565 Works

0 ns and 75 ns configurations of glycosylated ACE2-FC and its interaction with SARS-CoV-2 binding domains

Roland Faller, Austen Bernardi, Yihan Huang, Bradley Harris, Yongao Xiong, Somen Nandi & Karen McDonald
These are initial and final (75ns) configurations in PDB format of glycosylated ACE2-FC fusion proteins which are promising targets for a COVID-19 therapeutic. Some of them are in interaction witha fragment of the receptor-binding domain (RBD) of the Spike Protein S of the SARS-CoV-2 virus. We used two glycosylation variants for ACE2-FC, variant 1 is fully glycosylated with Man8 glycans, variant 2 is fully glycosylated with GnGnXF3. The Spike RBD is glycosylated with ANaF^6.

Oral Regeneration Is the Default Pathway Triggered by Injury in Hydra

Jack Cazet & Celina Juliano
In animals capable of whole-body regeneration, a single bisection injury can trigger two different types of regeneration. Currently, it is not well understood how this adaptive response is transcriptionally regulated. We therefore comprehensively characterized transcript abundance and chromatin accessibility during two types of regeneration—oral and aboral regeneration—in the cnidarian Hydra vulgaris. We found that there was an initial generalized response to injury that was not dependent on the type of structure being regenerated. Canonical Wnt...

Data from: Mechanisms and implications of a type IV functional response for short-term intake rate of dry matter in large mammalian herbivores

Jean C. Mezzalira, Olivier J. F. Bonnet, Paulo C. De F. Carvalho, Lidiane Fonseca, Carolina Bremm, Carlos C. Mezzalira & Emilio A. Laca
1. The functional response (i.e. the relationship between consumers’ intake rate and resource density) is central in plant-herbivore interactions. Its shape and the biological processes leading to it have significant implications for both foraging theory and ecology of grazing systems. 2. A type IV functional response (i.e. dome-shaped relationship) of short-term intake rate of dry matter (intake while grazing) has rarely been reported for large herbivores and the conditions that can lead to it are...

Data from: Ecological intensification and arbuscular mycorrhizas: a meta-analysis of tillage and cover crop effects

Timothy M. Bowles, Louise E. Jackson, Malina Loeher & Timothy R. Cavagnaro
1. Reliance on ecosystem services instead of synthetic, non-renewable inputs is increasingly seen as key to achieving food security in an environmentally sustainable way. This process, known as ecological intensification, will depend in large part on enhancing below-ground biological interactions that facilitate resource use efficiency. Arbuscular mycorrhizas (AM), associations formed between the roots of most terrestrial plant species and a specialized group of soil fungi, provide valuable ecosystem services, but the full magnitude of these...

Data from: Interactive effects of predator and prey harvest on ecological resilience of rocky reefs

Robert P. Dunn, Marissa L. Baskett & Kevin A. Hovel
A major goal of ecosystem-based fisheries management is to prevent fishery-induced shifts in community states. This requires an understanding of ecological resilience: the ability of an ecosystem to return to the same state following a perturbation, which can strongly depend on species interactions across trophic levels. We use a structured model of a temperate rocky reef to explore how multi-trophic level fisheries impact ecological resilience. Increasing fishing mortality of prey (urchins) has a minor effect...

Data from: Early- and late-flowering guilds respond differently to landscape spatial structure

Jesse E.D. Miller, Anthony R. Ives, Susan P. Harrison, Ellen I. Damschen & Jesse E. D. Miller
1. Species with unique phenologies have distinct trait syndromes and environmental affinities, yet there has been little exploration of whether community assembly processes differ for plants with different phenologies. In this study, we ask whether early- and late-blooming species differ in the ways that dispersal, persistence, and resource-acquisition traits shape plant occurrence patterns in patchy habitats. 2. We sampled plant communities in 51 Ozark dolomite glade grasslands, which range in size from <1 ha to...

