26 Works

Data from: Unravelling the immune signature of Plasmodium falciparum transmission-reducing immunity

Will J. R. Stone, Joseph J. Campo, André Lin Ouédraogo, Lisette Meerstein-Kessel, Isabelle Morlais, Dari Da, Anna Cohuet, Sandrine Nsango, Colin J. Sutherland, Marga Van De Vegte-Bolmer, Rianne Siebelink-Stoter, Geert-Jan Van Gemert, Wouter Graumans, Kjerstin Lanke, Adam D. Shandling, Jozelyn V. Pablo, Andy A. Teng, Sophie Jones, Roos M. De Jong, Amanda Fabra-García, John Bradley, Will Roeffen, Edwin Lasonder, Giuliana Gremo, Evelin Schwarzer … & Matthijs M. Jore
Infection with Plasmodium can elicit antibodies that inhibit parasite survival in the mosquito, when they are ingested in an infectious blood meal. Here, we determine the transmission-reducing activity (TRA) of naturally acquired antibodies from 648 malaria-exposed individuals using lab-based mosquito-feeding assays. Transmission inhibition is significantly associated with antibody responses to Pfs48/45, Pfs230, and to 43 novel gametocyte proteins assessed by protein microarray. In field-based mosquito-feeding assays the likelihood and rate of mosquito infection are significantly...

Crystal Cove Marine Conservation Area Citizen Science Monitoring

Crystal Cove Alliance
Crystal Cove Conservancy operates the Crystal Cove Marine Protected Are Citizen Science Cruise in partnership with Newport Landing Sportfishing. Under the supervision of trained Crystal Cove Conservancy staff, junior high school and high school students collect data on fish and plankton biodiversity and nearshore water quality in the Crystal Cove Marine Conservation Area, following protocols designed in partnership with UCI and other researchers. See README file for more detailed information.Data made available in the OC...

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: 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: 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: 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: 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: 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...

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...

Predicting drought tolerance from slope aspect preference in restored plant communities

Sarah Kimball, Megan Lulow, Kathleen Balazs & Travis Huxman
Plants employ strategies of tolerance, endurance, and avoidance to cope witharidity in space and time, yet understanding the differential importance of suchstrategies in determining patterns of abundance across a heterogeneous landscapeis a challenge. Are the species abundant in drier microhabitats also better able tosurvive drought? Are there relationships among occupied sites and temporaldynamics that derive from physiological capacities to cope with stress or dormancyduring unfavorable periods? We used a restoration project conducted on twoslope aspects...

Data from: Making it last: storage time and temperature have differential impacts on metabolite profiles of airway samples from cystic fibrosis patients

Stephen Wandro, Lisa Carmody, Tara Gallagher, John J. LiPuma & Katrine Whiteson
Metabolites of human or microbial origin have the potential to be important biomarkers of disease state in cystic fibrosis (CF). Clinical sample collection and storage conditions may impact metabolite abundances with clinical relevance. We measured the change in metabolite composition based on untargeted gas chromatography mass spectrometry (GC-MS) when CF sputum samples were stored at either 4°C, -20°C, or -80°C with one or two freeze-thaw cycles. Daily time points were taken for one week and...

Data from: Links between plant and fungal diversity in habitat fragments of coastal shrubland

Mia R. Maltz, Kathleen K. Treseder & Krista L. McGuire
Habitat fragmentation is widespread across ecosystems, detrimentally affecting biodiversity. Although most habitat fragmentation studies have been conducted on macroscopic organisms, microbial communities and fungal processes may also be threatened by fragmentation. This study investigated whether fragmentation, and the effects of fragmentation on plants, altered fungal diversity and function within a fragmented shrubland in southern California. Using fluorimetric techniques, we assayed enzymes from plant litter collected from fragments of varying sizes to investigate enzymatic responses to...

Data from: Interaction rewiring and the rapid turnover of plant-pollinator networks

Paul J. CaraDonna, William K. Petry, Ross M. Brennan, James L. Cunningham, Judith L. Bronstein, Nickolas M. Waser & Nathan J. Sanders
Whether species interactions are static or change over time has wide-reaching ecological and evolutionary consequences. However, species interaction networks are typically constructed from temporally aggregated interaction data, thereby implicitly assuming that interactions are fixed. This approach has advanced our understanding of communities, but it obscures the timescale at which interactions form (or dissolve) and the drivers and consequences of such dynamics. We address this knowledge gap by quantifying the within-season turnover of plant–pollinator interactions from...

