298 Works

Differentially expressed genes in the blood, spleen, and liver of Peromyscus leucopus and Mus musculus with or without treatment with lipopolysaccharide

Alan Barbour, Ana Milovic, Gabriela Balderrama-Gutierrez & Ali Mortazavi
Animals that are competent reservoirs of zoonotic pathogens commonly suffer little morbidity from the infections. To investigate mechanisms of this tolerance of infection, we used single-dose lipopolysaccharide (LPS) as an experimental model of inflammation and compared the responses by two rodents: Peromyscus leucopus, white-footed deermouse and reservoir for agents of Lyme disease and other zoonoses, and the house mouse Mus musculus. Four hours after injection with LPS or saline, blood, spleen and liver samples were...

Evaluating Promising Practices in Undergraduate STEM Lecture Courses

Mark Warschauer, Lynn Reimer, Kameryn Denaro, Gabe Orona, Katerina Schenke, Tutrang Nguyen, Amanda Niili, Di Xu, Sabrina Solanki & Tate Tamara
Observations were collected to examine instructional practices in large undergraduate lecture courses at UCI, particularly in STEM (science, technology, engineering, and mathematics). The study began in 2012 with the intention of documenting the relative presence or absence of practices that potentially promote more active and engaged learning (e.g., enhanced faculty-student interaction, enhanced peer interaction, greater attention to problem-solving strategies, more opportunities for personalized learning, opportunities to receive and communicate information across diverse channels and modalities,...

Seismic detection of oceanic internal gravity waves from subaerial seismometers

Kristen Davis, Heather Shaddox, Emily Brodsky & Thorne Lay
Oceanic internal gravity waves propagate along density stratification within the water column and are ubiquitous. They can propagate thousands of kilometers before breaking in shoaling bathymetry and the ensuing turbulent mixing affects coastal processes and climate feedbacks. Despite their importance, internal waves are intrinsically difficult to detect as they result in only minor amplitudedeflection of the sea surface; the need for global detection and long time series of internal waves motivates a search for geophysical...

Differentially expressed genes of Peromyscus leucopus fibroblast cultures treated with lipopolysaccharide or buffer alone

Alan Barbour, Youwen Zhang, Ana Milovic & Hippokratis Kiaris
This experiment and its results were part of a larger study of the differential responses of the white-footed deermouse Peromyscus leucopus and the house mouse Mus musculus to single injections of lipopolysaccharide (LPS). The entire study is presented in the associated manuscript in submission and in the listed pre-print. The aim of this particular experiment was to identify differentially expressed genes (DEG) of fibroblast cultures of P. leucopus. The experiment identified 543 DEGs that were...

Data From: TERRA-REF, An open reference data set from high resolution genomics, phenomics, and imaging sensors

David LeBauer, Burnette Maxwell, Jeffrey Demieville, Noah Fahlgren, Andrew French, Roman Garnett, Zhenbin Hu, Kimberly Huynh, Rob Kooper, Zongyang Li, Maitiniyazi Maimaitijiang, Jerome Mao, Todd Mockler, Geoffrey Morris, Maria Newcomb, Michael Ottman, Philip Ozersky, Sidike Paheding, Duke Pauli, Robert Pless, Wei Qin, Kristina Riemer, Gareth Rohde, William Rooney, Vasit Sagan … & Charles Zender
The ARPA-E funded TERRA-REF project is generating open-access reference datasets for the study of plant sensing, genomics, and phenomics. Sensor data were generated by a field scanner sensing platform that captures color, thermal, hyperspectral, and active flourescence imagery as well as three dimensional structure and associated environmental measurements. This dataset is provided alongside data collected using traditional field methods in order to support calibration and validation of algorithms used to extract plot level phenotypes from...

Data from: Black Abalone habitat assessment

Kelcey Chung & Julia Peay
The black abalone Haliotis cracherodii was once an abundant intertidal species that was commonly found in the rocky intertidal zones throughout California. Due to overfishing and a fatal disease called Withering Syndrome, the black abalone is currently federally listed as endangered and considered locally extinct through southern California. In order to recover black abalone populations in southern California, intervention and restoration must be conducted to facilitate the base population of this species. Habitat quantity and...

Data from: In-vitro cultivation of liveforevers (genus Dudleya) to reduce poaching and extinction

Kevin Alison
The genus Dudleya consists of many rare and endangered species. Recently, poaching has emerged as a critical threat to the continued survival of these plants in the wild. Conservationists will typically store seeds and grow new plants, but this method could limit propagation if viability and seed availably is unreliable. Nursery growing efforts have been limited by unreliable and scarce seed sources, and challenges to maintaining genetically isolated populations, as Dudleya species readily hybridize. Micropropagation...