Data from: Form–function relationships in a marine foundation species depend on scale: a shoot to global perspective from a distributed ecological experiment

Jennifer L. Ruesink, John J. Stachowicz, Pamela L. Reynolds, Christoffer Boström, Mathieu Cusson, James Douglass, Johan Eklöf, Aschwin H. Engelen, Masakazu Hori, Kevin Hovel, Katrin Iken, Per-Olav Moksnes, Masahiro Nakaoka, Mary I. O'Connor, Jeanine L. Olsen, Erik E. Sotka, Matthew A. Whalen, Emmett J. Duffy & J. Emmett Duffy
Form-function relationships in plants underlie their ecosystem roles in supporting higher trophic levels through primary production, detrital pathways, and habitat provision. For widespread, phenotypically-variable plants, productivity may differ not only across abiotic conditions, but also from distinct morphological or demographic traits. A single foundation species, eelgrass (Zostera marina), typically dominates north temperate seagrass meadows, which we studied across 14 sites spanning 32-61° N latitude and two ocean basins. Body size varied by nearly two orders...

Data from: Long-term climate and competition explain forest mortality patterns under extreme drought

Derek J. N. Young, Jens T. Stevens, J. Mason Earles, Jeffrey Moore, Adam Ellis, Amy L. Jirka & Andrew M. Latimer
Rising temperatures are amplifying drought-induced stress and mortality in forests globally. It remains uncertain, however, whether tree mortality across drought-stricken landscapes will be concentrated in particular climatic and competitive environments. We investigated the effects of long-term average climate [i.e. 35-year mean annual climatic water deficit (CWD)] and competition (i.e. tree basal area) on tree mortality patterns, using extensive aerial mortality surveys conducted throughout the forests of California during a 4-year statewide extreme drought lasting from...

Data from: Marine subsidies change short-term foraging activity and habitat utilization of terrestrial lizards

Heather V. Kenny, Amber N. Wright, Jonah Piovia-Scott, Louie Yang, David A. Spiller, Thomas W. Schoener & Louie H. Yang
Resource pulses are brief periods of unusually high resource abundance. While population and community responses to resource pulses have been relatively well-studied, how individual consumers respond to resource pulses has received less attention. Local consumers are the first to respond to a resource pulse, and the form and timing of individual responses may influence how the effects of the pulse are transmitted throughout the community. Previous studies in Bahamian food webs have shown that detritivores...

Data from: Predator-induced collapse of niche structure and coexistence on islands

Robert M. Pringle, Tyler R. Kartzinel, Todd M. Palmer, Timothy J. Thurman, Kena Fox-Dobbs, Charles C. Y. Xu, Matthew C. Hutchinson, Tyler C. Coverdale, Joshua H. Daskin, Dominic A. Evangelista, Kiyoko M. Gotanda, , Johanna E. Wegener, Jason J. Kolbe, Thomas W. Schoener, David A. Spiller, Jonathan B. Losos & Rowan D. H. Barrett
Biological invasions represent both a pressing environmental challenge and an opportunity to investigate fundamental ecological processes, such as the role of top predators in regulating species diversity and food-web structure. In whole-ecosystem manipulations of small Caribbean islands where brown anole lizards (Anolis sagrei) were the native top predator, we experimentally staged invasions by competitors (green anoles, A. smaragdinus) and/or novel top predators (curly-tailed lizards, Leiocephalus carinatus). We show that curly-tails destabilized coexistence of competing prey...

Data from: TSPO PET Using [18F]PBR111 reveals persistent neuroinflammation following acute diisopropylfluorophosphate intoxication in the rat

Brad A. Hobson, Douglas J. Rowland, Sílvia Sisó, Michelle A. Guignet, Zachary T. Harmany, Suren Bandara, Naomi Saito, Danielle J. Harvey, Donald A. Bruun, Joel R. Garbow, Abhijit J. Chaudhari & Pamela J. Lein
Acute intoxication with organophosphates (OPs) can trigger status epilepticus followed by persistent cognitive impairment and/or electroencephalographic abnormalities. Neuroinflammation is widely posited to influence these persistent neurological consequences. However, testing this hypothesis has been challenging, in part because traditional biometrics preclude longitudinal measures of neuroinflammation within the same animal. Therefore, we evaluated the performance of non-invasive positron emission tomography (PET), using the translocator protein (TSPO) radioligand [18F]PBR111 against classic histopathologic measures of neuroinflammation in a preclinical...

