameters including SHR mobility, oligomeric...

Data from: Rapid divergence and convergence of life-history in experimentally evolved Drosophila melanogaster

Molly K. Burke, Thomas T. Barter, Larry G. Cabral, James N. Kezos, Mark A. Phillips, Grant A. Rutledge, Kevin H. Phung, Richard H. Chen, Huy D. Nguyen, Laurence D. Mueller & Michael R. Rose
Laboratory selection experiments are alluring in their simplicity, power, and ability to inform us about how evolution works. A longstanding challenge facing evolution experiments with metazoans is that significant generational turnover takes a long time. In this work, we present data from a unique system of experimentally evolved laboratory populations of Drosophila melanogaster that have experienced three distinct life-history selection regimes. The goal of our study was to determine how quickly populations of a certain...

Data from: Fine-scale analysis of parasite resistance genes in the red flour beetle, Tribolium castaneum

Daibin Zhong, Aditi Pai, Mei-Hui Wang, Naomi Keech & Guiyun Yan
Parasite infection impacts population dynamics through effects on fitness and fecundity of the individual host. In addition to the known roles of environmental factors, host susceptibility to parasites has a genetic basis that has not been well characterized. We previously mapped quantitative trait loci (QTL) for susceptibility to rat tapeworm (Hymenolepis diminuta) infection in Tribolium castaneum using dominant AFLP markers, but the resistance genes were not identified. In the current study, we refined the QTL...

Data from: Bottom-up effects of host-plant species diversity and top-down effects of ants interactively increase plant performance

Xoaquín Moreira, Kailen A. Mooney, Rafael Zas & Luis Sampedro
While plant diversity is well known to increase primary productivity, whether these bottom-up effects are enhanced by reciprocal top-down effects from the third trophic level is unknown. We studied whether pine tree species diversity, aphid-tending ants and their interaction determined plant performance and arthropod community structure. Plant diversity had a positive effect on aphids, but only in the presence of mutualistic ants, leading to threefold greater number of both groups in the tri-specific cultures than...

Data from: Natural hybridization between divergent lineages in a selfing hermaphroditic fish

Andrey Tatarenkov, Ryan L. Earley, D.S. Taylor, William P. Davis & John C. Avise
By definition, mating between individuals is infrequent in highly selfing organisms, and so too, therefore, hybridization should be rare between genetically divergent lineages in predominantly self-fertilizing species. Notwithstanding these expectations, here we report a remarkable case of natural hybridization between highly diverged phylogeographic lineages of the mangrove rivulus, a small killifish that reproduces predominantly by self-fertilization and typically is found as highly homozygous lines in most parts of its extensive geographic range. Two distinctive genetic...

Data from: Copy number variation and expression analysis reveals a nonorthologous pinta gene family member involved in butterfly vision

Aide Macias-Muñoz, Kyle J. McCulloch & Adriana D. Briscoe
Vertebrate (CRALBP) and Drosophila (PINTA) proteins with a CRAL-TRIO domain transport retinal-based chromophores that bind to opsin proteins and are necessary for phototransduction. The CRAL-TRIO domain gene family is composed of genes that encode proteins with a common N-terminal structural domain. While there is an expansion of this gene family in Lepidoptera, there is no lepidopteran ortholog of pinta. Further, the function of these genes in lepidopterans has not yet been established. Here we explored...

Data from: Tritrophic interactions at a community level: effects of host-plant species quality on bird predation of caterpillars

Michael S. Singer, Timothy E. Farkas, Christian M. Skorik & Kailen A. Mooney
Effects of plant traits on herbivore-carnivore interactions are well documented in component communities, but are not well understood at the level of large, complex communities. We report on a two-year field experiment testing mechanisms by which variation in food quality among eight temperate forest tree species alters avian suppression of an assemblage of dietary generalist caterpillars. Plant quality and bird effects varied dramatically among tree species; high quality plants yielded herbivores of 50% greater mass...

Data from: Patterns of male fitness conform to predictions of evolutionary models of late-life

Parvin Shahrestani, Xuan Tran & Laurence D. Mueller
We studied lifetime male virility, a male fitness component, in five populations of Drosophila melanogaster. Virility was measured as the number of females, out of eight total, that a male could fertilize in 24 hours. Individual males were measured at weekly intervals until they died. Virility declined in an approximately linear fashion for the first three weeks of adult life. It then stayed low but relatively constant for another three weeks, exhibiting a clear plateau....

Data from: The genetic architecture of methotrexate toxicity is similar in Drosophila melanogaster and humans

Galina Kislukhin, Elizabeth G. King, Kelli N. Walters, Stuart J. Macdonald & Anthony D. Long
The severity of the toxic side effects of chemotherapy varies among patients, and much of this variation is likely genetically based. Here, we use the model system Drosophila melanogaster to genetically dissect the toxicity of methotrexate (MTX), a drug used primarily to treat childhood acute lymphoblastic leukemia and rheumatoid arthritis. We use the Drosophila Synthetic Population Resource, a panel of recombinant inbred lines derived from a multiparent advanced intercross, and quantify MTX toxicity as a...

Data from: Willing or unwilling to share primary biodiversity data: results and implications of an international survey

Xiaolei Huang, Bradford A. Hawkins, Fumin Lei, Gary L. Miller, Colin Favret, Ruiling Zhang & Gexia Qiao
Biodiversity science and conservation increasingly depend on the sharing and integration of large amounts of data, but many researchers resist sharing their primary biodiversity data. We recently conducted an international survey to ascertain the attitudes, experiences, and expectations regarding biodiversity data sharing and archiving of researchers. The results show that whereas most respondents are willing to share paper-related biodiversity data, more than sixty percent of respondents are unwilling to share primary data before publishing. Results...

Southeast Greenland Bed Elevation - v2

Romain Millan
We employ NASA's Operation IceBridge (OIB) high‐resolution airborne gravity from 2016, NASA's Ocean Melting Greenland (OMG) bathymetry from 2015, ice thickness from Operation IceBridge (OIB) from 2010‐2015, and BedMachine v3 to analyze 20 major southeast Greenland glaciers. The results reveal glacial fjords several hundreds of meters deeper than previously thought; the full extent of the marine‐based portions of the glaciers; deep troughs enabling warm, salty Atlantic Water (AW) to reach the glacier fronts and melt...

Jakobshavn Glacier Bed Elevation

Lu An
Jakobshavn Isbræ, West Greenland, which holds a 0.6-m sea level volume equivalent, has been speeding up and retreating since the late 1990s. Interpretation of its retreat has been hindered by difficulties in measuring its ice thickness with airborne radar depth sounders. Here, we employ high-resolution, helicopter-borne gravity data from 2012 to reconstruct its bed elevation within 50 km of the ocean margin using a three-dimensional inversion constrained by fjord bathymetry data offshore and a mass...

UCI Libraries' Chatbot Files (ANTswers)

Danielle Kane
ANTswers is an experimental chatbot that can answer questions about the UC Irvine Libraries. ANTswers is a web-based application, run on a remote library server and is accessed through a web interface page. ANTswers’ personality and persona is based on the UCI mascot, Peter the Anteater. ANTswers responds to simple and short questions. The first link in a response opens in a preview window, all other links open in a new window. Each transaction is...

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