126 Works

Host Factor Experiment (IM004-R)

Purpose: To look at the host response to different doses across 4 time points after infection. Samples were collected for both transcriptomics and proteomics.General Design: 20 week-old C57Bl6 mice; doses = 1E4 PFU; Time points of 1, 2, 4 and 7 days; ~5 mice/time point for infections; 3 mice/timepoint for time matched mocks

Host Factor Experiment (IM005-P)

Purpose: To obtain lung samples from C57BL6 mice infected with Vietnam/1203-CIP048_RG2/2004 (H5N1) for both transcriptional and proteomic analyses. Details: Time Points = 1, 2, 4 and 7 days post infection; 5 replicates/time point for infections; 3 mice/ time point for time matched mock infections. Infection dose was 10^4 PFU.

Host Factor Experiment (IM002-R)

Purpose: To obtain lung samples from BALB/c mice infected with A/CA/04/2009 (H1N1) or, mouse-adapted A/CA/04/2009 (H1N1) virus for transcriptional analysis. Details: Time Points = 1, 3 and 5 days post-infection; 2-3 replicates for infected and mock mice; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^6 pfu.

Host Factor Experiment (SCL006-R)

Purpose: To obtain samples for transcriptional analysis and proteomics in triplicate using wild typeicSARS urbani and icSARS Bat SRBD mutant in 2B4 cells/sorted Calu3 cells with high ACE2 expression. Overview of Experiment: Time Points = 0, 7, 12, 24, 30, 36, 48, 54, 60 and 72 hrs post infection. (Note: there is no time point at 7 h for icSARS Bat SRBD.) Done in triplicate for both RNA and Protein. Triplicates are defined as 3...

Host Factor Experiment (SCL005-P)

Purpose: To obtain samples for transcriptional and proteomic analysis using wild type and icSARS delta ORF6 virus in 2B-4 cells/sorted Calu-3 cells with high ACE2 expression. Details: Time Points = 0, 3, 7, 12, 24, 30, 36, 48, 54, 60 and 72h post infection; Done in triplicate for both RNA and protein; Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates; Time matched mocks...

Cadmium exposure persistently modulates the gut-liver axis in an Alzheimer’s disease mouse model

Angela Zhang, Megumi Matsushita, Zhengui Xia, Liang Zhang, Xiaojian Shi, Haiwei Gui & Julia Yue Cui
The human Apolipoprotein E4 (ApoE4) variant is the strongest known genetic risk factor for Alzheimer’s disease (AD). Cadmium (Cd) has been shown to impair learning and memory at a greater extent in humanized ApoE4 knock-in (ApoE4-KI) mice as compared to the ApoE3 (common allele)-KI mice. In this study, we determined the extent that cadmium interacts with the ApoE4 gene variants to modify the gut-liver axis, which is important for xenobiotic biotransformation and nutrient homeostasis. Large...

Nocturnal dispersal flight of crickets: behavioural and physiological responses to cool environmental temperatures

Caroline Williams, Baojun Sun, Christopher Huebner, Lisa Treidel, Kevin Roberts, G.J. Kenagy & Rebecca Clark
1. Flight of nocturnal insects may be limited by cool nighttime environmental temperatures. We used laboratory and field experiments to explore the thermal basis of nocturnal flight in wing-polymorphic Gryllus lineaticeps crickets consisting of long-winged (LW), flight-capable morphs and short-winged (SW), flight-incapable morphs. These crickets are a model for life history evolution and loss of flight, but their thermal requirements for flight have been unknown. We hypothesized that LW crickets achieve warm body temperatures required...