Data from: Brief in-hospital cognitive screening anticipates complex admissions and may detect dementia

David P. Bissig & Charles S. DeCarli
Objective: With the long-term goal of improving community health by screening for dementia, we tested the utility of integrating the Six-Item Screener (SIS) into our emergency department neurology consultations. Methods: In this cross-sectional observational study, we measured SIS performance within 24 hours of hospital arrival in 100 consecutive English-speaking patients aged ≥ 45 years. Performance was compared to patient age, previously charted cognitive impairment, and proxies for in-hospital complexity: whether or not a patient was...

Data from: Synthesizing the effects of large, wild herbivore exclusion on ecosystem function

Elizabeth S. Forbes, J. Hall Cushman, Deron E. Burkepile, Truman P. Young, Maggie Klope & Hillary S. Young
1. Wild large herbivores are declining worldwide. Despite extensive use of exclosure experiments to investigate herbivore impacts, there is little consensus on the effects of wild large herbivores on ecosystem function. 2. Of the ecosystem functions likely impacted, we reviewed the five most-studied in exclosure experiments: ecosystem resilience/resistance to disturbance, nutrient cycling, carbon cycling, plant regeneration, and primary productivity. 3. Experimental data on large wild herbivores’ effects on ecosystem functions were predominately derived from temperate...

Data from: Optimizing carbon storage and biodiversity co-benefits in reforested riparian zones

Kristen E. Dybala, Kristin Steger, Robert G. Walsh, David R. Smart, Thomas Gardali & Nathaniel E. Seavy
1. Climate change and biodiversity loss are two global challenges that can be addressed simultaneously through reforestation of previously cleared land. However, carbon markets can encourage reforestations that focus on maximizing carbon storage, potentially at the expense of biodiversity conservation. 2. To identify opportunities to optimize reforestation design and management to meet both goals, we examined the forest stand features associated with carbon stocks in biomass and soil as well as bird abundance and diversity...

Data from: How size and conspicuousness affect the efficacy of flash coloration

Sangryong Bae, Doyeon Kim, Thomas N. Sherratt, Tim Caro & Changku Kang
Some prey are cryptic at rest but expose conspicuous colors when in motion. Previous findings suggest that these “flash displays” deceive would-be predators by providing false information about the color of prey, tricking them into continuing to look for prey with the conspicuous color when the prey have actually returned to their cryptic resting state. These results raise questions about the properties of flash coloration that make it effective. Here, using humans as visual foragers...

Data from: The dynamics of open populations: integration of top–down, bottom–up and supply‐side influences on intertidal oysters

David L. Kimbro, James Wilson White, Edwin D. Grosholz & J. Wilson White
Most communities are structured not by a single process but by some combination of top–down, bottom–up and supply‐side (i.e. juvenile recruitment) factors. However, establishing how multiple processes interact remains a fundamental challenge. For example, the recruitment, growth, and mortality of estuarine species can vary along the steep and numerous environmental and biological gradients typical of these habitats, but the relative importance of those gradients is generally unknown. We took a novel approach to this question...

Data from: Adaptive radiation in labrid fishes: a central role for functional innovations during 65 My of relentless diversification

Edward D. Burress & Peter C. Wainwright
Early burst patterns of diversification have become closely linked with concepts of adaptive radiation, reflecting interest in the role of ecological opportunity in modulating diversification. But, this model has not been widely explored on coral reefs, where biodiversity is exceptional, but many lineages have high dispersal capabilities and a pan-tropical distribution. We analyze adaptive radiation in labrid fishes, arguably the most ecologically dominant and diverse radiation of fishes on coral reefs. We test for time-dependent...

Data from: Microbial communities in hummingbird feeders are distinct from floral nectar and influenced by bird visitation

Casie Lee, Lisa A. Tell, Tiffany Hilfer & Rachel L. Vannette
Human provisioning can shape resource availability for wildlife, but consequences for microbiota availability and exchange remain relatively unexplored. Here, we characterized microbial communities on bills and fecal material of two hummingbird species and their food resources, including hummingbird feeders and floral nectar. We experimentally manipulated bird visitation to feeders and examined effects on feeder microbial communities and sucrose solutions. Birds, feeders, and flowers hosted distinct bacterial and fungal communities. Flowers and feeders hosted remarkably different...

Data from: Do genomics and sex predict migration in a partially migratory salmonid fish, Oncorhynchus mykiss?