Physical processes determine spatial structure in water temperature and residence time on a wide reef flat

Kristen Davis, Emma Reid, Steven Lentz, Thomas DeCarlo & Anne Cohen
On coral reefs, flow determines residence time of water, influencing physical and chemical environments and creating observable microclimates within the reef structure. Understanding the physical mechanisms driving variability on coral reefs, which distinguishes them from the open ocean, can be important for understanding what contributes to thermal resilience of coral communities and predicting their response to future anomalies. In June 2014, a field experiment was conducted at Dongsha Atoll in the northern South China Sea...

Data from: How atmospheric chemistry and transport drive surface variability of N2O and CFC-11

Daniel Ruiz
Figure and table scripts, processed data from: NOAA observations, MLS measurements, GMI, UCI, and LMDz5 CTMs. This dataset includes processed numerical output from N2O tracer experiments that quantify the stratospheric signal of N2O, driven by atmospheric chemistry and transport, at Earth’s surface in observations and 3 CTMs. Nitrous oxide (N2O) is a long-lived greenhouse gas that affects atmospheric chemistry and climate. In this work we use satellite measurements of N2O, ozone (O3), and temperature from...

The tale of two ice shelves: Zachariae Isstrøm and Nioghalvfjerdsfjorden, Northeast Greenland

Lu An, Eric Rignot, Michael Wood, Josh Willis, Jeremie Mouginot & Shfaqat Khan
Oceanography and gravity data of Northeastern Greenland reveal ocean temperature and bathymetry in front of Zachariae Isstrøm (ZI) and Nioghalvfjerdsfjorden (79N), which hold a 1.1-m sea-level rise ice volume equivalent but underwent different evolutions. Sub-surface, warm, salty water of Atlantic origin has easier access to ZI than to 79N because of bathymetric barriers. We reconstruct ice removal by the ocean at the grounding line and floatation retreat from thinning to explain the observed grounding line...

Random peptide sequences binding amyloid monoclonal antibodies

Charles Glabe
Antibodies against Aß amyloid are indispensable research tools and potential therapeutics for Alzheimer’s Disease, but display several unusual properties, such as specificity for aggregated forms of the peptide, ability to distinguish polymorphic aggregate structures and ability to recognize generic aggregation-related epitopes formed by unrelated amyloid sequences. Understanding the mechanisms underlying these unusual properties of anti-amyloid antibodies and the structures of their corresponding epitopes is crucial for the understanding why antibodies display different therapeutic activities and...

Monitoring marine bound debris using UAS on the US-Mexico Border

Jochen Schubert, Napoleon Gudino, Steven Wright & Waylon Matson
The Tijuana river estuary suffers from overwhelming solid-waste contamination such as marine bound plastics, tires, and sediment. Funded by the US EPA's Border 2020 program (SOLTA-C-19-008), this project intends to establish a framework for bi-national monitoring of trans-boundary, marine bound trash (TBMBT) using light-weight unmanned aerial systems (UASs), also known as drones. The developed framework is intended to benefit 1) border authorities through the establishment of a low-cost, minimally invasive, operational standard to monitor TBMBT...

Combining metabolomics and experimental evolution reveals key mechanisms underlying longevity differences in laboratory evolved Drosophila melanogaster populations

Mark Phillips, Kenneth R. Arnold, Zer Vue, Heather K. Beasley, Edgar Garza-Lopez, Andrea G. Marshall, Derrick J. Morton, Melanie R. McReynolds, Thomas T. Barter & Antentor Hinton
Experimental evolution with Drosophila melanogaster has been used extensively for decades to study aging and longevity. In recent years, the addition of DNA and RNA sequencing to this framework has allowed researchers to leverage the statistical power inherent to experimental evolution to study the genetic basis of longevity itself. Here, we incorporated metabolomic data into to this framework to generate even deeper insights into the physiological and genetic mechanisms underlying longevity differences in three groups...

Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow

Diana Le Duc, Akhil Velluva, Molly Cassatt-Johnstone, Remi-Andre Olsen, Sina Baleka, Chen-Ching Lin, Johannes R. Lemke, John R. Southon, Alexander Burdin, Ming-Shan Wang, Sonja Grunewald, Wilfried Rosendahl, Ulrich Joger, Sereina Rutschmann, Thomas B. Hildebrandt, Guido Fritsch, James A. Estes, Janet Kelso, Love Dalén, Michael Hofreiter, Beth Shapiro & Torsten Schöneberg
Steller’s sea cow, an extinct sirenian and one of the largest Quaternary mammals, was described by Georg Steller in 1741 and eradicated by humans within 27 years. Here, we complement Steller’s descriptions with paleogenomic data from 12 individuals. We identified convergent evolution between Steller’s sea cow and cetaceans but not extant sirenians, suggesting a role of several genes in adaptation to cold environments. Among these are inactivations of lipoxygenase genes, which in humans and mouse...

Non-adaptive molecular evolution of seminal fluid proteins in drosophila

Alberto Civetta, Bahar Patlar, Vivek Jayaswal & Jose Ranz
Seminal fluid proteins (SFPs) are a group of reproductive proteins that are amongst the most evolutionarily divergent known. As SFPs can impact male and female fitness, these proteins have been proposed to evolve under post-copulatory sexual selection (PCSS). However, the fast change of the SFPs can also result from non-adaptive evolution, and the extent to which selective constraints prevent SFPs rapid evolution remains unknown. Using intra- and interspecific sequence information, along with genomics and functional...