Selection of indicators for assessing and managing the impacts of bottom trawling on seabed habitats

Jan Geert Hiddink, Michel Kaiser, Marija Sciberras, Robert McConnaughey, Tessa Mazor, Ray Hilborn, Jeremy Collie, C. Roland Pitcher, Ana Parma, Petri Suuronen, Adriaan Rijnsdorp & Simon Jennings
1. Bottom-trawl fisheries are the most-widespread source of anthropogenic physical disturbance to seabed habitats. Development of fisheries-, conservation- and ecosystem-based management strategies requires the selection of indicators of the impact of bottom trawling on the state of benthic biota. Many indicators have been proposed, but no rigorous test of a range of candidate indicators against 9 commonly-agreed criteria (concreteness, theoretical basis, public awareness, cost, measurement, historical data, sensitivity, responsiveness, specificity) has been performed. 2. Here,...

Data from: Quantifying spatiotemporal occupancy dynamics and multi-year core-use areas at a species range boundary

Nathan Hostetter, Daniel Ryan, David Grosshuesch, Timothy Catton, Sarah Malick-Wahls, Tamara Smith & Beth Gardner
Aim Many species face large-scale range contractions and predicted distributional shifts in response to climate change, shifting forest characteristics, and anthropogenic disturbances. Canada lynx (Lynx canadensis) are listed as threatened under the U.S. Endangered Species Act and were recently recommended for delisting. Predicted climate-driven losses in habitat quality and quantity may negatively affect the northeastern Minnesota lynx population, one of six remaining resident populations in the contiguous United States. We develop a large-scale monitoring protocol...

Morphological diversity in the sensory system of phyllostomid bats: implications for acoustic and dietary ecology

Leith Leiser-Miller & Sharlene Santana
1. Sensory systems perform fitness-relevant functions, and specialized sensory structures allow organisms to accomplish challenging tasks. However, broad comparative analyses of sensory morphologies and their performance are lacking for diverse mammalian radiations. 2. Neotropical leaf-nosed bats (Phyllostomidae) are one of the most ecologically diverse mammal groups; including a wide range of diets and foraging behaviors, and extreme morphological variation in external sensory structures used in echolocation (nose leaf and pinnae). 3. We coupled 3D geometric...

Swimming and defense - competing needs across ontogeny in armored fishes (Agonidae)

Matthew Kolmann, Cassandra Donatelli, Tessa Peixoto, Janne Pfeiffenberger & Adam Summers
Biological armors are potent model systems for understanding the complex series of competing demands on protective exoskeletons; after all, armored organisms are the product of millions of years of refined engineering under the harshest conditions. Fishes are no strangers to armor, with various types of armor plating common to the 400 million years of evolution in both jawed and jawless fishes. Here we focus on the poachers (Agonidae), a family of armored fishes native to...

In vivo x-ray diffraction and simultaneous EMG reveal the timecourse of myofilament lattice dilation and filament stretch

Sage Malingen, Anthony Asencio, Julie Cass, Weikang Ma, Thomas Irving & Thomas Daniel
Muscle function within an organism depends on the feedback between molecular and meter-scale processes. Although the motions of muscle’s contractile machinery are well described in isolated preparations, only a handful of experiments have documented the kinematics of the lattice occurring when multi-scale interactions are fully intact. We used time-resolved X-ray diffraction to record the kinematics of the myofilament lattice within a normal operating context: the tethered flight of Manduca sexta. As the primary flight muscles...

Genome-wide association results from: Transcriptomic stratification of late-onset Alzheimer’s cases reveals novel genetic modifiers of disease pathology

Greg Carter, Christoph Preuss, Nikhil Milind, Annat Haber, Guruprasad Ananda, Shubhabrata Mukherjee, Cai John, Sarah Shapley, Benjamin A. Logsdon & Paul K. Crane
Late-Onset Alzheimer’s disease (LOAD) is a common, complex genetic disorder well-known for its heterogeneous pathology. The genetic heterogeneity underlying common, complex diseases poses a major challenge for targeted therapies and the identification of novel disease-associated variants. Case-control approaches are often limited to examining a specific outcome in a group of heterogenous patients with different clinical characteristics. Here, we developed a novel approach to define relevant transcriptomic endophenotypes and stratify decedents based on molecular profiles in...