Suzanne J. Kelson, Michael R. Miller, Tasha Q. Thompson, Sean M. O'Rourke & Stephanie M. Carlson
Partial migration is a common phenomenon wherein populations include migratory and resident individuals. Whether an individual migrates or not has important ecological and management implications, particularly within protected populations. Within partially migratory populations of O. mykiss, migration is highly correlated with a specific genomic region, but it is unclear how well this region predicts migration at the individual level. Here, we relate sex and life history genotype, determined using >400 SNPs on the migratory-linked genomic...

Data from: Experiments reveal limited top-down control of key herbivores in southern California kelp forests

Robert P. Dunn & Kevin A. Hovel
Predator responses to gradients in prey density have important implications for population regulation and are a potential structuring force for subtidal marine communities, particularly on rocky reefs where herbivorous sea urchins can drive community state shifts. On rocky reefs in southern California where predatory sea otters have been extirpated, top-down control of sea urchins by alternative predators has been hypothesized but rarely tested experimentally. In laboratory feeding assays, predatory spiny lobsters (Panulirus interruptus) demonstrated a...

Data from: Can avian functional traits predict cultural ecosystem services?

Alejandra Echeverri, Daniel Karp, Robin Naidoo, Joseph Tobias, Jiaying Zhao & Kai Chan
The functional trait diversity of species assemblages can predict the provision of ecosystem services such as pollination and carbon sequestration, but it is unclear whether the same trait-based framework can be applied to identify the factors that underpin cultural ecosystem services and disservices. To explore the relationship between traits and the contribution of species to cultural ecosystem services and disservices, we conducted 404 questionnaire surveys with birdwatchers and local residents in Guanacaste, Costa Rica. We...

Data from: Climate outweighs native vs. non-native range-effects for genetics and common garden performance of a cosmopolitan weed

Christoph Rosche, Isabell Hensen, Adrian Schaar, Uzma Zehra, Marie Jasieniuk, Ragan M. Callaway, Damase P. Khasa, Mohammad M. Al-Gharaibeh, Ylva Lekberg, David U. Nagy, Robert W. Pal, Miki Okada, Karin Schrieber, Kathryn G. Turner, Susanne Lachmuth, Andrey Erst, Tomonori Tsunoda, Min Sheng, Robin Schmidt, Yanling Peng, Wenbo Luo, Yun Jäschke, Zafar A. Reshi & Manzoor A. Shah
Comparing genetic diversity, genetic differentiation and performance between native and non-native populations has advanced our knowledge of contemporary evolution and its ecological consequences. However, such between-range comparisons can be complicated by high among-population variation within native and non-native ranges. For example, native vs. non-native comparisons between small and non-representative subsets of populations for species with very large distributions have the potential to mislead because they may not sufficiently account for within-range adaptation to climatic conditions,...

Data from: Contrasting patterns in species and functional-trait diversity of bees in an agricultural landscape

Jessica R. K. Forrest, Robbin W. Thorp, Claire Kremen & Neal M. Williams
Land-use change frequently reduces local species diversity. Species losses will often result in loss of trait diversity, with likely consequences for community functioning. However, the converse need not be generally true: management approaches that succeed in retaining species richness could nevertheless fail to maintain trait diversity. We evaluated this possibility using bee communities in a California agroecosystem. We examined among-site patterns in bee species diversity and functional-trait diversity in a landscape composed of a mosaic...

Data from: Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulate field fitness

Rachel Kerwin, Julie Feusier, Jason Corwin, Matthew Rubin, Catherine Lin, Alise Muok, Brandon Larson, Baohua Li, Bindu Joseph, Marta Francisco, Daniel Copeland, Cynthia Weinig, Daniel J. Kliebenstein & Daniel J Kliebenstein
Natural populations persist in complex environments, where biotic stressors, such as pathogen and insect communities, fluctuate temporally and spatially. These shifting biotic pressures generate heterogeneous selective forces that can maintain standing natural variation within a species. To directly test if genes containing causal variation for the Arabidopsis thaliana defensive compounds, glucosinolates (GSL) control field fitness and are therefore subject to natural selection, we conducted a multi-year field trial using lines that vary in only specific...

Data from: BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction

Brad T. Townsley, Michael F. Covington, Yasunori Ichihashi, Kristina Zumstein & Neelima R. Sinha
Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing inherent properties of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing...

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