Experimental test of the combined effects of water availability and flowering time on pollinator visitation and seed set

M. Kate Gallagher & Diane Campbell
Climate change is likely to alter both flowering phenology and water availability for plants. Either of these changes alone can affect pollinator visitation and plant reproductive success. The relative impacts of phenology and water, and whether they interact in their impacts on plant reproductive success remain, however, largely unexplored. We manipulated flowering phenology and soil moisture in a factorial experiment with the subalpine perennial Mertensia ciliata (Boraginaceae). We examined responses of floral traits, floral abundance,...

Tuned inhibition in perceptual decision-making circuits can explain seemingly suboptimal confidence behavior: S4 data, evidence for tuned inhibition in macaque superior colliculus

Megan Peters, Brian Maniscalco, Brian Odegaard, Piercesare Grimaldi, Seong Hah Cho, Michele Basso & Hakwan Lau
This dataset contains online spike-sorted single-unit recordings from one Rhesus macaque who performed a dot-motion discrimination task while neural data was recorded with a 16-channel v-probe from superior colliculus neurons. Full methods for data collection, including description of the stimuli and task, surgical details, ethics statement, funding information, and other relevant details, are available in the above-referenced manuscript, section S4 Text.

The impact of Rhodiola Rosea on biomarkers of diabetes, inflammation, and microbiota in a leptin receptor-knockout mouse model

Robert Courville, Mahtab Jafari, Richard Van Etten, John Chaston, Jasmin Grace Juanson Arabit, Dara Kiani, Cindy Duy Nguyen, Nilamani Jena, Zhong-Ying Liu & Prasanthi Tata
Type 2 diabetes is the most prevalent endocrine disease in the world, and recently the gut microbiota have become a potential target for its management. Recent studies have illustrated that this disease may predispose individuals to certain microbiome compositions, and treatments like metformin have been shown to change gut microbiota and their associated metabolic pathways. However, given the limitations and side effects associated with pharmaceuticals currently being used for therapy of diabetes, there is a...

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: Does phenotypic plasticity for adult size versus food level in Drosophila melanogaster evolve in response to adaptation to different rearing densities?

Laurence D. Mueller & Larry G. Cabral
Recent studies using inbred lines of Drosophila have suggested that there is extensive genetic variability for phenotypic plasticity of body size versus food level. If true, we expect that the outcome of evolution at very different food levels should yield genotypes whose adult sizes show different patterns of phenotypic plasticity. We have tested this prediction with six independent populations of Drosophila melanogaster kept at extreme (low vs. high) densities for 125 generations. We found that...

Data from: Modeling effects of environmental change on wolf population dynamics, trait evolution, and life history

Tim Coulson, Daniel R. MacNulty, Daniel R. Stahler, Bridgett VonHoldt, Robert K. Wayne & Douglas W. Smith
Environmental change has been observed to generate simultaneous responses in population dynamics, life history, gene frequencies, and morphology in a number of species. But how common are such eco-evolutionary responses to environmental change likely to be? Are they inevitable, or do they require a specific type of change? Can we accurately predict eco-evolutionary responses? We address these questions using theory and data from the study of Yellowstone wolves. We show that environmental change is expected...

Data from: Minimal ProtoHox cluster inferred from bilaterian and cnidarian Hox complements

Daniel Chourrout, Frédéric Delsuc, Pascal Chourrout, Rolph B Edvardsen, Fabian Rentzsch, Eduard Renfer, Marit F. Jensen, Baoli Zhu, Pieter De Jong, Robert E. Steele & Ulrich Technau
Bilaterian animals have a Hox gene cluster essential for patterning the main body axis, and a ParaHox gene cluster. Comparison of Hox and ParaHox genes has led workers to postulate that both clusters originated from the duplication of an ancient cluster named ProtoHox, which contained up to four genes with at least the precursors of anterior and posterior Hox/ParaHox genes. However, the way in which genes diversified within the ProtoHox, Hox and ParaHox clusters remains...

Data from: UV photoreceptors and UV-yellow wing pigments in Heliconius butterflies allow a color signal to serve both mimicry and intraspecific communication

Seth M. Bybee, Furong Yuan, Monica D. Ramstetter, Jorge Llorente-Bousquets, Robert D. Reed, Daniel Osorio & Adriana D. Briscoe
Mimetic wing coloration evolves in butterflies in the context of predator confusion. Unless butterfly eyes have adaptations for discriminating mimetic color variation, mimicry also carries a risk of confusion for the butterflies themselves. Heliconius butterfly eyes, which express recently duplicated UV opsins, have such an adaptation. To examine bird and butterfly color vision as sources of selection on butterfly coloration we studied yellow wing pigmentation in the tribe Heliconiini. We confirmed using reflectance and mass...

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