Data from: Trait syndromes among North American trees are evolutionarily conserved and show adaptive value over broad geographic scales

Marta Rueda, Oscar Godoy & Bradford A. Hawkins
Adaptive syndromes and their evolutionary constraints represent a powerful construct for understanding plant distributions. However, it is unclear how the species requirements to face multiple stressors promotes syndrome formation and to which abiotic stressors these syndromes show adaptive value over broad geographic scales. We combined local occurrence data from the U.S. Forest Inventory and Analysis (FIA) of 219 angiosperm and 85 gymnosperm species living across the conterminous US with phylogenies and trait data to identify...

Data from: Age of heart disease presentation and dysmorphic nuclei in patients with LMNA mutations

Jason Q. Core, Mehrsa Mehrabi, Zachery R. Robinson, Alexander R. Ochs, Linda A. McCarthy, Michael V. Zaragoza & Anna Grosberg
Nuclear shape defects are a distinguishing characteristic in laminopathies, cancers, and other pathologies. Correlating these defects to the symptoms, mechanisms, and progression of disease requires unbiased, quantitative, and high-throughput means of quantifying nuclear morphology. To accomplish this, we developed a method of automatically segmenting fluorescently stained nuclei in 2D microscopy images and then classifying them as normal or dysmorphic based on three geometric features of the nucleus using a package of Matlab codes. As a...

Data from: A new genus of horse from Pleistocene North America

Peter D. Heintzman, Grant D. Zazula, Ross D.E. MacPhee, Eric Scott, James A. Cahill, Brianna K. McHorse, Joshua D. Kapp, Mathias Stiller, Matthew J. Wooller, Ludovic Orlando, John R. Southon, Duane G. Froese, Beth Shapiro & John Southon
The extinct “New World stilt-legged”, or NWSL, equids constitute a perplexing group of Pleistocene horses endemic to North America. Their slender distal limb bones resemble those of Asiatic asses, such as the Persian onager. Previous palaeogenetic studies, however, have suggested a closer relationship to caballine horses than to Asiatic asses. Here, we report complete mitochondrial and partial nuclear genomes from NWSL equids from across their geographic range. Although multiple NWSL equid species have been named,...

Data from: Connecting genomic patterns of local adaptation and niche suitability in teosintes

Jonas Aguirre-Liguori, Maud Tenaillon, Alejandra Vázquez-Lobo, Brandon Gaut, Juan Jaramillo-Correa, Salvador Montes-Hernandez, Valeria Souza, L. E. Eguiarte, J. P. Jaramillo-Correa & M. I. Tenaillon
The central-abundance hypothesis predicts that local adaptation is a function of the distance to the center of a species’ geographic range. To test this hypothesis, we gathered genomic diversity data from 49 populations, 646 individuals and 33,464 SNPs of two wild relatives of maize, the teosintes Zea mays ssp. parviglumis and Zea. mays. ssp. mexicana. We examined the association between the distance to their climatic and geographic centroids and the enrichment of SNPs bearing signals...

Data from: Evolutionary and structural analyses uncover a role for solvent interactions in the diversification of cocoonases in butterflies

Gilbert Smith, John E. Kelly, Aide Macias-Muñoz, Carter T. Butts, Rachel W. Martin & Adriana D. Briscoe
Multi-omic approaches promise to supply the power to detect genes underlying disease and fitness-related phenotypes. Optimal use of the resulting profusion of data requires detailed investigation of individual candidate genes, a challenging proposition. Here, we combine transcriptomic and genomic data with molecular modeling of candidate enzymes to characterize the evolutionary history and function of the serine protease cocoonase. Heliconius butterflies possess the unique ability to feed on pollen; recent work has identified cocoonase as a...

Data from: Experimental assemblage of novel plant-herbivore interactions: ecological host shifts after 40 million years of isolation

Carlos Garcia-Robledo, Carol C. Horvitz, W. John Kress, A. Nalleli Carvajal-Acosta, Terry L. Erwin & Charles L. Staines
Geographic isolation is the first step in insect herbivore diet specialization. Such specialization is postulated to increase insect fitness, but may simultaneously reduce insect ability to colonize novel hosts. During the Paleocene-Eocene, plants from the order Zingiberales became isolated either in the Paleotropics or in the Neotropics. During the Cretaceous, rolled-leaf beetles diversified in the Neotropics concurrently with neotropical Zingiberales. Using a community of Costa Rican rolled-leaf beetles and their Zingiberales host plants as study...