A dataset of plant and microbial community structure after long-term grazing and mowing in a semiarid steppe

Wenhuai Li, Jasna Hodzic, Jishuai Su, Shuxia Zheng & Yongfei Bai
Grazing and mowing are two dominant management regimes used in grasslands. Although many studies have focused on the effects of grazing intensity on plant community structure, far fewer test how grazing impacts the soil microbial community. Furthermore, the effects of long-term grazing and mowing on plant and microbial community structure are poorly understood. To elucidate how these management regimes affect plant and microbial communities, we collected data from 280 quadrats in a semiarid steppe after...

Data From: Ecosystem size shapes antipredator trait evolution in estuarine threespine stickleback

Ben A. Wasserman, Antoine Paccard, Travis M. Apgar, Simone Des Roches, Rowan D.H. Barrett, Andrew P. Hendry & Eric P. Palkovacs
Ecosystem size is known to influence both community structure and ecosystem processes. Less is known about the evolutionary consequences of ecosystem size. A few studies have shown that ecosystem size shapes the evolution of trophic diversity by shaping habitat heterogeneity, but the effects of ecosystem size on antipredator trait evolution have not been explored. Ecosystem size may impact antipredator trait evolution by shaping predator presence (larger ecosystems have longer food chains) and habitat complexity (larger...

Phylogeny and systematics of Crescentieae (Bignoniaceae), a Neotropical clade of cauliflorous and bat-pollinated trees

Audrey C Ragsac, Susan O Grose & Richard G Olmstead
The tribe Crescentieae includes Amphitecna (21 species), Crescentia (six species), and Parmentiera (10 species), three genera of understory trees with a center of diversity in Central America and a small number of species in the Antilles and northern South America. Species in Crescentieae are united by their fleshy, indehiscent fruit and cauliflorous, bat-pollinated flowers. The large fruits are presumed to have evolved to be mammal dispersed, although water dispersal is known to occur. To lay...

Microplastic changes the sinking and resuspension rates of marine mussel biodeposits

Lyda Harris
Microplastic (MP; < 5mm) is ubiquitous in marine environments and is likely transported by biotic benthic-pelagic coupling. Mussels are key benthic-pelagic couplers, concentrating particles from the water column into dense and nutrient rich biodeposits. This study examined how MP affects benthic-pelagic coupling processes of mussels exposed to feeding regimes with and without MP by measuring four attributes of biodeposits: 1) morphology, 2) quantity of algal and MP particles, 3) sinking rate, and 4) resuspension velocity....

Alignments of Sequence Data for Phylogenetic Analysis of Damsel

Emily McFarland, Carole Baldwin, D Ross Robertson, Luiz Rocha & Luke Tornabene
Initially described in 1882, Chromis enchrysurus, the Yellowtail Reeffish, was redescribed in 1982 to account for an observed color morph that possesses a white tail instead of a yellow one, but morphological and geographic boundaries between the two color morphs were not well understood. Taking advantage of newly collected material from submersible studies of deep reefs and photographs from rebreather dives, we sought to determine whether the white-tailed Chromis is actually a color morph of...

Pervasive mitonuclear coadaptation underlies fast development in interpopulation hybrids of a marine crustacean

Kin-Lan Han & Felipe Barreto
Cellular energy production requires coordinated interactions between genetic components from the nuclear and mitochondrial genomes. This coordination results in coadaptation of interacting elements within populations. Interbreeding between divergent gene pools can disrupt coadapted loci and result in hybrid fitness breakdown. While specific incompatible loci have been detected in mutiple eukaryotic taxa, the extent of the nuclear genome that is influenced by mitonuclear coadaptation is not clear in any species. Here, we used F2 hybrids between...

Data from: Increased diversity and concordant shifts in community structure of coral-associated Symbiodiniaceae and bacteria subjected to chronic human disturbance

Danielle Claar, Jamie McDevitt-Irwin, Melissa Garren, Rebecca Vega Thurber, Ruth Gates & Julia Baum
Coral-associated bacteria and endosymbiotic algae (Symbiodiniaceae spp.) are both vitally important for the biological function of corals. Yet little is known about their co-occurrence within corals, how their diversity varies across coral species, or how they are impacted by anthropogenic disturbances. Here, we sampled coral colonies (n = 472) from seven species, encompassing a range of life history traits, across a gradient of chronic human disturbance (n = 11 sites on Kiritimati (Christmas) atoll) in...

Data from: Planning for climate change through additions to a national protected area network: implications for cost and configuration

Joshua Lawler, D. Scott Rinnan, Julia Michalak, John Withey & Hugh Possingham
Expanding the network of protected areas is a core strategy for conserving biodiversity in the face of climate change. Here we explore the impacts on reserve network cost and configuration associated with planning for climate change in the United States using networks that prioritize areas projected to be climatically suitable for 1,460 species both today and into the future, climatic refugia, and areas likely to facilitate climate-driven species movements. For 14% of the species, networks...

Co-evolution of cleaning and feeding morphology in the western Atlantic and eastern Pacific gobies

Jonathan Huie, Christine Thacker & Luke Tornabene
Cleaning symbioses are mutualistic relationships where cleaners remove and consume ectoparasites from their clients. Cleaning behavior is rare in fishes and is a highly specialized feeding strategy only observed in around 200 species. Cleaner fishes vary in their degree of specialization, ranging from species that clean as juveniles or facultatively as adults, to nearly obligate or dedicated cleaners. Here we investigate whether these different levels of trophic specialization correspond with similar changes in feeding morphology....

Data from: Nutrient availability controls the impact of mammalian herbivores on soil carbon and nitrogen pools in grasslands

Judith Sitters, E.R. Jasper Wubs, Elisabeth S. Bakker, Thomas W. Crowther, Peter B. Adler, Sumanta Bagchi, Jonathan D. Bakker, Lori Biederman, Elizabeth T. Borer, Elsa E. Cleland, Nico Eisenhauer, Jennifer Firn, Laureano Gherardi, Nicole Hagenah, Yann Hautier, Sarah E. Hobbie, Johannes M.H. Knops, Andrew S. MacDougall, Rebecca L. McCulley, Joslin L. Moore, Brent Mortensen, Pablo L. Peri, Suzanne M. Prober, Charlotte Riggs, Anita C. Risch … &
Grasslands have been subject to considerable alteration due to human activities globally, including widespread changes in populations and composition of large mammalian herbivores and elevated supply of nutrients. Grassland soils remain important reservoirs of carbon (C) and nitrogen (N). Herbivores may affect both C and N pools and these changes likely interact with increases in soil nutrient availability. Given the scale of grassland soil fluxes, such changes can have striking consequences for atmospheric C concentrations...

Comparative phylogeography of West African amphibians and reptiles

Adam Leache, Jamie Oaks, Caleb Ofori-Boateng & Matthew Fujita
Comparative phylogeographic studies often support shared divergence times for co-distributed species with similar life histories and habitat specializations. During the late Holocene, West Africa experienced aridification and the turnover of rain forest habitats into savannas. These fragmented rain forests harbor impressive numbers of endemic and threatened species. In this setting, populations of co-distributed rain forest species are expected to have diverged simultaneously, whereas divergence events for species adapted to savanna and forest-edge habitats should be...

Feeding ecology has a stronger evolutionary influence on functional morphology than on body mass in mammals

David Grossnickle
Ecological specialization is a central driver of adaptive evolution. However, selective pressures may uniquely affect different ecomorphological traits (e.g., size and shape), complicating efforts to investigate the role of ecology in generating phenotypic diversity. Comparative studies can help remedy this issue by identifying specific relationships between ecologies and morphologies, thus elucidating functionally-relevant traits. Jaw shape is a dietary correlate that offers considerable insight on mammalian evolution, but few studies have examined the influence of diet...

Registration Year

  • 2020

Resource Types

  • Dataset


  • University of Washington
  • University of Queensland
  • Oregon State University
  • University of California, Berkeley
  • Smithsonian Institution
  • Arizona State University
  • University of California Los Angeles
  • Bangor University
  • Stanford University
  • University of Pretoria