Shifts in water availability mediate plant-pollinator interactions

M. Kate Gallagher & Diane Campbell
Altered precipitation patterns associated with anthropogenic climate change are expected to have many effects on plants and insect pollinators, but it is unknown if effects on pollination are mediated by changes in water availability. We tested the hypothesis that impacts of climate on plant–pollinator interactions operate through changes in water availability, and specifically that such effects occur through alteration of floral attractants. We manipulated water availability in two naturally occurring Mertensia ciliata (Boraginaceae) populations using...

Data from: Day/night upper thermal limits differ within Ectatomma ruidum ant colonies

Annika S. Nelson, Trey Scott, Maciej Barczyk, Terrence P. McGlynn, Arian Avalos, Elizabeth Clifton, Amlan Das, Andreia Figueiredo, Laura L. Figueroa, Mark Janowiecki, Sarah Pahlke, Jignasha D. Rana & Sean O'Donnell
In the tropics, daily temperature fluctuations can pose physiological challenges for ectothermic organisms, and upper thermal limits may affect foraging activity over the course of the day. Variation in upper thermal limits can occur among and within species, and for social insects such as ants, within colonies. Within colonies, upper thermal limits may differ among individuals or change for an individual throughout the day. Daytime foragers of the Neotropical ant Ectatomma ruidum have higher critical...

Data from: A species-specific multigene family mediates differential sperm displacement in Drosophila melanogaster

Vivek Jayawal, Jamie Jimenez, Robert Magie, Kien Nguyen, Bryan Clifton, Shudan Yeh, Jose M. Ranz & Vivek Jayaswal
Sperm competition is a post-copulatory sexual selection mechanism in species in which females mate with multiple males. Despite its evolutionary relevance in shaping male traits, the genetic mechanisms underlying sperm competition are poorly understood. A recently originated multigene family specific to D. melanogaster, Sdic, is important for the outcome of sperm competition in doubly-mated females, although the mechanistic nature of this phenotype remained unresolved. Here we compared doubly-mated females, second mated to either Sdic knockout...

Data from: Higher predation risk for insect prey at low latitudes and elevations

Tomas Roslin, Bess Hardwick, Vojtech Novotny, William K. Petry, Nigel R. Andrew, Ashley Asmus, Isabel C. Barrio, Yves Basset, Andrea Larissa Boesing, Timothy C. Bonebrake, Erin K. Cameron, Wesley Dáttilo, David A. Donoso, Pavel Drozd, Claudia L. Gray, David S. Hik, Sarah J. Hill, Tapani Hopkins, Shuyin Huang, Bonny Koane, Benita Laird-Hopkins, Liisa Laukkanen, Owen T. Lewis, Sol Milne, Isaiah Mwesige … & Eleanor M. Slade
Biotic interactions underlie ecosystem structure and function, but predicting interaction outcomes is difficult. We tested the hypothesis that biotic interaction strength increases toward the equator, using a global experiment with model caterpillars to measure predation risk. Across an 11,660-kilometer latitudinal gradient spanning six continents, we found increasing predation toward the equator, with a parallel pattern of increasing predation toward lower elevations. Patterns across both latitude and elevation were driven by arthropod predators, with no systematic...

Vegetation Change in the Natural Reserve of Orange County

Katherine Suding, Sara Jo Dickens & Samuel Bedgood
This data set describes vegetation change in 109 areas in the Nature Reserve of Orange County. The authors of this data were mainly interested in the success of artichoke thistle (Cynara cardunculus) control, but it could be approached in many different ways. Surveyors identified and recorded more than 375 plant species from the years 1998, 2008, and 2013.

Speech Intelligibility for Spectrally Degraded Sentences

Sierra Broussard & Kourosh Saberi
This data was collected to determine how amplitude and phase information differentially contribute to speech intelligibility. Listeners performed a word-identification task after hearing spectrally degraded sentences. Each stimulus was degraded by first dividing it into segments, then the amplitude and phase components of each segment were decorrelated independently to various degrees relative to those of the original segment. Segments were then concatenated into their original sequence to present to the listener. We used three segment...

Registration Year

  • 2017

Resource Types

  • Dataset


  • University of California, Irvine
  • University of California System
  • University of Alberta
  • University of California, Berkeley
  • National Autonomous University of Mexico
  • University of Connecticut
  • French National Centre for Scientific Research
  • University of Oxford
  • Bangor University
  • Plymouth University